Index: /issm/oecreview/Archive/13393-13976/Date.tex =================================================================== --- /issm/oecreview/Archive/13393-13976/Date.tex (revision 13980) +++ /issm/oecreview/Archive/13393-13976/Date.tex (revision 13980) @@ -0,0 +1,1 @@ +Nov-16-2012 Index: /issm/oecreview/Archive/13393-13976/ISSM-13397-13398.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13397-13398.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13397-13398.diff (revision 13980) @@ -0,0 +1,49 @@ +Index: ../trunk-jpl/src/dox/issm.dox +=================================================================== +--- ../trunk-jpl/src/dox/issm.dox (revision 13397) ++++ ../trunk-jpl/src/dox/issm.dox (revision 13398) +@@ -45,28 +45,28 @@ + LanguagefilesblankcommentcodeTotal + + +- C++ 50814595167625603687393 ++ C++ 50514316165645652287402 + + +- MATLAB 9256851132283046850547 ++ MATLAB 9136625130543016049839 + + +- C/C++ Header 37827582612981815188 ++ C/C++ Header 388306929831185517907 + + +- m4 79978082599336 ++ m4 6105279899310124 + + +- Python 5340061014242434 ++ Python 8126773936516911782 + + + Objective C 9980370468 + + +- Perl 32123240284 ++ Bourne Shell 55881268407 + + +- Bourne Shell 54775239361 ++ Perl 32123240284 + + + IDL 1184124146 +@@ -75,7 +75,7 @@ + C 123611 + + +- SUM: 18902578733397106984166168 ++ SUM: 19122793636727113707178370 + + + Index: /issm/oecreview/Archive/13393-13976/ISSM-13407-13408.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13407-13408.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13407-13408.diff (revision 13980) @@ -0,0 +1,37 @@ +Index: ../trunk-jpl/externalpackages/adolc/install-update-dev.sh +=================================================================== +--- ../trunk-jpl/externalpackages/adolc/install-update-dev.sh (revision 0) ++++ ../trunk-jpl/externalpackages/adolc/install-update-dev.sh (revision 13408) +@@ -0,0 +1,26 @@ ++#!/bin/bash ++set -eu ++ ++#This script is very specific to the larour larsen nightly using adolc. ++#It relies on just an update of adolc, and symlink to an existing adolc ++#repo. ++ ++#Some cleanup ++rm -rf install adolc_v220_issm ++ ++#symlink: ++ln -s /u/astrid-r1b/larour/issm-uci/trunk-jpl/externalpackages/adolc/adolc_v220_issm ./adolc_v220_issm ++ ++#update and compile ++cd adolc_v220_issm ++git pull ++ ++autoreconf -f -i ++./configure --prefix=$ISSM_DIR/externalpackages/adolc/install ++ ++if [ $# -eq 0 ]; then ++ make ++else ++ make -j $1 ++fi ++make install + +Property changes on: ../trunk-jpl/externalpackages/adolc/install-update-dev.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* Index: /issm/oecreview/Archive/13393-13976/ISSM-13408-13409.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13408-13409.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13408-13409.diff (revision 13980) @@ -0,0 +1,130 @@ +Index: ../trunk-jpl/externalpackages/adolc/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/adolc/install.sh (revision 13408) ++++ ../trunk-jpl/externalpackages/adolc/install.sh (revision 13409) +@@ -1,60 +0,0 @@ +-#!/bin/bash +-set -eu +- +-#some issues on macosx64 with ISSM's autoconf. you might want to run native to mac on this. +- +-#Some cleanup +-rm -rf install ADOL-C-2.2.0 src trunk +- +-#Create install directories +-mkdir install src +- +-#Download from ISSM server +-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C-2.2.0.tar.gz' 'ADOL-C-2.2.0.tar.gz' +- +-#Untar +-tar -zxvf ADOL-C-2.2.0.tar.gz +- +-#Move ADOL-C into install directory +-mv ADOL-C-2.2.0/* src +-rm -rf ADOL-C-2.2.0 +- +-#Compile ADOL-C +-cd src +- +-#export CC=gcc +-#export CXX=g++ +-#export CFLAGS="-arch x86_64" +-#export CXXFLAGS="-arch x86_64" +- +-./configure \ +- --prefix=$ISSM_DIR/externalpackages/adolc/install \ +- --enable-sparse \ +- --enable-docexa \ +- --enable-addexa \ +- --disable-shave +- +-if [ $# -eq 0 ]; then +- make +-else +- make -j $1 +-fi +-make install +- +- +-#Ok, bug with libtool: replace all LIBTOOL= by LIBTOOL=libtool +-#in all Makefiles +-for i in `find ./ -name Makefile ` +-do +- echo $i +- cat $i | sed 's/LIBTOOL =/LIBTOOL = libtool/g' > $i.bak +- mv $i.bak $i +-done +- +-#remake: +-if [ $# -eq 0 ]; then +- make +-else +- make -j $1 +-fi +-make install +Index: ../trunk-jpl/externalpackages/adolc/install-2.2.0.sh +=================================================================== +--- ../trunk-jpl/externalpackages/adolc/install-2.2.0.sh (revision 0) ++++ ../trunk-jpl/externalpackages/adolc/install-2.2.0.sh (revision 13409) +@@ -0,0 +1,60 @@ ++#!/bin/bash ++set -eu ++ ++#some issues on macosx64 with ISSM's autoconf. you might want to run native to mac on this. ++ ++#Some cleanup ++rm -rf install ADOL-C-2.2.0 src trunk ++ ++#Create install directories ++mkdir install src ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ADOL-C-2.2.0.tar.gz' 'ADOL-C-2.2.0.tar.gz' ++ ++#Untar ++tar -zxvf ADOL-C-2.2.0.tar.gz ++ ++#Move ADOL-C into install directory ++mv ADOL-C-2.2.0/* src ++rm -rf ADOL-C-2.2.0 ++ ++#Compile ADOL-C ++cd src ++ ++#export CC=gcc ++#export CXX=g++ ++#export CFLAGS="-arch x86_64" ++#export CXXFLAGS="-arch x86_64" ++ ++./configure \ ++ --prefix=$ISSM_DIR/externalpackages/adolc/install \ ++ --enable-sparse \ ++ --enable-docexa \ ++ --enable-addexa \ ++ --disable-shave ++ ++if [ $# -eq 0 ]; then ++ make ++else ++ make -j $1 ++fi ++make install ++ ++ ++#Ok, bug with libtool: replace all LIBTOOL= by LIBTOOL=libtool ++#in all Makefiles ++for i in `find ./ -name Makefile ` ++do ++ echo $i ++ cat $i | sed 's/LIBTOOL =/LIBTOOL = libtool/g' > $i.bak ++ mv $i.bak $i ++done ++ ++#remake: ++if [ $# -eq 0 ]; then ++ make ++else ++ make -j $1 ++fi ++make install Index: /issm/oecreview/Archive/13393-13976/ISSM-13409-13410.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13409-13410.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13409-13410.diff (revision 13980) @@ -0,0 +1,1307 @@ +Index: ../trunk-jpl/src/c/Container/Vertices.cpp +=================================================================== +--- ../trunk-jpl/src/c/Container/Vertices.cpp (revision 13409) ++++ ../trunk-jpl/src/c/Container/Vertices.cpp (revision 13410) +@@ -37,73 +37,73 @@ + /*}}}*/ + + /*Numerics management*/ +-/*FUNCTION Vertices::DistributeDofs{{{*/ +-void Vertices::DistributeDofs(int numberofobjects,int numberofdofsperobject){ ++/*FUNCTION Vertices::DistributePids{{{*/ ++void Vertices::DistributePids(int numberofobjects){ + + extern int num_procs; + extern int my_rank; + + int i; +- int dofcount=0; +- int* alldofcount=NULL; +- int* truedofs=NULL; +- int* alltruedofs=NULL; ++ int pidcount = 0; ++ int *allpidcount = NULL; ++ int *truepids = NULL; ++ int *alltruepids = NULL; + +- /*Go through objects, and distribute dofs locally, from 0 to numberofdofsperobject*/ ++ /*Go through objects, and distribute pids locally, from 0 to numberofpidsperobject*/ + for (i=0;iSize();i++){ + Vertex* vertex=(Vertex*)this->GetObjectByOffset(i); +- vertex->DistributeDofs(&dofcount); ++ vertex->DistributePids(&pidcount); + } + +- /* Now every object has distributed dofs, but locally, and with a dof count starting from +- * 0. This means the dofs between all the cpus are not unique. We now offset the dofs of eache +- * cpus by the total last dofs of the previus cpu, starting from 0. +- * First: bet number of dofs for each cpu*/ +- alldofcount=xNew(num_procs); ++ /* Now every object has distributed pids, but locally, and with a pid count starting from ++ * 0. This means the pids between all the cpus are not unique. We now offset the pids of each ++ * cpus by the total last pids of the previus cpu, starting from 0. ++ * First: get number of pids for each cpu*/ ++ allpidcount=xNew(num_procs); + #ifdef _HAVE_MPI_ +- MPI_Gather(&dofcount,1,MPI_INT,alldofcount,1,MPI_INT,0,MPI_COMM_WORLD); +- MPI_Bcast(alldofcount,num_procs,MPI_INT,0,MPI_COMM_WORLD); ++ MPI_Gather(&pidcount,1,MPI_INT,allpidcount,1,MPI_INT,0,MPI_COMM_WORLD); ++ MPI_Bcast(allpidcount,num_procs,MPI_INT,0,MPI_COMM_WORLD); + #else +- alldofcount[0]=dofcount; ++ allpidcount[0]=pidcount; + #endif + +- /* Every cpu should start its own dof count at the end of the dofcount from cpu-1*/ +- dofcount=0; ++ /* Every cpu should start its own pid count at the end of the pidcount from cpu-1*/ ++ pidcount=0; + if(my_rank!=0){ + for(i=0;iSize();i++){ + Vertex* vertex=(Vertex*)this->GetObjectByOffset(i); +- vertex->OffsetDofs(dofcount); ++ vertex->OffsetPids(pidcount); + } + + /* Finally, remember that cpus may have skipped some objects, because they were clones. For every +- * object that is not a clone, tell them to show their dofs, so that later on, they can get picked ++ * object that is not a clone, tell them to show their pids, so that later on, they can get picked + * up by their clones: */ +- truedofs =xNewZeroInit(numberofobjects*numberofdofsperobject); +- alltruedofs=xNewZeroInit(numberofobjects*numberofdofsperobject); ++ truepids =xNewZeroInit(numberofobjects); ++ alltruepids=xNewZeroInit(numberofobjects); + for (i=0;iSize();i++){ + Vertex* vertex=(Vertex*)this->GetObjectByOffset(i); +- vertex->ShowTrueDofs(truedofs); ++ vertex->ShowTruePids(truepids); + } + #ifdef _HAVE_MPI_ +- MPI_Allreduce((void*)truedofs,(void*)alltruedofs,numberofobjects*numberofdofsperobject,MPI_INT,MPI_MAX,MPI_COMM_WORLD); ++ MPI_Allreduce((void*)truepids,(void*)alltruepids,numberofobjects,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + #else +- for(i=0;iSize();i++){ ++ /* Now every cpu knows the true pids of everyone else that is not a clone*/ ++ for(i=0;iSize();i++){ + Vertex* vertex=(Vertex*)this->GetObjectByOffset(i); +- vertex->UpdateCloneDofs(alltruedofs); ++ vertex->UpdateClonePids(alltruepids); + } + + /* Free ressources: */ +- xDelete(alldofcount); +- xDelete(truedofs); +- xDelete(alltruedofs); ++ xDelete(allpidcount); ++ xDelete(truepids); ++ xDelete(alltruepids); + } + /*}}}*/ + /*FUNCTION Vertices::FlagClones{{{*/ +Index: ../trunk-jpl/src/c/Container/Vertices.h +=================================================================== +--- ../trunk-jpl/src/c/Container/Vertices.h (revision 13409) ++++ ../trunk-jpl/src/c/Container/Vertices.h (revision 13410) +@@ -18,17 +18,15 @@ + + public: + +- /*constructors, destructors: {{{*/ ++ /*constructors, destructors:*/ + Vertices(); + ~Vertices(); +- /*}}}*/ +- /*numerics: {{{*/ +- void DistributeDofs(int numberofnodes,int numdofspernode); ++ ++ /*numerics:*/ ++ void DistributePids(int numberofnodes); + void FlagClones(int numberofnodes); + int NumberOfVertices(void); + void Ranks(int* ranks); +- /*}}}*/ +- + }; + + #endif //ifndef _VERTICES_H_ +Index: ../trunk-jpl/src/c/modules/VerticesDofx/VerticesDofx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/VerticesDofx/VerticesDofx.cpp (revision 13409) ++++ ../trunk-jpl/src/c/modules/VerticesDofx/VerticesDofx.cpp (revision 13410) +@@ -10,24 +10,18 @@ + + void VerticesDofx( Vertices* vertices, Parameters* parameters) { + +- int i; +- +- int found=0; +- extern int num_procs; +- extern int my_rank; +- + /*intermediary: */ + int numberofvertices; + + /*figure out how many vertices we have: */ + numberofvertices=vertices->NumberOfVertices(); + +- /*Ensure that only for each cpu, the partition border vertices only will be taken into account once +- * across the cluster. To do so, we flag all the clone vertices: */ ++ /*Ensure that only for each cpu, the partition border vertices only will be ++ * taken into account once across the cluster. To do so, we flag all the ++ * clone vertices: */ + vertices->FlagClones(numberofvertices); + +- /*Go through all vertices and distribute 1 dof at a time. When a vertex has already been distributed his dof on a cpu, +- * all other cpus with the same vertex cannot distribute it anymore. Use clone field to be sure of that: */ +- vertices->DistributeDofs(numberofvertices,1); //only 1 dof per vertex. ++ /*Go through all vertices and distribute pids*/ ++ vertices->DistributePids(numberofvertices); + + } +Index: ../trunk-jpl/src/c/classes/objects/Materials/Matdamageice.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Materials/Matdamageice.cpp (revision 13409) ++++ ../trunk-jpl/src/c/classes/objects/Materials/Matdamageice.cpp (revision 13410) +@@ -209,7 +209,7 @@ + + /*Prepare index list*/ + int doflist1[3]; +- for(int i=0;i<3;i++) doflist1[i]=((Tria*)element)->nodes[i]->GetVertexDof(); ++ for(int i=0;i<3;i++) doflist1[i]=((Tria*)element)->nodes[i]->GetVertexPid(); + + /*Get input (either in element or material)*/ + Input* input=inputs->GetInput(input_enum); +@@ -639,7 +639,7 @@ + + case TriaEnum: { + IssmDouble values[3]; +- for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexDof()]; ++ for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexPid()]; + this->inputs->AddInput(new TriaP1Input(name,values)); + return; + } +@@ -681,7 +681,7 @@ + + case TriaEnum: { + IssmDouble values[3]; +- for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetSidList()]; //use sid list, to index into serial oriented vector ++ for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexSid()]; //use sid list, to index into serial oriented vector + this->inputs->AddInput(new TriaP1Input(name,values)); + /*Special case for rheology B in 2D: Pourave land for this solution{{{*/ + if(name==MaterialsRheologyBEnum){ +Index: ../trunk-jpl/src/c/classes/objects/Materials/Matice.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Materials/Matice.cpp (revision 13409) ++++ ../trunk-jpl/src/c/classes/objects/Materials/Matice.cpp (revision 13410) +@@ -189,7 +189,7 @@ + + /*Prepare index list*/ + int doflist1[3]; +- for(int i=0;i<3;i++) doflist1[i]=((Tria*)element)->nodes[i]->GetVertexDof(); ++ for(int i=0;i<3;i++) doflist1[i]=((Tria*)element)->nodes[i]->GetVertexPid(); + + /*Get input (either in element or material)*/ + Input* input=inputs->GetInput(input_enum); +@@ -559,7 +559,7 @@ + + case TriaEnum: { + IssmDouble values[3]; +- for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexDof()]; ++ for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexPid()]; + this->inputs->AddInput(new TriaP1Input(name,values)); + return; + } +@@ -601,7 +601,7 @@ + + case TriaEnum: { + IssmDouble values[3]; +- for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetSidList()]; //use sid list, to index into serial oriented vector ++ for (int i=0;i<3;i++) values[i]=vector[((Tria*)element)->nodes[i]->GetVertexSid()]; //index into serial oriented vector + this->inputs->AddInput(new TriaP1Input(name,values)); + /*Special case for rheology B in 2D: Pourave land for this solution{{{*/ + if(name==MaterialsRheologyBEnum){ +Index: ../trunk-jpl/src/c/classes/objects/Vertex.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Vertex.cpp (revision 13409) ++++ ../trunk-jpl/src/c/classes/objects/Vertex.cpp (revision 13410) +@@ -48,12 +48,12 @@ + /*all the initialization has been done by the initializer, just fill in the id: */ + this->id=vertex_id; + this->sid=vertex_sid; ++ this->pid=UNDEF; + this->x=vertex_x; + this->y=vertex_y; + this->z=vertex_z; + this->sigma=vertex_sigma; + this->connectivity=vertex_connectivity; +- this->dof=UNDEF; + + return; + } +@@ -66,12 +66,12 @@ + _printLine_("Vertex:"); + _printLine_(" id: " << id); + _printLine_(" sid: " << sid); ++ _printLine_(" pid: " << pid); + _printLine_(" x: " << x); + _printLine_(" y: " << y); + _printLine_(" z: " << z); + _printLine_(" sigma: " << sigma); + _printLine_(" connectivity: " << connectivity); +- _printLine_(" dof: " << dof); + _printLine_(" clone: " << clone); + + return; +@@ -106,71 +106,78 @@ + } + /*}}}*/ + +-/* DofObject routines: */ +-/*FUNCTION Vertex::DistributeDofs{{{*/ +-void Vertex::DistributeDofs(int* pdofcount){ ++/*Vertex management: */ ++/*FUNCTION Vertex::Connectivity{{{*/ ++int Vertex::Connectivity(void){return connectivity;} ++/*}}}*/ ++/*FUNCTION Vertex::Sid{{{*/ ++int Vertex::Sid(void){ return sid; } ++/*}}}*/ ++/*FUNCTION Vertex::UpdateVertexPosition {{{*/ ++void Vertex::UpdatePosition(Vector* vz,Parameters* parameters,IssmDouble* thickness,IssmDouble* bed){ + +- int i; +- extern int my_rank; +- int dofcount; ++ IssmDouble oldz,newz; ++ IssmDouble dt,velz; + +- dofcount=*pdofcount; ++ /*Get time stepping*/ ++ parameters->FindParam(&dt,TimesteppingTimeStepEnum); ++ ++ /*sigma remains constant. z=bed+sigma*thickness*/ ++ oldz = this->z; ++ newz = bed[this->pid]+sigma*thickness[this->pid]; ++ velz = (newz-oldz)/dt; ++ this->z = newz; ++ ++ /*put vz in vector*/ ++ vz->SetValue(this->pid,velz,INS_VAL); ++} ++/*}}}*/ ++/*FUNCTION Vertex::DistributePids{{{*/ ++void Vertex::DistributePids(int* ppidcount){ ++ ++ /*retrieve current pid*/ ++ int pidcount=*ppidcount; + +- if(this->clone){ +- /*This vertex is a clone! Don't distribute dofs, it will get them from another cpu!*/ +- return; +- } ++ /*This vertex is a clone! Don't distribute pids, it will get them from another cpu!*/ ++ if(this->clone) return; + +- /*This vertex should distribute his dof, go ahead: */ +- this->dof=dofcount; +- dofcount++; ++ /*This vertex should distribute its pid*/ ++ this->pid=pidcount; ++ pidcount++; + + /*Assign output pointers: */ +- *pdofcount=dofcount; +- ++ *ppidcount=pidcount; + } + /*}}}*/ +-/*FUNCTION Vertex::OffsetDofs{{{*/ +-void Vertex::OffsetDofs(int dofcount){ ++/*FUNCTION Vertex::OffsetPids{{{*/ ++void Vertex::OffsetPids(int pidcount){ + +- int i; +- extern int my_rank; +- +- if(this->clone){ +- /*This vertex is a clone, don't offset the dofs!: */ +- return; +- } ++ /*This vertex is a clone, don't offset the pids*/ ++ if(this->clone) return; + +- /*This vertex should offset his dof, go ahead: */ +- this->dof+=dofcount; ++ /*This vertex should offset his pid, go ahead: */ ++ this->pid+=pidcount; + } + /*}}}*/ +-/*FUNCTION Vertex::ShowTrueDofs{{{*/ +-void Vertex::ShowTrueDofs(int* truedofs){ ++/*FUNCTION Vertex::ShowTruePids{{{*/ ++void Vertex::ShowTruePids(int* truepids){ + +- int j; +- extern int my_rank; +- + /*Are we a clone? : */ + if(this->clone)return; + +- /*Ok, we are not a clone, just plug our dof into truedofs: */ +- truedofs[this->id-1]=this->dof; +- ++ /*Ok, we are not a clone, just plug our pid into truepids: */ ++ truepids[this->sid]=this->pid; + } + /*}}}*/ +-/*FUNCTION Vertex::UpdateCloneDofs{{{*/ +-void Vertex::UpdateCloneDofs(int* alltruedofs){ ++/*FUNCTION Vertex::UpdateClonePids{{{*/ ++void Vertex::UpdateClonePids(int* alltruepids){ + +- int j; +- extern int my_rank; +- +- /*If we are not a clone, don't update, we already have dofs!: */ +- if(this->clone==0)return; ++ /*If we are not a clone, don't update, we already have pids: */ ++ if(!this->clone)return; + +- /*Ok, we are a clone node, but we did not create the dof for this vertex +- * Therefore, our dof is garbage right now. Go pick it up in the alltruedofs: */ +- this->dof=alltruedofs[id-1]; ++ /*Ok, we are a clone node, but we did not create the pid for this vertex ++ * Therefore, our pid is garbage right now. Go pick it up in the alltruepids: */ ++ this->pid=alltruepids[this->pid]; + } + /*}}}*/ + /*FUNCTION Vertex::SetClone {{{*/ +@@ -178,41 +185,15 @@ + + extern int my_rank; + +- if (minranks[id-1]==my_rank){ +- this->clone=0; ++ if (minranks[this->sid]==my_rank){ ++ this->clone=false; + } + else{ + /*!there is a cpu with lower rank that has the same vertex, + therefore, I am a clone*/ +- this->clone=1; ++ this->clone=true; + } + + } + /*}}}*/ + +-/*Vertex management: */ +-/*FUNCTION Vertex::Connectivity{{{*/ +-int Vertex::Connectivity(void){return connectivity;} +-/*}}}*/ +-/*FUNCTION Vertex::Sid{{{*/ +-int Vertex::Sid(void){ return sid; } +-/*}}}*/ +-/*FUNCTION Vertex::UpdateVertexPosition {{{*/ +-void Vertex::UpdatePosition(Vector* vz,Parameters* parameters,IssmDouble* thickness,IssmDouble* bed){ +- +- IssmDouble oldz,newz; +- IssmDouble dt,velz; +- +- /*Get time stepping*/ +- parameters->FindParam(&dt,TimesteppingTimeStepEnum); +- +- /*sigma remains constant. z=bed+sigma*thickness*/ +- oldz = this->z; +- newz = bed[this->dof]+sigma*thickness[this->dof]; +- velz = (newz-oldz)/dt; +- this->z = newz; +- +- /*put vz in vector*/ +- vz->SetValue(this->dof,velz,INS_VAL); +-} +-/*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Vertex.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Vertex.h (revision 13409) ++++ ../trunk-jpl/src/c/classes/objects/Vertex.h (revision 13410) +@@ -21,19 +21,16 @@ + class Vertex: public Object{ + + public: +- +- int id; +- int sid; //sid for "serial" id, ie the rank of this vertex in the vertices dataset, if the dataset was serial on 1 cpu. ++ bool clone; ++ int id; // random index ++ int sid; // "serial" id (rank of this vertex if the dataset was on 1 cpu) ++ int pid; // "parallel" id + IssmDouble x; + IssmDouble y; + IssmDouble z; +- IssmDouble sigma; //sigma coordinate: (z-bed)/thickness +- int connectivity; //number of vertices connected to this vertex ++ IssmDouble sigma; //sigma coordinate: (z-bed)/thickness ++ int connectivity; //number of vertices connected to this vertex + +- /*dof management: */ +- int clone; +- int dof; //dof to recover values in a vertex indexed vector +- + /*Vertex constructors, destructors {{{*/ + Vertex(); + Vertex(int id, int sid,IssmDouble x, IssmDouble y, IssmDouble z, IssmDouble sigma, int connectivity); +@@ -49,17 +46,14 @@ + int ObjectEnum(); + Object* copy(); + /*}}}*/ +- /*DofObject routines {{{*/ +- void DistributeDofs(int* pdofcount); +- void OffsetDofs(int dofcount); +- void ShowTrueDofs(int* borderdofs); +- void UpdateCloneDofs(int* allborderdofs); +- void SetClone(int* minranks); +- /*}}}*/ +- /*Vertex management: {{{*/ ++ /*Vertex management:*/ + int Sid(void); + int Connectivity(void); + void UpdatePosition(Vector* vz,Parameters* parameters,IssmDouble* thickness,IssmDouble* bed); +- /*}}}*/ ++ void DistributePids(int* ppidcount); ++ void OffsetPids(int pidcount); ++ void ShowTruePids(int* borderpids); ++ void UpdateClonePids(int* allborderpids); ++ void SetClone(int* minranks); + }; + #endif /* _VERTEX_H */ +Index: ../trunk-jpl/src/c/classes/objects/Node.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Node.cpp (revision 13409) ++++ ../trunk-jpl/src/c/classes/objects/Node.cpp (revision 13410) +@@ -233,16 +233,6 @@ + else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!"); + + } /*}}}*/ +-/*FUNCTION Node::GetDofList1{{{*/ +-int Node::GetDofList1(void){ +- +- Vertex* vertex=NULL; +- +- vertex=(Vertex*)this->hvertex->delivers(); +- +- return vertex->dof; +-} +-/*}}}*/ + /*FUNCTION Node::GetDofList{{{*/ + void Node::GetDofList(int* outdoflist,int approximation_enum,int setenum){ + int i; +@@ -305,16 +295,6 @@ + } + } + /*}}}*/ +-/*FUNCTION Node::GetSidList{{{*/ +-int Node::GetSidList(void){ +- +- Vertex* vertex=NULL; +- +- vertex=(Vertex*)this->hvertex->delivers(); +- +- return vertex->sid; +-} +-/*}}}*/ + /*FUNCTION Node::GetLocalDofList{{{*/ + void Node::GetLocalDofList(int* outdoflist,int approximation_enum,int setenum){ + int i; +@@ -426,15 +406,25 @@ + return vertex->id; + } + /*}}}*/ +-/*FUNCTION Node::GetVertexDof {{{*/ +-int Node::GetVertexDof(void){ ++/*FUNCTION Node::GetVertexPid{{{*/ ++int Node::GetVertexPid(void){ + + Vertex* vertex=NULL; + + vertex=(Vertex*)hvertex->delivers(); +- return vertex->dof; ++ return vertex->pid; + } + /*}}}*/ ++/*FUNCTION Node::GetVertexSid{{{*/ ++int Node::GetVertexSid(void){ ++ ++ Vertex* vertex=NULL; ++ ++ vertex=(Vertex*)this->hvertex->delivers(); ++ ++ return vertex->sid; ++} ++/*}}}*/ + #ifdef _HAVE_DIAGNOSTIC_ + /*FUNCTION Node::GetCoordinateSystem{{{*/ + void Node::GetCoordinateSystem(IssmDouble* coord_system_out){ +@@ -445,16 +435,6 @@ + } + /*}}}*/ + #endif +-/*FUNCTION Node::SetVertexDof {{{*/ +-void Node::SetVertexDof(int in_dof){ +- +- Vertex* vertex=NULL; +- +- vertex=(Vertex*)hvertex->delivers(); +- vertex->dof=in_dof; +- +-} +-/*}}}*/ + /*FUNCTION Node::InAnalysis{{{*/ + bool Node::InAnalysis(int in_analysis_type){ + if (in_analysis_type==this->analysis_type) return true; +@@ -886,7 +866,7 @@ + } + /*}}}*/ + +-/* DofObject routines:*/ ++/* indexing routines:*/ + /*FUNCTION Node::DistributeDofs{{{*/ + void Node::DistributeDofs(int* pdofcount,int setenum){ + +@@ -934,7 +914,7 @@ + + } + /*}}}*/ +-/*FUNCTION Node::Off_setDofs{{{*/ ++/*FUNCTION Node::OffsetDofs{{{*/ + void Node::OffsetDofs(int dofcount,int setenum){ + + int i; +Index: ../trunk-jpl/src/c/classes/objects/Node.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Node.h (revision 13409) ++++ ../trunk-jpl/src/c/classes/objects/Node.h (revision 13410) +@@ -66,12 +66,9 @@ + void CreateNodalConstraints(Vector* ys); + void SetCurrentConfiguration(DataSet* nodes,Vertices* vertices); + int Sid(void); +- int GetVertexDof(void); +- int GetVertexId(void); + #ifdef _HAVE_DIAGNOSTIC_ + void GetCoordinateSystem(IssmDouble* coord_system_out); + #endif +- void SetVertexDof(int in_dof); + bool InAnalysis(int analysis_type); + int GetApproximation(); + int GetNumberOfDofs(int approximation_enum,int setenum); +@@ -85,8 +82,9 @@ + int GetConnectivity(); + void GetDofList(int* poutdoflist,int approximation_enum,int setenum); + void GetLocalDofList(int* poutdoflist,int approximation_enum,int setenum); +- int GetDofList1(void); +- int GetSidList(void); ++ int GetVertexId(void); ++ int GetVertexPid(void); ++ int GetVertexSid(void); + IssmDouble GetX(); + IssmDouble GetY(); + IssmDouble GetZ(); +Index: ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13409) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13410) +@@ -139,8 +139,8 @@ + area=this->GetArea(); + + /*Figure out the average for this element: */ +- this->GetSidList(&offsetsid[0]); +- this->GetDofList1(&offsetdof[0]); ++ this->GetVertexSidList(&offsetsid[0]); ++ this->GetVertexPidList(&offsetdof[0]); + mean=0; + for(i=0;i(qmu_part[offsetsid[i]]); +@@ -1054,14 +1054,6 @@ + *pdoflist=doflist; + } + /*}}}*/ +-/*FUNCTION Tria::GetDofList1 {{{*/ +-void Tria::GetDofList1(int* doflist){ +- +- int i; +- for(i=0;i<3;i++) doflist[i]=nodes[i]->GetDofList1(); +- +-} +-/*}}}*/ + /*FUNCTION Tria::GetElementType {{{*/ + int Tria::GetElementType(){ + +@@ -1179,11 +1171,19 @@ + delete gauss; + } + /*}}}*/ +-/*FUNCTION Tria::GetSidList {{{*/ +-void Tria::GetSidList(int* sidlist){ +- for(int i=0;iGetSidList(); ++/*FUNCTION Tria::GetVertexPidList {{{*/ ++void Tria::GetVertexPidList(int* doflist){ ++ ++ int i; ++ for(i=0;i<3;i++) doflist[i]=nodes[i]->GetVertexPid(); ++ + } + /*}}}*/ ++/*FUNCTION Tria::GetVertexSidList {{{*/ ++void Tria::GetVertexSidList(int* sidlist){ ++ for(int i=0;iGetVertexSid(); ++} ++/*}}}*/ + /*FUNCTION Tria::GetConnectivityList {{{*/ + void Tria::GetConnectivityList(int* connectivity){ + for(int i=0;iGetConnectivity(); +@@ -1242,20 +1242,20 @@ + /*FUNCTION Tria::GetVectorFromInputs{{{*/ + void Tria::GetVectorFromInputs(Vector* vector,int input_enum){ + +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + + /*Get out if this is not an element input*/ + if(!IsInput(input_enum)) return; + + /*Prepare index list*/ +- this->GetDofList1(&doflist1[0]); ++ this->GetVertexPidList(&vertexpidlist[0]); + + /*Get input (either in element or material)*/ + Input* input=inputs->GetInput(input_enum); + if(!input) _error_("Input " << EnumToStringx(input_enum) << " not found in element"); + + /*We found the enum. Use its values to fill into the vector, using the vertices ids: */ +- input->GetVectorFromInputs(vector,&doflist1[0]); ++ input->GetVectorFromInputs(vector,&vertexpidlist[0]); + } + /*}}}*/ + /*FUNCTION Tria::GetVectorFromResults{{{*/ +@@ -1267,11 +1267,11 @@ + _error_("Results of offset "<InstanceEnum())<<" when "<GetSidList(&doflist1[0]); ++ this->GetVertexSidList(&vertexpidlist[0]); + this->GetConnectivityList(&connectivity[0]); +- elementresult->GetVectorFromResults(vector,&doflist1[0],&connectivity[0],NUMVERTICES); ++ elementresult->GetVectorFromResults(vector,&vertexpidlist[0],&connectivity[0],NUMVERTICES); + } + else if(interp==P0Enum){ + elementresult->GetElementVectorFromResults(vector,sid); +@@ -1686,7 +1686,7 @@ + + /*Get values on the 3 vertices*/ + for (int i=0;i<3;i++){ +- values[i]=vector[this->nodes[i]->GetVertexDof()]; ++ values[i]=vector[this->nodes[i]->GetVertexPid()]; + } + + /*update input*/ +@@ -3431,7 +3431,7 @@ + /*FUNCTION Tria::ControlInputGetGradient{{{*/ + void Tria::ControlInputGetGradient(Vector* gradient,int enum_type,int control_index){ + +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + Input* input=NULL; + + if(enum_type==MaterialsRheologyBbarEnum || enum_type==MaterialsRheologyZbarEnum){ +@@ -3443,8 +3443,8 @@ + if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found"); + if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput"); + +- GradientIndexing(&doflist1[0],control_index); +- ((ControlInput*)input)->GetGradient(gradient,&doflist1[0]); ++ GradientIndexing(&vertexpidlist[0],control_index); ++ ((ControlInput*)input)->GetGradient(gradient,&vertexpidlist[0]); + + }/*}}}*/ + /*FUNCTION Tria::ControlInputScaleGradient{{{*/ +@@ -3466,7 +3466,7 @@ + /*FUNCTION Tria::ControlInputSetGradient{{{*/ + void Tria::ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index){ + +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + IssmDouble grad_list[NUMVERTICES]; + Input* grad_input=NULL; + Input* input=NULL; +@@ -3480,8 +3480,8 @@ + if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found"); + if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput"); + +- GradientIndexing(&doflist1[0],control_index); +- for(int i=0;iSetGradient(grad_input); +@@ -3555,7 +3555,7 @@ + void Tria::GradjBGradient(Vector* gradient,int weight_index,int control_index){ + + int i,ig; +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + IssmDouble Jdet,weight; + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble dbasis[NDOF2][NUMVERTICES]; +@@ -3565,7 +3565,7 @@ + + /*Retrieve all inputs we will be needing: */ + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + Input* rheologyb_input=material->inputs->GetInput(MaterialsRheologyBbarEnum); _assert_(rheologyb_input); + Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum); _assert_(weights_input); + +@@ -3585,7 +3585,7 @@ + /*Build gradje_g_gaussian vector (actually -dJ/ddrag): */ + for (i=0;iweight*(dbasis[0][i]*dk[0]+dbasis[1][i]*dk[1]); + } +- gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); ++ gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; +@@ -3595,7 +3595,7 @@ + void Tria::GradjZGradient(Vector* gradient,int weight_index,int control_index){ + + int i,ig; +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + IssmDouble Jdet,weight; + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble dbasis[NDOF2][NUMVERTICES]; +@@ -3605,7 +3605,7 @@ + + /*Retrieve all inputs we will be needing: */ + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + Input* rheologyz_input=material->inputs->GetInput(MaterialsRheologyZbarEnum); _assert_(rheologyz_input); + Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum); _assert_(weights_input); + +@@ -3625,7 +3625,7 @@ + /*Build gradje_g_gaussian vector (actually -dJ/ddrag): */ + for (i=0;iweight*(dbasis[0][i]*dk[0]+dbasis[1][i]*dk[1]); + } +- gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); ++ gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; +@@ -3750,7 +3750,7 @@ + + int i,ig; + int analysis_type; +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + int connectivity[NUMVERTICES]; + IssmDouble vx,vy,lambda,mu,alpha_complement,Jdet; + IssmDouble bed,thickness,Neff,drag; +@@ -3768,7 +3768,7 @@ + /*retrive parameters: */ + parameters->FindParam(&analysis_type,AnalysisTypeEnum); + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + this->GetConnectivityList(&connectivity[0]); + + /*Build frictoin element, needed later: */ +@@ -3826,7 +3826,7 @@ + //} + /*End Analytical gradient*/ + +- gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); ++ gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; +@@ -3837,7 +3837,7 @@ + void Tria::GradjDragGradient(Vector* gradient, int weight_index,int control_index){ + + int i,ig; +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + IssmDouble Jdet,weight; + IssmDouble xyz_list[NUMVERTICES][3]; + IssmDouble dbasis[NDOF2][NUMVERTICES]; +@@ -3848,7 +3848,7 @@ + /*Retrieve all inputs we will be needing: */ + if(IsFloating())return; + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + Input* dragcoefficient_input=inputs->GetInput(FrictionCoefficientEnum); _assert_(dragcoefficient_input); + Input* weights_input=inputs->GetInput(InversionCostFunctionsCoefficientsEnum); _assert_(weights_input); + +@@ -3871,7 +3871,7 @@ + _assert_(!xIsNan(grade_g[i])); + } + } +- gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); ++ gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; +@@ -3881,16 +3881,16 @@ + void Tria::GradjDhDtBalancedthickness(Vector* gradient,int control_index){ + + /*Intermediaries*/ +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + IssmDouble lambda[NUMVERTICES]; + IssmDouble gradient_g[NUMVERTICES]; + + /*Compute Gradient*/ +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + GetInputListOnVertices(&lambda[0],AdjointEnum); + for(int i=0;iSetValues(NUMVERTICES,doflist1,gradient_g,INS_VAL); ++ gradient->SetValues(NUMVERTICES,vertexpidlist,gradient_g,INS_VAL); + } + /*}}}*/ + /*FUNCTION Tria::GradjVxBalancedthickness{{{*/ +@@ -3898,7 +3898,7 @@ + + /*Intermediaries*/ + int i,ig; +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + IssmDouble thickness,Jdet; + IssmDouble basis[3]; + IssmDouble Dlambda[2],dp[2]; +@@ -3908,7 +3908,7 @@ + + /* Get node coordinates and dof list: */ + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + + /*Retrieve all inputs we will be needing: */ + Input* adjoint_input=inputs->GetInput(AdjointEnum); _assert_(adjoint_input); +@@ -3930,7 +3930,7 @@ + for(i=0;iweight*basis[i]; + } + +- gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); ++ gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; +@@ -3941,7 +3941,7 @@ + + /*Intermediaries*/ + int i,ig; +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + IssmDouble thickness,Jdet; + IssmDouble basis[3]; + IssmDouble Dlambda[2],dp[2]; +@@ -3951,7 +3951,7 @@ + + /* Get node coordinates and dof list: */ + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + + /*Retrieve all inputs we will be needing: */ + Input* adjoint_input=inputs->GetInput(AdjointEnum); _assert_(adjoint_input); +@@ -3972,7 +3972,7 @@ + + for(i=0;iweight*basis[i]; + } +- gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); ++ gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; +@@ -3987,7 +3987,7 @@ + + /*get gradient indices*/ + for(int i=0;inodes[i]->GetVertexDof() + control_index; ++ indexing[i]=num_controls*this->nodes[i]->GetVertexPid() + control_index; + } + + } +@@ -5204,14 +5204,14 @@ + /*FUNCTION Tria::GetVectorFromControlInputs{{{*/ + void Tria::GetVectorFromControlInputs(Vector* vector,int control_enum,int control_index,const char* data){ + +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + Input *input=NULL; + + /*Get out if this is not an element input*/ + if(!IsInput(control_enum)) return; + + /*Prepare index list*/ +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + + /*Get input (either in element or material)*/ + if(control_enum==MaterialsRheologyBbarEnum || control_enum==MaterialsRheologyZbarEnum){ +@@ -5226,14 +5226,14 @@ + _error_("input " << EnumToStringx(control_enum) << " is not a ControlInput"); + } + +- ((ControlInput*)input)->GetVectorFromInputs(vector,&doflist1[0],data); ++ ((ControlInput*)input)->GetVectorFromInputs(vector,&vertexpidlist[0],data); + } + /*}}}*/ + /*FUNCTION Tria::SetControlInputsFromVector{{{*/ + void Tria::SetControlInputsFromVector(IssmDouble* vector,int control_enum,int control_index){ + + IssmDouble values[NUMVERTICES]; +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + Input *input = NULL; + Input *new_input = NULL; + +@@ -5241,11 +5241,11 @@ + if(!IsInput(control_enum)) return; + + /*Prepare index list*/ +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + + /*Get values on vertices*/ + for (int i=0;inodes[i]->GetSidList()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!) ++ values[i]=vector[this->nodes[i]->GetVertexSidList()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!) + } + + /*Branch on the specified type of update: */ +@@ -5661,7 +5661,7 @@ + + /*create input values: */ + for(i=0;i<3;i++){ +- row=this->nodes[i]->GetSidList(); ++ row=this->nodes[i]->GetVertexSidList(); + values[i]=(IssmDouble)matrix[ncols*row+t]; + } + +Index: ../trunk-jpl/src/c/classes/objects/Elements/Tria.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Tria.h (revision 13409) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Tria.h (revision 13410) +@@ -189,8 +189,8 @@ + IssmDouble GetArea(void); + int GetElementType(void); + void GetDofList(int** pdoflist,int approximation_enum,int setenum); +- void GetDofList1(int* doflist); +- void GetSidList(int* sidlist); ++ void GetVertexPidList(int* doflist); ++ void GetVertexSidList(int* sidlist); + void GetConnectivityList(int* connectivity); + void GetInputListOnVertices(IssmDouble* pvalue,int enumtype); + void GetInputListOnVertices(IssmDouble* pvalue,int enumtype,IssmDouble defaultvalue); +Index: ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp (revision 13409) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp (revision 13410) +@@ -814,14 +814,22 @@ + *pdoflist=doflist; + } + /*}}}*/ +-/*FUNCTION Penta::GetDofList1 {{{*/ +-void Penta::GetDofList1(int* doflist){ ++/*FUNCTION Penta::GetVertexPidList {{{*/ ++void Penta::GetVertexPidList(int* doflist){ + + int i; +- for(i=0;i<6;i++) doflist[i]=nodes[i]->GetDofList1(); ++ for(i=0;i<6;i++) doflist[i]=nodes[i]->GetVertexPid(); + + } + /*}}}*/ ++/*FUNCTION Penta::GetVertexSidList{{{*/ ++void Penta::GetVertexSidList(int* sidlist){ ++ ++ int i; ++ for(i=0;iGetVertexSid(); ++ ++} ++/*}}}*/ + /*FUNCTION Penta::GetConnectivityList {{{*/ + void Penta::GetConnectivityList(int* connectivity){ + for(int i=0;iGetConnectivity(); +@@ -996,14 +1004,6 @@ + *phi=4*pow(epsilon_eff,2.0)*viscosity; + } + /*}}}*/ +-/*FUNCTION Penta::GetSidList{{{*/ +-void Penta::GetSidList(int* sidlist){ +- +- int i; +- for(i=0;iGetSidList(); +- +-} +-/*}}}*/ + /*FUNCTION Penta::GetSolutionFromInputs{{{*/ + void Penta::GetSolutionFromInputs(Vector* solution){ + +@@ -1134,20 +1134,20 @@ + /*FUNCTION Penta::GetVectorFromInputs{{{*/ + void Penta::GetVectorFromInputs(Vector* vector,int input_enum){ + +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + + /*Get out if this is not an element input*/ + if (!IsInput(input_enum)) return; + + /*Prepare index list*/ +- this->GetDofList1(&doflist1[0]); ++ this->GetVertexPidList(&vertexpidlist[0]); + + /*Get input (either in element or material)*/ + Input* input=inputs->GetInput(input_enum); + if(!input) _error_("Input " << EnumToStringx(input_enum) << " not found in element"); + + /*We found the enum. Use its values to fill into the vector, using the vertices ids: */ +- input->GetVectorFromInputs(vector,&doflist1[0]); ++ input->GetVectorFromInputs(vector,&vertexpidlist[0]); + } + /*}}}*/ + /*FUNCTION Penta::GetVectorFromResults{{{*/ +@@ -1159,11 +1159,11 @@ + _error_("Results of offset "<InstanceEnum())<<" when "<GetSidList(&doflist1[0]); ++ this->GetVertexSidList(&vertexpidlist[0]); + this->GetConnectivityList(&connectivity[0]); +- elementresult->GetVectorFromResults(vector,&doflist1[0],&connectivity[0],NUMVERTICES); ++ elementresult->GetVectorFromResults(vector,&vertexpidlist[0],&connectivity[0],NUMVERTICES); + } + else if(interp==P0Enum){ + elementresult->GetElementVectorFromResults(vector,sid); +@@ -1959,7 +1959,7 @@ + + /*Get values on the 6 vertices*/ + for (int i=0;i<6;i++){ +- values[i]=vector[this->nodes[i]->GetVertexDof()]; ++ values[i]=vector[this->nodes[i]->GetVertexPid()]; + } + + /*update input*/ +@@ -4462,7 +4462,7 @@ + /*FUNCTION Penta::ControlInputGetGradient{{{*/ + void Penta::ControlInputGetGradient(Vector* gradient,int enum_type,int control_index){ + +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + Input* input=NULL; + + if(enum_type==MaterialsRheologyBbarEnum){ +@@ -4480,8 +4480,8 @@ + if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found"); + if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput"); + +- GradientIndexing(&doflist1[0],control_index); +- ((ControlInput*)input)->GetGradient(gradient,&doflist1[0]); ++ GradientIndexing(&vertexpidlist[0],control_index); ++ ((ControlInput*)input)->GetGradient(gradient,&vertexpidlist[0]); + + }/*}}}*/ + /*FUNCTION Penta::ControlInputScaleGradient{{{*/ +@@ -4506,7 +4506,7 @@ + /*FUNCTION Penta::ControlInputSetGradient{{{*/ + void Penta::ControlInputSetGradient(IssmDouble* gradient,int enum_type,int control_index){ + +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + IssmDouble grad_list[NUMVERTICES]; + Input* grad_input=NULL; + Input* input=NULL; +@@ -4523,8 +4523,8 @@ + if (!input) _error_("Input " << EnumToStringx(enum_type) << " not found"); + if (input->ObjectEnum()!=ControlInputEnum) _error_("Input " << EnumToStringx(enum_type) << " is not a ControlInput"); + +- GradientIndexing(&doflist1[0],control_index); +- for(int i=0;iSetGradient(grad_input); + +@@ -4801,7 +4801,7 @@ + + /*get gradient indices*/ + for(int i=0;inodes[i]->GetVertexDof() + control_index; ++ indexing[i]=num_controls*this->nodes[i]->GetVertexPid() + control_index; + } + + } +@@ -4914,7 +4914,7 @@ + + int i,j,ig; + int analysis_type; +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + IssmDouble vx,vy,lambda,mu,alpha_complement,Jdet; + IssmDouble bed,thickness,Neff,drag; + IssmDouble xyz_list[NUMVERTICES][3]; +@@ -4931,7 +4931,7 @@ + + /*Retrieve all inputs and parameters*/ + parameters->FindParam(&analysis_type,AnalysisTypeEnum); +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); + for(i=0;iGetInput(AdjointxEnum); _assert_(adjointx_input); +@@ -4973,7 +4973,7 @@ + grade_g[i]+=grade_g_gaussian[i]; + } + } +- gradient->SetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); ++ gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL); + + /*Clean up and return*/ + delete gauss; +@@ -4985,7 +4985,7 @@ + + int i,j,ig; + int analysis_type; +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + IssmDouble bed,thickness,Neff; + IssmDouble lambda,mu,xi,Jdet,vx,vy,vz; + IssmDouble alpha_complement,drag; +@@ -5006,7 +5006,7 @@ + parameters->FindParam(&analysis_type,AnalysisTypeEnum); + GetVerticesCoordinates(&xyz_list[0][0], nodes, NUMVERTICES); + for(i=0;iGetInput(FrictionCoefficientEnum); _assert_(drag_input); + Input* vx_input =inputs->GetInput(VxEnum); _assert_(vx_input); + Input* vy_input =inputs->GetInput(VyEnum); _assert_(vy_input); +@@ -5066,7 +5066,7 @@ + for( i=0; iSetValues(NUMVERTICES,doflist1,grade_g,ADD_VAL); ++ gradient->SetValues(NUMVERTICES,vertexpidlist,grade_g,ADD_VAL); + + delete friction; + delete gauss; +@@ -5493,13 +5493,13 @@ + /*FUNCTION Penta::GetVectorFromControlInputs{{{*/ + void Penta::GetVectorFromControlInputs(Vector* vector,int control_enum,int control_index,const char* data){ + +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + + /*Get out if this is not an element input*/ + if(!IsInput(control_enum)) return; + + /*Prepare index list*/ +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + + /*Get input (either in element or material)*/ + Input* input=inputs->GetInput(control_enum); +@@ -5510,14 +5510,14 @@ + _error_("input " << EnumToStringx(control_enum) << " is not a ControlInput"); + } + +- ((ControlInput*)input)->GetVectorFromInputs(vector,&doflist1[0],data); ++ ((ControlInput*)input)->GetVectorFromInputs(vector,&vertexpidlist[0],data); + } + /*}}}*/ + /*FUNCTION Penta::SetControlInputsFromVector{{{*/ + void Penta::SetControlInputsFromVector(IssmDouble* vector,int control_enum,int control_index){ + + IssmDouble values[NUMVERTICES]; +- int doflist1[NUMVERTICES]; ++ int vertexpidlist[NUMVERTICES]; + Input *input = NULL; + Input *new_input = NULL; + +@@ -5525,11 +5525,11 @@ + if(!IsInput(control_enum)) return; + + /*Prepare index list*/ +- GradientIndexing(&doflist1[0],control_index); ++ GradientIndexing(&vertexpidlist[0],control_index); + + /*Get values on vertices*/ + for (int i=0;inodes[i]->GetSidList()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!) ++ values[i]=vector[this->nodes[i]->GetVertexSid()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!) + } + + /*Branch on the specified type of update: */ +@@ -5688,7 +5688,7 @@ + + /*create input values: */ + for(i=0;i<6;i++){ +- row=this->nodes[i]->GetSidList(); ++ row=this->nodes[i]->GetVertexSid(); + values[i]=(IssmDouble)matrix[ncols*row+t]; + } + +Index: ../trunk-jpl/src/c/classes/objects/Elements/Penta.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Penta.h (revision 13409) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Penta.h (revision 13410) +@@ -173,8 +173,8 @@ + ElementVector* CreatePVectorPrognostic(void); + ElementVector* CreatePVectorSlope(void); + void GetDofList(int** pdoflist,int approximation_enum,int setenum); +- void GetDofList1(int* doflist); +- void GetSidList(int* sidlist); ++ void GetVertexPidList(int* doflist); ++ void GetVertexSidList(int* sidlist); + void GetConnectivityList(int* connectivity); + int GetElementType(void); + void GetElementSizes(IssmDouble* hx,IssmDouble* hy,IssmDouble* hz); Index: /issm/oecreview/Archive/13393-13976/ISSM-13410-13411.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13410-13411.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13410-13411.diff (revision 13980) @@ -0,0 +1,321 @@ +Index: ../trunk-jpl/src/m/classes/plotoptions.py +=================================================================== +--- ../trunk-jpl/src/m/classes/plotoptions.py (revision 0) ++++ ../trunk-jpl/src/m/classes/plotoptions.py (revision 13411) +@@ -0,0 +1,125 @@ ++from collections import OrderedDict, Counter, defaultdict ++from pairoptions import * ++ ++class plotoptions(object): ++ ''' ++ PLOTOPTIONS class definition ++ ++ Usage: ++ plotoptions=plotoptions(*arg) ++ ''' ++ ++ def __init__(self,*arg): ++ self.numberofplots = 0 ++ self.figurenumber = 1 ++ self.list = OrderedDict() ++ ++ self.buildlist(*arg) ++ ++ def __repr__(self): #{{{ ++ s="\n" ++ s+=" numberofplots: %i\n" % self.numberofplots ++ s+=" figurenumber: %i\n" % self.figurenumber ++ if self.list: ++ s+=" list: (%ix%i)\n" % (len(self.list),2) ++ for item in self.list.iteritems(): ++ #s+=" options of plot number %i\n" % item ++ if isinstance(item[1],(str,unicode)): ++ s+=" field: %-10s value: '%s'\n" % (item[0],item[1]) ++ elif isinstance(item[1],(bool,int,long,float)): ++ s+=" field: %-10s value: '%g'\n" % (item[0],item[1]) ++ else: ++ s+=" field: %-10s value: '%s'\n" % (item[0],item[1]) ++ else: ++ s+=" list: empty\n" ++ return s ++ #}}} ++ def buildlist(self,*arg): #{{{ ++ #check length of input ++ if len(arg) % 2: ++ raise TypeError('error: an even number of options is required') ++ ++ #go through args and build list (like pairoptions) ++ rawoptions=pairoptions(*arg) ++ numoptions=len(arg)/2 ++ rawlist=[] # cannot be a dict since they do not support duplicate keys ++ ++ for i in xrange(numoptions): ++ if isinstance(arg[2*i],(str,unicode)): ++ rawlist.append([arg[2*i],arg[2*i+1]]) ++ else: ++ #option is not a string, ignore it ++ print "WARNING: option number %d is not a string and will be ignored." % (i+1) ++ ++ #get figure number ++ self.figurenumber=rawoptions.getfieldvalue('figure',1) ++ ++ #get number of subplots ++ numberofplots=Counter(x for sublist in rawlist for x in sublist if isinstance(x,(str,unicode)))['data'] ++ self.numberofplots=numberofplots ++ ++ #figure out whether alloptions flag is on ++ if rawoptions.getfieldvalue('alloptions','off') is 'on': ++ allflag=1 ++ else: ++ allflag=0 ++ ++ #initialize self.list (will need a list of dict's (or nested dict) for numberofplots>1) ++ #self.list=defaultdict(dict) ++ for i in xrange(numberofplots): ++ self.list[i]=pairoptions() ++ ++ #process plot options ++ for i in xrange(len(rawlist)): ++ ++ #if alloptions flag is on, apply to all plots ++ if (allflag and 'data' not in rawlist[i][0] and '#' not in rawlist[i][0]): ++ ++ for j in xrange(numberofplots): ++ self.list[j].addfield(rawlist[i][0],rawlist[i][1]) ++ ++ elif '#' in rawlist[i][0]: ++ ++ #get subplots associated ++ string=rawlist[i][0].split('#') ++ plotnums=string[-1].split(',') ++ field=string[0] ++ ++ #loop over plotnums ++ for k in xrange(len(plotnums)): ++ plotnum=plotnums[k] ++ ++ #Empty ++ if not plotnum: continue ++ ++ elif 'all' in plotnum: ++ for j in xrange(numberofplots): ++ self.list[j].addfield(field,rawlist[i][1]) ++ ++ elif '-' in plotnum: ++ nums=plotnum.split('-') ++ if len(nums)!=2: continue ++ if False in [x.isdigit() for x in nums]: ++ raise ValueError('error: in option i-j both i and j must be integers') ++ for j in xrange(int(nums[0])-1,int(nums[1])): ++ self.list[j].addfield(field,rawlist[i][1]) ++ ++ # Deal with #i ++ else: ++ #assign to subplot ++ if int(plotnum)>numberofplots: ++ raise ValueError('error: %s cannot be assigned %d which exceeds the number of subplots' % (field,plotnum)) ++ self.list[int(plotnum)-1].addfield(field,rawlist[i][1]) ++ else: ++ ++ #go through all subplots and assign key-value pairs ++ j=0 ++ while j <= numberofplots-1: ++ if not self.list[j].exist(rawlist[i][0]): ++ self.list[j].addfield(rawlist[i][0],rawlist[i][1]) ++ break ++ else: ++ j=j+1 ++ if j+1>numberofplots: ++ print "WARNING: too many instances of '%s' in options" % rawlist[i][0] ++ #}}} +Index: ../trunk-jpl/src/m/classes/pairoptions.py +=================================================================== +--- ../trunk-jpl/src/m/classes/pairoptions.py (revision 13410) ++++ ../trunk-jpl/src/m/classes/pairoptions.py (revision 13411) +@@ -40,7 +40,7 @@ + self.list[arg[2*i]] = arg[2*i+1]; + else: + #option is not a string, ignore it +- print "WARNING: option number %d '%s' is not a string and will be ignored." % (i+1,type(arg[2*i])) ++ print "WARNING: option number %d is not a string and will be ignored." % (i+1) + # }}} + + def addfield(self,field,value): # {{{ +@@ -127,18 +127,20 @@ + return False + # }}} + +-# function num = fieldoccurences(obj,field), % {{{ +-# %FIELDOCCURENCES - get number of occurence of a field +-# +-# %check input +-# if ~ischar(field), +-# error('fieldoccurences error message: field should be a string'); +-# end +-# +-# %get number of occurence +-# num=sum(strcmpi(field,obj.list(:,1))); +-# end % }}} ++ #def fieldoccurences(self,field): #{{{ ++ # ''' ++ # FIELDOCCURENCES - get number of occurence of a field ++ # ''' ++ # ++ # #check input ++ # if not isinstance(field,(str,unicode)): ++ # raise TypeError("fieldoccurences error message: field should be a string") + ++ # #get number of occurence ++ # # ?? ++ # #return num ++ # #% }}} ++ + def getfieldvalue(self,field,default=None): # {{{ + """ + GETOPTION - get the value of an option +Index: ../trunk-jpl/src/m/plot/plot_manager.py +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_manager.py (revision 0) ++++ ../trunk-jpl/src/m/plot/plot_manager.py (revision 13411) +@@ -0,0 +1,32 @@ ++from pairoptions import * ++import pylab as p ++from checkplotoptions import * ++from plot_mesh import * ++ ++def plot_manager(md,options,subplotwidth,nlines,ncols,i): ++ ''' ++ PLOT_MANAGER - distribute the plots called by plotmodel ++ ++ Usage: ++ plot_manager(md,options,subplotwidth,i); ++ ++ See also: PLOTMODEL, PLOT_UNIT ++ ''' ++ ++ #parse options and get a structure of options ++ options=checkplotoptions(md,options) ++ #print 'options:', options ++ ++ #get data to be plotted ++ data=options.getfieldvalue('data'); ++ ++ #figure out if this is a special plot ++ if isinstance(data,(str,unicode)): ++ ++ if data=='mesh': plot_mesh(md,options,nlines,ncols,i) ++ else: ++ print "WARNING: '%s' is not implemented or is not a valid string for option 'data'" % data ++ ++ else: ++ print "'data' not a string, plotting model properties yet to be implemented..." ++ +Index: ../trunk-jpl/src/m/plot/checkplotoptions.py +=================================================================== +--- ../trunk-jpl/src/m/plot/checkplotoptions.py (revision 0) ++++ ../trunk-jpl/src/m/plot/checkplotoptions.py (revision 13411) +@@ -0,0 +1,15 @@ ++def checkplotoptions(md,options): ++ ''' ++ CHECKPLOTOPTIONS - build a structure that holds all plot options ++ ++ Usage: ++ options=checkplotoptions(md,options) ++ ++ See also: PLOTMODEL ++ ++ NOTE: not fully implemented yet ++ ''' ++ ++ print "WARNING: checkplotoptions not implemented: options returned as passed" ++ return options ++ +Index: ../trunk-jpl/src/m/plot/plot_mesh.py +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_mesh.py (revision 0) ++++ ../trunk-jpl/src/m/plot/plot_mesh.py (revision 13411) +@@ -0,0 +1,24 @@ ++import pylab as p ++import matplotlib.tri as tri ++ ++def plot_mesh(md,options,nlines,ncols,i): ++ ''' ++ PLOT_MESH - plot model mesh ++ ++ Usage: ++ plot_mesh(md,options,nlines,ncols,i) ++ ++ See also: PLOTMODEL ++ ''' ++ ++ #TODO: implement processmesh ++ x=md.mesh.x ++ y=md.mesh.y ++ elements=md.mesh.elements ++ elements=elements-1 #since python indexes from zero ++ ++ p.subplot(nlines,ncols,i) ++ p.triplot(x,y,elements) ++ p.title('Mesh') ++ ++ print 'WARNING: options passed to plot_mesh not implemented yet' +Index: ../trunk-jpl/src/m/plot/plotmodel.py +=================================================================== +--- ../trunk-jpl/src/m/plot/plotmodel.py (revision 0) ++++ ../trunk-jpl/src/m/plot/plotmodel.py (revision 13411) +@@ -0,0 +1,55 @@ ++import pylab as p ++#from pairoptions import * ++from plotoptions import * ++from plot_manager import * ++ ++def plotmodel(md,*args): ++ ''' ++ at command prompt, type 'plotdoc' for additional documentation ++ ''' ++ ++ #First process options ++ options=plotoptions(*args) ++ ++ #get number of subplots ++ subplotwidth=math.ceil(math.sqrt(options.numberofplots)) ++ ++ #if nlines and ncols specified, then bypass ++ if options.list[0].exist('nlines'): ++ nlines=options.list[0].getfieldvalue('nlines') ++ nl=True ++ else: ++ nlines=subplotwidth ++ nl=False ++ ++ if options.list[0].exist('ncols'): ++ ncols=options.list[0].getfieldvalue('ncols') ++ nc=True ++ else: ++ ncols=subplotwidth ++ nc=False ++ ++ #check that nlines and ncols were given at the same time! ++ if not nl==nc: ++ raise StandardError('error: nlines and ncols need to be specified together, or not at all') ++ ++ #Get figure number and number of plots ++ figurenumber=options.figurenumber ++ numberofplots=options.numberofplots ++ ++ #Go through plots ++ if numberofplots: ++ ++ #Create figure ++ #plots will be visible by default if ipython is run in interactive mode (invoked by ipython --pylab) ++ #handling the 'visible' option will need some check on whether ipython is currently in interactive or non-interactive mode ++ p.figure(figurenumber) ++ ++ try: ++ for i in xrange(numberofplots): ++ plot_manager(options.list[i].getfieldvalue('model',md),options.list[i],subplotwidth,nlines,ncols,i) ++ except StandardError: ++ print 'error in plot_manager' ++ else: ++ raise StandardError('plotmodel error message: no output data found.') ++ Index: /issm/oecreview/Archive/13393-13976/ISSM-13411-13412.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13411-13412.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13411-13412.diff (revision 13980) @@ -0,0 +1,462 @@ +Index: ../trunk-jpl/src/c/matlab/io/PrintfFunction.cpp +=================================================================== +--- ../trunk-jpl/src/c/matlab/io/PrintfFunction.cpp (revision 13411) ++++ ../trunk-jpl/src/c/matlab/io/PrintfFunction.cpp (revision 13412) +@@ -18,8 +18,7 @@ + int n,size = 100; + int string_size; + extern int my_rank; +- extern int num_procs; +- ++ + //variable list of arguments + va_list args; + +Index: ../trunk-jpl/src/c/io/PrintfFunction.cpp +=================================================================== +--- ../trunk-jpl/src/c/io/PrintfFunction.cpp (revision 13411) ++++ ../trunk-jpl/src/c/io/PrintfFunction.cpp (revision 13412) +@@ -16,8 +16,6 @@ + int n,size = 100; + int string_size; + extern int my_rank; +- extern int num_procs; +- + //variable list of arguments + va_list args; + +Index: ../trunk-jpl/src/c/modules/ResetConstraintsx/ResetConstraintsx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ResetConstraintsx/ResetConstraintsx.cpp (revision 13411) ++++ ../trunk-jpl/src/c/modules/ResetConstraintsx/ResetConstraintsx.cpp (revision 13412) +@@ -12,11 +12,6 @@ + + void ResetConstraintsx(Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads,Materials* materials, Parameters* parameters){ + +- int i; +- +- extern int num_procs; +- extern int my_rank; +- + /*output: */ + int analysis_type; + +Index: ../trunk-jpl/src/c/modules/ConstraintsStatex/ConstraintsStatex.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ConstraintsStatex/ConstraintsStatex.cpp (revision 13411) ++++ ../trunk-jpl/src/c/modules/ConstraintsStatex/ConstraintsStatex.cpp (revision 13412) +@@ -12,11 +12,6 @@ + + void ConstraintsStatex(int* pconverged, int* pnum_unstable_constraints, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads,Materials* materials, Parameters* parameters){ + +- int i; +- +- extern int num_procs; +- extern int my_rank; +- + /*output: */ + int converged=0; + int num_unstable_constraints=0; +Index: ../trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp (revision 13411) ++++ ../trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp (revision 13412) +@@ -11,28 +11,24 @@ + + void MassFluxx(IssmDouble* pmass_flux, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,bool process_units){ + +- int i,j; +- extern int num_procs; +- extern int my_rank; ++ int i,j; ++ Element *element = NULL; ++ int element_id; + +- Element* element=NULL; +- int element_id; +- + /*output: */ + IssmDouble mass_flux=0; + IssmDouble all_mass_flux=0; +- + int counter; + + /*all segments: */ +- IssmDouble** array=NULL; +- int M; +- int* mdims_array=NULL; +- int* ndims_array=NULL; ++ IssmDouble **array = NULL; ++ int M; ++ int *mdims_array = NULL; ++ int *ndims_array = NULL; + + /*our segments of interest: */ +- IssmDouble* segments=NULL; +- int num_segments; ++ IssmDouble *segments = NULL; ++ int num_segments; + + /*First, figure out which segment to compute our mass flux on. Start with retrieving qmu_mass_flux_segments: */ + parameters->FindParam(&array,&M,&mdims_array,&ndims_array,QmuMassFluxSegmentsEnum); +Index: ../trunk-jpl/src/c/classes/DofIndexing.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/DofIndexing.cpp (revision 13411) ++++ ../trunk-jpl/src/c/classes/DofIndexing.cpp (revision 13412) +@@ -20,17 +20,17 @@ + /*FUNCTION DofIndexing::DofIndexing(){{{*/ + DofIndexing::DofIndexing(){ + +- this->gsize=UNDEF; +- this->fsize=UNDEF; +- this->ssize=UNDEF; +- this->clone=0; +- this->f_set=NULL; +- this->s_set=NULL; +- this->svalues=NULL; +- this->doftype=NULL; +- this->gdoflist=NULL; +- this->fdoflist=NULL; +- this->sdoflist=NULL; ++ this->gsize = UNDEF; ++ this->fsize = UNDEF; ++ this->ssize = UNDEF; ++ this->clone = false; ++ this->f_set = NULL; ++ this->s_set = NULL; ++ this->svalues = NULL; ++ this->doftype = NULL; ++ this->gdoflist = NULL; ++ this->fdoflist = NULL; ++ this->sdoflist = NULL; + + } + /*}}}*/ +@@ -42,12 +42,10 @@ + /*FUNCTION DofIndexing::DofIndexing(DofIndexing* in) -> copy{{{*/ + DofIndexing::DofIndexing(DofIndexing* in){ //copy constructor + +- int i; +- this->gsize=in->gsize; +- this->fsize=in->fsize; +- this->ssize=in->ssize; +- +- this->clone=in->clone; ++ this->gsize = in->gsize; ++ this->fsize = in->fsize; ++ this->ssize = in->ssize; ++ this->clone = in->clone; + + if(this->gsize>0){ + this->f_set=xNew(this->gsize); +@@ -57,11 +55,11 @@ + this->gdoflist=xNew(this->gsize); + } + else{ +- this->f_set=NULL; +- this->s_set=NULL; +- this->svalues=NULL; +- this->doftype=NULL; +- this->gdoflist=NULL; ++ this->f_set = NULL; ++ this->s_set = NULL; ++ this->svalues = NULL; ++ this->doftype = NULL; ++ this->gdoflist = NULL; + } + if(this->fsize>0 && this->fsize!=UNDEF)this->fdoflist=xNew(this->fsize); else this->fdoflist=NULL; + if(this->ssize>0 && this->ssize!=UNDEF)this->sdoflist=xNew(this->ssize); else this->sdoflist=NULL; +@@ -94,10 +92,8 @@ + /*FUNCTION DofIndexing::Init{{{*/ + void DofIndexing::Init(int in_gsize,int* in_doftype){ + +- int i; + this->gsize=in_gsize; +- +- this->clone=0; ++ this->clone=false; + + /*allocate: */ + if(this->gsize>0){ +@@ -108,7 +104,7 @@ + this->gdoflist=xNew(this->gsize); + } + +- for (i=0;igsize;i++){ ++ for(int i=0;igsize;i++){ + /*assume dof is free, no constraints, no rigid body constraint: */ + this->f_set[i]=true; + this->s_set[i]=false; +Index: ../trunk-jpl/src/c/classes/DofIndexing.h +=================================================================== +--- ../trunk-jpl/src/c/classes/DofIndexing.h (revision 13411) ++++ ../trunk-jpl/src/c/classes/DofIndexing.h (revision 13412) +@@ -17,7 +17,7 @@ + int ssize; //number of constrained dofs + + /*partitioning: */ +- int clone; //this node is replicated from another one ++ bool clone; //this node is replicated from another one + + /*boundary conditions sets: */ + bool* f_set; //is dof on f-set (on which we solve) +Index: ../trunk-jpl/src/c/classes/objects/Node.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Node.cpp (revision 13411) ++++ ../trunk-jpl/src/c/classes/objects/Node.cpp (revision 13412) +@@ -871,7 +871,6 @@ + void Node::DistributeDofs(int* pdofcount,int setenum){ + + int i; +- extern int my_rank; + int dofcount; + + dofcount=*pdofcount; +@@ -880,14 +879,12 @@ + if(setenum==FsetEnum) this->indexing.InitSet(setenum); + if(setenum==SsetEnum) this->indexing.InitSet(setenum); + +- + /*For clone nodfs, don't distribute dofs, we will get them from another cpu in UpdateCloneDofs!*/ + if(indexing.clone){ + return; + } + + /*This node should distribute dofs for setenum set (eg, f_set or s_set), go ahead: */ +- + if(setenum==GsetEnum){ + for(i=0;iindexing.gsize;i++){ + indexing.gdoflist[i]=dofcount+i; +@@ -908,17 +905,14 @@ + } + else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!"); + +- + /*Assign output pointers: */ + *pdofcount=dofcount; +- + } + /*}}}*/ + /*FUNCTION Node::OffsetDofs{{{*/ + void Node::OffsetDofs(int dofcount,int setenum){ + + int i; +- extern int my_rank; + + if(indexing.clone){ + /*This node is a clone, don't off_set the dofs!: */ +@@ -942,16 +936,24 @@ + void Node::ShowTrueDofs(int* truedofs, int ncols,int setenum){ + + int j; +- extern int my_rank; +- ++ + /*Are we a clone? : */ +- if(indexing.clone)return; ++ if(indexing.clone) return; + + /*Ok, we are not a clone, just plug our dofs into truedofs: */ +- if(setenum==GsetEnum)for(j=0;jindexing.gsize;j++) *(truedofs+ncols*sid+j)=indexing.gdoflist[j]; +- else if(setenum==FsetEnum)for(j=0;jindexing.fsize;j++) *(truedofs+ncols*sid+j)=indexing.fdoflist[j]; +- else if(setenum==SsetEnum)for(j=0;jindexing.ssize;j++) *(truedofs+ncols*sid+j)=indexing.sdoflist[j]; +- else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!"); ++ switch(setenum){ ++ case GsetEnum: ++ for(j=0;jindexing.gsize;j++) truedofs[ncols*sid+j]=indexing.gdoflist[j]; ++ break; ++ case FsetEnum: ++ for(j=0;jindexing.fsize;j++) truedofs[ncols*sid+j]=indexing.fdoflist[j]; ++ break; ++ case SsetEnum: ++ for(j=0;jindexing.ssize;j++) truedofs[ncols*sid+j]=indexing.sdoflist[j]; ++ break; ++ default: ++ _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!"); ++ } + + } + /*}}}*/ +@@ -959,19 +961,25 @@ + void Node::UpdateCloneDofs(int* alltruedofs,int ncols,int setenum){ + + int j; +- extern int my_rank; +- ++ + /*If we are not a clone, don't update, we already have dofs!: */ +- if(indexing.clone==0)return; ++ if(!indexing.clone)return; + +- + /*Ok, we are a clone node, but we did not create the dofs for this node. +- * * Therefore, our doflist is garbage right now. Go pick it up in the alltruedofs: */ +- if(setenum==GsetEnum)for(j=0;jindexing.gsize;j++) indexing.gdoflist[j]=*(alltruedofs+ncols*sid+j); +- else if(setenum==FsetEnum)for(j=0;jindexing.fsize;j++) indexing.fdoflist[j]=*(alltruedofs+ncols*sid+j); +- else if(setenum==SsetEnum)for(j=0;jindexing.ssize;j++) indexing.sdoflist[j]=*(alltruedofs+ncols*sid+j); +- else _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!"); +- ++ *Therefore, our doflist is garbage right now. Go pick it up in the alltruedofs: */ ++ switch(setenum){ ++ case GsetEnum: ++ for(j=0;jindexing.gsize;j++) indexing.gdoflist[j]=alltruedofs[ncols*sid+j]; ++ break; ++ case FsetEnum: ++ for(j=0;jindexing.fsize;j++) indexing.fdoflist[j]=alltruedofs[ncols*sid+j]; ++ break; ++ case SsetEnum: ++ for(j=0;jindexing.ssize;j++) indexing.sdoflist[j]=alltruedofs[ncols*sid+j]; ++ break; ++ default: ++ _error_("set of enum type " << EnumToStringx(setenum) << " not supported yet!"); ++ } + } + /*}}}*/ + /*FUNCTION Node::SetClone {{{*/ +@@ -980,13 +988,12 @@ + extern int my_rank; + + if (minranks[sid]==my_rank){ +- indexing.clone=0; ++ indexing.clone=false; + } + else{ + /*!there is a cpu with lower rank that has the same node, + therefore, I am a clone*/ +- indexing.clone=1; ++ indexing.clone=true; + } +- + } + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13411) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13412) +@@ -227,19 +227,18 @@ + void IoModel::FetchConstants(void){ + + extern int my_rank; +- extern int num_procs; + + /*record descriptions; */ + int record_enum; + int record_length; +- int record_code; //1 to 7 number ++ int record_code; //1 to 7 number + + /*records: */ +- int booleanint=0; +- int integer=0; +- IssmPDouble scalar=0; +- char* string=NULL; +- int string_size; ++ int booleanint = 0; ++ int integer = 0; ++ IssmPDouble scalar = 0; ++ char *string = NULL; ++ int string_size; + + /*Check that some fields have been allocated*/ + _assert_(this->fid || my_rank); +@@ -457,8 +456,6 @@ + void IoModel::FetchData(bool* pboolean,int data_enum){ + + extern int my_rank; +- extern int num_procs; +- + + /*output: */ + int booleanint; +@@ -487,7 +484,6 @@ + void IoModel::FetchData(int* pinteger,int data_enum){ + + extern int my_rank; +- extern int num_procs; + + /*output: */ + int integer; +@@ -514,10 +510,7 @@ + /*FUNCTION IoModel::FetchData(IssmDouble* pscalar,int data_enum){{{*/ + void IoModel::FetchData(IssmDouble* pscalar,int data_enum){ + +- + extern int my_rank; +- extern int num_procs; +- + + /*output: */ + IssmPDouble scalar; +@@ -545,8 +538,6 @@ + void IoModel::FetchData(char** pstring,int data_enum){ + + extern int my_rank; +- extern int num_procs; +- + + /*output: */ + char* string=NULL; +@@ -596,7 +587,6 @@ + void IoModel::FetchData(int** pmatrix,int* pM,int* pN,int data_enum){ + + extern int my_rank; +- extern int num_procs; + int i,j; + + /*output: */ +@@ -671,7 +661,6 @@ + void IoModel::FetchData(IssmDouble** pmatrix,int* pM,int* pN,int data_enum){ + + extern int my_rank; +- extern int num_procs; + + /*output: */ + int M,N; +@@ -736,8 +725,6 @@ + void IoModel::FetchData(char*** pstrings,int* pnumstrings,int data_enum){ + + extern int my_rank; +- extern int num_procs; +- + int i; + + /*output: */ +@@ -808,7 +795,6 @@ + int i; + + extern int my_rank; +- extern int num_procs; + + /*output: */ + IssmDouble** matrices=NULL; +@@ -897,12 +883,9 @@ + /*FUNCTION IoModel::FetchData(Option** poption,int data_enum){{{*/ + void IoModel::FetchData(Option** poption,int index){ + +- extern int my_rank; +- extern int num_procs; +- + /*output: */ +- int code; +- char *name = NULL; ++ int code; ++ char *name = NULL; + + /*First get option name*/ + this->FetchData(&name,index); +@@ -1219,7 +1202,6 @@ + FILE* IoModel::SetFilePointerToData(int* pcode,int* pvector_type, int data_enum){ + + extern int my_rank; +- extern int num_procs; + + int found=0; + int record_enum; +@@ -1314,7 +1296,6 @@ + + #ifdef _HAVE_ADOLC_ //cannot come here unless you are running AD mode, from DeclaredIndependents: + extern int my_rank; +- extern int num_procs; + + /*output: */ + int M,N; Index: /issm/oecreview/Archive/13393-13976/ISSM-13412-13413.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13412-13413.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13412-13413.diff (revision 13980) @@ -0,0 +1,895 @@ +Index: ../trunk-jpl/src/c/Container/Nodes.cpp +=================================================================== +--- ../trunk-jpl/src/c/Container/Nodes.cpp (revision 13412) ++++ ../trunk-jpl/src/c/Container/Nodes.cpp (revision 13413) +@@ -159,7 +159,6 @@ + /*Allocate ranks: */ + ranks=xNew(numnodes); + minranks=xNew(numnodes); +- + for(i=0;iSize();i++){ + +- int i; +- int rank; +- int sid; +- +- for(i=0;iSize();i++){ +- + Node* node=(Node*)this->GetObjectByOffset(i); + + /*Check that this node corresponds to our analysis currently being carried out: */ + if (node->InAnalysis(analysis_type)){ +- +- rank=node->MyRank(); ++ /*Plug rank into ranks, according to sid: */ + sid=node->Sid(); +- +- /*Plug rank into ranks, according to id: */ +- ranks[sid]=rank; ++ ranks[sid]=my_rank; + } + } +- return; + } + /*}}}*/ + /*FUNCTION Nodes::SetCurrentConfiguration{{{*/ +Index: ../trunk-jpl/src/c/Container/Vertices.cpp +=================================================================== +--- ../trunk-jpl/src/c/Container/Vertices.cpp (revision 13412) ++++ ../trunk-jpl/src/c/Container/Vertices.cpp (revision 13413) +@@ -176,20 +176,15 @@ + /*FUNCTION Vertices::Ranks{{{*/ + void Vertices::Ranks(int* ranks){ + ++ extern int my_rank; ++ int sid; ++ + /*Go through a dataset, and for each object, report it cpu: */ +- +- int i; +- int rank; +- int sid; +- +- for(i=0;iSize();i++){ ++ for(int i=0;iSize();i++){ ++ /*Plug rank into ranks, according to id: */ + Vertex* vertex=(Vertex*)this->GetObjectByOffset(i); +- rank=vertex->MyRank(); + sid=vertex->Sid(); +- +- /*Plug rank into ranks, according to id: */ +- ranks[sid]=rank; ++ ranks[sid]=my_rank; + } +- return; + } + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/DofIndexing.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/DofIndexing.cpp (revision 13412) ++++ ../trunk-jpl/src/c/classes/DofIndexing.cpp (revision 13413) +@@ -203,4 +203,3 @@ + _printLine_(""); + } + /*}}}*/ +- +Index: ../trunk-jpl/src/c/classes/Patch.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Patch.cpp (revision 13412) ++++ ../trunk-jpl/src/c/classes/Patch.cpp (revision 13413) +@@ -2,7 +2,7 @@ + * \brief: implementation of the Patch object + */ + +-/*Include files: {{{*/ ++/*Include files */ + #ifdef HAVE_CONFIG_H + #include + #else +@@ -18,26 +18,23 @@ + #include "../EnumDefinitions/EnumDefinitions.h" + #include "../shared/shared.h" + #include "../include/include.h" +-/*}}}*/ + + /*Object constructors and destructors:*/ + /*FUNCTION Patch::Patch() default constructor {{{*/ + Patch::Patch(){ +- this->numrows=0; +- this->numcols=0; +- this->maxvertices=0; +- this->maxnodes=0; +- this->values=NULL; ++ this->numrows = 0; ++ this->numcols = 0; ++ this->maxvertices = 0; ++ this->maxnodes = 0; ++ this->values = NULL; + } + /*}}}*/ + /*FUNCTION Patch::Patch(int numrows, int maxvertices, int maxnodes){{{*/ + Patch::Patch(int in_numrows, int in_maxvertices, int in_maxnodes){ + +- int i,j; + this->numrows=in_numrows; + this->maxvertices=in_maxvertices; + this->maxnodes=in_maxnodes; +- + this->numcols=1 //enum_type + +1 //step + +1 //time +@@ -51,9 +48,9 @@ + this->values=NULL; + } + else{ +- this->values=xNew(this->numcols*this->numrows); +- for(i=0;inumrows;i++){ +- for(j=0;jnumcols;j++){ ++ this->values=xNew(this->numcols*this->numrows); ++ for(int i=0;inumrows;i++){ ++ for(int j=0;jnumcols;j++){ + this->values[i*this->numcols+j]=NAN; + } + } +@@ -97,8 +94,7 @@ + row=this->values+count*this->numcols; + + /*Let's remember what is on a row: +- enum_type step time element_id interpolation vertices_ids nodal_values +- */ ++ enum_type step time element_id interpolation vertices_ids nodal_values */ + row[0]=enum_type; + row[1]=(IssmDouble)step; + row[2]=time; +Index: ../trunk-jpl/src/c/classes/Hook.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Hook.cpp (revision 13412) ++++ ../trunk-jpl/src/c/classes/Hook.cpp (revision 13413) +@@ -2,7 +2,6 @@ + * \brief: implementation of the Hook object: see Hook.h for more explanations. + */ + +- + #ifdef HAVE_CONFIG_H + #include + #else +@@ -17,32 +16,27 @@ + #include "../shared/shared.h" + #include "../include/include.h" + +- + /*Constructor/Destructors*/ + /*FUNCTION Hook::Hook(){{{*/ + Hook::Hook(){ +- this->num=0; +- this->objects=NULL; +- this->ids=NULL; +- this->offsets=NULL; +- return; ++ this->num = 0; ++ this->objects = NULL; ++ this->ids = NULL; ++ this->offsets = NULL; + } + /*}}}*/ + /*FUNCTION Hook::Hook(int* ids, int num){{{*/ + Hook::Hook(int* in_ids, int in_num){ + +- /*Intermediaries*/ +- int i; +- + /*Get number of objects to hook*/ + this->num=in_num; + + /*Get out if num=0*/ + if (num==0){ + /*Empty hook*/ +- this->ids=NULL; +- this->objects=NULL; +- this->offsets=NULL; ++ this->ids = NULL; ++ this->objects = NULL; ++ this->offsets = NULL; + } + else{ + /*Allocate: */ +@@ -51,21 +45,19 @@ + this->offsets=xNew(this->num); + + /*Copy ids: */ +- for (i=0;inum;i++){ +- this->ids[i]=in_ids[i]; +- this->objects[i]=NULL; +- this->offsets[i]=0; ++ for(int i=0;inum;i++){ ++ this->ids[i] = in_ids[i]; ++ this->objects[i] = NULL; ++ this->offsets[i] = 0; + } + } + } + /*}}}*/ + /*FUNCTION Hook::~Hook(){{{*/ + Hook::~Hook(){ +- /*deallocate: */ + xDelete(this->objects); + xDelete(this->ids); + xDelete(this->offsets); +- return; + } + /*}}}*/ + +@@ -120,8 +112,6 @@ + /*FUNCTION Hook::copy {{{*/ + Object* Hook::copy(void){ + +- int i; +- + /*output: */ + Hook* output=NULL; + +@@ -131,15 +121,15 @@ + /*copy in the fields: */ + output->num=this->num; + if(output->num){ +- output->objects=xNew(output->num); +- output->ids=xNew(output->num); +- output->offsets=xNew(output->num); ++ output->objects = xNew(output->num); ++ output->ids = xNew(output->num); ++ output->offsets = xNew(output->num); + } + +- for(i=0;inum;i++){ +- output->objects[i]=this->objects[i]; +- output->offsets[i]=this->offsets[i]; +- output->ids[i]=this->ids[i]; ++ for(int i=0;inum;i++){ ++ output->objects[i] = this->objects[i]; ++ output->offsets[i] = this->offsets[i]; ++ output->ids[i] = this->ids[i]; + } + + return (Object*)output; +@@ -230,8 +220,6 @@ + /*FUNCTION Hook::Spawn{{{*/ + Hook* Hook::Spawn(int* indices, int numindices){ + +- int i; +- + /*output: */ + Hook* output=NULL; + +@@ -245,20 +233,20 @@ + } + + /*Else, check that we are requesting a half of num*/ +- if (numindices>this->num) _error_("Cannot spawn hook with " << numindices << " objects from a Hook of " << this->num << " objects"); ++ if(numindices>this->num) _error_("Cannot spawn hook with " << numindices << " objects from a Hook of " << this->num << " objects"); + + /*go pickup the correct objects, ids and offsets :*/ + output->num=numindices; + if(output->num<1) _error_("Trying to spawn an empty ElementProperties!"); + +- output->objects=xNew(output->num); +- output->ids=xNew(output->num); +- output->offsets=xNew(output->num); ++ output->objects = xNew(output->num); ++ output->ids = xNew(output->num); ++ output->offsets = xNew(output->num); + +- for(i=0;inum;i++){ +- output->objects[i]=this->objects[indices[i]]; +- output->ids[i]=this->ids[indices[i]]; +- output->offsets[i]=this->offsets[indices[i]]; ++ for(int i=0;inum;i++){ ++ output->objects[i] = this->objects[indices[i]]; ++ output->ids[i] = this->ids[indices[i]]; ++ output->offsets[i] = this->offsets[indices[i]]; + } + + return output; +Index: ../trunk-jpl/src/c/classes/DofIndexing.h +=================================================================== +--- ../trunk-jpl/src/c/classes/DofIndexing.h (revision 13412) ++++ ../trunk-jpl/src/c/classes/DofIndexing.h (revision 13413) +@@ -12,27 +12,26 @@ + public: + + /*sizes: */ +- int gsize; //number of dofs for a node +- int fsize; //number of dofs solver for +- int ssize; //number of constrained dofs ++ int gsize; //number of dofs for a node ++ int fsize; //number of dofs solver for ++ int ssize; //number of constrained dofs + + /*partitioning: */ +- bool clone; //this node is replicated from another one ++ bool clone; //this node is replicated from another one + + /*boundary conditions sets: */ +- bool* f_set; //is dof on f-set (on which we solve) +- bool* s_set; //is dof on s-set (on which boundary conditions -dirichlet- are applied) +- IssmDouble* svalues; //list of constraint values. size g_size, for ease of use. ++ bool *f_set; //is dof on f-set (on which we solve) ++ bool *s_set; //is dof on s-set (on which boundary conditions -dirichlet- are applied) ++ IssmDouble *svalues; //list of constraint values. size g_size, for ease of use. + + /*types of dofs: */ +- int* doftype; //approximation type of the dofs (used only for coupling), size g_size ++ int *doftype; //approximation type of the dofs (used only for coupling), size g_size + + /*list of degrees of freedom: */ +- int* gdoflist; //dof list in g_set +- int* fdoflist; //dof list in f_set +- int* sdoflist; //dof list in s_set ++ int *gdoflist; //dof list in g_set ++ int *fdoflist; //dof list in f_set ++ int *sdoflist; //dof list in s_set + +- + /*DofIndexing constructors, destructors {{{*/ + DofIndexing(); + DofIndexing(int g_size); +Index: ../trunk-jpl/src/c/classes/Patch.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Patch.h (revision 13412) ++++ ../trunk-jpl/src/c/classes/Patch.h (revision 13413) +@@ -19,7 +19,6 @@ + VzEnum 2 .8 2 P1 1 3 4 4.5 3.2 2.5 + */ + +- + #ifndef _PATCH_H_ + #define _PATCH_H_ + +@@ -28,12 +27,11 @@ + + public: + +- int numrows; //number of results held in Patch object +- int numcols; //number of columns +- int maxvertices; //maxvertices corresponds to largest amount of vertices on a given element, determined by the geometry. +- int maxnodes; // maxnodes corresponds to the largest amout of nodes on a given element, determined by the interpolation type. +- +- IssmDouble* values; //result values ++ int numrows; //number of results held in Patch object ++ int numcols; //number of columns ++ int maxvertices; //largest amount of vertices on a given element, determined by geometry ++ int maxnodes; //the largest amout of nodes on a given element, determined by interpolation ++ IssmDouble *values; //result values + + Patch(); + Patch(int numrows, int maxvertices, int maxnodes); +Index: ../trunk-jpl/src/c/classes/Hook.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Hook.h (revision 13412) ++++ ../trunk-jpl/src/c/classes/Hook.h (revision 13413) +@@ -18,10 +18,10 @@ + + private: + +- int num; //number of objects being hooked onto +- Object** objects; //list of object pointers. we do not allocate objects, just a list a pointers, that will get to point to the real objects from a dataset. +- int* ids; //list of object ids, to go look for them in datasets. +- int* offsets; //list of object offsets into datasets, to speed up lookup. ++ int num; //number of objects being hooked onto ++ Object **objects; //list of object pointers ++ int *ids; //list of object ids, to go look for them in datasets. ++ int *offsets; //list of object offsets into datasets, to speed up lookup. + + public: + +Index: ../trunk-jpl/src/c/classes/objects/Contour.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Contour.h (revision 13412) ++++ ../trunk-jpl/src/c/classes/objects/Contour.h (revision 13413) +@@ -21,28 +21,28 @@ + + public: + +- int id; +- int nods; //number of vertices in the contour +- doubletype* x; +- doubletype* y; +- bool closed; //is this contour closed? ++ int id; ++ int nods; //number of vertices in the contour ++ doubletype *x; ++ doubletype *y; ++ bool closed; //is this contour closed? + + /*Contour constructors, destructors :*/ +- /*FUNCTION Contour() default constructor {{{*/ ++ /*FUNCTION Contour() {{{*/ + Contour(){ +- this->id=0; +- this->nods=0; +- this->x=NULL; +- this->y=NULL; +- this->closed=false; ++ this->id = 0; ++ this->nods = 0; ++ this->x = NULL; ++ this->y = NULL; ++ this->closed = false; + } + /*}}}*/ + /*FUNCTION Contour(int pid, int nods, doubletype* x, doubletype* y,bool closed) {{{*/ + Contour(int pid,int pnods, doubletype* px, doubletype* py,bool pclosed){ + +- this->id=pid; +- this->nods=pnods; +- this->closed=pclosed; ++ this->id = pid; ++ this->nods = pnods; ++ this->closed = pclosed; + if(nods){ + this->x=xNew(nods); + xMemCpy(this->x,px,nods); +@@ -51,27 +51,23 @@ + } + } + /*}}}*/ +- /*FUNCTION Contour() default constructor {{{*/ ++ /*FUNCTION ~Contour() {{{*/ + ~Contour(){ + xDelete(this->x); + xDelete(this->y); + } + /*}}}*/ + +- + /*Object virtual function resolutoin: */ + /*FUNCTION Echo(){{{*/ + void Echo(void){ +- +- int i; +- +- _printLine_("Contour: " << id); +- _printLine_(" nods: " << nods); +- _printLine_(" closed: " << (closed?"true":"false")); ++ _printLine_(" Contour: " << id); ++ _printLine_(" nods: " << nods); ++ _printLine_(" closed: " << (closed?"true":"false")); + if(nods){ +- _printLine_(" x,y:"); +- for(i=0;i* ug, IssmDouble* vector_serial,int setenum); + void VecReduce(Vector* vector, IssmDouble* ug_serial,int setnum); +- +- /*}}}*/ +- /*Dof Object routines {{{*/ + void DistributeDofs(int* pdofcount,int setenum); + void OffsetDofs(int dofcount,int setenum); + void ShowTrueDofs(int* truerows,int ncols,int setenum); +Index: ../trunk-jpl/src/c/classes/Update.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Update.h (revision 13412) ++++ ../trunk-jpl/src/c/classes/Update.h (revision 13413) +@@ -32,4 +32,3 @@ + }; + + #endif //ifndef _UPDATE_H_ +- +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13412) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13413) +@@ -23,20 +23,20 @@ + + /*FUNCTION IoModel::IoModel(){{{*/ + IoModel::IoModel(){ +- this->fid=NULL; +- this->data=NULL; +- this->independents=NULL; +- this->constants=NULL; ++ this->fid = NULL; ++ this->data = NULL; ++ this->independents = NULL; ++ this->constants = NULL; + +- this->my_elements=NULL; +- this->my_nodes=NULL; +- this->my_vertices=NULL; +- this->singlenodetoelementconnectivity=NULL; +- this->numbernodetoelementconnectivity=NULL; ++ this->my_elements = NULL; ++ this->my_nodes = NULL; ++ this->my_vertices = NULL; ++ this->singlenodetoelementconnectivity = NULL; ++ this->numbernodetoelementconnectivity = NULL; + +- this->nodecounter=0; +- this->loadcounter=0; +- this->constraintcounter=0; ++ this->nodecounter = 0; ++ this->loadcounter = 0; ++ this->constraintcounter = 0; + } + /*}}}*/ + /*FUNCTION IoModel::IoModel(FILE* iomodel_handle){{{*/ +@@ -61,15 +61,15 @@ + for(int i=0;iindependents[i]=false; + + /*Initialize permanent data: */ +- this->my_elements=NULL; +- this->my_nodes=NULL; +- this->my_vertices=NULL; +- this->singlenodetoelementconnectivity=NULL; +- this->numbernodetoelementconnectivity=NULL; ++ this->my_elements = NULL; ++ this->my_nodes = NULL; ++ this->my_vertices = NULL; ++ this->singlenodetoelementconnectivity = NULL; ++ this->numbernodetoelementconnectivity = NULL; + +- this->nodecounter=0; +- this->loadcounter=0; +- this->constraintcounter=0; ++ this->nodecounter = 0; ++ this->loadcounter = 0; ++ this->constraintcounter = 0; + } + /*}}}*/ + /*FUNCTION IoModel::~IoModel(){{{*/ +@@ -199,15 +199,13 @@ + /*FUNCTION IoModel::DeleteData(int num,...){{{*/ + void IoModel::DeleteData(int num,...){ + +- va_list ap; +- int dataenum; +- int i; +- DoubleMatParam* parameter=NULL; ++ va_list ap; ++ int dataenum; ++ DoubleMatParam *parameter = NULL; + + /*Go through the entire list of enums and delete the corresponding data from the iomodel-data dataset: */ +- + va_start(ap,num); +- for(i = 0; i SetFilePointerToData(&code,NULL,data_enum); +@@ -549,8 +546,6 @@ + + if(code!=4)_error_("expecting a string for enum " << EnumToStringx(data_enum)); + +- /*Now fetch: */ +- + /*We have to read a string from disk. First read the dimensions of the string, then the string: */ + if(my_rank==0){ + if(fread(&string_size,sizeof(int),1,fid)!=1) _error_("could not read length of string "); +@@ -578,7 +573,6 @@ + string[0]='\0'; + } + +- + /*Assign output pointers: */ + *pstring=string; + } +@@ -602,8 +596,6 @@ + + if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(data_enum)); + +- /*Now fetch: */ +- + /*We have to read a matrix from disk. First read the dimensions of the matrix, then the whole matrix: */ + /*numberofelements: */ + if(my_rank==0){ +@@ -672,8 +664,6 @@ + fid=this->SetFilePointerToData(&code,&vector_type,data_enum); + if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(data_enum)); + +- /*Now fetch: */ +- + /*We have to read a matrix from disk. First read the dimensions of the matrix, then the whole matrix: */ + /*numberofelements: */ + if(my_rank==0){ +@@ -793,14 +783,13 @@ + void IoModel::FetchData(IssmDouble*** pmatrices,int** pmdims,int** pndims, int* pnumrecords,int data_enum){ + + int i; +- + extern int my_rank; + + /*output: */ +- IssmDouble** matrices=NULL; +- int* mdims=NULL; +- int* ndims=NULL; +- int numrecords=0; ++ IssmDouble **matrices = NULL; ++ int *mdims = NULL; ++ int *ndims = NULL; ++ int numrecords = 0; + + /*intermediary: */ + int M, N; +@@ -929,17 +918,17 @@ + /*FUNCTION IoModel::FetchData(int num,...){{{*/ + void IoModel::FetchData(int num,...){ + +- va_list ap; +- int dataenum; +- IssmDouble* matrix=NULL; +- int M,N; +- int i; ++ va_list ap; ++ int dataenum; ++ IssmDouble *matrix = NULL; ++ int M,N; + +- /*Go through the entire list of enums and fetch the corresponding data. Add it to the iomodel->data dataset. Everything +- *we fetch is a IssmDouble* : */ ++ /*Go through the entire list of enums and fetch the corresponding data. ++ * Add it to the iomodel->data dataset. Everything ++ * we fetch is a IssmDouble* : */ + + va_start(ap,num); +- for(i=0; idata[dataenum]=matrix; + } + va_end(ap); +- + } + /*}}}*/ + /*FUNCTION IoModel::FetchDataToInput{{{*/ +@@ -982,7 +970,6 @@ + int nel; + int numberofelements; + +- + /*variables being fetched: */ + bool boolean; + int integer; +@@ -1308,8 +1295,6 @@ + fid=this->SetFilePointerToData(&code,&vector_type,independent_enum); + if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(independent_enum)); + +- /*Now fetch: */ +- + /*We have to read a matrix from disk. First read the dimensions of the matrix, then the whole matrix: */ + /*numberofelements: */ + if(my_rank==0){ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13412) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13413) +@@ -2,7 +2,6 @@ + * \brief: implementation of the FemModel object + */ + +- + #ifdef HAVE_CONFIG_H + #include + #else +@@ -32,10 +31,10 @@ + if(my_rank==0) IOMODEL = pfopen(inputfilename ,"rb"); + + /*Initialize internal data: */ +- this->nummodels=nummodels; +- this->solution_type=in_solution_type; +- this->analysis_counter=nummodels-1; //point to last analysis_type carried out. +- this->results=new Results(); //not initialized by CreateDataSets ++ this->nummodels = nummodels; ++ this->solution_type = in_solution_type; ++ this->analysis_counter = nummodels-1; //point to last analysis_type carried out. ++ this->results = new Results(); //not initialized by CreateDataSets + + /*Dynamically allocate whatever is a list of length nummodels: */ + analysis_type_list=xNew(nummodels); +@@ -73,9 +72,7 @@ + + /*Add output file name to parameters: */ + this->parameters->AddObject(new StringParam(OutputfilenameEnum,outputfilename)); +- + } +- + /*}}}*/ + /*FUNCTION FemModel::destructor {{{*/ + FemModel::~FemModel(){ +@@ -152,8 +149,6 @@ + /*}}}*/ + /*FUNCTION FemModel::SetCurrentConfiguration(int configuration_type){{{*/ + void FemModel::SetCurrentConfiguration(int configuration_type){ +- +- /*overload: analysis_type = configuration_type: */ + this->SetCurrentConfiguration(configuration_type,configuration_type); + } + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/IoModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.h (revision 13412) ++++ ../trunk-jpl/src/c/classes/IoModel.h (revision 13413) +@@ -18,13 +18,13 @@ + class IoModel { + + private: +- Parameters *constants; //this dataset holds all IssmDouble, int, bool and char *parameters read in from the input file.* ++ Parameters *constants; //this dataset holds all IssmDouble, int, bool and char from input + + public: +- IssmDouble **data; //this dataset holds temporary data, memory intensive. ++ IssmDouble **data; //this dataset holds temporary data, memory intensive. + + /*This data needs to stay memory resident at all time, even if it's memory intensive: */ +- FILE *fid; //pointer to input file ++ FILE *fid; //pointer to input file + bool *my_elements; + bool *my_nodes; + int *my_vertices; +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 13412) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 13413) +@@ -27,20 +27,20 @@ + + public: + +- int nummodels; +- int solution_type; +- int* analysis_type_list; //list of analyses this femmodel is going to carry out +- int analysis_counter; //counter into analysis_type_list +- +- Elements* elements; //elements (one set for all analyses) +- Nodes* nodes; //one set of nodes +- Vertices* vertices; //one set of vertices +- Constraints* constraints; //one set of constraints. each constraint knows which analysis_type it handles +- Loads* loads; //one set of constraints. each constraint knows which analysis_type it handles +- Materials* materials; //one set of materials, for each element +- Parameters* parameters; //one set of parameters, independent of the analysis_type +- Results* results; //results that cannot be fit into the elements (such as one time constants, arrays, strings, etc ...) ++ int nummodels; ++ int solution_type; ++ int *analysis_type_list; //list of analyses this femmodel is going to carry out ++ int analysis_counter; //counter into analysis_type_list + ++ Elements *elements; //elements (one set for all analyses) ++ Nodes *nodes; //one set of nodes ++ Vertices *vertices; //one set of vertices ++ Constraints *constraints; //one set of constraints. each constraint knows which analysis_type it handles ++ Loads *loads; //one set of constraints. each constraint knows which analysis_type it handles ++ Materials *materials; //one set of materials, for each element ++ Parameters *parameters; //one set of parameters, independent of the analysis_type ++ Results *results; //results that cannot be fit into the elements ++ + /*constructors, destructors: */ + FemModel(char* rootpath, char* inputfilename, char* outputfilename, const int solution_type,const int* analyses,const int nummodels); + ~FemModel(); Index: /issm/oecreview/Archive/13393-13976/ISSM-13413-13414.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13413-13414.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13413-13414.diff (revision 13980) @@ -0,0 +1,2361 @@ +Index: ../trunk-jpl/src/c/include/types.h +=================================================================== +--- ../trunk-jpl/src/c/include/types.h (revision 13413) ++++ ../trunk-jpl/src/c/include/types.h (revision 13414) +@@ -39,6 +39,4 @@ + typedef IssmDouble IssmPDouble; + #endif + +-typedef bool IssmBool; +- + #endif //ifndef _TYPES_H_ +Index: ../trunk-jpl/src/c/classes/objects/Contour.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Contour.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Contour.h (revision 13414) +@@ -82,12 +82,6 @@ + return id; + } + /*}}}*/ +- /*FUNCTION MyRank{{{*/ +- int MyRank(void){ +- extern int my_rank; +- return my_rank; +- } +- /*}}}*/ + /*FUNCTION ObjectEnum{{{*/ + int ObjectEnum(void){ + return ContourEnum; +Index: ../trunk-jpl/src/c/classes/objects/Materials/Matdamageice.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Materials/Matdamageice.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Materials/Matdamageice.cpp (revision 13414) +@@ -81,12 +81,6 @@ + /*FUNCTION Matdamageice::Id {{{*/ + int Matdamageice::Id(void){ return mid; } + /*}}}*/ +-/*FUNCTION Matdamageice::MyRank {{{*/ +-int Matdamageice::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Matdamageice::ObjectEnum{{{*/ + int Matdamageice::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Materials/Matice.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Materials/Matice.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Materials/Matice.cpp (revision 13414) +@@ -81,12 +81,6 @@ + /*FUNCTION Matice::Id {{{*/ + int Matice::Id(void){ return mid; } + /*}}}*/ +-/*FUNCTION Matice::MyRank {{{*/ +-int Matice::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Matice::ObjectEnum{{{*/ + int Matice::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Materials/Matpar.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Materials/Matpar.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Materials/Matpar.cpp (revision 13414) +@@ -84,12 +84,6 @@ + /*FUNCTION Matpar::Id {{{*/ + int Matpar::Id(void){ return mid; } + /*}}}*/ +-/*FUNCTION Matpar::MyRank {{{*/ +-int Matpar::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Matpar::ObjectEnum{{{*/ + int Matpar::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Materials/Matdamageice.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Materials/Matdamageice.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Materials/Matdamageice.h (revision 13414) +@@ -27,7 +27,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Materials/Matice.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Materials/Matice.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Materials/Matice.h (revision 13414) +@@ -14,8 +14,8 @@ + class Matice: public Material{ + + private: +- int mid; +- Hook* helement; ++ int mid; ++ Hook *helement; + + public: + /*Matice constructors, destructors: {{{*/ +@@ -27,7 +27,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Materials/Matpar.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Materials/Matpar.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Materials/Matpar.h (revision 13414) +@@ -42,12 +42,11 @@ + ~Matpar(); + + /*Object virtual functions definitions:{{{ */ +- void Echo(); +- void DeepEcho(); +- int Id(); +- int MyRank(); +- int ObjectEnum(); +- Object* copy(); ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int ObjectEnum(); ++ Object *copy(); + /*}}}*/ + /*Update virtual functions resolution: {{{*/ + void InputUpdateFromVector(IssmDouble* vector, int name, int type); +Index: ../trunk-jpl/src/c/classes/objects/Inputs/DoubleInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/DoubleInput.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/DoubleInput.h (revision 13414) +@@ -28,7 +28,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Inputs/ControlInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/ControlInput.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/ControlInput.cpp (revision 13414) +@@ -83,12 +83,6 @@ + /*FUNCTION ControlInput::Id{{{*/ + int ControlInput::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION ControlInput::MyRank{{{*/ +-int ControlInput::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION ControlInput::ObjectEnum{{{*/ + int ControlInput::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Inputs/ControlInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/ControlInput.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/ControlInput.h (revision 13414) +@@ -33,7 +33,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Inputs/DatasetInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/DatasetInput.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/DatasetInput.cpp (revision 13414) +@@ -54,12 +54,6 @@ + /*FUNCTION DatasetInput::Id{{{*/ + int DatasetInput::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION DatasetInput::MyRank{{{*/ +-int DatasetInput::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION DatasetInput::ObjectEnum{{{*/ + int DatasetInput::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Inputs/DatasetInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/DatasetInput.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/DatasetInput.h (revision 13414) +@@ -16,10 +16,9 @@ + class DatasetInput: public Input{ + + public: +- int enum_type; ++ int enum_type; ++ Inputs *inputs; + +- Inputs* inputs; +- + /*DatasetInput constructors, destructors: {{{*/ + DatasetInput(); + DatasetInput(int enum_type); +@@ -29,7 +28,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Inputs/IntInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/IntInput.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/IntInput.cpp (revision 13414) +@@ -47,12 +47,6 @@ + /*FUNCTION IntInput::Id{{{*/ + int IntInput::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION IntInput::MyRank{{{*/ +-int IntInput::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION IntInput::ObjectEnum{{{*/ + int IntInput::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Inputs/BoolInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/BoolInput.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/BoolInput.cpp (revision 13414) +@@ -22,8 +22,8 @@ + return; + } + /*}}}*/ +-/*FUNCTION BoolInput::BoolInput(IssmDouble* values){{{*/ +-BoolInput::BoolInput(int in_enum_type,IssmBool in_value){ ++/*FUNCTION BoolInput::BoolInput(int in_enum_type,bool in_value){{{*/ ++BoolInput::BoolInput(int in_enum_type,bool in_value){ + + enum_type=in_enum_type; + value=in_value; +@@ -52,12 +52,6 @@ + /*FUNCTION BoolInput::Id{{{*/ + int BoolInput::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION BoolInput::MyRank{{{*/ +-int BoolInput::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION BoolInput::ObjectEnum{{{*/ + int BoolInput::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Inputs/IntInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/IntInput.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/IntInput.h (revision 13414) +@@ -29,7 +29,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Inputs/BoolInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/BoolInput.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/BoolInput.h (revision 13414) +@@ -17,21 +17,20 @@ + + public: + /*just hold 3 values for 3 vertices: */ +- int enum_type; +- IssmBool value; ++ int enum_type; ++ bool value; + + /*BoolInput constructors, destructors: {{{*/ + BoolInput(); +- BoolInput(int enum_type,IssmBool value); ++ BoolInput(int enum_type,bool value); + ~BoolInput(); + /*}}}*/ + /*Object virtual functions definitions:{{{ */ +- void Echo(); +- void DeepEcho(); +- int Id(); +- int MyRank(); +- int ObjectEnum(); +- Object* copy(); ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int ObjectEnum(); ++ Object *copy(); + /*}}}*/ + /*BoolInput management: {{{*/ + int InstanceEnum(); +Index: ../trunk-jpl/src/c/classes/objects/Inputs/TriaP1Input.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/TriaP1Input.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/TriaP1Input.cpp (revision 13414) +@@ -63,12 +63,6 @@ + /*FUNCTION TriaP1Input::Id{{{*/ + int TriaP1Input::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION TriaP1Input::MyRank{{{*/ +-int TriaP1Input::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION TriaP1Input::ObjectEnum{{{*/ + int TriaP1Input::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Inputs/TriaP1Input.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/TriaP1Input.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/TriaP1Input.h (revision 13414) +@@ -17,7 +17,7 @@ + + public: + /*just hold 3 values for 3 vertices: */ +- int enum_type; ++ int enum_type; + IssmDouble values[3]; + + /*TriaP1Input constructors, destructors: {{{*/ +@@ -26,12 +26,11 @@ + ~TriaP1Input(); + /*}}}*/ + /*Object virtual functions definitions:{{{ */ +- void Echo(); +- void DeepEcho(); +- int Id(); +- int MyRank(); +- int ObjectEnum(); +- Object* copy(); ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int ObjectEnum(); ++ Object *copy(); + /*}}}*/ + /*TriaP1Input management: {{{*/ + int InstanceEnum(); +Index: ../trunk-jpl/src/c/classes/objects/Inputs/TransientInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/TransientInput.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/TransientInput.cpp (revision 13414) +@@ -78,12 +78,6 @@ + /*FUNCTION TransientInput::Id{{{*/ + int TransientInput::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION TransientInput::MyRank{{{*/ +-int TransientInput::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION TransientInput::ObjectEnum{{{*/ + int TransientInput::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Inputs/PentaP1Input.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/PentaP1Input.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/PentaP1Input.cpp (revision 13414) +@@ -63,12 +63,6 @@ + /*FUNCTION PentaP1Input::Id{{{*/ + int PentaP1Input::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION PentaP1Input::MyRank{{{*/ +-int PentaP1Input::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION PentaP1Input::ObjectEnum{{{*/ + int PentaP1Input::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Inputs/DoubleInput.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/DoubleInput.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/DoubleInput.cpp (revision 13414) +@@ -52,12 +52,6 @@ + /*FUNCTION DoubleInput::Id{{{*/ + int DoubleInput::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION DoubleInput::MyRank{{{*/ +-int DoubleInput::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION DoubleInput::ObjectEnum{{{*/ + int DoubleInput::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Inputs/TransientInput.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/TransientInput.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/TransientInput.h (revision 13414) +@@ -16,11 +16,11 @@ + class TransientInput: public Input{ + + public: +- int enum_type; +- int numtimesteps; +- Inputs* inputs; +- IssmDouble* timesteps; +- Parameters* parameters; //to find current time. ++ int enum_type; ++ int numtimesteps; ++ Inputs *inputs; ++ IssmDouble *timesteps; ++ Parameters *parameters; //to find current time. + + /*TransientInput constructors, destructors: {{{*/ + TransientInput(); +@@ -32,7 +32,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Inputs/PentaP1Input.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Inputs/PentaP1Input.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Inputs/PentaP1Input.h (revision 13414) +@@ -17,7 +17,7 @@ + + public: + /*just hold 6 values for 6 vertices: */ +- int enum_type; ++ int enum_type; + IssmDouble values[6]; + + /*PentaP1Input constructors, destructors: {{{*/ +@@ -26,12 +26,11 @@ + ~PentaP1Input(); + /*}}}*/ + /*Object virtual functions definitions:{{{ */ +- void Echo(); +- void DeepEcho(); +- int Id(); +- int MyRank(); +- int ObjectEnum(); +- Object* copy(); ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int ObjectEnum(); ++ Object *copy(); + /*}}}*/ + /*PentaP1Input management: {{{*/ + int InstanceEnum(); +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Icon.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Icon.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Icon.h (revision 13414) +@@ -44,10 +44,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Point.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Point.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Point.h (revision 13414) +@@ -36,10 +36,6 @@ + void Read(FILE* fid,char* kstr); + void WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_LinearRing.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_LinearRing.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_LinearRing.h (revision 13414) +@@ -38,10 +38,6 @@ + void Read(FILE* fid,char* kstr); + void WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Feature.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Feature.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Feature.h (revision 13414) +@@ -44,10 +44,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_StyleSelector.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_StyleSelector.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_StyleSelector.h (revision 13414) +@@ -29,10 +29,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_LatLonBox.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_LatLonBox.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_LatLonBox.h (revision 13414) +@@ -35,10 +35,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Attribute.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Attribute.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Attribute.h (revision 13414) +@@ -30,10 +30,6 @@ + virtual void DeepEcho(); + virtual void DeepEcho(const char* indent); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_PolyStyle.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_PolyStyle.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_PolyStyle.h (revision 13414) +@@ -32,10 +32,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Object.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Object.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Object.h (revision 13414) +@@ -31,10 +31,6 @@ + virtual void DeepEcho(); + virtual void DeepEcho(const char* indent); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_SubStyle.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_SubStyle.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_SubStyle.h (revision 13414) +@@ -29,10 +29,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_LineString.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_LineString.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_LineString.h (revision 13414) +@@ -38,10 +38,6 @@ + void Read(FILE* fid,char* kstr); + void WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Overlay.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Overlay.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Overlay.h (revision 13414) +@@ -36,10 +36,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Container.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Container.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Container.h (revision 13414) +@@ -33,10 +33,6 @@ + void Read(FILE* fid,char* kstr); + void WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Polygon.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Polygon.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Polygon.h (revision 13414) +@@ -40,10 +40,6 @@ + void Read(FILE* fid,char* kstr); + void WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Geometry.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Geometry.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Geometry.h (revision 13414) +@@ -29,10 +29,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_ColorStyle.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_ColorStyle.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_ColorStyle.h (revision 13414) +@@ -35,9 +35,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; + void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Placemark.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Placemark.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Placemark.h (revision 13414) +@@ -34,10 +34,6 @@ + void Read(FILE* fid,char* kstr); + void WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Unknown.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Unknown.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Unknown.h (revision 13414) +@@ -32,10 +32,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_GroundOverlay.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_GroundOverlay.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_GroundOverlay.h (revision 13414) +@@ -36,10 +36,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Style.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Style.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Style.h (revision 13414) +@@ -38,10 +38,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Comment.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Comment.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Comment.h (revision 13414) +@@ -30,10 +30,6 @@ + virtual void DeepEcho(); + virtual void DeepEcho(const char* indent); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_MultiGeometry.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_MultiGeometry.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_MultiGeometry.h (revision 13414) +@@ -34,10 +34,6 @@ + void Read(FILE* fid,char* kstr); + void WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_LineStyle.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_LineStyle.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_LineStyle.h (revision 13414) +@@ -31,10 +31,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Folder.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Folder.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Folder.h (revision 13414) +@@ -30,10 +30,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_Document.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_Document.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_Document.h (revision 13414) +@@ -30,10 +30,6 @@ + void Write(FILE* fid,const char* indent); + void Read(FILE* fid,char* kstr); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/KML/KML_File.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/KML/KML_File.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/KML/KML_File.h (revision 13414) +@@ -31,10 +31,6 @@ + void Read(FILE* fid,char* kstr); + void WriteExp(FILE* fid,const char* nstr,int sgn,double cm,double sp); + int Id(){_error_("Not implemented yet.");}; +- int MyRank(){_error_("Not implemented yet.");}; +- void Marshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; +- int MarshallSize(){_error_("Not implemented yet.");}; +- void Demarshall(char** pmarshalled_dataset){_error_("Not implemented yet.");}; + int ObjectEnum(){_error_("Not implemented yet.");}; + Object* copy(){_error_("Not implemented yet.");}; + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/DoubleVecParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DoubleVecParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/DoubleVecParam.h (revision 13414) +@@ -22,9 +22,9 @@ + class DoubleVecParam: public Param{ + + private: +- int enum_type; +- IssmDouble* values; +- int M; ++ int enum_type; ++ IssmDouble *values; ++ int M; + + public: + /*DoubleVecParam constructors, destructors: {{{*/ +@@ -36,7 +36,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/DoubleMatParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DoubleMatParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/DoubleMatParam.h (revision 13414) +@@ -22,10 +22,10 @@ + class DoubleMatParam: public Param{ + + protected: +- int enum_type; +- IssmDouble* value; +- int M; +- int N; ++ int enum_type; ++ IssmDouble *value; ++ int M; ++ int N; + + public: + /*DoubleMatParam constructors, destructors: {{{*/ +@@ -37,7 +37,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/GenericParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/GenericParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/GenericParam.h (revision 13414) +@@ -48,7 +48,6 @@ + } + void Echo() {DeepEcho();}; + int Id(){ return -1; }; +- int MyRank() { extern int my_rank; return my_rank;} ; + int ObjectEnum() {return AdolcParamEnum;}; + + // the "copy" has to implement the base class abstract function +Index: ../trunk-jpl/src/c/classes/objects/Params/FileParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/FileParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/FileParam.h (revision 13414) +@@ -35,7 +35,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/IntVecParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/IntVecParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/IntVecParam.cpp (revision 13414) +@@ -84,12 +84,6 @@ + /*FUNCTION IntVecParam::Id{{{*/ + int IntVecParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION IntVecParam::MyRank{{{*/ +-int IntVecParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION IntVecParam::ObjectEnum{{{*/ + int IntVecParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/BoolParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/BoolParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/BoolParam.cpp (revision 13414) +@@ -25,8 +25,8 @@ + return; + } + /*}}}*/ +-/*FUNCTION BoolParam::BoolParam(int enum_type,IssmBool value){{{*/ +-BoolParam::BoolParam(int in_enum_type,IssmBool in_value){ ++/*FUNCTION BoolParam::BoolParam(int enum_type,bool value){{{*/ ++BoolParam::BoolParam(int in_enum_type,bool in_value){ + + enum_type=in_enum_type; + value=in_value; +@@ -55,12 +55,6 @@ + /*FUNCTION BoolParam::Id{{{*/ + int BoolParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION BoolParam::MyRank{{{*/ +-int BoolParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION BoolParam::ObjectEnum{{{*/ + int BoolParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/IntMatParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/IntMatParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/IntMatParam.cpp (revision 13414) +@@ -71,12 +71,6 @@ + /*FUNCTION IntMatParam::Id{{{*/ + int IntMatParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION IntMatParam::MyRank{{{*/ +-int IntMatParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION IntMatParam::ObjectEnum{{{*/ + int IntMatParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/IntParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/IntParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/IntParam.h (revision 13414) +@@ -36,7 +36,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/StringParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/StringParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/StringParam.cpp (revision 13414) +@@ -57,12 +57,6 @@ + /*FUNCTION StringParam::Id{{{*/ + int StringParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION StringParam::MyRank{{{*/ +-int StringParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION StringParam::ObjectEnum{{{*/ + int StringParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/VectorParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/VectorParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/VectorParam.h (revision 13414) +@@ -36,7 +36,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/DoubleVecParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DoubleVecParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/DoubleVecParam.cpp (revision 13414) +@@ -68,12 +68,6 @@ + /*FUNCTION DoubleVecParam::Id{{{*/ + int DoubleVecParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION DoubleVecParam::MyRank{{{*/ +-int DoubleVecParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION DoubleVecParam::ObjectEnum{{{*/ + int DoubleVecParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/MatrixParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/MatrixParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/MatrixParam.h (revision 13414) +@@ -36,7 +36,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/StringArrayParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/StringArrayParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/StringArrayParam.h (revision 13414) +@@ -38,7 +38,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/DoubleMatParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DoubleMatParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/DoubleMatParam.cpp (revision 13414) +@@ -71,12 +71,6 @@ + /*FUNCTION DoubleMatParam::Id{{{*/ + int DoubleMatParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION DoubleMatParam::MyRank{{{*/ +-int DoubleMatParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION DoubleMatParam::ObjectEnum{{{*/ + int DoubleMatParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/TransientParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/TransientParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/TransientParam.h (revision 13414) +@@ -2,7 +2,6 @@ + * \brief: header file for triavertexinput object + */ + +- + #ifndef _TRANSIENTPARAM_H_ + #define _TRANSIENTPARAM_H_ + +@@ -22,10 +21,10 @@ + class TransientParam: public Param{ + + protected: +- int enum_type; +- int N; +- IssmDouble* values; +- IssmDouble* timesteps; ++ int enum_type; ++ int N; ++ IssmDouble *values; ++ IssmDouble *timesteps; + + public: + /*TransientParam constructors, destructors: {{{*/ +@@ -37,7 +36,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/FileParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/FileParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/FileParam.cpp (revision 13414) +@@ -55,12 +55,6 @@ + /*FUNCTION FileParam::Id{{{*/ + int FileParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION FileParam::MyRank{{{*/ +-int FileParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION FileParam::ObjectEnum{{{*/ + int FileParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/DoubleParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DoubleParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/DoubleParam.h (revision 13414) +@@ -23,7 +23,7 @@ + + private: + /*just hold 3 values for 3 vertices: */ +- int enum_type; ++ int enum_type; + IssmDouble value; + + public: +@@ -36,7 +36,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/DoubleMatArrayParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DoubleMatArrayParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/DoubleMatArrayParam.h (revision 13414) +@@ -22,11 +22,11 @@ + class DoubleMatArrayParam: public Param{ + + private: +- int enum_type; +- IssmDouble** array; //array of matrices +- int M; //size of array +- int* mdim_array; //m-dimensions of matrices in the array +- int* ndim_array; //n-dimensions -f matrices in the array ++ int enum_type; ++ IssmDouble **array; //array of matrices ++ int M; //size of array ++ int *mdim_array; //m-dimensions of matrices in the array ++ int *ndim_array; //n-dimensions -f matrices in the array + + public: + /*DoubleMatArrayParam constructors, destructors: {{{*/ +@@ -38,7 +38,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/IntParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/IntParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/IntParam.cpp (revision 13414) +@@ -55,12 +55,6 @@ + /*FUNCTION IntParam::Id{{{*/ + int IntParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION IntParam::MyRank{{{*/ +-int IntParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION IntParam::ObjectEnum{{{*/ + int IntParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/IntVecParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/IntVecParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/IntVecParam.h (revision 13414) +@@ -37,7 +37,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/BoolParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/BoolParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/BoolParam.h (revision 13414) +@@ -24,18 +24,17 @@ + public: + /*just hold 3 values for 3 vertices: */ + int enum_type; +- IssmBool value; ++ bool value; + + /*BoolParam constructors, destructors: {{{*/ + BoolParam(); +- BoolParam(int enum_type,IssmBool value); ++ BoolParam(int enum_type,bool value); + ~BoolParam(); + /*}}}*/ + /*Object virtual functions definitions:{{{ */ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/IntMatParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/IntMatParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/IntMatParam.h (revision 13414) +@@ -37,7 +37,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/VectorParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/VectorParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/VectorParam.cpp (revision 13414) +@@ -65,12 +65,6 @@ + /*FUNCTION VectorParam::Id{{{*/ + int VectorParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION VectorParam::MyRank{{{*/ +-int VectorParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION VectorParam::ObjectEnum{{{*/ + int VectorParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/MatrixParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/MatrixParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/MatrixParam.cpp (revision 13414) +@@ -63,12 +63,6 @@ + /*FUNCTION MatrixParam::Id{{{*/ + int MatrixParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION MatrixParam::MyRank{{{*/ +-int MatrixParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION MatrixParam::ObjectEnum{{{*/ + int MatrixParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/StringArrayParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/StringArrayParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/StringArrayParam.cpp (revision 13414) +@@ -85,12 +85,6 @@ + /*FUNCTION StringArrayParam::Id{{{*/ + int StringArrayParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION StringArrayParam::MyRank{{{*/ +-int StringArrayParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION StringArrayParam::ObjectEnum{{{*/ + int StringArrayParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/TransientParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/TransientParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/TransientParam.cpp (revision 13414) +@@ -73,12 +73,6 @@ + /*FUNCTION TransientParam::Id{{{*/ + int TransientParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION TransientParam::MyRank{{{*/ +-int TransientParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION TransientParam::ObjectEnum{{{*/ + int TransientParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/DoubleParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DoubleParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/DoubleParam.cpp (revision 13414) +@@ -52,12 +52,6 @@ + /*FUNCTION DoubleParam::Id{{{*/ + int DoubleParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION DoubleParam::MyRank{{{*/ +-int DoubleParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION DoubleParam::ObjectEnum{{{*/ + int DoubleParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/DoubleMatArrayParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DoubleMatArrayParam.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/DoubleMatArrayParam.cpp (revision 13414) +@@ -120,12 +120,6 @@ + /*FUNCTION DoubleMatArrayParam::Id{{{*/ + int DoubleMatArrayParam::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION DoubleMatArrayParam::MyRank{{{*/ +-int DoubleMatArrayParam::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION DoubleMatArrayParam::ObjectEnum{{{*/ + int DoubleMatArrayParam::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Params/StringParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/StringParam.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Params/StringParam.h (revision 13414) +@@ -23,8 +23,8 @@ + + private: + /*just hold 3 values for 3 vertices: */ +- int enum_type; +- char* value; ++ int enum_type; ++ char *value; + + public: + /*StringParam constructors, destructors: {{{*/ +@@ -36,7 +36,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Segment.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Segment.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Segment.h (revision 13414) +@@ -14,31 +14,30 @@ + class Segment: public Object{ + + public: +- int eid; ++ int eid; + doubletype x1; + doubletype y1; + doubletype x2; + doubletype y2; + +- + /*Segment constructors, destructors :*/ + /*FUNCTION Segment() default constructor {{{*/ + Segment(){ +- this->eid=UNDEF; +- this->x1=UNDEF; +- this->y1=UNDEF; +- this->x2=UNDEF; +- this->y2=UNDEF; ++ this->eid = UNDEF; ++ this->x1 = UNDEF; ++ this->y1 = UNDEF; ++ this->x2 = UNDEF; ++ this->y2 = UNDEF; + } + /*}}}*/ + /*FUNCTION Segment(int eid, doubletype x1,doubletype y1,doubletype x2, doubletype y2){{{*/ + Segment(int segment_eid, doubletype segment_x1,doubletype segment_y1,doubletype segment_x2, doubletype segment_y2){ + +- this->eid=segment_eid; +- this->x1=segment_x1; +- this->y1=segment_y1; +- this->x2=segment_x2; +- this->y2=segment_y2; ++ this->eid = segment_eid; ++ this->x1 = segment_x1; ++ this->y1 = segment_y1; ++ this->x2 = segment_x2; ++ this->y2 = segment_y2; + + } + /*}}}*/ +@@ -66,13 +65,6 @@ + /*FUNCTION Id{{{*/ + int Id(void){ return eid; } + /*}}}*/ +- /*FUNCTION MyRank{{{*/ +- int MyRank(void){ +- extern int my_rank; +- +- return my_rank; +- } +- /*}}}*/ + /*FUNCTION ObjectEnum{{{*/ + int ObjectEnum(void){ + +@@ -83,9 +75,7 @@ + /*FUNCTION copy {{{*/ + Object* copy() { + return new Segment(this->eid,this->x1,this->y1,this->x2,this->y2); +- + } +- + /*}}}*/ + + }; +Index: ../trunk-jpl/src/c/classes/objects/Options/GenericOption.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Options/GenericOption.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Options/GenericOption.h (revision 13414) +@@ -28,12 +28,12 @@ + + public: + +- char* name; +- OptionType value; ++ char *name; ++ OptionType value; + +- int numel; //in case OptionType is an array +- int ndims; //in case OptionType is a multi-dimensional array: */ +- int* size; ++ int numel; //in case OptionType is an array ++ int ndims; //in case OptionType is a multi-dimensional array: */ ++ int *size; + + /*GenericOption constructors, destructors*/ + GenericOption(){ /*{{{*/ +@@ -80,7 +80,6 @@ + _printLine_(indent << " value: " << value);; + } /*}}}*/ + int Id(){_error_("Not implemented yet");}; +- int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){return GenericOptionEnum;}; + Object* copy(){_error_("Not implemented yet");}; + +Index: ../trunk-jpl/src/c/classes/objects/Options/Option.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Options/Option.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Options/Option.h (revision 13414) +@@ -16,21 +16,18 @@ + class Option: public Object { + + public: +- + +- /*Option constructors, destructors {{{*/ ++ /*Option constructors, destructors*/ + Option(){}; + ~Option(){}; +- /*}}}*/ +- /*Object virtual functions definitions:{{{*/ ++ ++ /*Object virtual functions definitions*/ + virtual void Echo()= 0; + virtual void DeepEcho()= 0; + virtual void DeepEcho(char *indent)=0; + int Id(){_error_("Not implemented yet"); }; +- int MyRank(){_error_("Not implemented yet"); }; + int ObjectEnum(){return OptionEnum; }; + Object *copy(){_error_("Not implemented yet"); }; +- /*}}}*/ + + /*virtual functions: */ + virtual char* Name()=0; +@@ -40,4 +37,3 @@ + + }; + #endif /* _OPTIONOBJECT_H */ +- +Index: ../trunk-jpl/src/c/classes/objects/Vertex.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Vertex.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Vertex.cpp (revision 13414) +@@ -85,12 +85,6 @@ + /*FUNCTION Vertex::Id{{{*/ + int Vertex::Id(void){ return id; } + /*}}}*/ +-/*FUNCTION Vertex::MyRank {{{*/ +-int Vertex::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Vertex::ObjectEnum{{{*/ + int Vertex::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Loads/Icefront.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Loads/Icefront.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Loads/Icefront.h (revision 13414) +@@ -47,7 +47,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Loads/Numericalflux.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Loads/Numericalflux.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Loads/Numericalflux.cpp (revision 13414) +@@ -182,12 +182,6 @@ + return id; + } + /*}}}*/ +-/*FUNCTION Numericalflux::MyRank {{{*/ +-int Numericalflux::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Numericalflux::ObjectEnum{{{*/ + int Numericalflux::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Loads/Penpair.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Loads/Penpair.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Loads/Penpair.cpp (revision 13414) +@@ -78,12 +78,6 @@ + /*FUNCTION Penpair::Id {{{*/ + int Penpair::Id(void){ return id; } + /*}}}*/ +-/*FUNCTION Penpair::MyRank {{{*/ +-int Penpair::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Penpair::ObjectEnum{{{*/ + int Penpair::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Loads/Riftfront.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Loads/Riftfront.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Loads/Riftfront.h (revision 13414) +@@ -31,21 +31,21 @@ + Element **elements; + + /*computational: */ +- int penalty_lock; +- bool active; +- bool frozen; +- int counter; +- bool prestable; +- bool material_converged; +- IssmDouble normal[2]; +- IssmDouble length; +- IssmDouble fraction; +- int state; +- +- Parameters* parameters; //pointer to solution parameters +- Inputs* inputs; ++ int penalty_lock; ++ bool active; ++ bool frozen; ++ int counter; ++ bool prestable; ++ bool material_converged; ++ IssmDouble normal[2]; ++ IssmDouble length; ++ IssmDouble fraction; ++ int state; + ++ Parameters *parameters; //pointer to solution parameters ++ Inputs *inputs; + ++ + /*Riftfrontconstructors,destructors: {{{*/ + Riftfront(); + Riftfront(int riftfront_id,int i, IoModel* iomodel,int analysis_type); +@@ -55,7 +55,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Loads/Numericalflux.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Loads/Numericalflux.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Loads/Numericalflux.h (revision 13414) +@@ -19,21 +19,19 @@ + class Numericalflux: public Load { + + public: +- int id; ++ int id; + int analysis_type; + + /*Hooks*/ +- Hook* helement; +- Hook* hnodes; ++ Hook *helement; ++ Hook *hnodes; + + /*Corresponding fields*/ +- Element* element; +- Node** nodes; ++ Element *element; ++ Node **nodes; ++ Parameters *parameters; ++ Inputs *inputs; + +- Parameters *parameters; +- Inputs *inputs; +- +- + /*Numericalflux constructors,destructors {{{*/ + Numericalflux(); + Numericalflux(int numericalflux_id,int i, IoModel* iomodel,int analysis_type); +@@ -43,7 +41,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Loads/Penpair.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Loads/Penpair.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Loads/Penpair.h (revision 13414) +@@ -16,14 +16,12 @@ + class Penpair: public Load{ + + private: +- int id; +- int analysis_type; +- +- Hook* hnodes; //hook to 2 nodes +- Node** nodes; ++ int id; ++ int analysis_type; ++ Hook *hnodes; //hook to 2 nodes ++ Node **nodes; ++ Parameters *parameters; //pointer to solution parameters + +- Parameters* parameters; //pointer to solution parameters +- + public: + + /*Penpair constructors, destructors: {{{*/ +@@ -35,7 +33,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Loads/Load.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Loads/Load.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Loads/Load.h (revision 13414) +@@ -4,7 +4,6 @@ + * It is derived from Load, so DataSets can contain them. + */ + +- + #ifndef _LOAD_H_ + #define _LOAD_H_ + +@@ -24,8 +23,6 @@ + public: + + virtual ~Load(){}; +- +- /*Virtual functions: {{{*/ + virtual void Configure(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters)=0; + virtual void SetCurrentConfiguration(Elements* elements,Loads* loads,Nodes* nodes,Vertices* vertices,Materials* materials,Parameters* parameters)=0; + virtual void CreateKMatrix(Matrix* Kff, Matrix* Kfs)=0; +@@ -35,6 +32,5 @@ + virtual void PenaltyCreateKMatrix(Matrix* Kff, Matrix* Kfs, IssmDouble kmax)=0; + virtual void PenaltyCreatePVector(Vector* pf, IssmDouble kmax)=0; + virtual bool InAnalysis(int analysis_type)=0; +- /*}}}*/ + }; + #endif +Index: ../trunk-jpl/src/c/classes/objects/Loads/Pengrid.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Loads/Pengrid.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Loads/Pengrid.cpp (revision 13414) +@@ -125,12 +125,6 @@ + /*FUNCTION Pengrid::Id {{{*/ + int Pengrid::Id(void){ return id; } + /*}}}*/ +-/*FUNCTION Pengrid::MyRank {{{*/ +-int Pengrid::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Pengrid::ObjectEnum{{{*/ + int Pengrid::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Loads/Icefront.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Loads/Icefront.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Loads/Icefront.cpp (revision 13414) +@@ -156,12 +156,6 @@ + /*FUNCTION Icefront::Id {{{*/ + int Icefront::Id(void){ return id; } + /*}}}*/ +-/*FUNCTION Icefront::MyRank {{{*/ +-int Icefront::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Icefront::ObjectEnum{{{*/ + int Icefront::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Loads/Pengrid.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Loads/Pengrid.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Loads/Pengrid.h (revision 13414) +@@ -48,7 +48,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Loads/Riftfront.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Loads/Riftfront.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Loads/Riftfront.cpp (revision 13414) +@@ -185,12 +185,6 @@ + /*FUNCTION Riftfront::Id {{{*/ + int Riftfront::Id(void){ return id; } + /*}}}*/ +-/*FUNCTION Riftfront::MyRank {{{*/ +-int Riftfront::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Riftfront::ObjectEnum{{{*/ + int Riftfront::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Vertex.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Vertex.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Vertex.h (revision 13414) +@@ -42,7 +42,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/ExternalResults/GenericExternalResult.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/ExternalResults/GenericExternalResult.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/ExternalResults/GenericExternalResult.h (revision 13414) +@@ -98,10 +98,6 @@ + int Id(void){ /*{{{*/ + return -1; + } /*}}}*/ +- int MyRank(void){ /*{{{*/ +- extern int my_rank; +- return my_rank; +- } /*}}}*/ + int ObjectEnum(void){ /*{{{*/ + _error_("template ObjectEnum not implemented for this ResultType\n"); + } /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Node.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Node.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Node.cpp (revision 13414) +@@ -57,20 +57,20 @@ + //intialize inputs, and add as many inputs per element as requested: + this->inputs=new Inputs(); + if (iomodel->Data(MeshVertexonbedEnum)) +- this->inputs->AddInput(new BoolInput(MeshVertexonbedEnum,reCast(iomodel->Data(MeshVertexonbedEnum)[io_index]))); ++ this->inputs->AddInput(new BoolInput(MeshVertexonbedEnum,reCast(iomodel->Data(MeshVertexonbedEnum)[io_index]))); + if (iomodel->Data(MeshVertexonsurfaceEnum)) +- this->inputs->AddInput(new BoolInput(MeshVertexonsurfaceEnum,reCast(iomodel->Data(MeshVertexonsurfaceEnum)[io_index]))); ++ this->inputs->AddInput(new BoolInput(MeshVertexonsurfaceEnum,reCast(iomodel->Data(MeshVertexonsurfaceEnum)[io_index]))); + if (iomodel->Data(MaskVertexonfloatingiceEnum)) +- this->inputs->AddInput(new BoolInput(MaskVertexonfloatingiceEnum,reCast(iomodel->Data(MaskVertexonfloatingiceEnum)[io_index]))); ++ this->inputs->AddInput(new BoolInput(MaskVertexonfloatingiceEnum,reCast(iomodel->Data(MaskVertexonfloatingiceEnum)[io_index]))); + if (iomodel->Data(MaskVertexongroundediceEnum)) +- this->inputs->AddInput(new BoolInput(MaskVertexongroundediceEnum,reCast(iomodel->Data(MaskVertexongroundediceEnum)[io_index]))); ++ this->inputs->AddInput(new BoolInput(MaskVertexongroundediceEnum,reCast(iomodel->Data(MaskVertexongroundediceEnum)[io_index]))); + if (analysis_type==DiagnosticHorizAnalysisEnum) + this->inputs->AddInput(new IntInput(ApproximationEnum,reCast(iomodel->Data(FlowequationVertexEquationEnum)[io_index]))); + /*set single point constraints: */ + + /*spc all nodes on water*/ + if (!iomodel->Data(MaskVertexonwaterEnum)) _error_("iomodel->nodeonwater is NULL"); +- if (reCast(iomodel->Data(MaskVertexonwaterEnum)[io_index])){ ++ if (reCast(iomodel->Data(MaskVertexonwaterEnum)[io_index])){ + for(k=1;k<=gsize;k++){ + this->FreezeDof(k); + } +@@ -136,7 +136,7 @@ + if (dim==3){ + /*On a 3d mesh, we may have collapsed elements, hence dead nodes. Freeze them out: */ + _assert_(iomodel->Data(MeshVertexonbedEnum)); +- if (!(reCast(iomodel->Data(MeshVertexonbedEnum)[io_index]))){ ++ if (!(reCast(iomodel->Data(MeshVertexonbedEnum)[io_index]))){ + for(k=1;k<=gsize;k++){ + this->FreezeDof(k); + } +@@ -187,13 +187,6 @@ + /*FUNCTION Node::Id{{{*/ + int Node::Id(void){ return id; } + /*}}}*/ +-/*FUNCTION Node::MyRank{{{*/ +-int Node::MyRank(void){ +- extern int my_rank; +- +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Node::ObjectEnum{{{*/ + int Node::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Constraints/SpcDynamic.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Constraints/SpcDynamic.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Constraints/SpcDynamic.h (revision 13414) +@@ -32,7 +32,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Constraints/SpcStatic.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Constraints/SpcStatic.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Constraints/SpcStatic.h (revision 13414) +@@ -31,7 +31,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Constraints/SpcTransient.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Constraints/SpcTransient.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Constraints/SpcTransient.h (revision 13414) +@@ -33,7 +33,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Constraints/Constraint.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Constraints/Constraint.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Constraints/Constraint.h (revision 13414) +@@ -4,7 +4,6 @@ + * It is derived from Object, so DataSets can contain them. + */ + +- + #ifndef _CONSTRAINT_H_ + #define _CONSTRAINT_H_ + +@@ -23,6 +22,5 @@ + virtual void ConstrainNode(Nodes* nodes,Parameters* parameters)=0; + virtual bool InAnalysis(int analysis_type)=0; + +- + }; + #endif +Index: ../trunk-jpl/src/c/classes/objects/Constraints/SpcDynamic.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Constraints/SpcDynamic.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Constraints/SpcDynamic.cpp (revision 13414) +@@ -65,12 +65,6 @@ + /*FUNCTION SpcDynamic::Id {{{*/ + int SpcDynamic::Id(void){ return sid; } + /*}}}*/ +-/*FUNCTION SpcDynamic::MyRank {{{*/ +-int SpcDynamic::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION SpcDynamic::ObjectEnum{{{*/ + int SpcDynamic::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Constraints/SpcStatic.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Constraints/SpcStatic.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Constraints/SpcStatic.cpp (revision 13414) +@@ -68,12 +68,6 @@ + /*FUNCTION SpcStatic::Id {{{*/ + int SpcStatic::Id(void){ return sid; } + /*}}}*/ +-/*FUNCTION SpcStatic::MyRank {{{*/ +-int SpcStatic::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION SpcStatic::ObjectEnum{{{*/ + int SpcStatic::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Constraints/SpcTransient.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Constraints/SpcTransient.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Constraints/SpcTransient.cpp (revision 13414) +@@ -80,12 +80,6 @@ + /*FUNCTION SpcTransient::Id {{{*/ + int SpcTransient::Id(void){ return sid; } + /*}}}*/ +-/*FUNCTION SpcTransient::MyRank {{{*/ +-int SpcTransient::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION SpcTransient::ObjectEnum{{{*/ + int SpcTransient::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/Node.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Node.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Node.h (revision 13414) +@@ -39,12 +39,11 @@ + ~Node(); + /*}}}*/ + /*Object virtual functions definitions:{{{ */ +- void Echo(); +- void DeepEcho(); +- int Id(); +- int MyRank(); +- int ObjectEnum(); +- Object* copy(){_error_("Not implemented yet (similar to Elements)");}; ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int ObjectEnum(); ++ Object *copy() {_error_("Not implemented yet (similar to Elements)"); }; + /*}}}*/ + /*Update virtual functions definitions: {{{*/ + void InputUpdateFromVector(IssmDouble* vector, int name, int type); +Index: ../trunk-jpl/src/c/classes/objects/ElementResults/TriaP1ElementResult.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/ElementResults/TriaP1ElementResult.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/ElementResults/TriaP1ElementResult.h (revision 13414) +@@ -31,7 +31,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/ElementResults/PentaP1ElementResult.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/ElementResults/PentaP1ElementResult.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/ElementResults/PentaP1ElementResult.cpp (revision 13414) +@@ -60,12 +60,6 @@ + /*FUNCTION PentaP1ElementResult::Id{{{*/ + int PentaP1ElementResult::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION PentaP1ElementResult::MyRank{{{*/ +-int PentaP1ElementResult::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION PentaP1ElementResult::ObjectEnum{{{*/ + int PentaP1ElementResult::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/ElementResults/DoubleElementResult.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/ElementResults/DoubleElementResult.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/ElementResults/DoubleElementResult.cpp (revision 13414) +@@ -57,12 +57,6 @@ + /*FUNCTION DoubleElementResult::Id{{{*/ + int DoubleElementResult::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION DoubleElementResult::MyRank{{{*/ +-int DoubleElementResult::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION DoubleElementResult::ObjectEnum{{{*/ + int DoubleElementResult::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/ElementResults/BoolElementResult.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/ElementResults/BoolElementResult.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/ElementResults/BoolElementResult.cpp (revision 13414) +@@ -57,12 +57,6 @@ + /*FUNCTION BoolElementResult::Id{{{*/ + int BoolElementResult::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION BoolElementResult::MyRank{{{*/ +-int BoolElementResult::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION BoolElementResult::ObjectEnum{{{*/ + int BoolElementResult::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/ElementResults/PentaP1ElementResult.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/ElementResults/PentaP1ElementResult.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/ElementResults/PentaP1ElementResult.h (revision 13414) +@@ -32,7 +32,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/ElementResults/DoubleElementResult.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/ElementResults/DoubleElementResult.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/ElementResults/DoubleElementResult.h (revision 13414) +@@ -33,7 +33,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/ElementResults/ElementResultLocal.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/ElementResults/ElementResultLocal.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/ElementResults/ElementResultLocal.h (revision 13414) +@@ -8,4 +8,3 @@ + class Parameters; + + #endif //ifndef _ELEMENTRESULTLOCAL_H_ +- +Index: ../trunk-jpl/src/c/classes/objects/ElementResults/BoolElementResult.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/ElementResults/BoolElementResult.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/ElementResults/BoolElementResult.h (revision 13414) +@@ -33,7 +33,6 @@ + void Echo(); + void DeepEcho(); + int Id(); +- int MyRank(); + int ObjectEnum(); + Object* copy(); + /*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/ElementResults/TriaP1ElementResult.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/ElementResults/TriaP1ElementResult.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/ElementResults/TriaP1ElementResult.cpp (revision 13414) +@@ -59,12 +59,6 @@ + /*FUNCTION TriaP1ElementResult::Id{{{*/ + int TriaP1ElementResult::Id(void){ return -1; } + /*}}}*/ +-/*FUNCTION TriaP1ElementResult::MyRank{{{*/ +-int TriaP1ElementResult::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION TriaP1ElementResult::ObjectEnum{{{*/ + int TriaP1ElementResult::ObjectEnum(void){ + +Index: ../trunk-jpl/src/c/classes/objects/ElementResults/ElementResult.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/ElementResults/ElementResult.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/ElementResults/ElementResult.h (revision 13414) +@@ -2,7 +2,6 @@ + * \brief abstract class for ElementResult object + */ + +- + #ifndef _ELEMENTRESULT_H_ + #define _ELEMENTRESULT_H_ + +@@ -16,7 +15,6 @@ + public: + + virtual ~ElementResult(){}; +- + virtual ElementResult* SpawnTriaElementResult(int* indices)=0; + virtual IssmDouble GetTime(void)=0; + virtual int GetStep(void)=0; +Index: ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13414) +@@ -2039,12 +2039,6 @@ + this->inputs->AddInput(new TriaP1Input(BedEnum,&b[0])); + } + /*}}}*/ +-/*FUNCTION Tria::MyRank {{{*/ +-int Tria::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Tria::NodalValue {{{*/ + int Tria::NodalValue(IssmDouble* pvalue, int index, int natureofdataenum,bool process_units){ + +Index: ../trunk-jpl/src/c/classes/objects/Elements/Tria.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Tria.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Tria.h (revision 13414) +@@ -28,17 +28,17 @@ + + public: + +- int id; +- int sid; ++ int id; ++ int sid; + +- Node **nodes; // 3 nodes +- Material *material; // 1 material ice +- Matpar *matpar; // 1 material parameter +- int horizontalneighborsids[3]; ++ Node **nodes; // 3 nodes ++ Material *material; // 1 material ice ++ Matpar *matpar; // 1 material parameter ++ int horizontalneighborsids[3]; + +- Parameters *parameters; //pointer to solution parameters +- Inputs *inputs; +- Results *results; ++ Parameters *parameters; //pointer to solution parameters ++ Inputs *inputs; ++ Results *results; + + /*Tria constructors, destructors {{{*/ + Tria(); +@@ -46,12 +46,11 @@ + ~Tria(); + /*}}}*/ + /*Object virtual functions definitions:{{{ */ +- void Echo(); +- void DeepEcho(); +- int Id(); +- int MyRank(); +- int ObjectEnum(); +- Object* copy(); ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int ObjectEnum(); ++ Object *copy(); + /*}}}*/ + /*Update virtual functions resolution: {{{*/ + void InputUpdateFromSolution(IssmDouble* solutiong); +Index: ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp (revision 13414) +@@ -2252,12 +2252,6 @@ + return minlength; + } + /*}}}*/ +-/*FUNCTION Penta::MyRank {{{*/ +-int Penta::MyRank(void){ +- extern int my_rank; +- return my_rank; +-} +-/*}}}*/ + /*FUNCTION Penta::NodalValue {{{*/ + int Penta::NodalValue(IssmDouble* pvalue, int index, int natureofdataenum,bool process_units){ + +Index: ../trunk-jpl/src/c/classes/objects/Elements/Penta.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Penta.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Penta.h (revision 13414) +@@ -33,15 +33,15 @@ + int id; + int sid; + +- Node **nodes; // 6 nodes +- Material *material; // 1 material ice +- Matpar *matpar; // 1 material parameter +- Penta **verticalneighbors; // 2 neighbors: first one under, second one above ++ Node **nodes; // 6 nodes ++ Material *material; // 1 material ice ++ Matpar *matpar; // 1 material parameter ++ Penta **verticalneighbors; // 2 neighbors: first one under, second one above + int horizontalneighborsids[3]; + +- Parameters *parameters; //pointer to solution parameters ++ Parameters *parameters; //pointer to solution parameters + Inputs *inputs; +- Results *results; ++ Results *results; + + /*Penta constructors and destructor: {{{*/ + Penta(); +@@ -49,12 +49,11 @@ + ~Penta(); + /*}}}*/ + /*Object virtual functions definitions: {{{*/ +- Object* copy(); +- void DeepEcho(); +- void Echo(); +- int ObjectEnum(); +- int Id(); +- int MyRank(); ++ Object *copy(); ++ void DeepEcho(); ++ void Echo(); ++ int ObjectEnum(); ++ int Id(); + /*}}}*/ + /*Update virtual functions definitions: {{{*/ + void InputUpdateFromConstant(bool constant, int name); +Index: ../trunk-jpl/src/c/classes/kriging/Quadtree.h +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/Quadtree.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/kriging/Quadtree.h (revision 13414) +@@ -28,7 +28,6 @@ + void Echo(); + void DeepEcho() {_error_("not implemented yet"); }; + int Id() {_error_("not implemented yet"); }; +- int MyRank() {_error_("not implemented yet"); }; + int ObjectEnum(){_error_("not implemented yet"); }; + Object *copy() {_error_("not implemented yet"); }; + +Index: ../trunk-jpl/src/c/classes/kriging/Observation.h +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/Observation.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/kriging/Observation.h (revision 13414) +@@ -25,7 +25,6 @@ + void Echo(); + void DeepEcho() {_error_("Not implemented yet"); }; + int Id() {_error_("Not implemented yet"); }; +- int MyRank() {_error_("Not implemented yet"); }; + int ObjectEnum(){_error_("Not implemented yet"); }; + Object *copy() {_error_("Not implemented yet"); }; + +Index: ../trunk-jpl/src/c/classes/kriging/ExponentialVariogram.h +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/ExponentialVariogram.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/kriging/ExponentialVariogram.h (revision 13414) +@@ -24,7 +24,6 @@ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; +- int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + +Index: ../trunk-jpl/src/c/classes/kriging/GaussianVariogram.h +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/GaussianVariogram.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/kriging/GaussianVariogram.h (revision 13414) +@@ -25,7 +25,6 @@ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; +- int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + +Index: ../trunk-jpl/src/c/classes/kriging/SphericalVariogram.h +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/SphericalVariogram.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/kriging/SphericalVariogram.h (revision 13414) +@@ -24,7 +24,6 @@ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; +- int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + +Index: ../trunk-jpl/src/c/classes/kriging/PowerVariogram.h +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/PowerVariogram.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/kriging/PowerVariogram.h (revision 13414) +@@ -24,7 +24,6 @@ + void Echo(); + void DeepEcho(){_error_("Not implemented yet");}; + int Id(){_error_("Not implemented yet");}; +- int MyRank(){_error_("Not implemented yet");}; + int ObjectEnum(){_error_("Not implemented yet");}; + Object* copy(){_error_("Not implemented yet");}; + +Index: ../trunk-jpl/src/c/classes/bamg/BamgQuadtree.h +=================================================================== +--- ../trunk-jpl/src/c/classes/bamg/BamgQuadtree.h (revision 13413) ++++ ../trunk-jpl/src/c/classes/bamg/BamgQuadtree.h (revision 13414) +@@ -33,7 +33,6 @@ + void Echo() {_error_("not implemented yet"); }; + void DeepEcho() {_error_("not implemented yet"); }; + int Id() {_error_("not implemented yet"); }; +- int MyRank() {_error_("not implemented yet"); }; + int ObjectEnum() {_error_("not implemented yet"); }; + Object *copy() {_error_("not implemented yet"); }; + }; Index: /issm/oecreview/Archive/13393-13976/ISSM-13414-13415.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13414-13415.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13414-13415.diff (revision 13980) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13414) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13415) +@@ -5549,7 +5549,7 @@ + + /*Get values on the 3 vertices*/ + for (i=0;i<3;i++){ +- values[i]=vector[this->nodes[i]->GetVertexSidList()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!) ++ values[i]=vector[this->nodes[i]->GetVertexSid()]; //careful, vector of values here is not parallel distributed, but serial distributed (from a serial Dakota core!) + } + + /*Branch on the specified type of update: */ +@@ -5655,7 +5655,7 @@ + + /*create input values: */ + for(i=0;i<3;i++){ +- row=this->nodes[i]->GetVertexSidList(); ++ row=this->nodes[i]->GetVertexSid(); + values[i]=(IssmDouble)matrix[ncols*row+t]; + } + Index: /issm/oecreview/Archive/13393-13976/ISSM-13415-13416.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13415-13416.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13415-13416.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/classes/objects/Vertex.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Vertex.cpp (revision 13415) ++++ ../trunk-jpl/src/c/classes/objects/Vertex.cpp (revision 13416) +@@ -171,7 +171,7 @@ + + /*Ok, we are a clone node, but we did not create the pid for this vertex + * Therefore, our pid is garbage right now. Go pick it up in the alltruepids: */ +- this->pid=alltruepids[this->pid]; ++ this->pid=alltruepids[this->sid]; + } + /*}}}*/ + /*FUNCTION Vertex::SetClone {{{*/ Index: /issm/oecreview/Archive/13393-13976/ISSM-13416-13417.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13416-13417.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13416-13417.diff (revision 13980) @@ -0,0 +1,345 @@ +Index: ../trunk-jpl/src/m/classes/plotoptions.py +=================================================================== +--- ../trunk-jpl/src/m/classes/plotoptions.py (revision 13416) ++++ ../trunk-jpl/src/m/classes/plotoptions.py (revision 13417) +@@ -92,10 +92,12 @@ + #Empty + if not plotnum: continue + ++ # '#all' + elif 'all' in plotnum: + for j in xrange(numberofplots): + self.list[j].addfield(field,rawlist[i][1]) + ++ # '#i-j' + elif '-' in plotnum: + nums=plotnum.split('-') + if len(nums)!=2: continue +Index: ../trunk-jpl/src/m/plot/plot_mesh.py +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_mesh.py (revision 13416) ++++ ../trunk-jpl/src/m/plot/plot_mesh.py (revision 13417) +@@ -1,5 +1,6 @@ + import pylab as p +-import matplotlib.tri as tri ++from processmesh import processmesh ++from applyoptions import applyoptions + + def plot_mesh(md,options,nlines,ncols,i): + ''' +@@ -11,14 +12,14 @@ + See also: PLOTMODEL + ''' + +- #TODO: implement processmesh +- x=md.mesh.x +- y=md.mesh.y +- elements=md.mesh.elements +- elements=elements-1 #since python indexes from zero ++ x,y,z,elements,is2d=processmesh(md,[],options) + +- p.subplot(nlines,ncols,i) +- p.triplot(x,y,elements) +- p.title('Mesh') ++ if is2d: ++ p.subplot(nlines,ncols,i) ++ p.triplot(x,y,elements) ++ else: ++ print 'WARNING: only 2D mesh plot is currently implemented' + +- print 'WARNING: options passed to plot_mesh not implemented yet' ++ #apply options ++ options.addfielddefault('title','Mesh') ++ applyoptions(md,[],options) +Index: ../trunk-jpl/src/m/plot/processmesh.py +=================================================================== +--- ../trunk-jpl/src/m/plot/processmesh.py (revision 0) ++++ ../trunk-jpl/src/m/plot/processmesh.py (revision 13417) +@@ -0,0 +1,86 @@ ++from math import isnan ++ ++def processmesh(md,data,options): ++ """ ++ PROCESSMESH - process the mesh for plotting ++ ++ Usage: ++ [x y z elements is2d]=processmech(md,data,options) ++ ++ See also: PLOTMODEL, PROCESSDATA ++ """ ++ ++ #some checks ++ if md.mesh.numberofvertices==0: ++ raise ValueError('processmesh error: mesh is empty') ++ if md.mesh.numberofvertices==md.mesh.numberofelements: ++ raise ValueError('processmesh error: the number of elements is the same as the number of nodes') ++ ++ if not data or not isinstance(data,dict): ++ ++ if 'latlon' not in options.getfieldvalue('coord','xy').lower(): #convert to lower case for comparison ++ x=md.mesh.x ++ if not isnan(md.mesh.x2d): x2d=md.mesh.x2d ++ y=md.mesh.y ++ if not isnan(md.mesh.y2d): y2d=md.mesh.y2d ++ else: ++ x=md.mesh.long ++ y=md.mesh.lat ++ ++ z_field=options.getfieldvalue('z',md.mesh.z) ++ #if isinstance(z_field,basestring): # how could z be a string? ++ # z=md.(z_field) ++ if isinstance(z_field,(int,long,float)): # isnumeric ++ z=z_field ++ else: ++ z=md.mesh.z ++ ++ if not isnan(md.mesh.elements2d): ++ elements2d=md.mesh.elements2d ++ elements2d=elements2d-1 ++ # subtract one since python indexes from zero ++ elements=md.mesh.elements ++ elements=elements-1 ++ ++ #is it a 2D plot? ++ if md.mesh.dimension==2: ++ is2d=1 ++ elif md.mesh.dimension==3: ++ if options.getfieldvalue('layer',0)>=1: ++ is2d=1 ++ else: ++ is2d=0 ++ else: ++ raise ValueError('processmesh error: dim = %d not supported') ++ ++ #layer projection? ++ if options.getfieldvalue('layer',0)>=1: ++ if 'latlon' in options.getfieldvalue('coord','xy').lower(): ++ raise ValueError('processmesh error: cannot work with 3D mesh in lat-lon coords') ++ #we modify (w/c?) the mesh temporarily to a 2D mesh from which the 3D mesh was extruded ++ x=x2d ++ y=y2d ++ z=zeros(size(x2d)) ++ elements=elements2d ++ ++ else: ++ #Process mesh for plotting (triangulation for 2D, polycollection for 3D?) ++ if md.mesh.dimension==2: ++ is2d=1 ++ else: ++ # process polycollection here for 3D plot ++ is2d=0 ++ ++ #units ++ if options.exist('unit'): ++ unit=options.getfieldvalue('unit') ++ x=x*unit ++ y=y*unit ++ z=z*unit ++ ++ ##is model a member of planet class? (won't work until planet class defined) ++ #if isinstance(md,planet): ++ # isplanet=1 ++ #else: ++ # isplanet=0 ++ return x,y,z,elements,is2d +Index: ../trunk-jpl/src/m/plot/plotmodel.py +=================================================================== +--- ../trunk-jpl/src/m/plot/plotmodel.py (revision 13416) ++++ ../trunk-jpl/src/m/plot/plotmodel.py (revision 13417) +@@ -1,7 +1,8 @@ + import pylab as p + #from pairoptions import * +-from plotoptions import * +-from plot_manager import * ++from plotoptions import plotoptions ++from plot_manager import plot_manager ++from math import ceil, sqrt + + def plotmodel(md,*args): + ''' +@@ -12,7 +13,7 @@ + options=plotoptions(*args) + + #get number of subplots +- subplotwidth=math.ceil(math.sqrt(options.numberofplots)) ++ subplotwidth=ceil(sqrt(options.numberofplots)) + + #if nlines and ncols specified, then bypass + if options.list[0].exist('nlines'): +@@ -43,13 +44,20 @@ + #Create figure + #plots will be visible by default if ipython is run in interactive mode (invoked by ipython --pylab) + #handling the 'visible' option will need some check on whether ipython is currently in interactive or non-interactive mode +- p.figure(figurenumber) ++ ++ #if figsize specified ++ if options.list[0].exist('figsize'): ++ figsize=options.list[0].getfieldvalue('figsize') ++ p.figure(figurenumber,figsize=figsize) ++ else: ++ p.figure(figurenumber) ++ + +- try: +- for i in xrange(numberofplots): +- plot_manager(options.list[i].getfieldvalue('model',md),options.list[i],subplotwidth,nlines,ncols,i) +- except StandardError: +- print 'error in plot_manager' ++ #try: ++ for i in xrange(numberofplots): ++ plot_manager(options.list[i].getfieldvalue('model',md),options.list[i],subplotwidth,nlines,ncols,i) ++ #except StandardError: ++ # print 'error in plot_manager' + else: + raise StandardError('plotmodel error message: no output data found.') + +Index: ../trunk-jpl/src/m/plot/applyoptions.py +=================================================================== +--- ../trunk-jpl/src/m/plot/applyoptions.py (revision 0) ++++ ../trunk-jpl/src/m/plot/applyoptions.py (revision 13417) +@@ -0,0 +1,145 @@ ++from matplotlib.font_manager import FontProperties ++import pylab as p ++ ++def applyoptions(md,data,options): ++ ''' ++ APPLYOPTIONS - apply options to current plot ++ ++ Usage: ++ applyoptions(md,data,options) ++ ++ See also: PLOTMODEL, PARSE_OPTIONS ++ ''' ++ ++ #some defaults (this seems to be adding a field that already exists...) ++ #if not isnan(md.mesh.hemisphere): ++ # options.addfielddefault('hemisphere',md.mesh.hemisphere) ++ ++ #font ++ fontsize=options.getfieldvalue('fontsize',14) ++ fontweight=options.getfieldvalue('fontweight','normal') ++ fontfamily=options.getfieldvalue('fontfamily','sans-serif') ++ font={ ++ 'fontsize' :fontsize, ++ 'fontweight' :fontweight, ++ 'family' :fontfamily ++ } ++ ++ #title ++ if options.exist('title'): ++ title=options.getfieldvalue('title') ++ if options.exist('titlefontsize'): ++ titlefontsize=options.getfieldvalue('titlefontsize') ++ else: ++ titlefontsize=fontsize ++ if options.exist('titlefontweight'): ++ titlefontweight=options.getfieldvalue('titlefontweight') ++ else: ++ titlefontweight=fontweight ++ #title font ++ titlefont=font.copy() ++ titlefont['size']=titlefontsize ++ titlefont['weight']=titlefontweight ++ p.title(title,**titlefont) ++ ++ #xlabel, ylabel, zlabel ++ if options.exist('labelfontsize'): ++ labelfontsize=options.getfieldvalue('labelfontsize') ++ else: ++ labelfontsize=fontsize ++ if options.exist('labelfontweight'): ++ labelfontweight=options.getfieldvalue('labelfontweight') ++ else: ++ labelfontweight=fontweight ++ ++ #font dict for labels ++ labelfont=font.copy() ++ labelfont['fontsize']=labelfontsize ++ labelfont['fontweight']=labelfontweight ++ ++ if options.exist('xlabel'): ++ p.xlabel(options.getfieldvalue('xlabel'),**labelfont) ++ if options.exist('ylabel'): ++ p.ylabel(options.getfieldvalue('ylabel'),**labelfont) ++ if options.exist('zlabel'): ++ p.zlabel(options.getfieldvalue('zlabel'),**labelfont) ++ ++ #xticks, yticks, zticks ++ ++ #view ++ ++ #axis ++ ++ #box ++ ++ #xlim, ylim, zlim ++ if options.exist('xlim'): ++ p.xlim(options.getfieldvalue('xlim')) ++ if options.exist('ylim'): ++ p.xlim(options.getfieldvalue('ylim')) ++ if options.exist('zlim'): ++ p.xlim(options.getfieldvalue('zlim')) ++ ++ #latlon ++ ++ #Basinzoom ++ ++ #ShowBasins ++ ++ #Caxis ++ ++ #shading ++ ++ #grid ++ if options.exist('grid'): ++ p.grid() ++ ++ #colormap ++ ++ #wrapping ++ ++ #colorbar ++ ++ #area ++ ++ #expdisp ++ ++ #text ++ ++ #north arrow ++ ++ #scale ruler ++ ++ #streamlines ++ ++ #contours ++ ++ #YTickLabel ++ ++ #XTickLabel ++ ++ #xtick ++ ++ #ytick ++ ++ #axis positions ++ ++ #figure position ++ ++ #axes position ++ ++ #showregion ++ ++ #flat edges of a partition ++ ++ #scatter ++ ++ #backgroundcolor ++ ++ #figurebackgroundcolor ++ ++ #lighting ++ ++ #point cloud ++ ++ #inset Index: /issm/oecreview/Archive/13393-13976/ISSM-13417-13418.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13417-13418.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13417-13418.diff (revision 13980) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/m/regional/regionaltransient2d.m +=================================================================== +--- ../trunk-jpl/src/m/regional/regionaltransient2d.m (revision 13417) ++++ ../trunk-jpl/src/m/regional/regionaltransient2d.m (revision 13418) +@@ -30,7 +30,7 @@ + end + + %take every fields from model +-mde=modelextract(md1,area); ++mde=md1.extract(area); + mde.private.bamg=[]; + mde.mesh.extractedvertices=nan; + mde.mesh.extractedelements=nan; +@@ -130,7 +130,7 @@ + + %Diagnostic. Don't spc the icefront vertices. + if ~isnan(md2.diagnostic.icefront) +- md1s=modelextract(md1,area); ++ md1s=md1.extract(area); + %md2.diagnostic.icefront=[md2.mesh.segments 2]; + e2=md2.mesh.segments(:,end); + e1=md1s.mesh.segments(:,end); Index: /issm/oecreview/Archive/13393-13976/ISSM-13418-13419.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13418-13419.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13418-13419.diff (revision 13980) @@ -0,0 +1,20 @@ +Index: ../trunk-jpl/externalpackages/adolc/install-dev.sh +=================================================================== +--- ../trunk-jpl/externalpackages/adolc/install-dev.sh (revision 13418) ++++ ../trunk-jpl/externalpackages/adolc/install-dev.sh (revision 13419) +@@ -2,12 +2,12 @@ + set -eu + + #Some cleanup +-rm -rf install adolc_v220_issm ++rm -rf install adolc*issm + +-git clone -b 2.3.x_ISSM git://gitorious.org/~utke/adol-c/adolc_v220_issm.git ++git clone -b 2.3.x_ISSM git://git.mcs.anl.gov/adol-c.git adolc_issm + + #Compile ADOL-C +-cd adolc_v220_issm ++cd adolc_issm + + autoreconf -f -i + ./configure --prefix=$ISSM_DIR/externalpackages/adolc/install Index: /issm/oecreview/Archive/13393-13976/ISSM-13419-13420.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13419-13420.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13419-13420.diff (revision 13980) @@ -0,0 +1,21 @@ +Index: ../trunk-jpl/src/m/classes/thermal.py +=================================================================== +--- ../trunk-jpl/src/m/classes/thermal.py (revision 13419) ++++ ../trunk-jpl/src/m/classes/thermal.py (revision 13420) +@@ -1,4 +1,5 @@ + #module imports ++import numpy + from fielddisplay import fielddisplay + from EnumDefinitions import * + from checkfield import * +@@ -69,7 +70,9 @@ + md = checkfield(md,'thermal.stabilization','numel',[1],'values',[0,1,2]) + md = checkfield(md,'thermal.spctemperature','forcing',1) + if EnthalpyAnalysisEnum() in analyses and (md.thermal.isenthalpy or solution==EnthalpySolutionEnum()) and md.mesh.dimension==3: +- md = checkfield(md,'thermal.spctemperature','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*(md.geometry.surface-md.mesh.z),'message',"spctemperature should be below the adjusted melting point") ++ pos=numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[1:md.mesh.numberofvertices,:]))) ++ replicate=numpy.tile(md.geometry.surface-md.mesh.z,(1,numpy.size(md.thermal.spctemperature,axis=1))) ++ md = checkfield(md,'thermal.spctemperature(numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[1:md.mesh.numberofvertices,:]))))','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") + md = checkfield(md,'thermal.isenthalpy','numel',[1],'values',[0,1]) + + return md Index: /issm/oecreview/Archive/13393-13976/ISSM-13420-13421.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13420-13421.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13420-13421.diff (revision 13980) @@ -0,0 +1,16 @@ +Index: ../trunk-jpl/src/m/classes/thermal.py +=================================================================== +--- ../trunk-jpl/src/m/classes/thermal.py (revision 13420) ++++ ../trunk-jpl/src/m/classes/thermal.py (revision 13421) +@@ -70,9 +70,9 @@ + md = checkfield(md,'thermal.stabilization','numel',[1],'values',[0,1,2]) + md = checkfield(md,'thermal.spctemperature','forcing',1) + if EnthalpyAnalysisEnum() in analyses and (md.thermal.isenthalpy or solution==EnthalpySolutionEnum()) and md.mesh.dimension==3: +- pos=numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[1:md.mesh.numberofvertices,:]))) ++ pos=numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices-1,:]))) + replicate=numpy.tile(md.geometry.surface-md.mesh.z,(1,numpy.size(md.thermal.spctemperature,axis=1))) +- md = checkfield(md,'thermal.spctemperature(numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[1:md.mesh.numberofvertices,:]))))','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") ++ md = checkfield(md,'thermal.spctemperature(numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices-1,:]))))','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") + md = checkfield(md,'thermal.isenthalpy','numel',[1],'values',[0,1]) + + return md Index: /issm/oecreview/Archive/13393-13976/ISSM-13421-13422.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13421-13422.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13421-13422.diff (revision 13980) @@ -0,0 +1,16 @@ +Index: ../trunk-jpl/src/m/classes/thermal.py +=================================================================== +--- ../trunk-jpl/src/m/classes/thermal.py (revision 13421) ++++ ../trunk-jpl/src/m/classes/thermal.py (revision 13422) +@@ -70,9 +70,9 @@ + md = checkfield(md,'thermal.stabilization','numel',[1],'values',[0,1,2]) + md = checkfield(md,'thermal.spctemperature','forcing',1) + if EnthalpyAnalysisEnum() in analyses and (md.thermal.isenthalpy or solution==EnthalpySolutionEnum()) and md.mesh.dimension==3: +- pos=numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices-1,:]))) ++ pos=numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices,:]))) + replicate=numpy.tile(md.geometry.surface-md.mesh.z,(1,numpy.size(md.thermal.spctemperature,axis=1))) +- md = checkfield(md,'thermal.spctemperature(numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices-1,:]))))','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") ++ md = checkfield(md,'thermal.spctemperature(numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices,:]))))','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") + md = checkfield(md,'thermal.isenthalpy','numel',[1],'values',[0,1]) + + return md Index: /issm/oecreview/Archive/13393-13976/ISSM-13422-13423.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13422-13423.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13422-13423.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/m/miscellaneous/fielddisplay.py +=================================================================== +--- ../trunk-jpl/src/m/miscellaneous/fielddisplay.py (revision 13422) ++++ ../trunk-jpl/src/m/miscellaneous/fielddisplay.py (revision 13423) +@@ -127,7 +127,7 @@ + elif isinstance(comment,list): + string="%s%-23s: %-15s -- %s" % (offset,name,characterization,comment[0]) + for commenti in comment: +- string+="\n%s%-23s %-15s %s" % (offset,'','',comment[i]) ++ string+="\n%s%-23s %-15s %s" % (offset,'','',commenti) + else: + raise RuntimeError("fielddisplay error message: format for comment not supported yet") + Index: /issm/oecreview/Archive/13393-13976/ISSM-13423-13424.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13423-13424.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13423-13424.diff (revision 13980) @@ -0,0 +1,169 @@ +Index: ../trunk-jpl/src/m/classes/pairoptions.py +=================================================================== +--- ../trunk-jpl/src/m/classes/pairoptions.py (revision 13423) ++++ ../trunk-jpl/src/m/classes/pairoptions.py (revision 13424) +@@ -52,7 +52,7 @@ + # }}} + + def addfielddefault(self,field,value): # {{{ +- """ADDFIELDDEFAULT - add a field to an options list if it does not exist""" ++ """ADDFIELDDEFAULT - add a field to an options list if it does not already exist""" + if isinstance(field,(str,unicode)): + if field not in self.list: + self.list[field] = value +Index: ../trunk-jpl/src/m/plot/plot_manager.py +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_manager.py (revision 13423) ++++ ../trunk-jpl/src/m/plot/plot_manager.py (revision 13424) +@@ -23,10 +23,13 @@ + #figure out if this is a special plot + if isinstance(data,(str,unicode)): + +- if data=='mesh': plot_mesh(md,options,nlines,ncols,i) ++ # convert string to lower case for a case-insensitive comparison ++ if data.lower()=='mesh': plot_mesh(md,options,nlines,ncols,i) + else: + print "WARNING: '%s' is not implemented or is not a valid string for option 'data'" % data + ++ #elif data in vars(md): + else: + print "'data' not a string, plotting model properties yet to be implemented..." + ++ +Index: ../trunk-jpl/src/m/plot/applyoptions.py +=================================================================== +--- ../trunk-jpl/src/m/plot/applyoptions.py (revision 13423) ++++ ../trunk-jpl/src/m/plot/applyoptions.py (revision 13424) +@@ -1,4 +1,3 @@ +-from matplotlib.font_manager import FontProperties + import pylab as p + + def applyoptions(md,data,options): +@@ -15,7 +14,7 @@ + #if not isnan(md.mesh.hemisphere): + # options.addfielddefault('hemisphere',md.mesh.hemisphere) + +- #font ++ #font {{{ + fontsize=options.getfieldvalue('fontsize',14) + fontweight=options.getfieldvalue('fontweight','normal') + fontfamily=options.getfieldvalue('fontfamily','sans-serif') +@@ -24,8 +23,9 @@ + 'fontweight' :fontweight, + 'family' :fontfamily + } ++ #}}} + +- #title ++ #title {{{ + if options.exist('title'): + title=options.getfieldvalue('title') + if options.exist('titlefontsize'): +@@ -41,8 +41,9 @@ + titlefont['size']=titlefontsize + titlefont['weight']=titlefontweight + p.title(title,**titlefont) ++ #}}} + +- #xlabel, ylabel, zlabel ++ #xlabel, ylabel, zlabel {{{ + if options.exist('labelfontsize'): + labelfontsize=options.getfieldvalue('labelfontsize') + else: +@@ -63,22 +64,67 @@ + p.ylabel(options.getfieldvalue('ylabel'),**labelfont) + if options.exist('zlabel'): + p.zlabel(options.getfieldvalue('zlabel'),**labelfont) ++ #}}} + +- #xticks, yticks, zticks ++ #xticks, yticks, zticks (tick locations) {{{ ++ if options.exist('xticks'): ++ if options.exist('xticklabels'): ++ xticklabels=options.getfieldvalue('xticklabels') ++ p.xticks(options.getfieldvalue('xticks'),xticklabels) ++ else: ++ p.xticks(options.getfieldvalue('xticks')) ++ if options.exist('yticks'): ++ if options.exist('yticklabels'): ++ yticklabels=options.getfieldvalue('yticklabels') ++ p.yticks(options.getfieldvalue('yticks'),yticklabels) ++ else: ++ p.yticks(options.getfieldvalue('yticks')) ++ if options.exist('zticks'): ++ if options.exist('zticklabels'): ++ zticklabels=options.getfieldvalue('zticklabels') ++ p.zticks(options.getfieldvalue('zticks'),zticklabels) ++ else: ++ p.zticks(options.getfieldvalue('zticks')) ++ #}}} + ++ #xticklabels,yticklabels,zticklabels {{{ ++ if options.exist('xticklabels'): ++ xticklabels=options.getfieldvalue('xticklabels') ++ xtickloc=p.xticks()[0] ++ p.xticks(xtickloc,xticklabels) ++ if options.exist('yticklabels'): ++ yticklabels=options.getfieldvalue('yticklabels') ++ ytickloc=p.yticks()[0] ++ p.yticks(ytickloc,yticklabels) ++ if options.exist('zticklabels'): ++ zticklabels=options.getfieldvalue('zticklabels') ++ ztickloc=p.zticks()[0] ++ p.zticks(ztickloc,zticklabels) ++ #}}} ++ ++ #ticklabelfontsize {{{ ++ if options.exist('ticklabelfontsize'): ++ ax=p.gca() ++ for label in ax.get_xticklabels() + ax.get_yticklabels(): ++ label.set_fontsize(options.getfieldvalue('ticklabelfontsize')) ++ if int(md.mesh.dimension)==3: ++ for label in ax.get_zticklabels(): ++ label.set_fontsize(options.getfieldvalue('ticklabelfontsize')) ++ #}}} + #view + + #axis + + #box + +- #xlim, ylim, zlim ++ #xlim, ylim, zlim {{{ + if options.exist('xlim'): + p.xlim(options.getfieldvalue('xlim')) + if options.exist('ylim'): + p.xlim(options.getfieldvalue('ylim')) + if options.exist('zlim'): + p.xlim(options.getfieldvalue('zlim')) ++ #}}} + + #latlon + +@@ -90,9 +136,10 @@ + + #shading + +- #grid ++ #grid {{{ + if options.exist('grid'): + p.grid() ++ #}}} + + #colormap + +@@ -114,14 +161,9 @@ + + #contours + +- #YTickLabel + +- #XTickLabel + +- #xtick + +- #ytick +- + #axis positions + + #figure position Index: /issm/oecreview/Archive/13393-13976/ISSM-13424-13425.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13424-13425.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13424-13425.diff (revision 13980) @@ -0,0 +1,419 @@ +Index: ../trunk-jpl/src/c/Container/Parameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/Container/Parameters.cpp (revision 13424) ++++ ../trunk-jpl/src/c/Container/Parameters.cpp (revision 13425) +@@ -296,7 +296,25 @@ + _error_("could not find parameter " << EnumToStringx(enum_type)); + } + /*}}}*/ ++/*FUNCTION Parameters::FindParam(DataSet** pdataset,int enum_type){{{*/ ++void Parameters::FindParam(DataSet** pdataset,int enum_type){ ++ _assert_(this); + ++ vector::iterator object; ++ Param* param=NULL; ++ ++ for ( object=objects.begin() ; object < objects.end(); object++ ){ ++ ++ param=(Param*)(*object); ++ if(param->InstanceEnum()==enum_type){ ++ param->GetParameterValue(pdataset); ++ return; ++ } ++ } ++ _error_("could not find parameter " << EnumToStringx(enum_type)); ++} ++/*}}}*/ ++ + /*FUNCTION Parameters::SetParam(bool boolean,int enum_type);{{{*/ + void Parameters::SetParam(bool boolean,int enum_type){ + +Index: ../trunk-jpl/src/c/Container/Parameters.h +=================================================================== +--- ../trunk-jpl/src/c/Container/Parameters.h (revision 13424) ++++ ../trunk-jpl/src/c/Container/Parameters.h (revision 13425) +@@ -43,6 +43,7 @@ + void FindParam(Vector** pvec,int enum_type); + void FindParam(Matrix** pmat,int enum_type); + void FindParam(FILE** pfid,int enum_type); ++ void FindParam(DataSet** pdataset, int enum_type); + + void SetParam(bool boolean,int enum_type); + void SetParam(int integer,int enum_type); +Index: ../trunk-jpl/src/c/classes/objects/Params/DoubleVecParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DoubleVecParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/DoubleVecParam.h (revision 13425) +@@ -55,6 +55,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} + void GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");} + void SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");} +Index: ../trunk-jpl/src/c/classes/objects/Params/GenericParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/GenericParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/GenericParam.h (revision 13425) +@@ -78,6 +78,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a Mat");} + void GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold a bool");} + void SetValue(int integer){_error_("Param "<< EnumToStringx(myEnumVal) << " cannot hold an integer");} +Index: ../trunk-jpl/src/c/classes/objects/Params/DoubleMatParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DoubleMatParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/DoubleMatParam.h (revision 13425) +@@ -56,6 +56,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} + void GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");} + void SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");} +Index: ../trunk-jpl/src/c/classes/objects/Params/Param.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/Param.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/Param.h (revision 13425) +@@ -40,6 +40,7 @@ + virtual void GetParameterValue(Vector** pvec)=0; + virtual void GetParameterValue(Matrix** pmat)=0; + virtual void GetParameterValue(FILE** pfid)=0; ++ virtual void GetParameterValue(DataSet** pdataset)=0; + + virtual void SetValue(bool boolean)=0; + virtual void SetValue(int integer)=0; +Index: ../trunk-jpl/src/c/classes/objects/Params/FileParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/FileParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/FileParam.h (revision 13425) +@@ -54,6 +54,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} + void GetParameterValue(FILE** pfid){*pfid=value;}; ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");} + void SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");} +Index: ../trunk-jpl/src/c/classes/objects/Params/DataSetParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DataSetParam.h (revision 0) ++++ ../trunk-jpl/src/c/classes/objects/Params/DataSetParam.h (revision 13425) +@@ -0,0 +1,80 @@ ++/*! \file DataSetParam.h ++ * \brief: header file for triavertexinput object ++ */ ++ ++ ++#ifndef _DATASETPARAM_H_ ++#define _DATASETPARAM_H_ ++ ++/*Headers:*/ ++/*{{{*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "./Param.h" ++#include "../../../include/include.h" ++#include "../../../shared/shared.h" ++/*}}}*/ ++ ++class DataSetParam: public Param{ ++ ++ private: ++ int enum_type; ++ DataSet* value; ++ ++ public: ++ /*DataSetParam constructors, destructors: {{{*/ ++ DataSetParam(); ++ DataSetParam(int enum_type,DataSet* dataset); ++ ~DataSetParam(); ++ /*}}}*/ ++ /*Object virtual functions definitions:{{{ */ ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int MyRank(); ++ int ObjectEnum(); ++ Object* copy(); ++ /*}}}*/ ++ /*Param vritual function definitions: {{{*/ ++ int InstanceEnum(){return enum_type;} ++ void GetParameterValue(bool* pbool){ _error_("Param "<< EnumToStringx(enum_type) << " cannot return a bool");} ++ void GetParameterValue(int* pinteger){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");} ++ void GetParameterValue(int** pintarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");} ++ void GetParameterValue(int** pintarray,int* pM,int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");} ++ void GetParameterValue(IssmDouble* pIssmDouble){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble");} ++ void GetParameterValue(IssmDouble* pdouble,IssmDouble time){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble for a given time");} ++ void GetParameterValue(FILE** pfile){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a file pointer");} ++ void GetParameterValue(char** pstring){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string");} ++ void GetParameterValue(char*** pstringarray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a string array");} ++ void GetParameterValue(IssmDouble** pIssmDoublearray,int* pM){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");} ++ void GetParameterValue(IssmDouble** pIssmDoublearray,int* pM, int* pN){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a IssmDouble array");} ++ void GetParameterValue(IssmDouble*** parray, int* pM,int** pmdims, int** pndims){_error_("DataSet param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return a matrix array");} ++ void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} ++ void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} ++ void GetParameterValue(DataSet** pdataset); ++ ++ void SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");} ++ void SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");} ++ void SetValue(IssmDouble scalar){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");} ++ void SetValue(char* string){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string");} ++ void SetValue(FILE* fid){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a file pointer");} ++ void SetValue(char** stringarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a string array");} ++ void SetValue(IssmDouble* IssmDoublearray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");} ++ void SetValue(IssmDouble* pIssmDoublearray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a IssmDouble array");} ++ void SetValue(int* intarray,int M){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");} ++ void SetValue(int* pintarray,int M,int N){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a int array");} ++ void SetValue(Vector* vec){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Vec");} ++ void SetValue(Matrix* mat){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a Mat");} ++ void SetValue(DataSet* dataset){_error_("DataSet param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot hold a DataSet yet");} ++ void SetValue(IssmDouble** array, int M, int* mdim_array, int* ndim_array){_error_("DataSet param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot hold an array of matrices");} ++ void UnitConversion(int direction_enum); ++ ++ void GetParameterName(char**pname); ++ ++ /*}}}*/ ++}; ++#endif /* _INTPARAM_H */ +Index: ../trunk-jpl/src/c/classes/objects/Params/IntParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/IntParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/IntParam.h (revision 13425) +@@ -55,6 +55,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} + void GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a bool");} + void SetValue(int integer){this->value=integer;} +Index: ../trunk-jpl/src/c/classes/objects/Params/VectorParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/VectorParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/VectorParam.h (revision 13425) +@@ -55,6 +55,7 @@ + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} + void GetParameterValue(Vector** poutput); + void GetParameterValue(FILE** pfid){_error_("Vector of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Vector of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot hold a boolean");} + void SetValue(int integer){_error_("Vector of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot hold an integer");} +Index: ../trunk-jpl/src/c/classes/objects/Params/MatrixParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/MatrixParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/MatrixParam.h (revision 13425) +@@ -55,6 +55,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a vec");} + void GetParameterValue(Matrix** poutput); + void GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");} + void SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");} +Index: ../trunk-jpl/src/c/classes/objects/Params/StringArrayParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/StringArrayParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/StringArrayParam.h (revision 13425) +@@ -57,6 +57,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} + void GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");} + void SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");} +Index: ../trunk-jpl/src/c/classes/objects/Params/TransientParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/TransientParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/TransientParam.h (revision 13425) +@@ -55,6 +55,7 @@ + void GetParameterValue(Vector** pvec){_error_("Parameter " <** pmat){_error_("Parameter " <** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} + void GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){this->value=(IssmDouble)boolean;} + void SetValue(int integer){this->value=(IssmDouble)integer;} +Index: ../trunk-jpl/src/c/classes/objects/Params/DoubleMatArrayParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DoubleMatArrayParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/DoubleMatArrayParam.h (revision 13425) +@@ -57,6 +57,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a Mat");} + void GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << "cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold a boolean");} + void SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << "cannot hold an integer");} +Index: ../trunk-jpl/src/c/classes/objects/Params/DataSetParam.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/DataSetParam.cpp (revision 0) ++++ ../trunk-jpl/src/c/classes/objects/Params/DataSetParam.cpp (revision 13425) +@@ -0,0 +1,95 @@ ++/*!\file DataSetParam.c ++ * \brief: implementation of the DataSetParam object ++ */ ++ ++/*header files: */ ++/*{{{*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "../objects.h" ++#include "../../../EnumDefinitions/EnumDefinitions.h" ++#include "../../../shared/shared.h" ++#include "../../../Container/Container.h" ++#include "../../../include/include.h" ++/*}}}*/ ++ ++/*DataSetParam constructors and destructor*/ ++/*FUNCTION DataSetParam::DataSetParam(){{{*/ ++DataSetParam::DataSetParam(){ ++ value=NULL; ++ return; ++} ++/*}}}*/ ++/*FUNCTION DataSetParam::DataSetParam(int enum_type,DataSet *value){{{*/ ++DataSetParam::DataSetParam(int in_enum_type,DataSet* in_value){ ++ ++ enum_type=in_enum_type; ++ value=in_value->Copy();; ++} ++/*}}}*/ ++/*FUNCTION DataSetParam::~DataSetParam(){{{*/ ++DataSetParam::~DataSetParam(){ ++ delete value; ++} ++/*}}}*/ ++ ++/*Object virtual functions definitions:*/ ++/*FUNCTION DataSetParam::Echo {{{*/ ++void DataSetParam::Echo(void){ ++ this->DeepEcho(); ++} ++/*}}}*/ ++/*FUNCTION DataSetParam::DeepEcho{{{*/ ++void DataSetParam::DeepEcho(void){ ++ ++ _printLine_("DataSetParam:"); ++ _printLine_(" enum: " << this->enum_type << " (" << EnumToStringx(this->enum_type) << ")"); ++ this->value->Echo(); ++} ++/*}}}*/ ++/*FUNCTION DataSetParam::Id{{{*/ ++int DataSetParam::Id(void){ return -1; } ++/*}}}*/ ++/*FUNCTION DataSetParam::MyRank{{{*/ ++int DataSetParam::MyRank(void){ ++ extern int my_rank; ++ return my_rank; ++} ++/*}}}*/ ++/*FUNCTION DataSetParam::ObjectEnum{{{*/ ++int DataSetParam::ObjectEnum(void){ ++ ++ return DataSetParamEnum; ++ ++} ++/*}}}*/ ++/*FUNCTION DataSetParam::copy{{{*/ ++Object* DataSetParam::copy() { ++ ++ return new DataSetParam(this->enum_type,this->value); ++ ++} ++/*}}}*/ ++ ++/*DataSetParam virtual functions definitions: */ ++/*FUNCTION DataSetParam::GetParameterName{{{*/ ++void DataSetParam::GetParameterName(char**pname){ ++ EnumToStringx(pname,this->enum_type); ++} ++/*}}}*/ ++/*FUNCTION DataSetParam::UnitConversion{{{*/ ++void DataSetParam::UnitConversion(int direction_enum){ ++ /*do nothing, no unit conversion*/ ++} ++/*}}}*/ ++/*FUNCTION DataSetParam::GetParameterValue{{{*/ ++void DataSetParam::GetParameterValue(DataSet** pdataset){ ++ *pdataset=value->Copy(); ++} ++/*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Params/IntVecParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/IntVecParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/IntVecParam.h (revision 13425) +@@ -56,6 +56,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} + void GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");} + void SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");} +Index: ../trunk-jpl/src/c/classes/objects/Params/BoolParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/BoolParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/BoolParam.h (revision 13425) +@@ -54,6 +54,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} + void GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){this->value=boolean;} + void SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an int");} +Index: ../trunk-jpl/src/c/classes/objects/Params/IntMatParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/IntMatParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/IntMatParam.h (revision 13425) +@@ -56,6 +56,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} + void GetParameterValue(FILE** pfid){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");} + void SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");} +Index: ../trunk-jpl/src/c/classes/objects/Params/StringParam.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Params/StringParam.h (revision 13424) ++++ ../trunk-jpl/src/c/classes/objects/Params/StringParam.h (revision 13425) +@@ -55,6 +55,7 @@ + void GetParameterValue(Vector** pvec){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Vec");} + void GetParameterValue(Matrix** pmat){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a Mat");} + void GetParameterValue(FILE** pfid){_error_("Bool param of enum " << enum_type << " (" << EnumToStringx(enum_type) << ") cannot return a FILE");} ++ void GetParameterValue(DataSet** pdataset){_error_("Param "<< EnumToStringx(enum_type) << " cannot return a DataSet");} + + void SetValue(bool boolean){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold a boolean");} + void SetValue(int integer){_error_("Param "<< EnumToStringx(enum_type) << " cannot hold an integer");} Index: /issm/oecreview/Archive/13393-13976/ISSM-13425-13426.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13425-13426.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13425-13426.diff (revision 13980) @@ -0,0 +1,441 @@ +Index: ../trunk-jpl/src/c/classes/objects/objects.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/objects.h (revision 13425) ++++ ../trunk-jpl/src/c/classes/objects/objects.h (revision 13426) +@@ -12,6 +12,8 @@ + #include "./Contour.h" + #include "./Vertex.h" + #include "./Node.h" ++#include "./DependentObject.h" ++#include "./IndependentObject.h" + #include "./Segment.h" + + /*Constraints: */ +@@ -118,5 +120,6 @@ + #include "./Params/StringArrayParam.h" + #include "./Params/StringParam.h" + #include "./Params/TransientParam.h" ++#include "./Params/DataSetParam.h" + + #endif +Index: ../trunk-jpl/src/c/classes/objects/DependentObject.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/DependentObject.h (revision 0) ++++ ../trunk-jpl/src/c/classes/objects/DependentObject.h (revision 13426) +@@ -0,0 +1,38 @@ ++/*!\file: DependentObject.h ++ * \brief prototype for DependentObject.h ++ */ ++ ++#ifndef _DEPENDENTOBJECT_H_ ++#define _DEPENDENTOBJECT_H_ ++ ++/*{{{*/ ++#include "./Object.h" ++#include "../../shared/shared.h" ++/*}}}*/ ++ ++class DependentObject: public Object{ ++ ++ public: ++ ++ int name; ++ int type; /*0: scalar, 1: vertex*/ ++ ++ /*DependentObject constructors, destructors {{{*/ ++ DependentObject(); ++ DependentObject(int name, int type); ++ ~DependentObject(); ++ /*}}}*/ ++ /*Object virtual functions definitions:{{{ */ ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int MyRank(); ++ int ObjectEnum(); ++ Object* copy(void); ++ /*}}}*/ ++ ++ /*DependentObject methods: */ ++ int NumDependents(void); ++ ++}; ++#endif //ifndef _DEPENDENTOBJECT_H_ +Index: ../trunk-jpl/src/c/classes/objects/IndependentObject.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/IndependentObject.cpp (revision 0) ++++ ../trunk-jpl/src/c/classes/objects/IndependentObject.cpp (revision 13426) +@@ -0,0 +1,224 @@ ++/*!\file IndependentObject.c ++ * \brief: implementation of the IndependentObject object ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "./objects.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++#include "../../shared/shared.h" ++#include "../../Container/Container.h" ++#include "../../include/include.h" ++#include "../IoModel.h" ++ ++/*IndependentObject constructors and destructor*/ ++/*FUNCTION IndependentObject::IndependentObject(){{{*/ ++IndependentObject::IndependentObject(){ ++ this->name=NoneEnum; ++ this->type=0; ++ this->numberofvertices=0; ++} ++/*}}}*/ ++/*FUNCTION IndependentObject::IndependentObject(int in_name, int in_type,int in_numberofvertices){{{*/ ++IndependentObject::IndependentObject(int in_name, int in_type,int in_numberofvertices){ ++ ++ this->numberofvertices=0; ++ this->name=in_name; ++ this->type=in_type; ++ if(in_type!=0 && in_type!=1)_error_("cannot create an IndependentObject of type " << in_type); ++ if(this->type==1)this->numberofvertices=in_numberofvertices; ++ ++} ++/*}}}*/ ++/*FUNCTION IndependentObject::~IndependentObject() {{{*/ ++IndependentObject::~IndependentObject(){ //destructor ++} ++/*}}}*/ ++ ++/*Object virtual functions definitions:*/ ++/*FUNCTION IndependentObject::Echo{{{*/ ++void IndependentObject::Echo(void){ ++ ++ _printLine_("IndependentObject:"); ++ _printLine_(" name: " << EnumToStringx(this->name)); ++ if(this->type==0) ++ _printLine_(" type: scalar"); ++ else if(this->type==1) ++ _printLine_(" type: vertex"); ++ else ++ _error_(" unknown type: " << this->type); ++ _printLine_(" numberofvertices: " << this->numberofvertices); ++} ++/*}}}*/ ++/*FUNCTION IndependentObject::DeepEcho{{{*/ ++void IndependentObject::DeepEcho(void){ ++ this->Echo(); ++} ++/*}}}*/ ++/*FUNCTION IndependentObject::Id{{{*/ ++int IndependentObject::Id(void){ return -1; } ++/*}}}*/ ++/*FUNCTION IndependentObject::MyRank{{{*/ ++int IndependentObject::MyRank(void){ ++ extern int my_rank; ++ ++ return my_rank; ++} ++/*}}}*/ ++/*FUNCTION IndependentObject::ObjectEnum{{{*/ ++int IndependentObject::ObjectEnum(void){ ++ ++ return IndependentObjectEnum; ++ ++} ++/*}}}*/ ++/*FUNCTION IndependentObject::copy{{{*/ ++Object* IndependentObject::copy(void) { ++ return new IndependentObject(name,type,numberofvertices); ++} /*}}}*/ ++ ++ ++/*IndependentObject methods: */ ++/*FUNCTION IndependentObject::FetchIndependent{{{*/ ++void IndependentObject::FetchIndependent(IoModel* iomodel){ ++ ++ extern int my_rank; ++ FILE* fid=NULL; ++ ++ #ifdef _HAVE_ADOLC_ //cannot come here unless you are running AD mode, from DeclaredIndependents: ++ ++ /*Branch according to the type of variable: */ ++ if(type==0){ /*scalar: {{{*/ ++ ++ /*output: */ ++ IssmPDouble pscalar; ++ IssmDouble scalar; //same as pscalar, except it's an ADOLC independent variable ++ IssmDouble* scalar_slot=NULL; ++ int code; ++ ++ /*Set file pointer to beginning of the data: */ ++ fid=iomodel->SetFilePointerToData(&code,NULL,name); ++ ++ if(code!=3)_error_("expecting a IssmDouble for enum " << EnumToStringx(name)); ++ ++ /*We have to read a scalar from disk. First read the dimensions of the scalar, then the scalar: */ ++ if(my_rank==0){ ++ if(fread(&pscalar,sizeof(IssmPDouble),1,fid)!=1)_error_("could not read scalar "); ++ } ++ ++ /*Now, before we even broadcast this to other nodes, declare the scalar as an independent variable!: */ ++ scalar<<=pscalar; ++ ++ #ifdef _HAVE_MPI_ ++ MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); ++ #endif ++ ++ ++ /*Ok, we are almost done. scalar is now an independent variable. We don't want this variable to be fetched again in the ++ *future, which would effectively write over the independency in the ADOLC tape! So we are going to keep track of this ++ independent variable inthe iomodel->data[name] data slot. Because this data slot holds double*, we allocate a sizeof(double) ++ space for it: */ ++ scalar_slot=xNew(1); *scalar_slot=scalar; ++ ++ iomodel->data[name]=scalar_slot; ++ iomodel->independents[name]=true; ++ ++ ++ } /*}}}*/ ++ else if(type==1){ /* vector: {{{*/ ++ ++ FILE* fid=NULL; ++ int M,N; ++ IssmPDouble* buffer=NULL; //a buffer to read the data from disk ++ IssmDouble* matrix=NULL; //our independent variable ++ int code=0; ++ int vector_type=0; ++ ++ /*Set file pointer to beginning of the data: */ ++ fid=iomodel->SetFilePointerToData(&code,&vector_type,name); ++ if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(name)); ++ ++ /*We have to read a matrix from disk. First read the dimensions of the matrix, then the whole matrix: */ ++ /*numberofelements: */ ++ if(my_rank==0){ ++ if(fread(&M,sizeof(int),1,fid)!=1) _error_("could not read number of rows for matrix "); ++ } ++ #ifdef _HAVE_MPI_ ++ MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif ++ ++ if(my_rank==0){ ++ if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix "); ++ } ++ #ifdef _HAVE_MPI_ ++ MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif ++ ++ /*Now allocate matrix: */ ++ if(M*N){ ++ buffer=xNew(M*N); ++ matrix=xNew(M*N); ++ ++ /*Read matrix on node 0, then broadcast: */ ++ if(my_rank==0){ ++ if(fread(buffer,M*N*sizeof(IssmPDouble),1,fid)!=1) _error_("could not read matrix "); ++ ++ /*Now, before we even broadcast this to other nodes, declare the whole matrix as a independent variable!: */ ++ for (int i=0;i(buffer); ++ } ++ else _error_("cannot declare the independent variable " << EnumToStringx(name) << "if it's empty!"); ++ ++ /*Ok, we are almost done. Matrix is now a independent matrix. We don't want this matrix to be fetched again in the ++ *future, which would effectively write over the independency in the ADOLC tape! So we are going to keep track of this ++ independent matrix inthe iomodel->data[name] data slot: */ ++ iomodel->data[name]=matrix; ++ iomodel->independents[name]=true; ++ }/*}}}*/ ++ else _error_("should not have a type of " << type); ++ ++ #endif ++} ++/*}}}*/ ++/*FUNCTION IndependentObject::NumIndependents{{{*/ ++int IndependentObject::NumIndependents(void){ ++ ++ /*Branch according to the type of variable: */ ++ if(type==0){ /*scalar:*/ ++ return 1; ++ } ++ else if(type==1){ /* vector:*/ ++ return this->numberofvertices; ++ } ++ else _error_("should not have a type of " << type); ++} ++/*}}}*/ ++/*FUNCTION IndependentObject::FillIndependents{{{*/ ++void IndependentObject::FillIndependents(IssmDouble** data, IssmDouble* xp){ ++ ++ int i; ++ ++ /*Branch according to the type of variable: */ ++ if(type==0){ /*scalar:*/ ++ xp[0]=*(data[name]); ++ } ++ else if(type==1){ /* vector:*/ ++ IssmDouble* values=data[name]; ++ for(i=0;inumberofvertices;i++){ ++ xp[i]=values[i]; ++ } ++ } ++ else _error_("should not have a type of " << type); ++} ++/*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/IndependentObject.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/IndependentObject.h (revision 0) ++++ ../trunk-jpl/src/c/classes/objects/IndependentObject.h (revision 13426) +@@ -0,0 +1,43 @@ ++/*!\file: IndependentObject.h ++ * \brief prototype for IndependentObject.h ++ */ ++ ++#ifndef _INDEPENDENTOBJECT_H_ ++#define _INDEPENDENTOBJECT_H_ ++ ++ ++/*{{{*/ ++#include "./Object.h" ++#include "../../shared/shared.h" ++/*}}}*/ ++class IoModel; ++ ++class IndependentObject: public Object{ ++ ++ public: ++ ++ int name; ++ int type; /*0: scalar, 1: vertex*/ ++ int numberofvertices; ++ ++ /*IndependentObject constructors, destructors {{{*/ ++ IndependentObject(); ++ IndependentObject(int name, int type, int numberofvertices); ++ ~IndependentObject(); ++ /*}}}*/ ++ /*Object virtual functions definitions:{{{ */ ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int MyRank(); ++ int ObjectEnum(); ++ Object* copy(void); ++ /*}}}*/ ++ /*IndependentObject methods: {{{*/ ++ void FetchIndependent(IoModel* iomodel); ++ int NumIndependents(void); ++ void FillIndependents(IssmDouble** data, IssmDouble* xp); ++ /*}}}*/ ++ ++}; ++#endif //ifndef _INDEPENDENTOBJECT_H_ +Index: ../trunk-jpl/src/c/classes/objects/DependentObject.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/DependentObject.cpp (revision 0) ++++ ../trunk-jpl/src/c/classes/objects/DependentObject.cpp (revision 13426) +@@ -0,0 +1,96 @@ ++/*!\file DependentObject.c ++ * \brief: implementation of the DependentObject object ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include ++#include ++#include "./objects.h" ++#include "../../EnumDefinitions/EnumDefinitions.h" ++#include "../../shared/shared.h" ++#include "../../Container/Container.h" ++#include "../../include/include.h" ++ ++/*DependentObject constructors and destructor*/ ++/*FUNCTION DependentObject::DependentObject(){{{*/ ++DependentObject::DependentObject(){ ++ this->name=NoneEnum; ++ this->type=0; ++} ++/*}}}*/ ++/*FUNCTION DependentObject::DependentObject(int in_name, int in_type){{{*/ ++DependentObject::DependentObject(int in_name, int in_type){ ++ ++ this->name=in_name; ++ this->type=in_type; ++ if(in_type!=0 && in_type!=1)_error_("cannot create an DependentObject of type " << in_type); ++ if(in_type==1)_error_("not implemented yet!"); ++ ++} ++/*}}}*/ ++/*FUNCTION DependentObject::~DependentObject() {{{*/ ++DependentObject::~DependentObject(){ //destructor ++} ++/*}}}*/ ++ ++ ++/*Object virtual functions definitions:*/ ++/*FUNCTION DependentObject::Echo{{{*/ ++void DependentObject::Echo(void){ ++ ++ _printLine_("DependentObject:"); ++ _printLine_(" name: " << EnumToStringx(this->name)); ++ if(this->type==0) ++ _printLine_(" type: scalar"); ++ else if(this->type==1) ++ _printLine_(" type: vertex"); ++ else ++ _error_(" unknown type: " << this->type); ++} ++/*}}}*/ ++/*FUNCTION DependentObject::DeepEcho{{{*/ ++void DependentObject::DeepEcho(void){ ++ this->Echo(); ++} ++/*}}}*/ ++/*FUNCTION DependentObject::Id{{{*/ ++int DependentObject::Id(void){ return -1; } ++/*}}}*/ ++/*FUNCTION DependentObject::MyRank{{{*/ ++int DependentObject::MyRank(void){ ++ extern int my_rank; ++ ++ return my_rank; ++} ++/*}}}*/ ++/*FUNCTION DependentObject::ObjectEnum{{{*/ ++int DependentObject::ObjectEnum(void){ ++ ++ return DependentObjectEnum; ++ ++} ++/*}}}*/ ++/*FUNCTION DependentObject::copy{{{*/ ++Object* DependentObject::copy(void) { ++ return new DependentObject(name,type); ++} /*}}}*/ ++ ++/*DependentObject methods: */ ++/*FUNCTION DependentObject::NumDependents{{{*/ ++int DependentObject::NumDependents(void){ ++ ++ /*Branch according to the type of variable: */ ++ if(type==0){ /*scalar:*/ ++ return 1; ++ } ++ else if(type==1){ /* vector:*/ ++ _error_("not implemented yet!"); ++ } ++ else _error_("should not have a type of " << type); ++} ++/*}}}*/ Index: /issm/oecreview/Archive/13393-13976/ISSM-13426-13427.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13426-13427.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13426-13427.diff (revision 13980) @@ -0,0 +1,527 @@ +Index: ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13426) ++++ ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13427) +@@ -12,13 +12,20 @@ + enum definitions{ + /*Model fields {{{1*/ + AutodiffIsautodiffEnum, +- AutodiffDependentsEnum, + AutodiffNumDependentsEnum, +- AutodiffIndependentsEnum, ++ AutodiffNumDependentObjectsEnum, ++ AutodiffDependentObjectNamesEnum, ++ AutodiffDependentObjectTypesEnum, ++ AutodiffDependentObjectsEnum, + AutodiffNumIndependentsEnum, ++ AutodiffNumIndependentObjectsEnum, ++ AutodiffIndependentObjectNamesEnum, ++ AutodiffIndependentObjectTypesEnum, ++ AutodiffIndependentObjectsEnum, + AutodiffJacobianEnum, + AutodiffXpEnum, +- AutodiffFosForwardOutputEnum, ++ AutodiffDriverEnum, ++ AutodiffFosForwardIndexEnum, + BalancethicknessSpcthicknessEnum, + BalancethicknessStabilizationEnum, + BalancethicknessThickeningRateEnum, +@@ -30,6 +37,7 @@ + ConstantsGEnum, + ConstantsReferencetemperatureEnum, + ConstantsYtsEnum, ++ DependentObjectEnum, + DiagnosticAbstolEnum, + DiagnosticIcefrontEnum, + DiagnosticIsnewtonEnum, +@@ -69,6 +77,7 @@ + HydrologyQEnum, + HydrologySpcwatercolumnEnum, + HydrologyStabilizationEnum, ++ IndependentObjectEnum, + InversionControlParametersEnum, + InversionCostFunctionEnum, + InversionCostFunctionThresholdEnum, +@@ -272,6 +281,7 @@ + DatasetInputEnum, + DofIndexingEnum, + DoubleInputEnum, ++ DataSetParamEnum, + DoubleMatArrayParamEnum, + DoubleMatParamEnum, + DoubleParamEnum, +Index: ../trunk-jpl/src/m/enum/AutodiffFosForwardOutputEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffFosForwardOutputEnum.m (revision 13426) ++++ ../trunk-jpl/src/m/enum/AutodiffFosForwardOutputEnum.m (revision 13427) +@@ -1,11 +0,0 @@ +-function macro=AutodiffFosForwardOutputEnum() +-%AUTODIFFFOSFORWARDOUTPUTENUM - Enum of AutodiffFosForwardOutput +-% +-% WARNING: DO NOT MODIFY THIS FILE +-% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +-% Please read src/c/EnumDefinitions/README for more information +-% +-% Usage: +-% macro=AutodiffFosForwardOutputEnum() +- +-macro=StringToEnum('AutodiffFosForwardOutput'); +Index: ../trunk-jpl/src/m/enum/AutodiffDependentsEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffDependentsEnum.m (revision 13426) ++++ ../trunk-jpl/src/m/enum/AutodiffDependentsEnum.m (revision 13427) +@@ -1,11 +0,0 @@ +-function macro=AutodiffDependentsEnum() +-%AUTODIFFDEPENDENTSENUM - Enum of AutodiffDependents +-% +-% WARNING: DO NOT MODIFY THIS FILE +-% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +-% Please read src/c/EnumDefinitions/README for more information +-% +-% Usage: +-% macro=AutodiffDependentsEnum() +- +-macro=StringToEnum('AutodiffDependents'); +Index: ../trunk-jpl/src/m/enum/AutodiffIndependentsEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffIndependentsEnum.m (revision 13426) ++++ ../trunk-jpl/src/m/enum/AutodiffIndependentsEnum.m (revision 13427) +@@ -1,11 +0,0 @@ +-function macro=AutodiffIndependentsEnum() +-%AUTODIFFINDEPENDENTSENUM - Enum of AutodiffIndependents +-% +-% WARNING: DO NOT MODIFY THIS FILE +-% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +-% Please read src/c/EnumDefinitions/README for more information +-% +-% Usage: +-% macro=AutodiffIndependentsEnum() +- +-macro=StringToEnum('AutodiffIndependents'); +Index: ../trunk-jpl/src/m/enum/AutodiffIndependentObjectTypesEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffIndependentObjectTypesEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffIndependentObjectTypesEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=AutodiffIndependentObjectTypesEnum() ++%AUTODIFFINDEPENDENTOBJECTTYPESENUM - Enum of AutodiffIndependentObjectTypes ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffIndependentObjectTypesEnum() ++ ++macro=StringToEnum('AutodiffIndependentObjectTypes'); +Index: ../trunk-jpl/src/m/enum/AutodiffFosForwardIndexEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffFosForwardIndexEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffFosForwardIndexEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=AutodiffFosForwardIndexEnum() ++%AUTODIFFFOSFORWARDINDEXENUM - Enum of AutodiffFosForwardIndex ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffFosForwardIndexEnum() ++ ++macro=StringToEnum('AutodiffFosForwardIndex'); +Index: ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13426) ++++ ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13427) +@@ -8,4 +8,4 @@ + % Usage: + % macro=MaximumNumberOfEnums() + +-macro=474; ++macro=484; +Index: ../trunk-jpl/src/m/enum/AutodiffIndependentObjectNamesEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffIndependentObjectNamesEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffIndependentObjectNamesEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=AutodiffIndependentObjectNamesEnum() ++%AUTODIFFINDEPENDENTOBJECTNAMESENUM - Enum of AutodiffIndependentObjectNames ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffIndependentObjectNamesEnum() ++ ++macro=StringToEnum('AutodiffIndependentObjectNames'); +Index: ../trunk-jpl/src/m/enum/AutodiffDriverEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffDriverEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffDriverEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=AutodiffDriverEnum() ++%AUTODIFFDRIVERENUM - Enum of AutodiffDriver ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffDriverEnum() ++ ++macro=StringToEnum('AutodiffDriver'); +Index: ../trunk-jpl/src/m/enum/AutodiffDependentObjectTypesEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffDependentObjectTypesEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffDependentObjectTypesEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=AutodiffDependentObjectTypesEnum() ++%AUTODIFFDEPENDENTOBJECTTYPESENUM - Enum of AutodiffDependentObjectTypes ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffDependentObjectTypesEnum() ++ ++macro=StringToEnum('AutodiffDependentObjectTypes'); +Index: ../trunk-jpl/src/m/enum/DataSetParamEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/DataSetParamEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/DataSetParamEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=DataSetParamEnum() ++%DATASETPARAMENUM - Enum of DataSetParam ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=DataSetParamEnum() ++ ++macro=StringToEnum('DataSetParam'); +Index: ../trunk-jpl/src/m/enum/AutodiffDependentObjectNamesEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffDependentObjectNamesEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffDependentObjectNamesEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=AutodiffDependentObjectNamesEnum() ++%AUTODIFFDEPENDENTOBJECTNAMESENUM - Enum of AutodiffDependentObjectNames ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffDependentObjectNamesEnum() ++ ++macro=StringToEnum('AutodiffDependentObjectNames'); +Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py +=================================================================== +--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13426) ++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13427) +@@ -18,36 +18,56 @@ + + return StringToEnum('AutodiffIsautodiff')[0] + +-def AutodiffDependentsEnum(): ++def AutodiffNumDependentsEnum(): + """ +- AUTODIFFDEPENDENTSENUM - Enum of AutodiffDependents ++ AUTODIFFNUMDEPENDENTSENUM - Enum of AutodiffNumDependents + + Usage: +- macro=AutodiffDependentsEnum() ++ macro=AutodiffNumDependentsEnum() + """ + +- return StringToEnum('AutodiffDependents')[0] ++ return StringToEnum('AutodiffNumDependents')[0] + +-def AutodiffNumDependentsEnum(): ++def AutodiffNumDependentObjectsEnum(): + """ +- AUTODIFFNUMDEPENDENTSENUM - Enum of AutodiffNumDependents ++ AUTODIFFNUMDEPENDENTOBJECTSENUM - Enum of AutodiffNumDependentObjects + + Usage: +- macro=AutodiffNumDependentsEnum() ++ macro=AutodiffNumDependentObjectsEnum() + """ + +- return StringToEnum('AutodiffNumDependents')[0] ++ return StringToEnum('AutodiffNumDependentObjects')[0] + +-def AutodiffIndependentsEnum(): ++def AutodiffDependentObjectNamesEnum(): + """ +- AUTODIFFINDEPENDENTSENUM - Enum of AutodiffIndependents ++ AUTODIFFDEPENDENTOBJECTNAMESENUM - Enum of AutodiffDependentObjectNames + + Usage: +- macro=AutodiffIndependentsEnum() ++ macro=AutodiffDependentObjectNamesEnum() + """ + +- return StringToEnum('AutodiffIndependents')[0] ++ return StringToEnum('AutodiffDependentObjectNames')[0] + ++def AutodiffDependentObjectTypesEnum(): ++ """ ++ AUTODIFFDEPENDENTOBJECTTYPESENUM - Enum of AutodiffDependentObjectTypes ++ ++ Usage: ++ macro=AutodiffDependentObjectTypesEnum() ++ """ ++ ++ return StringToEnum('AutodiffDependentObjectTypes')[0] ++ ++def AutodiffDependentObjectsEnum(): ++ """ ++ AUTODIFFDEPENDENTOBJECTSENUM - Enum of AutodiffDependentObjects ++ ++ Usage: ++ macro=AutodiffDependentObjectsEnum() ++ """ ++ ++ return StringToEnum('AutodiffDependentObjects')[0] ++ + def AutodiffNumIndependentsEnum(): + """ + AUTODIFFNUMINDEPENDENTSENUM - Enum of AutodiffNumIndependents +@@ -58,6 +78,46 @@ + + return StringToEnum('AutodiffNumIndependents')[0] + ++def AutodiffNumIndependentObjectsEnum(): ++ """ ++ AUTODIFFNUMINDEPENDENTOBJECTSENUM - Enum of AutodiffNumIndependentObjects ++ ++ Usage: ++ macro=AutodiffNumIndependentObjectsEnum() ++ """ ++ ++ return StringToEnum('AutodiffNumIndependentObjects')[0] ++ ++def AutodiffIndependentObjectNamesEnum(): ++ """ ++ AUTODIFFINDEPENDENTOBJECTNAMESENUM - Enum of AutodiffIndependentObjectNames ++ ++ Usage: ++ macro=AutodiffIndependentObjectNamesEnum() ++ """ ++ ++ return StringToEnum('AutodiffIndependentObjectNames')[0] ++ ++def AutodiffIndependentObjectTypesEnum(): ++ """ ++ AUTODIFFINDEPENDENTOBJECTTYPESENUM - Enum of AutodiffIndependentObjectTypes ++ ++ Usage: ++ macro=AutodiffIndependentObjectTypesEnum() ++ """ ++ ++ return StringToEnum('AutodiffIndependentObjectTypes')[0] ++ ++def AutodiffIndependentObjectsEnum(): ++ """ ++ AUTODIFFINDEPENDENTOBJECTSENUM - Enum of AutodiffIndependentObjects ++ ++ Usage: ++ macro=AutodiffIndependentObjectsEnum() ++ """ ++ ++ return StringToEnum('AutodiffIndependentObjects')[0] ++ + def AutodiffJacobianEnum(): + """ + AUTODIFFJACOBIANENUM - Enum of AutodiffJacobian +@@ -78,16 +138,26 @@ + + return StringToEnum('AutodiffXp')[0] + +-def AutodiffFosForwardOutputEnum(): ++def AutodiffDriverEnum(): + """ +- AUTODIFFFOSFORWARDOUTPUTENUM - Enum of AutodiffFosForwardOutput ++ AUTODIFFDRIVERENUM - Enum of AutodiffDriver + + Usage: +- macro=AutodiffFosForwardOutputEnum() ++ macro=AutodiffDriverEnum() + """ + +- return StringToEnum('AutodiffFosForwardOutput')[0] ++ return StringToEnum('AutodiffDriver')[0] + ++def AutodiffFosForwardIndexEnum(): ++ """ ++ AUTODIFFFOSFORWARDINDEXENUM - Enum of AutodiffFosForwardIndex ++ ++ Usage: ++ macro=AutodiffFosForwardIndexEnum() ++ """ ++ ++ return StringToEnum('AutodiffFosForwardIndex')[0] ++ + def BalancethicknessSpcthicknessEnum(): + """ + BALANCETHICKNESSSPCTHICKNESSENUM - Enum of BalancethicknessSpcthickness +@@ -198,6 +268,16 @@ + + return StringToEnum('ConstantsYts')[0] + ++def DependentObjectEnum(): ++ """ ++ DEPENDENTOBJECTENUM - Enum of DependentObject ++ ++ Usage: ++ macro=DependentObjectEnum() ++ """ ++ ++ return StringToEnum('DependentObject')[0] ++ + def DiagnosticAbstolEnum(): + """ + DIAGNOSTICABSTOLENUM - Enum of DiagnosticAbstol +@@ -588,6 +668,16 @@ + + return StringToEnum('HydrologyStabilization')[0] + ++def IndependentObjectEnum(): ++ """ ++ INDEPENDENTOBJECTENUM - Enum of IndependentObject ++ ++ Usage: ++ macro=IndependentObjectEnum() ++ """ ++ ++ return StringToEnum('IndependentObject')[0] ++ + def InversionControlParametersEnum(): + """ + INVERSIONCONTROLPARAMETERSENUM - Enum of InversionControlParameters +@@ -2538,6 +2628,16 @@ + + return StringToEnum('DoubleInput')[0] + ++def DataSetParamEnum(): ++ """ ++ DATASETPARAMENUM - Enum of DataSetParam ++ ++ Usage: ++ macro=DataSetParamEnum() ++ """ ++ ++ return StringToEnum('DataSetParam')[0] ++ + def DoubleMatArrayParamEnum(): + """ + DOUBLEMATARRAYPARAMENUM - Enum of DoubleMatArrayParam +@@ -4756,5 +4856,5 @@ + macro=MaximumNumberOfEnums() + """ + +- return 474 ++ return 484 + +Index: ../trunk-jpl/src/m/enum/AutodiffIndependentObjectsEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffIndependentObjectsEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffIndependentObjectsEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=AutodiffIndependentObjectsEnum() ++%AUTODIFFINDEPENDENTOBJECTSENUM - Enum of AutodiffIndependentObjects ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffIndependentObjectsEnum() ++ ++macro=StringToEnum('AutodiffIndependentObjects'); +Index: ../trunk-jpl/src/m/enum/DependentObjectEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/DependentObjectEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/DependentObjectEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=DependentObjectEnum() ++%DEPENDENTOBJECTENUM - Enum of DependentObject ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=DependentObjectEnum() ++ ++macro=StringToEnum('DependentObject'); +Index: ../trunk-jpl/src/m/enum/AutodiffNumIndependentObjectsEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffNumIndependentObjectsEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffNumIndependentObjectsEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=AutodiffNumIndependentObjectsEnum() ++%AUTODIFFNUMINDEPENDENTOBJECTSENUM - Enum of AutodiffNumIndependentObjects ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffNumIndependentObjectsEnum() ++ ++macro=StringToEnum('AutodiffNumIndependentObjects'); +Index: ../trunk-jpl/src/m/enum/AutodiffDependentObjectsEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffDependentObjectsEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffDependentObjectsEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=AutodiffDependentObjectsEnum() ++%AUTODIFFDEPENDENTOBJECTSENUM - Enum of AutodiffDependentObjects ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffDependentObjectsEnum() ++ ++macro=StringToEnum('AutodiffDependentObjects'); +Index: ../trunk-jpl/src/m/enum/AutodiffNumDependentObjectsEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffNumDependentObjectsEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffNumDependentObjectsEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=AutodiffNumDependentObjectsEnum() ++%AUTODIFFNUMDEPENDENTOBJECTSENUM - Enum of AutodiffNumDependentObjects ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffNumDependentObjectsEnum() ++ ++macro=StringToEnum('AutodiffNumDependentObjects'); +Index: ../trunk-jpl/src/m/enum/IndependentObjectEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/IndependentObjectEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/IndependentObjectEnum.m (revision 13427) +@@ -0,0 +1,11 @@ ++function macro=IndependentObjectEnum() ++%INDEPENDENTOBJECTENUM - Enum of IndependentObject ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=IndependentObjectEnum() ++ ++macro=StringToEnum('IndependentObject'); Index: /issm/oecreview/Archive/13393-13976/ISSM-13427-13428.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13427-13428.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13427-13428.diff (revision 13980) @@ -0,0 +1,28 @@ +Index: ../trunk-jpl/src/c/solutions/prognostic_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/prognostic_core.cpp (revision 13427) ++++ ../trunk-jpl/src/c/solutions/prognostic_core.cpp (revision 13428) +@@ -16,6 +16,7 @@ + /*parameters: */ + bool save_results; + bool issmbgradients,ispdd,isdelta18o; ++ int solution_type; + + /*activate formulation: */ + femmodel->SetCurrentConfiguration(PrognosticAnalysisEnum); +@@ -25,6 +26,7 @@ + femmodel->parameters->FindParam(&issmbgradients,SurfaceforcingsIssmbgradientsEnum); + femmodel->parameters->FindParam(&ispdd,SurfaceforcingsIspddEnum); + femmodel->parameters->FindParam(&isdelta18o,SurfaceforcingsIsdelta18oEnum); ++ femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); + + if(issmbgradients){ + _printf_(VerboseSolution()," call smb gradients module\n"); +@@ -45,4 +47,7 @@ + if(VerboseSolution()) _pprintLine_(" saving results"); + InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ThicknessEnum); + } ++ ++ ++ if(solution_type=PrognosticSolutionEnum)RequestedDependentsx(femmodel->results,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + } Index: /issm/oecreview/Archive/13393-13976/ISSM-13428-13429.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13428-13429.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13428-13429.diff (revision 13980) @@ -0,0 +1,228 @@ +Index: ../trunk-jpl/src/m/classes/autodiff.m +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.m (revision 13428) ++++ ../trunk-jpl/src/m/classes/autodiff.m (revision 13429) +@@ -8,6 +8,7 @@ + isautodiff = false; + dependents = {}; + independents = {}; ++ driver = 'fos_forward'; + end + methods + function obj = autodiff(varargin) % {{{ +@@ -23,47 +24,84 @@ + end % }}} + function md = checkconsistency(obj,md,solution,analyses) % {{{ + +- %Early return +- if ~obj.isautodiff, return; end ++ %Early return ++ if ~obj.isautodiff, return; end + ++ %Driver value: ++ md = checkfield(md,'autodiff.driver','values',{'fos_forward'}); ++ + end % }}} + function disp(obj) % {{{ + disp(sprintf(' automatic differentiation parameters:')); + fielddisplay(obj,'isautodiff','indicates if the automatic differentiation is activated'); +- fielddisplay(obj,'dependents','list of dependent variables ; ex: {''Thickness'',''FrictionCoefficient''}'); +- fielddisplay(obj,'independents','list of independent variables ; ex: {''IceVolume'',''MassFlux''}'); ++ fielddisplay(obj,'dependents','list of dependent variables'); ++ fielddisplay(obj,'independents','list of independent variables'); ++ fielddisplay(obj,'driver','ADOLC driver'); + end % }}} + function marshall(obj,fid) % {{{ + + WriteData(fid,'object',obj,'fieldname','isautodiff','format','Boolean'); ++ WriteData(fid,'object',obj,'fieldname','driver','format','String'); + + %early return + if ~obj.isautodiff, return; end + + %process dependent variables +- num_dependents=numel(obj.dependents); +- WriteData(fid,'data',num_dependents,'enum',AutodiffNumDependentsEnum(),'format','Integer'); +- +- if(num_dependents), +- data=zeros(1,num_dependents); +- for i=1:num_dependents, +- data(i)=StringToEnum(obj.dependents{i}); ++ num_dependent_objects=numel(obj.dependents); ++ WriteData(fid,'data',num_dependent_objects,'enum',AutodiffNumDependentObjectsEnum(),'format','Integer'); ++ ++ if(num_dependent_objects), ++ names=zeros(num_dependent_objects,1); ++ types=zeros(num_dependent_objects,1); ++ ++ for i=1:num_dependent_objects, ++ dep=obj.dependents{i}; ++ ++ names(i)=StringToEnum(dep.name); ++ types(i)=dep.typetoscalar(); + end +- WriteData(fid,'data',data,'enum',AutodiffDependentsEnum(),'format','DoubleMat','mattype',3); ++ WriteData(fid,'data',names,'enum',AutodiffDependentObjectNamesEnum(),'format','IntMat','mattype',3); ++ WriteData(fid,'data',types,'enum',AutodiffDependentObjectTypesEnum(),'format','IntMat','mattype',3); + end + ++ + %process independent variables +- num_independents=numel(obj.independents); +- WriteData(fid,'data',num_independents,'enum',AutodiffNumIndependentsEnum(),'format','Integer'); +- +- if(num_independents) +- data=zeros(1,num_independents); +- for i=1:num_independents, +- data(i)=StringToEnum(obj.independents{i}); ++ num_independent_objects=numel(obj.independents); ++ WriteData(fid,'data',num_independent_objects,'enum',AutodiffNumIndependentObjectsEnum(),'format','Integer'); ++ ++ if(num_independent_objects), ++ names=zeros(num_independent_objects,1); ++ types=zeros(num_independent_objects,1); ++ ++ for i=1:num_independent_objects, ++ indep=obj.independents{i}; ++ ++ names(i)=StringToEnum(indep.name); ++ types(i)=indep.typetoscalar(); + end +- WriteData(fid,'data',data,'enum',AutodiffIndependentsEnum(),'format','DoubleMat','mattype',3); ++ WriteData(fid,'data',names,'enum',AutodiffIndependentObjectNamesEnum(),'format','IntMat','mattype',3); ++ WriteData(fid,'data',types,'enum',AutodiffIndependentObjectTypesEnum(),'format','IntMat','mattype',3); + end + ++ %if driver is fos_forward, build index: ++ if strcmpi(obj.driver,'fos_forward'), ++ index=0; ++ ++ for i=1:num_independent_objects, ++ indep=obj.independents{i}; ++ if ~isnan(indep.fos_forward_index), ++ index=index+indep.fos_forward_index; ++ break; ++ else ++ if strcmpi(indep.type,'scalar'), ++ index=index+1; ++ else ++ index=index+indep.nods; ++ end ++ end ++ end ++ WriteData(fid,'data',index-1,'enum',AutodiffFosForwardIndexEnum(),'format','Integer'); %c-index numbering. ++ end + end % }}} + end + end +Index: ../trunk-jpl/src/m/classes/dependent.m +=================================================================== +--- ../trunk-jpl/src/m/classes/dependent.m (revision 0) ++++ ../trunk-jpl/src/m/classes/dependent.m (revision 13429) +@@ -0,0 +1,46 @@ ++%DEPENDENT class definition ++% ++% Usage: ++% dependent=dependent(); ++ ++classdef dependent ++ properties (SetAccess=public) ++ name = ''; ++ type = ''; ++ end ++ methods ++ function obj= dependent(varargin) % {{{ ++ ++ %use provided options to change fields ++ options=pairoptions(varargin{:}); ++ ++ %OK get other fields ++ obj=AssignObjectFields(pairoptions(varargin{:}),obj); ++ ++ end ++ %}}} ++ function obj = setdefaultparameters(obj) % {{{ ++ %do nothing ++ ++ end % }}} ++ function md = checkconsistency(obj,md,solution,analyses) % {{{ ++ %do nothing for now ++ ++ end % }}} ++ function disp(obj) % {{{ ++ disp(sprintf(' dependent variable :')); ++ ++ fielddisplay(obj,'name','variable name (must match corresponding Enum)'); ++ fielddisplay(obj,'type','type of variable (''vertex'' or ''scalar'')'); ++ ++ end % }}} ++ function scalar=typetoscalar(obj) % {{{ ++ if strcmpi(obj.type,'scalar'), ++ scalar=0; ++ elseif strcmpi(obj.type,'vertex'), ++ scalar=1; ++ end ++ ++ end % }}} ++ end ++end +Index: ../trunk-jpl/src/m/classes/independent.m +=================================================================== +--- ../trunk-jpl/src/m/classes/independent.m (revision 0) ++++ ../trunk-jpl/src/m/classes/independent.m (revision 13429) +@@ -0,0 +1,55 @@ ++%INDEPENDENT class definition ++% ++% Usage: ++% independent=independent(); ++ ++classdef independent ++ properties (SetAccess=public) ++ name = ''; ++ type = ''; ++ fos_forward_index = NaN; ++ nods = 0; ++ end ++ methods ++ function obj= independent(varargin) % {{{ ++ ++ %use provided options to change fields ++ options=pairoptions(varargin{:}); ++ ++ %OK get other fields ++ obj=AssignObjectFields(pairoptions(varargin{:}),obj); ++ ++ end ++ %}}} ++ function obj = setdefaultparameters(obj) % {{{ ++ %do nothing ++ ++ end % }}} ++ function md = checkconsistency(obj,md,solution,analyses) % {{{ ++ %do nothing for now ++ if ~isnan(obj.fos_forward_index), ++ if obj.nods==0, ++ error('independent checkconsistency error: nods should be set to the size of the independent variable'); ++ end ++ end ++ ++ end % }}} ++ function disp(obj) % {{{ ++ disp(sprintf(' independent variable :')); ++ ++ fielddisplay(obj,'name','variable name (must match corresponding Enum)'); ++ fielddisplay(obj,'type','type of variable (''vertex'' or ''scalar'')'); ++ if ~isnan(obj.fos_forward_index), ++ fielddisplay(obj,'fos_forward_index','index for fos_foward driver of ADOLC'); ++ end ++ ++ end % }}} ++ function scalar=typetoscalar(obj) % {{{ ++ if strcmpi(obj.type,'scalar'), ++ scalar=0; ++ elseif strcmpi(obj.type,'vertex'), ++ scalar=1; ++ end ++ end % }}} ++ end ++end Index: /issm/oecreview/Archive/13393-13976/ISSM-13429-13430.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13429-13430.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13429-13430.diff (revision 13980) @@ -0,0 +1,193 @@ +Index: ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13429) ++++ ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13430) +@@ -18,13 +18,20 @@ + + if(stage==1){ + if (strcmp(name,"AutodiffIsautodiff")==0) return AutodiffIsautodiffEnum; +- else if (strcmp(name,"AutodiffDependents")==0) return AutodiffDependentsEnum; + else if (strcmp(name,"AutodiffNumDependents")==0) return AutodiffNumDependentsEnum; +- else if (strcmp(name,"AutodiffIndependents")==0) return AutodiffIndependentsEnum; ++ else if (strcmp(name,"AutodiffNumDependentObjects")==0) return AutodiffNumDependentObjectsEnum; ++ else if (strcmp(name,"AutodiffDependentObjectNames")==0) return AutodiffDependentObjectNamesEnum; ++ else if (strcmp(name,"AutodiffDependentObjectTypes")==0) return AutodiffDependentObjectTypesEnum; ++ else if (strcmp(name,"AutodiffDependentObjects")==0) return AutodiffDependentObjectsEnum; + else if (strcmp(name,"AutodiffNumIndependents")==0) return AutodiffNumIndependentsEnum; ++ else if (strcmp(name,"AutodiffNumIndependentObjects")==0) return AutodiffNumIndependentObjectsEnum; ++ else if (strcmp(name,"AutodiffIndependentObjectNames")==0) return AutodiffIndependentObjectNamesEnum; ++ else if (strcmp(name,"AutodiffIndependentObjectTypes")==0) return AutodiffIndependentObjectTypesEnum; ++ else if (strcmp(name,"AutodiffIndependentObjects")==0) return AutodiffIndependentObjectsEnum; + else if (strcmp(name,"AutodiffJacobian")==0) return AutodiffJacobianEnum; + else if (strcmp(name,"AutodiffXp")==0) return AutodiffXpEnum; +- else if (strcmp(name,"AutodiffFosForwardOutput")==0) return AutodiffFosForwardOutputEnum; ++ else if (strcmp(name,"AutodiffDriver")==0) return AutodiffDriverEnum; ++ else if (strcmp(name,"AutodiffFosForwardIndex")==0) return AutodiffFosForwardIndexEnum; + else if (strcmp(name,"BalancethicknessSpcthickness")==0) return BalancethicknessSpcthicknessEnum; + else if (strcmp(name,"BalancethicknessStabilization")==0) return BalancethicknessStabilizationEnum; + else if (strcmp(name,"BalancethicknessThickeningRate")==0) return BalancethicknessThickeningRateEnum; +@@ -36,6 +43,7 @@ + else if (strcmp(name,"ConstantsG")==0) return ConstantsGEnum; + else if (strcmp(name,"ConstantsReferencetemperature")==0) return ConstantsReferencetemperatureEnum; + else if (strcmp(name,"ConstantsYts")==0) return ConstantsYtsEnum; ++ else if (strcmp(name,"DependentObject")==0) return DependentObjectEnum; + else if (strcmp(name,"DiagnosticAbstol")==0) return DiagnosticAbstolEnum; + else if (strcmp(name,"DiagnosticIcefront")==0) return DiagnosticIcefrontEnum; + else if (strcmp(name,"DiagnosticIsnewton")==0) return DiagnosticIsnewtonEnum; +@@ -75,6 +83,7 @@ + else if (strcmp(name,"HydrologyQ")==0) return HydrologyQEnum; + else if (strcmp(name,"HydrologySpcwatercolumn")==0) return HydrologySpcwatercolumnEnum; + else if (strcmp(name,"HydrologyStabilization")==0) return HydrologyStabilizationEnum; ++ else if (strcmp(name,"IndependentObject")==0) return IndependentObjectEnum; + else if (strcmp(name,"InversionControlParameters")==0) return InversionControlParametersEnum; + else if (strcmp(name,"InversionCostFunction")==0) return InversionCostFunctionEnum; + else if (strcmp(name,"InversionCostFunctionThreshold")==0) return InversionCostFunctionThresholdEnum; +@@ -128,7 +137,10 @@ + else if (strcmp(name,"MeshElementonsurface")==0) return MeshElementonsurfaceEnum; + else if (strcmp(name,"MeshElements2d")==0) return MeshElements2dEnum; + else if (strcmp(name,"MeshElements")==0) return MeshElementsEnum; +- else if (strcmp(name,"MeshLowerelements")==0) return MeshLowerelementsEnum; ++ else stage=2; ++ } ++ if(stage==2){ ++ if (strcmp(name,"MeshLowerelements")==0) return MeshLowerelementsEnum; + else if (strcmp(name,"MeshNumberofedges")==0) return MeshNumberofedgesEnum; + else if (strcmp(name,"MeshNumberofelements2d")==0) return MeshNumberofelements2dEnum; + else if (strcmp(name,"MeshNumberofelements")==0) return MeshNumberofelementsEnum; +@@ -137,10 +149,7 @@ + else if (strcmp(name,"MeshNumberofvertices")==0) return MeshNumberofverticesEnum; + else if (strcmp(name,"MeshUpperelements")==0) return MeshUpperelementsEnum; + else if (strcmp(name,"MeshVertexonbed")==0) return MeshVertexonbedEnum; +- else stage=2; +- } +- if(stage==2){ +- if (strcmp(name,"MeshVertexonsurface")==0) return MeshVertexonsurfaceEnum; ++ else if (strcmp(name,"MeshVertexonsurface")==0) return MeshVertexonsurfaceEnum; + else if (strcmp(name,"MeshX")==0) return MeshXEnum; + else if (strcmp(name,"MeshY")==0) return MeshYEnum; + else if (strcmp(name,"MeshZ")==0) return MeshZEnum; +@@ -251,7 +260,10 @@ + else if (strcmp(name,"NoneApproximation")==0) return NoneApproximationEnum; + else if (strcmp(name,"HutterApproximation")==0) return HutterApproximationEnum; + else if (strcmp(name,"MacAyealApproximation")==0) return MacAyealApproximationEnum; +- else if (strcmp(name,"MacAyealPattynApproximation")==0) return MacAyealPattynApproximationEnum; ++ else stage=3; ++ } ++ if(stage==3){ ++ if (strcmp(name,"MacAyealPattynApproximation")==0) return MacAyealPattynApproximationEnum; + else if (strcmp(name,"MacAyealStokesApproximation")==0) return MacAyealStokesApproximationEnum; + else if (strcmp(name,"L1L2Approximation")==0) return L1L2ApproximationEnum; + else if (strcmp(name,"PattynApproximation")==0) return PattynApproximationEnum; +@@ -260,10 +272,7 @@ + else if (strcmp(name,"Constraints")==0) return ConstraintsEnum; + else if (strcmp(name,"Loads")==0) return LoadsEnum; + else if (strcmp(name,"Materials")==0) return MaterialsEnum; +- else stage=3; +- } +- if(stage==3){ +- if (strcmp(name,"Nodes")==0) return NodesEnum; ++ else if (strcmp(name,"Nodes")==0) return NodesEnum; + else if (strcmp(name,"Parameters")==0) return ParametersEnum; + else if (strcmp(name,"Vertices")==0) return VerticesEnum; + else if (strcmp(name,"Results")==0) return ResultsEnum; +@@ -276,6 +285,7 @@ + else if (strcmp(name,"DatasetInput")==0) return DatasetInputEnum; + else if (strcmp(name,"DofIndexing")==0) return DofIndexingEnum; + else if (strcmp(name,"DoubleInput")==0) return DoubleInputEnum; ++ else if (strcmp(name,"DataSetParam")==0) return DataSetParamEnum; + else if (strcmp(name,"DoubleMatArrayParam")==0) return DoubleMatArrayParamEnum; + else if (strcmp(name,"DoubleMatParam")==0) return DoubleMatParamEnum; + else if (strcmp(name,"DoubleParam")==0) return DoubleParamEnum; +@@ -373,7 +383,10 @@ + else if (strcmp(name,"TemperatureSurface")==0) return TemperatureSurfaceEnum; + else if (strcmp(name,"TemperatureBasal")==0) return TemperatureBasalEnum; + else if (strcmp(name,"ThicknessAbsMisfit")==0) return ThicknessAbsMisfitEnum; +- else if (strcmp(name,"Type")==0) return TypeEnum; ++ else stage=4; ++ } ++ if(stage==4){ ++ if (strcmp(name,"Type")==0) return TypeEnum; + else if (strcmp(name,"Vel")==0) return VelEnum; + else if (strcmp(name,"Velocity")==0) return VelocityEnum; + else if (strcmp(name,"VxAverage")==0) return VxAverageEnum; +@@ -383,10 +396,7 @@ + else if (strcmp(name,"Vy")==0) return VyEnum; + else if (strcmp(name,"VyPicard")==0) return VyPicardEnum; + else if (strcmp(name,"Vz")==0) return VzEnum; +- else stage=4; +- } +- if(stage==4){ +- if (strcmp(name,"VzMacAyeal")==0) return VzMacAyealEnum; ++ else if (strcmp(name,"VzMacAyeal")==0) return VzMacAyealEnum; + else if (strcmp(name,"VzPattyn")==0) return VzPattynEnum; + else if (strcmp(name,"VzPicard")==0) return VzPicardEnum; + else if (strcmp(name,"VzStokes")==0) return VzStokesEnum; +@@ -496,11 +506,14 @@ + else if (strcmp(name,"OptionCell")==0) return OptionCellEnum; + else if (strcmp(name,"OptionChar")==0) return OptionCharEnum; + else if (strcmp(name,"OptionStruct")==0) return OptionStructEnum; +- else if (strcmp(name,"OptionDouble")==0) return OptionDoubleEnum; ++ else stage=5; ++ } ++ if(stage==5){ ++ if (strcmp(name,"OptionDouble")==0) return OptionDoubleEnum; + else if (strcmp(name,"OptionLogical")==0) return OptionLogicalEnum; + else if (strcmp(name,"Paterson")==0) return PatersonEnum; + else if (strcmp(name,"Arrhenius")==0) return ArrheniusEnum; +- else stage=5; ++ else stage=6; + } + /*If we reach this point, the string provided has not been found*/ + _error_("Enum " << name << " not found"); +Index: ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13429) ++++ ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13430) +@@ -17,13 +17,20 @@ + switch(en){ + + case AutodiffIsautodiffEnum : return "AutodiffIsautodiff"; +- case AutodiffDependentsEnum : return "AutodiffDependents"; + case AutodiffNumDependentsEnum : return "AutodiffNumDependents"; +- case AutodiffIndependentsEnum : return "AutodiffIndependents"; ++ case AutodiffNumDependentObjectsEnum : return "AutodiffNumDependentObjects"; ++ case AutodiffDependentObjectNamesEnum : return "AutodiffDependentObjectNames"; ++ case AutodiffDependentObjectTypesEnum : return "AutodiffDependentObjectTypes"; ++ case AutodiffDependentObjectsEnum : return "AutodiffDependentObjects"; + case AutodiffNumIndependentsEnum : return "AutodiffNumIndependents"; ++ case AutodiffNumIndependentObjectsEnum : return "AutodiffNumIndependentObjects"; ++ case AutodiffIndependentObjectNamesEnum : return "AutodiffIndependentObjectNames"; ++ case AutodiffIndependentObjectTypesEnum : return "AutodiffIndependentObjectTypes"; ++ case AutodiffIndependentObjectsEnum : return "AutodiffIndependentObjects"; + case AutodiffJacobianEnum : return "AutodiffJacobian"; + case AutodiffXpEnum : return "AutodiffXp"; +- case AutodiffFosForwardOutputEnum : return "AutodiffFosForwardOutput"; ++ case AutodiffDriverEnum : return "AutodiffDriver"; ++ case AutodiffFosForwardIndexEnum : return "AutodiffFosForwardIndex"; + case BalancethicknessSpcthicknessEnum : return "BalancethicknessSpcthickness"; + case BalancethicknessStabilizationEnum : return "BalancethicknessStabilization"; + case BalancethicknessThickeningRateEnum : return "BalancethicknessThickeningRate"; +@@ -35,6 +42,7 @@ + case ConstantsGEnum : return "ConstantsG"; + case ConstantsReferencetemperatureEnum : return "ConstantsReferencetemperature"; + case ConstantsYtsEnum : return "ConstantsYts"; ++ case DependentObjectEnum : return "DependentObject"; + case DiagnosticAbstolEnum : return "DiagnosticAbstol"; + case DiagnosticIcefrontEnum : return "DiagnosticIcefront"; + case DiagnosticIsnewtonEnum : return "DiagnosticIsnewton"; +@@ -74,6 +82,7 @@ + case HydrologyQEnum : return "HydrologyQ"; + case HydrologySpcwatercolumnEnum : return "HydrologySpcwatercolumn"; + case HydrologyStabilizationEnum : return "HydrologyStabilization"; ++ case IndependentObjectEnum : return "IndependentObject"; + case InversionControlParametersEnum : return "InversionControlParameters"; + case InversionCostFunctionEnum : return "InversionCostFunction"; + case InversionCostFunctionThresholdEnum : return "InversionCostFunctionThreshold"; +@@ -269,6 +278,7 @@ + case DatasetInputEnum : return "DatasetInput"; + case DofIndexingEnum : return "DofIndexing"; + case DoubleInputEnum : return "DoubleInput"; ++ case DataSetParamEnum : return "DataSetParam"; + case DoubleMatArrayParamEnum : return "DoubleMatArrayParam"; + case DoubleMatParamEnum : return "DoubleMatParam"; + case DoubleParamEnum : return "DoubleParam"; Index: /issm/oecreview/Archive/13393-13976/ISSM-13430-13431.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13430-13431.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13430-13431.diff (revision 13980) @@ -0,0 +1,37 @@ +Index: ../trunk-jpl/test/NightlyRun/ad.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/ad.m (revision 13430) ++++ ../trunk-jpl/test/NightlyRun/ad.m (revision 13431) +@@ -5,22 +5,15 @@ + md.cluster=generic('name',oshostname(),'np',3); + md.diagnostic.requested_outputs=StressTensorEnum; + md.autodiff.isautodiff=true; +-md.autodiff.independents={'Thickness','Surface'}; +-md.autodiff.dependents={'IceVolume'}; +-%md=solve(md,TransientSolutionEnum); +-md=solve(md,PrognosticSolutionEnum); + +-%Fields and tolerances to track changes +-field_names ={'Vx','Vy','Vel','Pressure',... +- 'StressTensorxx','StressTensoryy','StressTensorxy'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,... +- 1e-13,1e-13,1e-13}; +-field_values={... +- (md.results.TransientSolution.Vx),... +- (md.results.TransientSolution.Vy),... +- (md.results.TransientSolution.Vel),... +- (md.results.TransientSolution.Pressure),... +- (md.results.TransientSolution.StressTensorxx),... +- (md.results.TransientSolution.StressTensoryy),... +- (md.results.TransientSolution.StressTensorxy),... ++md.autodiff.independents={... ++ independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',1), ... ++ independent('name','Surface','type','vertex','nods',md.mesh.numberofvertices)... + }; ++ ++md.autodiff.dependents={... ++ dependent('name','IceVolume','type','scalar')... ++ }; ++md.autodiff.driver='fos_forward'; ++ ++md=solve(md,PrognosticSolutionEnum); Index: /issm/oecreview/Archive/13393-13976/ISSM-13431-13432.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13431-13432.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13431-13432.diff (revision 13980) @@ -0,0 +1,847 @@ +Index: ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13431) ++++ ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13432) +@@ -11,31 +11,47 @@ + + + void AutodiffDriversx(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters,Results* results){ +- bool isautodiff = false; ++ ++ ++ int i; ++ int dummy; ++ bool isautodiff = false; ++ int num_dependents; ++ int num_independents; ++ IssmDouble *axp = NULL; ++ int configuration_type; ++ int solveSize; ++ int edf_n ,edf_m; ++ double *xp = NULL; ++ int anIndepNum; ++ ++ + /*AD mode on?: */ + parameters->FindParam(&isautodiff,AutodiffIsautodiffEnum); ++ + if(isautodiff){ ++ + #ifdef _HAVE_ADOLC_ +- int num_dependents; ++ + parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); +- int num_independents; + parameters->FindParam(&num_independents,AutodiffNumIndependentsEnum); ++ + if(!(num_dependents*num_independents)) return; +- int numberofvertices; +- parameters->FindParam(&numberofvertices,MeshNumberofverticesEnum); ++ + /*retrieve state variable: */ +- IssmDouble *axp = NULL; +- parameters->FindParam(&axp,&num_independents,AutodiffXpEnum); ++ parameters->FindParam(&axp,&dummy,AutodiffXpEnum); ++ + /* driver argument */ +- double *xp=xNew(num_independents); +- for(int i=0;i(num_independents); ++ for(i=0;i(axp[i]); + } ++ + /* get the dimension for the solverx arguments*/ +- int configuration_type; + parameters->FindParam(&configuration_type,ConfigurationTypeEnum); +- int solveSize=nodes->NumberOfDofs(configuration_type,FsetEnum); +- int edf_n=solveSize*(solveSize+1), edf_m=solveSize; ++ solveSize=nodes->NumberOfDofs(configuration_type,FsetEnum); ++ edf_n=solveSize*(solveSize+1); ++ edf_m=solveSize; + + /*get the EDF pointer:*/ + ext_diff_fct *anEDF_for_solverx_p=dynamic_cast * >(parameters->FindParamObject(AdolcParamEnum))->GetParameterValue().myEDF_for_solverx_p; +@@ -46,6 +62,7 @@ + anEDF_for_solverx_p->fov_forward=EDF_fov_forward_for_solverx; + anEDF_for_solverx_p->fos_reverse=EDF_fos_reverse_for_solverx; + // anEDF_for_solverx_p->fov_reverse=EDF_fov_reverse_for_solverx; ++ + /*allocate the space for the parameters to invoke the forward methods:*/ + anEDF_for_solverx_p->dp_x=xNew(edf_n); + anEDF_for_solverx_p->dp_X=xNew(edf_n); +@@ -57,15 +74,17 @@ + anEDF_for_solverx_p->dpp_U=xNew(num_dependents,edf_m); + anEDF_for_solverx_p->dp_Z=xNew(edf_n); + anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,edf_n); ++ + /* Call AD driver:*/ + // single direction: + double *tangentDir=xNewZeroInit(num_independents); +- unsigned int anIndepNum=55; // <---------- make this selectable via config ++ parameters->FindParam(&anIndepNum,AutodiffFosForwardIndexEnum); + tangentDir[anIndepNum]=1.0; + double *theJacVecProduct=xNew(num_dependents); + double *theOutput=xNew(num_dependents); + if (fos_forward(1,num_dependents,num_independents, 0, xp, tangentDir, theOutput, theJacVecProduct )) + _error_("fos_forward returned non-zero error code"); ++ + results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,theJacVecProduct,num_dependents,1,1,0.0)); + + #if 0 +@@ -86,9 +105,11 @@ + xDelete(anEDF_for_solverx_p->dpp_U); + xDelete(anEDF_for_solverx_p->dp_Z); + xDelete(anEDF_for_solverx_p->dpp_Z); ++ + /*Free ressources: */ + xDelete(xp); +- xDelete(axp); // did we allocate this? ++ xDelete(axp); ++ + #else + _error_("Should not be requesting AD drivers when an AD library is not available!"); + #endif +Index: ../trunk-jpl/src/c/modules/RequestedDependentsx/RequestedDependentsx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/RequestedDependentsx/RequestedDependentsx.cpp (revision 13431) ++++ ../trunk-jpl/src/c/modules/RequestedDependentsx/RequestedDependentsx.cpp (revision 13432) +@@ -13,14 +13,12 @@ + + + int i; +- int output_enum; + bool isautodiff = false; + IssmDouble output_value; +- Element *element = NULL; +- int *dependent_enums = NULL; + + int num_dependents; + IssmPDouble *dependents; ++ DataSet* dependent_objects=NULL; + + /*AD mode on?: */ + parameters->FindParam(&isautodiff,AutodiffIsautodiffEnum); +@@ -28,16 +26,18 @@ + if(isautodiff){ + #ifdef _HAVE_ADOLC_ + parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); ++ parameters->FindParam(&dependent_objects,AutodiffDependentObjectsEnum); + if(num_dependents){ + dependents=xNew(num_dependents); +- parameters->FindParam(&dependent_enums,&num_dependents,AutodiffDependentsEnum); + + /*Go through our dependent variables, and compute the response:*/ +- for(i=0;iSize();i++){ ++ DependentObject* dep=(DependentObject*)dependent_objects->GetObjectByOffset(i); ++ Responsex(&output_value,elements,nodes,vertices,loads,materials,parameters,dep->name,false,0); + output_value>>=dependents[i]; + } + } ++ delete dependent_objects; + #else + _error_("Should not be requesting dependents when an AD library is not available!"); + #endif +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13431) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13432) +@@ -13,15 +13,19 @@ + + void CreateParametersAutodiff(Parameters** pparameters,IoModel* iomodel,int solution_type,int analysis_type){ + +- int i,j; ++ int i; + Parameters *parameters = NULL; + bool autodiff_analysis; +- int* dependents = NULL; +- int num_dependents; +- int* independents = NULL; +- int num_independents; +- int numberofvertices; ++ int num_dependent_objects; ++ int num_dep=0; ++ int* names=NULL; ++ int* types=NULL; ++ int dummy; ++ + IssmDouble* xp=NULL; ++ IssmDouble* xp_backup=NULL; ++ int num_ind,local_num_ind; ++ DataSet* dependent_objects=NULL; + + /*Get parameters: */ + parameters=*pparameters; +@@ -31,34 +35,60 @@ + + if(autodiff_analysis){ + +- iomodel->Constant(&num_independents,AutodiffNumIndependentsEnum); +- iomodel->Constant(&num_dependents,AutodiffNumDependentsEnum); +- iomodel->Constant(&numberofvertices,MeshNumberofverticesEnum); ++ /*retrieve driver: */ ++ parameters->AddObject(iomodel->CopyConstantObject(AutodiffDriverEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject(AutodiffFosForwardIndexEnum)); + +- /*recover dependents: */ +- parameters->AddObject(iomodel->CopyConstantObject(AutodiffNumDependentsEnum)); +- if(num_dependents){ +- iomodel->FetchData(&dependents,NULL,&num_dependents,AutodiffDependentsEnum); +- parameters->AddObject(new IntVecParam(AutodiffDependentsEnum,dependents,num_dependents)); ++ /*Deal with dependents first: {{{*/ ++ iomodel->Constant(&num_dependent_objects,AutodiffNumDependentObjectsEnum); ++ dependent_objects=new DataSet(); ++ num_dep=0; ++ ++ if(num_dependent_objects){ ++ iomodel->FetchData(&names,&dummy,&dummy,AutodiffDependentObjectNamesEnum); ++ iomodel->FetchData(&types,&dummy,&dummy,AutodiffDependentObjectTypesEnum); ++ ++ for(i=0;iAddObject(dep); ++ num_dep+=dep->NumDependents(); ++ } ++ ++ /*Free ressources:*/ ++ xDelete(names); ++ xDelete(types); + } ++ parameters->AddObject(new DataSetParam(AutodiffDependentObjectsEnum,dependent_objects)); ++ parameters->AddObject(new IntParam(AutodiffNumDependentsEnum,num_dep)); + +- /*recover independents: */ +- parameters->AddObject(iomodel->CopyConstantObject(AutodiffNumIndependentsEnum)); +- if(num_independents){ +- iomodel->FetchData(&independents,NULL,&num_independents,AutodiffIndependentsEnum); +- parameters->AddObject(new IntVecParam(AutodiffIndependentsEnum,independents,num_independents)); ++ delete dependent_objects; ++ /*}}}*/ + +- /*Build state vector, value at which we compute our gradients of dependent variables in adolc: the xp vector */ +- xp=xNew(num_independents*numberofvertices); +- for(i=0;idata[independents[i]]; +- for(j=0;jDeclareIndependents. Just do some more processing. ++ *In particular, figure out num_independents, and create the state vector xp, or size num_independents x 1 :*/ ++ num_ind=0; ++ for(i=0;iindependent_objects->Size();i++){ ++ IndependentObject* ind=(IndependentObject*)iomodel->independent_objects->GetObjectByOffset(i); ++ num_ind+=ind->NumIndependents(); ++ } ++ if(num_ind){ ++ xp=xNew(num_ind); ++ xp_backup=xp; ++ for(i=0;iindependent_objects->Size();i++){ ++ IndependentObject* ind=(IndependentObject*)iomodel->independent_objects->GetObjectByOffset(i); ++ ind->FillIndependents(iomodel->data,xp); ++ local_num_ind=ind->NumIndependents(); xp=xp+local_num_ind; + } +- parameters->AddObject(new DoubleVecParam(AutodiffXpEnum,xp,num_independents*numberofvertices)); ++ xp=xp_backup; parameters->AddObject(new DoubleVecParam(AutodiffXpEnum,xp,num_ind)); + } ++ parameters->AddObject(new IntParam(AutodiffNumIndependentsEnum,num_ind)); + ++ /*Don't forget to copy iomodel->independent_objects to parameters: */ ++ parameters->AddObject(new DataSetParam(AutodiffIndependentObjectsEnum,iomodel->independent_objects)); ++ /*}}}*/ ++ + /*Assign output pointer: */ + *pparameters=parameters; + } +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.cpp (revision 13431) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.cpp (revision 13432) +@@ -19,7 +19,7 @@ + void ModelProcessorx(Elements** pelements, Nodes** pnodes, Vertices** pvertices, Materials** pmaterials, Constraints** pconstraints, Loads** ploads, Parameters** pparameters, FILE* IOMODEL,char* rootpath,const int solution_type,const int nummodels,const int* analysis_type_list){ + + int i,analysis_type,dim,verbose; +- bool isthermal,isprognostic,isdiagnostic,isgroundingline,isenthalpy,autodiff; ++ bool isthermal,isprognostic,isdiagnostic,isgroundingline,isenthalpy; + + /*output: */ + Elements *elements = NULL; +@@ -42,13 +42,7 @@ + iomodel->Constant(&isprognostic,TransientIsprognosticEnum); + iomodel->Constant(&isdiagnostic,TransientIsdiagnosticEnum); + iomodel->Constant(&isgroundingline,TransientIsgroundinglineEnum); +- iomodel->Constant(&autodiff,AutodiffIsautodiffEnum); + +- /*If we are running in AD mode, we need to declare our independent variables now, before +- *and prevent them from being erased during successive calls to iomodel->FetchData and +- iomodel->DeleteData:*/ +- if(autodiff)iomodel->DeclareIndependents(); +- + SetVerbosityLevel(verbose); + + for(i=0;ifid = NULL; +- this->data = NULL; +- this->independents = NULL; +- this->constants = NULL; ++ this->fid=NULL; ++ this->data=NULL; ++ this->independents=NULL; ++ this->constants=NULL; + +- this->my_elements = NULL; +- this->my_nodes = NULL; +- this->my_vertices = NULL; +- this->singlenodetoelementconnectivity = NULL; +- this->numbernodetoelementconnectivity = NULL; ++ this->my_elements=NULL; ++ this->my_nodes=NULL; ++ this->my_vertices=NULL; ++ this->singlenodetoelementconnectivity=NULL; ++ this->numbernodetoelementconnectivity=NULL; + +- this->nodecounter = 0; +- this->loadcounter = 0; +- this->constraintcounter = 0; ++ this->nodecounter=0; ++ this->loadcounter=0; ++ this->constraintcounter=0; + } + /*}}}*/ + /*FUNCTION IoModel::IoModel(FILE* iomodel_handle){{{*/ + IoModel::IoModel(FILE* iomodel_handle){ +- ++ + /*First, keep track of the file handle: */ + this->fid=iomodel_handle; + + /*Check that Enums are Synchronized*/ + this->CheckEnumSync(); + ++ /*Initialize data: */ ++ this->data=xNew(MaximumNumberOfEnums); ++ for(int i=0;idata[i]=NULL; ++ ++ /*If we are running in AD mode, we need to declare our independent variables now, ++ *and prevent them from being erased during successive calls to iomodel->FetchConstants, iomodel->FetchData and ++ iomodel->DeleteData:*/ ++ this->DeclareIndependents(); ++ + /*Initialize and read constants:*/ + this->constants=new Parameters(); + this->FetchConstants(); /*this routine goes through the input file, and fetches bools, ints, IssmDoubles and strings only, nothing memory intensive*/ + +- /*Initialize data: */ +- this->data=xNew(MaximumNumberOfEnums); +- for(int i=0;idata[i]=NULL; +- +- /*Initialize array detecting whether data[i] is an independent AD mode variable: */ +- this->independents=xNew(MaximumNumberOfEnums); +- for(int i=0;iindependents[i]=false; +- + /*Initialize permanent data: */ +- this->my_elements = NULL; +- this->my_nodes = NULL; +- this->my_vertices = NULL; +- this->singlenodetoelementconnectivity = NULL; +- this->numbernodetoelementconnectivity = NULL; ++ this->my_elements=NULL; ++ this->my_nodes=NULL; ++ this->my_vertices=NULL; ++ this->singlenodetoelementconnectivity=NULL; ++ this->numbernodetoelementconnectivity=NULL; + +- this->nodecounter = 0; +- this->loadcounter = 0; +- this->constraintcounter = 0; ++ this->nodecounter=0; ++ this->loadcounter=0; ++ this->constraintcounter=0; + } + /*}}}*/ + /*FUNCTION IoModel::~IoModel(){{{*/ +@@ -90,6 +91,7 @@ + + xDelete(this->data); + xDelete(this->independents); ++ delete this->independent_objects; + xDelete(this->my_elements); + xDelete(this->my_nodes); + xDelete(this->my_vertices); +@@ -196,16 +198,74 @@ + return this->data[data_enum]; + } + /*}}}*/ ++/*FUNCTION IoModel::DeclareIndependents{{{*/ ++void IoModel::DeclareIndependents(void){ ++ ++ ++ int i; ++ bool autodiff = false; ++ int num_independent_objects; ++ ++ int *names = NULL; ++ int *types = NULL; ++ ++ int numberofvertices; ++ int dummy; ++ ++ ++ /*Initialize array detecting whether data[i] is an independent AD mode variable: */ ++ this->independents=xNew(MaximumNumberOfEnums); ++ for(i=0;iindependents[i]=false; ++ ++ this->FetchData(&autodiff,AutodiffIsautodiffEnum); ++ if(autodiff){ ++ ++ this->FetchData(&numberofvertices,MeshNumberofverticesEnum); ++ ++ #ifdef _HAVE_ADOLC_ ++ /*build dataset made of independent objects: */ ++ this->independent_objects=new DataSet(); ++ this->FetchData(&num_independent_objects,AutodiffNumIndependentObjectsEnum); ++ if(num_independent_objects){ ++ this->FetchData(&names,&dummy,&dummy,AutodiffIndependentObjectNamesEnum); ++ this->FetchData(&types,&dummy,&dummy,AutodiffIndependentObjectTypesEnum); ++ ++ /*create independent objects, and at the same time, fetch the corresponding independent variables, ++ *and declare them as such in ADOLC: */ ++ for(i=0;iindependent_objects->AddObject(independent_object); ++ ++ /*now go fetch the independent variable: */ ++ independent_object->FetchIndependent(this); //supply the pointer to iomodel. ++ } ++ xDelete(names); ++ xDelete(types); ++ } ++ #else ++ /*if we asked for AD computations, we have a problem!: */ ++ _error_("Cannot carry out AD mode computations without support of ADOLC compiled in!"); ++ #endif ++ } ++ ++} ++/*}}}*/ + /*FUNCTION IoModel::DeleteData(int num,...){{{*/ + void IoModel::DeleteData(int num,...){ + +- va_list ap; +- int dataenum; +- DoubleMatParam *parameter = NULL; ++ va_list ap; ++ int dataenum; ++ int i; ++ DoubleMatParam* parameter=NULL; + + /*Go through the entire list of enums and delete the corresponding data from the iomodel-data dataset: */ ++ + va_start(ap,num); +- for(int i=0; ifid || my_rank); +@@ -298,11 +360,19 @@ + + break; + case 3: +- /*Read the scalar and broadcast it to other cpus:*/ +- if(fread(&scalar,sizeof(IssmPDouble),1,this->fid)!=1) _error_("could not read scalar "); +- #ifdef _HAVE_MPI_ +- MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); +- #endif ++ /*Read the scalar and broadcast it to other cpus. However, if this record has already ++ * been read in DeclareIndependents, we should not re-read it, but grab it from the iomodel->data ++ * slots: */ ++ if(this->independents[record_enum]){ ++ scalar=*(this->data[record_enum]); ++ } ++ else{ ++ if(fread(&pscalar,sizeof(IssmPDouble),1,this->fid)!=1) _error_("could not read scalar "); ++ #ifdef _HAVE_MPI_ ++ MPI_Bcast(&pscalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); ++ #endif ++ scalar=reCast(pscalar); ++ } + + /*create DoubleParam: */ + this->constants->AddObject(new DoubleParam(record_enum,scalar)); +@@ -454,6 +524,8 @@ + void IoModel::FetchData(bool* pboolean,int data_enum){ + + extern int my_rank; ++ extern int num_procs; ++ + + /*output: */ + int booleanint; +@@ -472,6 +544,7 @@ + MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); + #endif + ++ /*cast to bool: */ + /*Assign output pointers: */ + *pboolean=(bool)booleanint; + +@@ -481,6 +554,7 @@ + void IoModel::FetchData(int* pinteger,int data_enum){ + + extern int my_rank; ++ extern int num_procs; + + /*output: */ + int integer; +@@ -507,11 +581,14 @@ + /*FUNCTION IoModel::FetchData(IssmDouble* pscalar,int data_enum){{{*/ + void IoModel::FetchData(IssmDouble* pscalar,int data_enum){ + ++ + extern int my_rank; ++ extern int num_procs; ++ + + /*output: */ +- IssmPDouble scalar; +- int code; ++ IssmPDouble scalar; ++ int code; + + /*Set file pointer to beginning of the data: */ + fid=this->SetFilePointerToData(&code,NULL,data_enum); +@@ -535,6 +612,8 @@ + void IoModel::FetchData(char** pstring,int data_enum){ + + extern int my_rank; ++ extern int num_procs; ++ + + /*output: */ + char* string=NULL; +@@ -546,6 +625,8 @@ + + if(code!=4)_error_("expecting a string for enum " << EnumToStringx(data_enum)); + ++ /*Now fetch: */ ++ + /*We have to read a string from disk. First read the dimensions of the string, then the string: */ + if(my_rank==0){ + if(fread(&string_size,sizeof(int),1,fid)!=1) _error_("could not read length of string "); +@@ -573,6 +654,7 @@ + string[0]='\0'; + } + ++ + /*Assign output pointers: */ + *pstring=string; + } +@@ -581,6 +663,7 @@ + void IoModel::FetchData(int** pmatrix,int* pM,int* pN,int data_enum){ + + extern int my_rank; ++ extern int num_procs; + int i,j; + + /*output: */ +@@ -596,6 +679,8 @@ + + if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(data_enum)); + ++ /*Now fetch: */ ++ + /*We have to read a matrix from disk. First read the dimensions of the matrix, then the whole matrix: */ + /*numberofelements: */ + if(my_rank==0){ +@@ -653,6 +738,7 @@ + void IoModel::FetchData(IssmDouble** pmatrix,int* pM,int* pN,int data_enum){ + + extern int my_rank; ++ extern int num_procs; + + /*output: */ + int M,N; +@@ -664,6 +750,8 @@ + fid=this->SetFilePointerToData(&code,&vector_type,data_enum); + if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(data_enum)); + ++ /*Now fetch: */ ++ + /*We have to read a matrix from disk. First read the dimensions of the matrix, then the whole matrix: */ + /*numberofelements: */ + if(my_rank==0){ +@@ -715,6 +803,8 @@ + void IoModel::FetchData(char*** pstrings,int* pnumstrings,int data_enum){ + + extern int my_rank; ++ extern int num_procs; ++ + int i; + + /*output: */ +@@ -783,13 +873,15 @@ + void IoModel::FetchData(IssmDouble*** pmatrices,int** pmdims,int** pndims, int* pnumrecords,int data_enum){ + + int i; ++ + extern int my_rank; ++ extern int num_procs; + + /*output: */ +- IssmDouble **matrices = NULL; +- int *mdims = NULL; +- int *ndims = NULL; +- int numrecords = 0; ++ IssmDouble** matrices=NULL; ++ int* mdims=NULL; ++ int* ndims=NULL; ++ int numrecords=0; + + /*intermediary: */ + int M, N; +@@ -872,9 +964,12 @@ + /*FUNCTION IoModel::FetchData(Option** poption,int data_enum){{{*/ + void IoModel::FetchData(Option** poption,int index){ + ++ extern int my_rank; ++ extern int num_procs; ++ + /*output: */ +- int code; +- char *name = NULL; ++ int code; ++ char *name = NULL; + + /*First get option name*/ + this->FetchData(&name,index); +@@ -918,17 +1013,17 @@ + /*FUNCTION IoModel::FetchData(int num,...){{{*/ + void IoModel::FetchData(int num,...){ + +- va_list ap; +- int dataenum; +- IssmDouble *matrix = NULL; +- int M,N; ++ va_list ap; ++ int dataenum; ++ IssmDouble* matrix=NULL; ++ int M,N; ++ int i; + +- /*Go through the entire list of enums and fetch the corresponding data. +- * Add it to the iomodel->data dataset. Everything +- * we fetch is a IssmDouble* : */ ++ /*Go through the entire list of enums and fetch the corresponding data. Add it to the iomodel->data dataset. Everything ++ *we fetch is a IssmDouble* : */ + + va_start(ap,num); +- for(int i=0; idata[dataenum]=matrix; + } + va_end(ap); ++ + } + /*}}}*/ + /*FUNCTION IoModel::FetchDataToInput{{{*/ +@@ -970,6 +1066,7 @@ + int nel; + int numberofelements; + ++ + /*variables being fetched: */ + bool boolean; + int integer; +@@ -1189,6 +1286,7 @@ + FILE* IoModel::SetFilePointerToData(int* pcode,int* pvector_type, int data_enum){ + + extern int my_rank; ++ extern int num_procs; + + int found=0; + int record_enum; +@@ -1249,93 +1347,3 @@ + return fid; + } + /*}}}*/ +-/*FUNCTION IoModel::DeclareIndependents{{{*/ +-void IoModel::DeclareIndependents(void){ +- +- bool autodiff=false; +- int dummy; +- int i; +- int num_independents; +- int* independents=NULL; +- +- #ifdef _HAVE_ADOLC_ +- /*recover independent enums: */ +- this->Constant(&num_independents,AutodiffNumIndependentsEnum); +- if(num_independents){ +- this->FetchData(&independents,&dummy,&dummy,AutodiffIndependentsEnum); +- +- /*now go fetch the independent variables for each independent enum: */ +- for(i=0;iFetchIndependent(independents[i]); +- } +- xDelete(independents); +- } +- #else +- /*if we asked for AD computations, we have a problem!: */ +- this->Constant(&autodiff,AutodiffIsautodiffEnum); +- if(autodiff)_error_("Cannot carry out AD mode computations without support of ADOLC compiled in!"); +- #endif +- +-} +-/*}}}*/ +-/*FUNCTION IoModel::FetchIndependent{{{*/ +-void IoModel::FetchIndependent(int independent_enum){ +- +- #ifdef _HAVE_ADOLC_ //cannot come here unless you are running AD mode, from DeclaredIndependents: +- extern int my_rank; +- +- /*output: */ +- int M,N; +- IssmPDouble* buffer=NULL; //a buffer to read the data from disk +- IssmDouble* matrix=NULL; //our independent variable +- int code=0; +- int vector_type=0; +- +- /*Set file pointer to beginning of the data: */ +- fid=this->SetFilePointerToData(&code,&vector_type,independent_enum); +- if((code!=5) && (code!=6) && (code!=7))_error_("expecting a IssmDouble, integer or boolean matrix for enum " << EnumToStringx(independent_enum)); +- +- /*We have to read a matrix from disk. First read the dimensions of the matrix, then the whole matrix: */ +- /*numberofelements: */ +- if(my_rank==0){ +- if(fread(&M,sizeof(int),1,fid)!=1) _error_("could not read number of rows for matrix "); +- } +- #ifdef _HAVE_MPI_ +- MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); +- #endif +- +- if(my_rank==0){ +- if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix "); +- } +- #ifdef _HAVE_MPI_ +- MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); +- #endif +- +- /*Now allocate matrix: */ +- if(M*N){ +- buffer=xNew(M*N); +- matrix=xNew(M*N); +- +- /*Read matrix on node 0, then broadcast: */ +- if(my_rank==0){ +- if(fread(buffer,M*N*sizeof(IssmPDouble),1,fid)!=1) _error_("could not read matrix "); +- +- /*Now, before we even broadcast this to other nodes, declare the whole matrix as a independent variable!: */ +- for (int i=0;i(buffer); +- } +- else _error_("cannot declare the independent variable " << EnumToStringx(independent_enum) << "if it's empty!"); +- +- /*Ok, we are almost done. Matrix is now a independent matrix. We don't want this matrix to be fetched again in the +- *future, which would effectively write over the independency in the ADOLC tape! So we are going to keep track of this +- independent matrix inthe iomodel->data[independent_enum] data slot: */ +- this->data[independent_enum]=matrix; +- this->independents[independent_enum]=true; +- #endif +-} +-/*}}}*/ +Index: ../trunk-jpl/src/c/classes/IoModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.h (revision 13431) ++++ ../trunk-jpl/src/c/classes/IoModel.h (revision 13432) +@@ -38,6 +38,7 @@ + + /*for AD mode: to keep track of our independent variables we fetch:*/ + bool* independents; ++ DataSet* independent_objects; + + /*Methods*/ + ~IoModel(); Index: /issm/oecreview/Archive/13393-13976/ISSM-13432-13433.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13432-13433.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13432-13433.diff (revision 13980) @@ -0,0 +1,137 @@ +Index: ../trunk-jpl/test/NightlyRun/test3001.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3001.m (revision 13432) ++++ ../trunk-jpl/test/NightlyRun/test3001.m (revision 13433) +@@ -5,6 +5,7 @@ + md.cluster=generic('name',oshostname(),'np',3); + md.diagnostic.requested_outputs=StressTensorEnum; + md.autodiff.isautodiff=true; ++md.verbose=verbose('autodiff',true); + md=solve(md,DiagnosticSolutionEnum); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test3005.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3005.m (revision 13432) ++++ ../trunk-jpl/test/NightlyRun/test3005.m (revision 13433) +@@ -4,6 +4,7 @@ + md=setflowequation(md,'macayeal','all'); + md.cluster=generic('name',oshostname(),'np',3); + md.autodiff.isautodiff=true; ++md.verbose=verbose('autodiff',true); + md=solve(md,PrognosticSolutionEnum); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test3009.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3009.m (revision 13432) ++++ ../trunk-jpl/test/NightlyRun/test3009.m (revision 13433) +@@ -9,6 +9,7 @@ + md.transient.isthermal=1; + md.transient.isgroundingline=0; + md.autodiff.isautodiff=true; ++md.verbose=verbose('autodiff',true); + md=solve(md,TransientSolutionEnum); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test3010.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3010.m (revision 13432) ++++ ../trunk-jpl/test/NightlyRun/test3010.m (revision 13433) +@@ -6,6 +6,7 @@ + md.transient.requested_outputs=IceVolumeEnum(); + + md.autodiff.isautodiff=true; ++md.verbose=verbose('autodiff',true); + md=solve(md,TransientSolutionEnum); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test3002.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3002.m (revision 13432) ++++ ../trunk-jpl/test/NightlyRun/test3002.m (revision 13433) +@@ -5,6 +5,7 @@ + md=setflowequation(md,'macayeal','all'); + md.cluster=generic('name',oshostname(),'np',3); + md.autodiff.isautodiff=true; ++md.verbose=verbose('autodiff',true); + md=solve(md,DiagnosticSolutionEnum); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test3006.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3006.m (revision 13432) ++++ ../trunk-jpl/test/NightlyRun/test3006.m (revision 13433) +@@ -7,6 +7,7 @@ + md.prognostic.stabilization=3; + md.prognostic.spcthickness=md.geometry.thickness; + md.autodiff.isautodiff=true; ++md.verbose=verbose('autodiff',true); + md=solve(md,PrognosticSolutionEnum); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/ad.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/ad.m (revision 13432) ++++ ../trunk-jpl/test/NightlyRun/ad.m (revision 13433) +@@ -5,6 +5,7 @@ + md.cluster=generic('name',oshostname(),'np',3); + md.diagnostic.requested_outputs=StressTensorEnum; + md.autodiff.isautodiff=true; ++md.verbose=verbose('autodiff',true); + + md.autodiff.independents={... + independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',1), ... +@@ -17,3 +18,4 @@ + md.autodiff.driver='fos_forward'; + + md=solve(md,PrognosticSolutionEnum); ++%md=solve(md,TransientSolutionEnum); +Index: ../trunk-jpl/test/NightlyRun/test3003.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3003.m (revision 13432) ++++ ../trunk-jpl/test/NightlyRun/test3003.m (revision 13433) +@@ -6,6 +6,7 @@ + md.cluster=generic('name',oshostname(),'np',3); + md.diagnostic.requested_outputs=StressTensorEnum; + md.autodiff.isautodiff=true; ++md.verbose=verbose('autodiff',true); + md=solve(md,DiagnosticSolutionEnum); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test3007.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3007.m (revision 13432) ++++ ../trunk-jpl/test/NightlyRun/test3007.m (revision 13433) +@@ -5,6 +5,7 @@ + md=extrude(md,5,3); + md.cluster=generic('name',oshostname(),'np',3); + md.autodiff.isautodiff=true; ++md.verbose=verbose('autodiff',true); + md=solve(md,PrognosticSolutionEnum); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test3004.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3004.m (revision 13432) ++++ ../trunk-jpl/test/NightlyRun/test3004.m (revision 13433) +@@ -5,6 +5,7 @@ + md=setflowequation(md,'stokes','all'); + md.cluster=generic('name',oshostname(),'np',3); + md.autodiff.isautodiff=true; ++md.verbose=verbose('autodiff',true); + md=solve(md,DiagnosticSolutionEnum); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test3008.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3008.m (revision 13432) ++++ ../trunk-jpl/test/NightlyRun/test3008.m (revision 13433) +@@ -6,6 +6,7 @@ + md.timestepping.time_step=0; + md.cluster=generic('name',oshostname(),'np',3); + md.autodiff.isautodiff=true; ++md.verbose=verbose('autodiff',true); + md=solve(md,ThermalSolutionEnum); + + %Fields and tolerances to track changes Index: /issm/oecreview/Archive/13393-13976/ISSM-13433-13434.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13433-13434.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13433-13434.diff (revision 13980) @@ -0,0 +1,38 @@ +Index: ../trunk-jpl/src/c/solutions/prognostic_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/prognostic_core.cpp (revision 13433) ++++ ../trunk-jpl/src/c/solutions/prognostic_core.cpp (revision 13434) +@@ -49,5 +49,5 @@ + } + + +- if(solution_type=PrognosticSolutionEnum)RequestedDependentsx(femmodel->results,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); ++ if(solution_type==PrognosticSolutionEnum)RequestedDependentsx(femmodel->results,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + } +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13433) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13434) +@@ -186,13 +186,15 @@ + #ifdef _HAVE_ADOLC_ + if(autodiff){ + tapestats(1,tape_stats); //reading of tape statistics +- _pprintLine_(" ADOLC statistics: "); +- _pprintLine_(" "< 2^$POWER = $BINARY" + +- #Add Verbosity Matlab file{{{ +- cat < $ISSM_DIR"/src/m/shared/"$(echo $FILENAME".m") +-function bool=$(echo $FILENAME)() +-%$(echo $FILENAME | awk {'print toupper($1)'}) - Return true if $(echo $LEVELNAME | awk {'print tolower($1)'}) level is activated +-% +-% WARNING: DO NOT MODIFY THIS FILE +-% this file has been automatically generated by src/c/shared/Numerics/Synchronize.sh +-% Please read src/c/shared/Numerics/README for more information +-% +-% Usage: +-% bool=$FILENAME() +- +-bool=logical(bitand(GetVerbosityLevel(),$BINARY)); +-END +- #}}} + #Add case to verbose.m FIELDS{{{ + if [ $i -eq 1 ]; then cat <> FIELDS + %BEGINFIELDS +@@ -134,7 +119,7 @@ + /*FUNCTION SetVerbosityLevel {{{*/ + void SetVerbosityLevel(int level){ + +- if(level<0) _error2_("vebosity level should be a positive integer (user provided " << level << ")"); ++ if(level<0) _error_("vebosity level should be a positive integer (user provided " << level << ")"); + + verbositylevel = level; + +Index: ../trunk-jpl/src/c/shared/Numerics/Verbosity.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Numerics/Verbosity.cpp (revision 13434) ++++ ../trunk-jpl/src/c/shared/Numerics/Verbosity.cpp (revision 13435) +@@ -27,6 +27,7 @@ + bool VerboseConvergence(void){return (GetVerbosityLevel() & 16);} /* 2^4*/ + bool VerboseControl(void){return (GetVerbosityLevel() & 32);} /* 2^5*/ + bool VerboseQmu(void){return (GetVerbosityLevel() & 64);} /* 2^6*/ ++bool VerboseAutodiff(void){return (GetVerbosityLevel() & 128);} /* 2^7*/ + + /*Verbosity Setup*/ + static int verbositylevel=-1; +@@ -40,8 +41,6 @@ + }/*}}}*/ + /*FUNCTION GetVerbosityLevel {{{*/ + int GetVerbosityLevel(void){ +- + _assert_(verbositylevel>=0); + return verbositylevel; +- + }/*}}}*/ +Index: ../trunk-jpl/src/c/shared/Numerics/Verbosity.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Numerics/Verbosity.h (revision 13434) ++++ ../trunk-jpl/src/c/shared/Numerics/Verbosity.h (revision 13435) +@@ -13,6 +13,7 @@ + bool VerboseConvergence(void); + bool VerboseControl(void); + bool VerboseQmu(void); ++bool VerboseAutodiff(void); + + /*Setup Verbosity level*/ + void SetVerbosityLevel(int level); +Index: ../trunk-jpl/src/m/classes/verbose.m +=================================================================== +--- ../trunk-jpl/src/m/classes/verbose.m (revision 13434) ++++ ../trunk-jpl/src/m/classes/verbose.m (revision 13435) +@@ -8,6 +8,7 @@ + % convergence : convergence criteria + % control : control method + % qmu : sensitivity analysis ++% autodiff : AD analysis + % + % Usage: + % verbose=verbose(); +@@ -22,13 +23,14 @@ + properties (SetAccess=public) + % {{{ + %BEGINFIELDS +- mprocessor = false; +- module = false; +- solution = false; +- solver = false; +- convergence = false; +- control = false; +- qmu = false; ++ mprocessor=false; ++ module=false; ++ solution=false; ++ solver=false; ++ convergence=false; ++ control=false; ++ qmu=false; ++ autodiff=false; + %ENDFIELDS + % }}} + end +@@ -82,6 +84,7 @@ + if (verbose.convergence), binary=bitor(binary,16); end + if (verbose.control), binary=bitor(binary,32); end + if (verbose.qmu), binary=bitor(binary,64); end ++ if (verbose.autodiff), binary=bitor(binary,128); end + %ENDVERB2BIN + + end +@@ -89,13 +92,14 @@ + function verbose=BinaryToVerbose(verbose,binary) % {{{ + + %BEGINBIN2VERB +- verbose.mprocessor =logical(bitand(binary, 1)); +- verbose.module =logical(bitand(binary, 2)); +- verbose.solution =logical(bitand(binary, 4)); +- verbose.solver =logical(bitand(binary, 8)); +- verbose.convergence=logical(bitand(binary,16)); +- verbose.control =logical(bitand(binary,32)); +- verbose.qmu =logical(bitand(binary,64)); ++ if bitand(binary,1), verbose.mprocessor=true; else verbose.mprocessor=false; end ++ if bitand(binary,2), verbose.module=true; else verbose.module=false; end ++ if bitand(binary,4), verbose.solution=true; else verbose.solution=false; end ++ if bitand(binary,8), verbose.solver=true; else verbose.solver=false; end ++ if bitand(binary,16), verbose.convergence=true; else verbose.convergence=false; end ++ if bitand(binary,32), verbose.control=true; else verbose.control=false; end ++ if bitand(binary,64), verbose.qmu=true; else verbose.qmu=false; end ++ if bitand(binary,128), verbose.autodiff=true; else verbose.autodiff=false; end + %ENDBIN2VERB + + end +@@ -114,6 +118,7 @@ + disp(sprintf(' %15s : %s','convergence',mat2str(verbose.convergence))); + disp(sprintf(' %15s : %s','control',mat2str(verbose.control))); + disp(sprintf(' %15s : %s','qmu',mat2str(verbose.qmu))); ++ disp(sprintf(' %15s : %s','autodiff',mat2str(verbose.autodiff))); + %ENDDISP + + end Index: /issm/oecreview/Archive/13393-13976/ISSM-13435-13436.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13435-13436.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13435-13436.diff (revision 13980) @@ -0,0 +1,776 @@ +Index: ../trunk-jpl/src/m/mesh/meshconvert.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/meshconvert.py (revision 13435) ++++ ../trunk-jpl/src/m/mesh/meshconvert.py (revision 13436) +@@ -51,7 +51,7 @@ + md.mesh.elementonbed=numpy.ones(md.mesh.numberofelements) + md.mesh.elementonsurface=numpy.ones(md.mesh.numberofelements) + md.mesh.vertexonboundary=numpy.zeros(md.mesh.numberofvertices) +- md.mesh.vertexonboundary[md.mesh.segments[:,0:1].astype(int)-1]=1 ++ md.mesh.vertexonboundary[md.mesh.segments[:,0:2].astype(int)-1]=1 + + return md + +Index: ../trunk-jpl/src/m/mesh/bamg.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.py (revision 0) ++++ ../trunk-jpl/src/m/mesh/bamg.py (revision 13436) +@@ -0,0 +1,486 @@ ++import os.path ++import numpy ++from collections import OrderedDict ++from pairoptions import * ++from bamggeom import * ++from bamgmesh import * ++from expread import * ++from expwrite import * ++from MatlabFuncs import * ++from BamgMesher import * ++ ++def bamg(md,*args): ++ """ ++ BAMG - mesh generation ++ ++ Available options (for more details see ISSM website http://issm.jpl.nasa.gov/): ++ ++ - domain : followed by an ARGUS file that prescribes the domain outline ++ - hmin : minimum edge length (default is 10^-100) ++ - hmax : maximum edge length (default is 10^100) ++ - hVertices : imposed edge length for each vertex (geometry or mesh) ++ - hminVertices : minimum edge length for each vertex (mesh) ++ - hmaxVertices : maximum edge length for each vertex (mesh) ++ ++ - anisomax : maximum ratio between the smallest and largest edges (default is 10^30) ++ - coeff : coefficient applied to the metric (2-> twice as many elements, default is 1) ++ - cutoff : scalar used to compute the metric when metric type 2 or 3 are applied ++ - err : error used to generate the metric from a field ++ - errg : geometric error (default is 0.1) ++ - field : field of the model that will be used to compute the metric ++ to apply several fields, use one column per field ++ - gradation : maximum ratio between two adjacent edges ++ - Hessiantype : 0 -> use double P2 projection (default) ++ 1 -> use Green formula ++ - KeepVertices : try to keep initial vertices when adaptation is done on an existing mesh (default 1) ++ - MaxCornerAngle : maximum angle of corners in degree (default is 10) ++ - maxnbv : maximum number of vertices used to allocate memory (default is 10^6) ++ - maxsubdiv : maximum subdivision of exisiting elements (default is 10) ++ - metric : matrix (numberofnodes x 3) used as a metric ++ - Metrictype : 1 -> absolute error c/(err coeff^2) * Abs(H) (default) ++ 2 -> relative error c/(err coeff^2) * Abs(H)/max(s,cutoff*max(s)) ++ 3 -> rescaled absolute error c/(err coeff^2) * Abs(H)/(smax-smin) ++ - nbjacoby : correction used by Hessiantype=1 (default is 1) ++ - nbsmooth : number of metric smoothing procedure (default is 3) ++ - omega : relaxation parameter of the smoothing procedure (default is 1.8) ++ - power : power applied to the metric (default is 1) ++ - splitcorners : split triangles whuch have 3 vertices on the outline (default is 1) ++ - geometricalmetric : take the geometry into account to generate the metric (default is 0) ++ - verbose : level of verbosity (default is 1) ++ ++ - rifts : followed by an ARGUS file that prescribes the rifts ++ - toltip : tolerance to move tip on an existing point of the domain outline ++ - tracks : followed by an ARGUS file that prescribes the tracks that the mesh will stick to ++ - RequiredVertices : mesh vertices that are required. [x,y,ref]; ref is optional ++ - tol : if the distance between 2 points of the domain outline is less than tol, they ++ will be merged ++ ++ Examples: ++ md=bamg(md,'domain','DomainOutline.exp','hmax',3000); ++ md=bamg(md,'field',[md.inversion.vel_obs md.geometry.thickness],'hmax',20000,'hmin',1000); ++ md=bamg(md,'metric',A,'hmin',1000,'hmax',20000,'gradation',3,'anisomax',1); ++ """ ++ ++ #process options ++ options=pairoptions(*args) ++# options=deleteduplicates(options,1); ++ ++ #initialize the structures required as input of Bamg ++ bamg_options=OrderedDict() ++ bamg_geometry=bamggeom() ++ bamg_mesh=bamgmesh() ++ ++ # Bamg Geometry parameters {{{ ++ if options.exist('domain'): ++ ++ #Check that file exists ++ domainfile=options.getfieldvalue('domain') ++ if not os.path.exists(domainfile): ++ raise IOError("bamg error message: file '%s' not found" % domainfile) ++ domain=expread(domainfile) ++ ++ #Build geometry ++ count=0 ++ for i,domaini in enumerate(domain): ++ ++ #Check that the domain is closed ++ if (domaini['x'][0]!=domaini['x'][-1] or domaini['y'][0]!=domaini['y'][-1]): ++ raise RuntimeError("bamg error message: all contours provided in ''domain'' should be closed") ++ ++ #Checks that all holes are INSIDE the principle domain outline ++ if i: ++ flags=ContourToNodes(domaini['x'],domaini['y'],domain[0],0) ++ if numpy.any(numpy.logical_not(flags)): ++ raise RuntimeError("bamg error message: All holes should be strictly inside the principal domain") ++ ++ #Add all points to bamg_geometry ++ nods=domaini['nods']-1 #the domain are closed 0=end ++ bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,numpy.hstack((domaini['x'][0:nods].reshape(-1,1),domaini['y'][0:nods].reshape(-1,1),numpy.ones((nods,1)))))) ++ bamg_geometry.Edges =numpy.vstack((bamg_geometry.Edges, numpy.hstack((numpy.arange(count+1,count+nods+1).reshape(-1,1),numpy.hstack((numpy.arange(count+2,count+nods+1),count+1)).reshape(-1,1),1.*numpy.ones((nods,1)))))) ++ if i: ++ bamg_geometry.SubDomains=numpy.vstack((bamg_geometry.SubDomains,[2,count+1,1,1])) ++ ++ #update counter ++ count=+nods ++ ++ #take care of rifts ++ if options.exist('rifts'): ++ ++ #Check that file exists ++ riftfile=options.getfieldvalue('rifts') ++ if not os.path.exists(riftfile): ++ raise IOError("bamg error message: file '%s' not found" % riftfile) ++ rift=expread(riftfile) ++ ++ for i,rifti in enumerate(rift): ++ ++ #detect whether all points of the rift are inside the domain ++ flags=ContourToNodes(rifti['x'],rifti['y'],domain[0],0) ++ if numpy.all(numpy.logical_not(flags)): ++ raise RuntimeError("one rift has all its points outside of the domain outline") ++ ++ elif numpy.any(numpy.logical_not(flags)): ++ raise RuntimeError("bamg.m for rifts is not complete.") ++ #We LOTS of work to do ++ print("Rift tip outside of or on the domain has been detected and is being processed...") ++ """ ++ ++ %check that only one point is outside (for now) ++ if sum(~flags)~=1, ++ error('bamg error message: only one point outside of the domain is supported yet'); ++ end ++ ++ %Move tip outside to the first position ++ if flags(1)==0, ++ %OK, first point is outside (do nothing), ++ elseif (flags(end)==0), ++ rift(i).x=flipud(rift(i).x); ++ rift(i).y=flipud(rift(i).y); ++ else ++ error('bamg error message: only a rift tip can be outside of the domain'); ++ end ++ ++ %Get cordinate of intersection point ++ x1=rift(i).x(1); y1=rift(i).y(1); ++ x2=rift(i).x(2); y2=rift(i).y(2); ++ for j=1:length(domain[0]['x'])-1; ++ if SegIntersect([x1 y1; x2 y2],[domain[0]['x'](j) domain[0]['y'](j); domain[0]['x'](j+1) domain[0]['y'](j+1)]), ++ ++ %Get position of the two nodes of the edge in domain ++ i1=j; ++ i2=mod(j+1,domain[0]['nods']); ++ ++ %rift is crossing edge [i1 i2] of the domain ++ %Get coordinate of intersection point (http://mathworld.wolfram.com/Line-LineIntersection.html) ++ x3=domain[0]['x'](i1); y3=domain[0]['y'](i1); ++ x4=domain[0]['x'](i2); y4=domain[0]['y'](i2); ++ x=det([det([x1 y1; x2 y2]) x1-x2;det([x3 y3; x4 y4]) x3-x4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); ++ y=det([det([x1 y1; x2 y2]) y1-y2;det([x3 y3; x4 y4]) y3-y4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); ++ ++ segdis= sqrt((x4-x3)**2+(y4-y3)**2); ++ tipdis=[sqrt((x-x3)**2+(y-y3)**2) sqrt((x-x4)**2+(y-y4)**2)]; ++ ++ if (min(tipdis)/segdis) < getfieldvalue(options,'toltip',0), ++ disp('moving tip-domain intersection point'); ++ ++ %Get position of the closest point ++ if tipdis(1)>tipdis(2), ++ pos=i2; ++ else ++ pos=i1; ++ end ++ ++ %This point is only in Vertices (number pos). ++ %OK, now we can add our own rift ++ nods=rift(i).nods-1; ++ bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(2:end) rift(i).y(2:end) ones(nods,1)]]; ++ bamg_geometry.Edges=[bamg_geometry.Edges;... ++ pos count+1 (1+i);... ++ [transpose(count+1:count+nods-1) transpose([count+2:count+nods]) (1+i)*ones(nods-1,1)]]; ++ count=count+nods; ++ ++ break; ++ ++ else ++ %Add intersection point to Vertices ++ bamg_geometry.Vertices=[bamg_geometry.Vertices; x y 1]; ++ count=count+1; ++ ++ %Decompose the crossing edge in 2 subedges ++ pos=find(bamg_geometry.Edges(:,1)==i1 & bamg_geometry.Edges(:,2)==i2); ++ if isempty(pos) error('bamg error message: a problem occured...'); end ++ bamg_geometry.Edges=[bamg_geometry.Edges(1:pos-1,:);... ++ bamg_geometry.Edges(pos,1) count bamg_geometry.Edges(pos,3);... ++ count bamg_geometry.Edges(pos,2) bamg_geometry.Edges(pos,3);... ++ bamg_geometry.Edges(pos+1:end,:)]; ++ ++ %OK, now we can add our own rift ++ nods=rift(i).nods-1; ++ bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(2:end) rift(i).y(2:end) ones(nods,1)]]; ++ bamg_geometry.Edges=[bamg_geometry.Edges;... ++ count count+1 2 ;... ++ [transpose(count+1:count+nods-1) transpose([count+2:count+nods]) (1+i)*ones(nods-1,1)]]; ++ count=count+nods; ++ ++ break; ++ end ++ end ++ end ++ """ ++ else: ++ nods=rifti['nods']-1 ++ bamg_geometry.Vertices=numpy.vstack(bamg_geometry.Vertices, numpy.hstack(rifti['x'][:],rifti['y'][:],numpy.ones((nods+1,1)))) ++ bamg_geometry.Edges =numpy.vstack(bamg_geometry.Edges, numpy.hstack(numpy.arange(count+1,count+nods).reshape(-1,1),numpy.arange(count+2,count+nods+1).reshape(-1,1),i*numpy.ones((nods,1)))) ++ count=+nods+1 ++ ++ #Deal with tracks ++ if options.exist('tracks'): ++ ++ #read tracks ++ track=options.getfieldvalue('tracks') ++ if all(isinstance(track,(str,unicode))): ++ A=expread(track) ++ track=numpy.hstack((A.x.reshape(-1,1),A.y.reshape(-1,1))) ++ else: ++ track=float(track) #for some reason, it is of class "single" ++ if numpy.size(track,axis=1)==2: ++ track=numpy.hstack((track,3.*numpy.ones((size(track,axis=0),1)))) ++ ++ #only keep those inside ++ flags=ContourToNodes(track[:,0],track[:,1],domainfile,0) ++ track=track[numpy.nonzero(flags),:] ++ ++ #Add all points to bamg_geometry ++ nods=numpy.size(track,axis=0) ++ bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,track)) ++ bamg_geometry.Edges =numpy.vstack((bamg_geometry.Edges,numpy.hstack((numpy.arange(count+1,count+nods).reshape(-1,1),numpy.arange(count+2,count+nods+1).reshape(-1,1),3.*numpy.ones((nods-1,1)))))) ++ ++ #update counter ++ count+=nods ++ ++ #Deal with vertices that need to be kept by mesher ++ if options.exist('RequiredVertices'): ++ ++ #recover RequiredVertices ++ requiredvertices=float(options.getfieldvalue('RequiredVertices')) #for some reason, it is of class "single" ++ if numpy.size(requiredvertices,axis=1)==2: ++ requiredvertices=numpy.hstack((requiredvertices,4.*numpy.ones((numpy.size(requiredvertices,axis=0),1)))) ++ ++ #only keep those inside ++ flags=ContourToNodes(requiredvertices[:,0],domain[0],0) ++ requiredvertices=requiredvertices[numpy.nonzero(flags),:] ++ ++ #Add all points to bamg_geometry ++ nods=numpy.size(requiredvertices,axis=0) ++ bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,requiredvertices)) ++ ++ #update counter ++ count+=nods ++ ++ #process geom ++ #bamg_geometry=processgeometry(bamg_geometry,options.getfieldvalue('tol',float(nan)),domain[0]) ++ ++ elif isinstance(md.private.bamg,dict) and 'geometry' in md.private.bamg: ++ bamg_geometry=bamggeom(md.private.bamg['geometry']) ++ else: ++ #do nothing... ++ pass ++ #}}} ++ # Bamg Mesh parameters {{{ ++ if options.exist('domain') and md.mesh.numberofvertices and md.mesh.dimension==2: ++ ++ if isinstance(md.private.bamg,dict) and 'mesh' in md.private.bamg: ++ bamg_mesh=bamgmesh(md.private.bamg['mesh']) ++ else: ++ bamg_mesh.Vertices=numpy.hstack((md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),numpy.ones((md.mesh.numberofvertices,1)))) ++ bamg_mesh.Triangles=numpy.hstack((md.mesh.elements,numpy.ones((md.mesh.numberofelements,1)))) ++ ++ if isinstance(md.rifts.riftstruct,dict): ++ raise TypeError("bamg error message: rifts not supported yet. Do meshprocessrift AFTER bamg") ++ #}}} ++ # Bamg Options {{{ ++ bamg_options['Crack']=options.getfieldvalue('Crack',0) ++ bamg_options['anisomax']=options.getfieldvalue('anisomax',10.**30) ++ bamg_options['coeff']=options.getfieldvalue('coeff',1.) ++ bamg_options['cutoff']=options.getfieldvalue('cutoff',10.**-5) ++ bamg_options['err']=options.getfieldvalue('err',numpy.array([[0.01]])) ++ bamg_options['errg']=options.getfieldvalue('errg',0.1) ++ bamg_options['field']=options.getfieldvalue('field',numpy.empty((0,1))) ++ bamg_options['gradation']=options.getfieldvalue('gradation',1.5) ++ bamg_options['Hessiantype']=options.getfieldvalue('Hessiantype',0) ++ bamg_options['hmin']=options.getfieldvalue('hmin',10.**-100) ++ bamg_options['hmax']=options.getfieldvalue('hmax',10.**100) ++ bamg_options['hminVertices']=options.getfieldvalue('hminVertices',numpy.empty((0,1))) ++ bamg_options['hmaxVertices']=options.getfieldvalue('hmaxVertices',numpy.empty((0,1))) ++ bamg_options['hVertices']=options.getfieldvalue('hVertices',numpy.empty((0,1))) ++ bamg_options['KeepVertices']=options.getfieldvalue('KeepVertices',1) ++ bamg_options['MaxCornerAngle']=options.getfieldvalue('MaxCornerAngle',10.) ++ bamg_options['maxnbv']=options.getfieldvalue('maxnbv',10**6) ++ bamg_options['maxsubdiv']=options.getfieldvalue('maxsubdiv',10.) ++ bamg_options['metric']=options.getfieldvalue('metric',numpy.empty((0,1))) ++ bamg_options['Metrictype']=options.getfieldvalue('Metrictype',0) ++ bamg_options['nbjacobi']=options.getfieldvalue('nbjacobi',1) ++ bamg_options['nbsmooth']=options.getfieldvalue('nbsmooth',3) ++ bamg_options['omega']=options.getfieldvalue('omega',1.8) ++ bamg_options['power']=options.getfieldvalue('power',1.) ++ bamg_options['splitcorners']=options.getfieldvalue('splitcorners',1) ++ bamg_options['geometricalmetric']=options.getfieldvalue('geometricalmetric',0) ++ bamg_options['verbose']=options.getfieldvalue('verbose',1) ++ #}}} ++ ++ #call Bamg ++ bamgmesh_out,bamggeom_out=BamgMesher(bamg_mesh.__dict__,bamg_geometry.__dict__,bamg_options) ++ ++ # plug results onto model ++ md.private.bamg=OrderedDict() ++ md.private.bamg['mesh']=bamgmesh(bamgmesh_out) ++ md.private.bamg['geometry']=bamggeom(bamggeom_out) ++ md.mesh.x=bamgmesh_out['Vertices'][:,0].copy() ++ md.mesh.y=bamgmesh_out['Vertices'][:,1].copy() ++ md.mesh.elements=bamgmesh_out['Triangles'][:,0:3].copy() ++ md.mesh.edges=bamgmesh_out['IssmEdges'].copy() ++ md.mesh.segments=bamgmesh_out['IssmSegments'][:,0:3].copy() ++ md.mesh.segmentmarkers=bamgmesh_out['IssmSegments'][:,3].copy() ++ ++ #Fill in rest of fields: ++ md.mesh.dimension=2 ++ md.mesh.numberofelements=numpy.size(md.mesh.elements,axis=0) ++ md.mesh.numberofvertices=numpy.size(md.mesh.x); ++ md.mesh.numberofedges=numpy.size(md.mesh.edges,axis=0) ++ md.mesh.z=numpy.zeros(md.mesh.numberofvertices) ++ md.mesh.vertexonbed=numpy.ones(md.mesh.numberofvertices) ++ md.mask.vertexonwater=numpy.zeros(md.mesh.numberofvertices) ++ md.mesh.vertexonsurface=numpy.ones(md.mesh.numberofvertices) ++ md.mesh.elementonbed=numpy.ones(md.mesh.numberofelements) ++ md.mesh.elementonsurface=numpy.ones(md.mesh.numberofelements) ++ md.mesh.vertexonboundary=numpy.zeros(md.mesh.numberofvertices) ++ md.mesh.vertexonboundary[md.mesh.segments[:,0:2].astype(int)-1]=1 ++ md.mesh.elementconnectivity=md.private.bamg['mesh'].ElementConnectivity ++ md.mesh.elementconnectivity[numpy.nonzero(numpy.isnan(md.mesh.elementconnectivity))]=0 ++ ++ #Check for orphan ++ if numpy.any(numpy.logical_not(numpy.in1d(numpy.arange(1,md.mesh.numberofvertices+1),md.mesh.elements.flat))): ++ raise RuntimeError("Output mesh has orphans. Decrease MaxCornerAngle to prevent outside points (ex: 0.01)") ++ ++ return md ++ ++def processgeometry(geom,tol,outline): # {{{ ++ ++ raise RuntimeError("bamg.m/processgeometry is not complete.") ++ #Deal with edges ++ print("Checking Edge crossing...") ++ i=0 ++ while (ii) ++ geom.Edges[posedges]=geom.Edges[posedges]-1 ++ ++ #update counter ++ i-=1 ++ ++ if num: ++ print("WARNING: %d points outside the domain outline have been removed" % num) ++ ++ """ ++ %Check point spacing ++ if ~isnan(tol), ++ disp('Checking point spacing...'); ++ i=0; ++ while (ij); ++ geom.Edges(posedges)=geom.Edges(posedges)-1; ++ ++ %update counter ++ j=j-1; ++ ++ end ++ end ++ end ++ end ++ %remove empty edges ++ geom.Edges(find(geom.Edges(:,1)==geom.Edges(:,2)),:)=[]; ++ """ ++ return geom ++# }}} ++ +Index: ../trunk-jpl/src/m/mesh/bamg.m +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.m (revision 13435) ++++ ../trunk-jpl/src/m/mesh/bamg.m (revision 13436) +@@ -54,15 +54,15 @@ + + %initialize the structures required as input of Bamg + bamg_options=struct(); +-bamg_geometry=bamggeom; +-bamg_mesh=bamgmesh; ++bamg_geometry=bamggeom(); ++bamg_mesh=bamgmesh(); + + % Bamg Geometry parameters {{{ + if exist(options,'domain'), + + %Check that file exists + domainfile=getfieldvalue(options,'domain'); +- if ~exist(domainfile,'file') error(['bamg error message: file ' domainfile ' not found ']); end ++ if ~exist(domainfile,'file') error(['bamg error message: file ' domainfile ' not found']); end + domain=expread(domainfile); + + %Build geometry +@@ -78,14 +78,14 @@ + if i>1, + flags=ContourToNodes(domain(i).x,domain(i).y,domain(1),0); + if any(~flags), +- error('bamg error message: All holes should be stricly inside the principal domain'); ++ error('bamg error message: All holes should be strictly inside the principal domain'); + end + end + + %Add all points to bamg_geometry + nods=domain(i).nods-1; %the domain are closed 1=end; + bamg_geometry.Vertices=[bamg_geometry.Vertices; [domain(i).x(1:nods) domain(i).y(1:nods) ones(nods,1)]]; +- bamg_geometry.Edges =[bamg_geometry.Edges; [transpose(count+1:count+nods) transpose([count+2:count+nods count+1]) 1*ones(nods,1)]]; ++ bamg_geometry.Edges =[bamg_geometry.Edges; [transpose(count+1:count+nods) transpose([count+2:count+nods count+1]) 1.*ones(nods,1)]]; + if i>1, bamg_geometry.SubDomains=[bamg_geometry.SubDomains; 2 count+1 1 1]; end + + %update counter +@@ -104,16 +104,16 @@ + + for i=1:length(rift), + +- %detect wether all points of the rift are inside the domain ++ %detect whether all points of the rift are inside the domain + flags=ContourToNodes(rift(i).x,rift(i).y,domain(1),0); + if ~flags, +- error('one Rift has all his points outside of the domain outline'), ++ error('one rift has all its points outside of the domain outline'), + + elseif any(~flags), + %We LOTS of work to do + disp('Rift tip outside of or on the domain has been detected and is being processed...'); + +- %check that only one point is outsie (for now) ++ %check that only one point is outside (for now) + if sum(~flags)~=1, + error('bamg error message: only one point outside of the domain is supported yet'); + end +@@ -159,7 +159,7 @@ + end + + %This point is only in Vertices (number pos). +- %OK, no we can add our own rift ++ %OK, now we can add our own rift + nods=rift(i).nods-1; + bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(2:end) rift(i).y(2:end) ones(nods,1)]]; + bamg_geometry.Edges=[bamg_geometry.Edges;... +@@ -182,7 +182,7 @@ + count bamg_geometry.Edges(pos,2) bamg_geometry.Edges(pos,3);... + bamg_geometry.Edges(pos+1:end,:)]; + +- %OK, no we can add our own rift ++ %OK, now we can add our own rift + nods=rift(i).nods-1; + bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(2:end) rift(i).y(2:end) ones(nods,1)]]; + bamg_geometry.Edges=[bamg_geometry.Edges;... +@@ -209,12 +209,12 @@ + %read tracks + track=getfieldvalue(options,'tracks'); + if all(ischar(track)), +- A=expread(track); ++ A=expread(track); + track=[A.x A.y]; + else + track=double(track); %for some reason, it is of class "single" + end +- if(size(track,2)==2), track=[track 3*ones(size(track,1),1)]; end ++ if(size(track,2)==2), track=[track 3.*ones(size(track,1),1)]; end + + %only keep those inside + flags=ContourToNodes(track(:,1),track(:,2),domainfile,0); +@@ -223,7 +223,7 @@ + %Add all points to bamg_geometry + nods=size(track,1); + bamg_geometry.Vertices=[bamg_geometry.Vertices; track]; +- bamg_geometry.Edges=[bamg_geometry.Edges; [transpose(count+1:count+nods-1) transpose([count+2:count+nods]) 3*ones(nods-1,1)]]; ++ bamg_geometry.Edges=[bamg_geometry.Edges; [transpose(count+1:count+nods-1) transpose([count+2:count+nods]) 3.*ones(nods-1,1)]]; + + %update counter + count=count+nods; +@@ -234,7 +234,7 @@ + + %recover RequiredVertices + requiredvertices=double(getfieldvalue(options,'RequiredVertices')); %for some reason, it is of class "single" +- if(size(requiredvertices,2)==2), requiredvertices=[requiredvertices 4*ones(size(requiredvertices,1),1)]; end ++ if(size(requiredvertices,2)==2), requiredvertices=[requiredvertices 4.*ones(size(requiredvertices,1),1)]; end + + %only keep those inside + flags=ContourToNodes(requiredvertices(:,1),requiredvertices(:,2),domain(1),0); +@@ -275,29 +275,29 @@ + %}}} + % Bamg Options {{{ + bamg_options.Crack=getfieldvalue(options,'Crack',0); +-bamg_options.anisomax=getfieldvalue(options,'anisomax',10^30); +-bamg_options.coeff=getfieldvalue(options,'coeff',1); +-bamg_options.cutoff=getfieldvalue(options,'cutoff',10^-5); ++bamg_options.anisomax=getfieldvalue(options,'anisomax',10.^30); ++bamg_options.coeff=getfieldvalue(options,'coeff',1.); ++bamg_options.cutoff=getfieldvalue(options,'cutoff',10.^-5); + bamg_options.err=getfieldvalue(options,'err',0.01); + bamg_options.errg=getfieldvalue(options,'errg',0.1); + bamg_options.field=getfieldvalue(options,'field',[]); + bamg_options.gradation=getfieldvalue(options,'gradation',1.5); + bamg_options.Hessiantype=getfieldvalue(options,'Hessiantype',0); +-bamg_options.hmin=getfieldvalue(options,'hmin',10^-100); +-bamg_options.hmax=getfieldvalue(options,'hmax',10^100); ++bamg_options.hmin=getfieldvalue(options,'hmin',10.^-100); ++bamg_options.hmax=getfieldvalue(options,'hmax',10.^100); + bamg_options.hminVertices=getfieldvalue(options,'hminVertices',[]); + bamg_options.hmaxVertices=getfieldvalue(options,'hmaxVertices',[]); + bamg_options.hVertices=getfieldvalue(options,'hVertices',[]); + bamg_options.KeepVertices=getfieldvalue(options,'KeepVertices',1); +-bamg_options.MaxCornerAngle=getfieldvalue(options,'MaxCornerAngle',10); ++bamg_options.MaxCornerAngle=getfieldvalue(options,'MaxCornerAngle',10.); + bamg_options.maxnbv=getfieldvalue(options,'maxnbv',10^6); +-bamg_options.maxsubdiv=getfieldvalue(options,'maxsubdiv',10); ++bamg_options.maxsubdiv=getfieldvalue(options,'maxsubdiv',10.); + bamg_options.metric=getfieldvalue(options,'metric',[]); + bamg_options.Metrictype=getfieldvalue(options,'Metrictype',0); + bamg_options.nbjacobi=getfieldvalue(options,'nbjacobi',1); + bamg_options.nbsmooth=getfieldvalue(options,'nbsmooth',3); + bamg_options.omega=getfieldvalue(options,'omega',1.8); +-bamg_options.power=getfieldvalue(options,'power',1); ++bamg_options.power=getfieldvalue(options,'power',1.); + bamg_options.splitcorners=getfieldvalue(options,'splitcorners',1); + bamg_options.geometricalmetric=getfieldvalue(options,'geometricalmetric',0); + bamg_options.verbose=getfieldvalue(options,'verbose',1); +@@ -333,8 +333,6 @@ + md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0; + + %Check for orphan +-reshape(md.mesh.elements,3*md.mesh.numberofelements,1); +-(~ismember(1:md.mesh.numberofvertices,sort(unique(reshape(md.mesh.elements,3*md.mesh.numberofelements,1))))); + if any(~ismember(1:md.mesh.numberofvertices,sort(unique(reshape(md.mesh.elements,3*md.mesh.numberofelements,1))))) + error('Output mesh has orphans. Decrease MaxCornerAngle to prevent outside points (ex: 0.01)'); + end +Index: ../trunk-jpl/src/m/classes/bamggeom.py +=================================================================== +--- ../trunk-jpl/src/m/classes/bamggeom.py (revision 13435) ++++ ../trunk-jpl/src/m/classes/bamggeom.py (revision 13436) +@@ -1,3 +1,5 @@ ++import numpy ++ + class bamggeom(object): + """ + BAMGGEOM class definition +@@ -7,14 +9,14 @@ + """ + + def __init__(self,*args): # {{{ +- self.Vertices=[] +- self.Edges=[] +- self.TangentAtEdges=[] +- self.Corners=[] +- self.RequiredVertices=[] +- self.RequiredEdges=[] +- self.CrackedEdges=[] +- self.SubDomains=[] ++ self.Vertices=numpy.empty((0,3)) ++ self.Edges=numpy.empty((0,3)) ++ self.TangentAtEdges=numpy.empty((0,0)) ++ self.Corners=numpy.empty((0,1)) ++ self.RequiredVertices=numpy.empty((0,1)) ++ self.RequiredEdges=numpy.empty((0,1)) ++ self.CrackedEdges=numpy.empty((0,0)) ++ self.SubDomains=numpy.empty((0,4)) + + if not len(args): + # if no input arguments, create a default object +Index: ../trunk-jpl/src/m/classes/bamgmesh.py +=================================================================== +--- ../trunk-jpl/src/m/classes/bamgmesh.py (revision 13435) ++++ ../trunk-jpl/src/m/classes/bamgmesh.py (revision 13436) +@@ -1,3 +1,5 @@ ++import numpy ++ + class bamgmesh(object): + """ + BAMGMESH class definition +@@ -7,22 +9,22 @@ + """ + + def __init__(self,*args): # {{{ +- self.Vertices=[] +- self.Edges=[] +- self.Triangles=[] +- self.Quadrilaterals=[] +- self.IssmEdges=[] +- self.IssmSegments=[] +- self.VerticesOnGeomVertex=[] +- self.VerticesOnGeomEdge=[] +- self.EdgesOnGeomEdge=[] +- self.SubDomains=[] +- self.SubDomainsFromGeom=[] +- self.ElementConnectivity=[] +- self.NodalConnectivity=[] +- self.NodalElementConnectivity=[] +- self.CrackedVertices=[] +- self.CrackedEdges=[] ++ self.Vertices=numpy.empty((0,3)) ++ self.Edges=numpy.empty((0,3)) ++ self.Triangles=numpy.empty((0,0)) ++ self.Quadrilaterals=numpy.empty((0,0)) ++ self.IssmEdges=numpy.empty((0,0)) ++ self.IssmSegments=numpy.empty((0,0)) ++ self.VerticesOnGeomVertex=numpy.empty((0,0)) ++ self.VerticesOnGeomEdge=numpy.empty((0,0)) ++ self.EdgesOnGeomEdge=numpy.empty((0,0)) ++ self.SubDomains=numpy.empty((0,4)) ++ self.SubDomainsFromGeom=numpy.empty((0,0)) ++ self.ElementConnectivity=numpy.empty((0,0)) ++ self.NodalConnectivity=numpy.empty((0,0)) ++ self.NodalElementConnectivity=numpy.empty((0,0)) ++ self.CrackedVertices=numpy.empty((0,0)) ++ self.CrackedEdges=numpy.empty((0,0)) + + if not len(args): + # if no input arguments, create a default object +Index: ../trunk-jpl/src/m/miscellaneous/MatlabFuncs.py +=================================================================== +--- ../trunk-jpl/src/m/miscellaneous/MatlabFuncs.py (revision 13435) ++++ ../trunk-jpl/src/m/miscellaneous/MatlabFuncs.py (revision 13436) +@@ -52,9 +52,24 @@ + b=[item in s for item in a] + + else: +- b=numpy.empty_like(a) +- for i,item in enumerate(a.flat): +- b.flat[i]=item in s ++ if not isinstance(s,numpy.ndarray): ++ b=numpy.empty_like(a) ++ for i,item in enumerate(a.flat): ++ b.flat[i]=item in s ++ else: ++ b=numpy.in1d(a.flat,s.flat).reshape(a.shape) + + return b + ++def det(a): ++ import numpy ++ ++ if a.shape==(1,): ++ return a[0] ++ elif a.shape==(1,1): ++ return a[0,0] ++ elif a.shape==(2,2): ++ return a[0,0]*a[1,1]-a[0,1]*a[1,0] ++ else: ++ raise TypeError("MatlabFunc.det only implemented for shape (2, 2), not for shape %s." % str(a.shape)) ++ Index: /issm/oecreview/Archive/13393-13976/ISSM-13436-13437.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13436-13437.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13436-13437.diff (revision 13980) @@ -0,0 +1,60 @@ +Index: ../trunk-jpl/test/NightlyRun/test119.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test119.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test119.py (revision 13437) +@@ -0,0 +1,30 @@ ++import numpy ++import time ++from model import * ++from bamg import * ++from MatlabFuncs import * ++ ++#Simple mesh ++md=bamg(model(),'domain','../Exp/Square.exp','hmax',100000.) ++x1=md.mesh.x ++y1=md.mesh.y ++ ++#hVertices ++md=bamg(model(),'domain','../Exp/Square.exp','hmax',300000.,'hVertices',numpy.array([10000.,100000.,400000.,100000.]).reshape(-1,1)) ++x2=md.mesh.x ++y2=md.mesh.y ++ ++#big mesh ++t0=time.time() ++md=bamg(model(),'domain','../Exp/Square.exp','hmax',3000.) ++nbelements=md.mesh.numberofelements ++elapsedtime=time.time()-t0 ++ ++#Fields and tolerances to track changes ++field_names =['x1','y1','x2','y2','nbelements','elapsed time'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,0.5] ++field_values=[\ ++ x1, y1,\ ++ x2, y2,\ ++ nbelements,elapsedtime,\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test119.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test119.m (revision 13436) ++++ ../trunk-jpl/test/NightlyRun/test119.m (revision 13437) +@@ -1,17 +1,17 @@ + + %Simple mesh +-md=bamg(model,'domain','../Exp/Square.exp','hmax',100000); ++md=bamg(model,'domain','../Exp/Square.exp','hmax',100000.); + x1=md.mesh.x; + y1=md.mesh.y; + + %hVertices +-md=bamg(model,'domain','../Exp/Square.exp','hmax',300000,'hvertices',[10000 100000 400000 100000]'); ++md=bamg(model,'domain','../Exp/Square.exp','hmax',300000.,'hVertices',[10000. 100000. 400000. 100000.]'); + x2=md.mesh.x; + y2=md.mesh.y; + + %big mesh + t0=clock; +-md=bamg(model,'domain','../Exp/Square.exp','hmax',3000); ++md=bamg(model,'domain','../Exp/Square.exp','hmax',3000.); + nbelements=md.mesh.numberofelements; + elapsedtime=etime(clock,t0); + Index: /issm/oecreview/Archive/13393-13976/ISSM-13437-13438.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13437-13438.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13437-13438.diff (revision 13980) @@ -0,0 +1,442 @@ +Index: ../trunk-jpl/test/NightlyRun/runme.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/runme.m (revision 13437) ++++ ../trunk-jpl/test/NightlyRun/runme.m (revision 13438) +@@ -105,7 +105,7 @@ + elseif strcmpi(benchmark,'mesh'), + test_ids=intersect(test_ids,[1401:1499]); + elseif strcmpi(benchmark,'adolc'), +- test_ids=intersect(test_ids,[3001:3010]); ++ test_ids=intersect(test_ids,[3001:3020]); + elseif strcmpi(benchmark,'validation'), + test_ids=intersect(test_ids,[1001:1999]); + elseif strcmpi(benchmark,'tranforcing'), +Index: ../trunk-jpl/test/NightlyRun/ad.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/ad.m (revision 13437) ++++ ../trunk-jpl/test/NightlyRun/ad.m (revision 13438) +@@ -3,13 +3,11 @@ + md=parameterize(md,'../Par/SquareShelfConstrained.par'); + md=setflowequation(md,'macayeal','all'); + md.cluster=generic('name',oshostname(),'np',3); +-md.diagnostic.requested_outputs=StressTensorEnum; ++ + md.autodiff.isautodiff=true; +-md.verbose=verbose('autodiff',true); +- ++index=1; + md.autodiff.independents={... +- independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',1), ... +- independent('name','Surface','type','vertex','nods',md.mesh.numberofvertices)... ++ independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',index) + }; + + md.autodiff.dependents={... +@@ -17,5 +15,4 @@ + }; + md.autodiff.driver='fos_forward'; + +-md=solve(md,PrognosticSolutionEnum); +-%md=solve(md,TransientSolutionEnum); ++md=solve(md,TransientSolutionEnum); +Index: ../trunk-jpl/test/NightlyRun/test3015.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3015.m (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3015.m (revision 13438) +@@ -0,0 +1,77 @@ ++%This test runs test3005 with autodiff on, and checks that ++%the value of the scalar forward difference match a step-wise differential ++ ++%First configure ++md=triangle(model,'../Exp/Square.exp',50000); ++md=setmask(md,'all',''); ++md=parameterize(md,'../Par/SquareShelfConstrained.par'); ++md=setflowequation(md,'macayeal','all'); ++md.cluster=generic('name',oshostname(),'np',3); ++md.prognostic.requested_outputs=IceVolumeEnum; ++md.verbose=verbose('autodiff',true); ++ ++%setup autodiff parameters ++index=1; %this is the scalar component we are checking against ++md.autodiff.independents={... ++ independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',index) ++ }; ++ ++md.autodiff.dependents={... ++ dependent('name','IceVolume','type','scalar')... ++ }; ++md.autodiff.driver='fos_forward'; ++ ++%parameters for the step-wise devivative ++delta=.001; ++h1=md.geometry.thickness(index); ++h0=h1*(1-delta); ++h2=h1*(1+delta); ++deltaH=(h2-h0); ++ ++%save model: ++md2=md; ++ ++%evaluate derivative by forward and backward stepping ++%forward ++md=md2; ++md.autodiff.isautodiff=false; ++md.geometry.thickness(index)=h0; ++md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; ++md.geometry.surface=md.geometry.bed+md.geometry.thickness; ++md=SetIceShelfBC(md); ++ ++md=solve(md,PrognosticSolutionEnum); ++V0=md.results.PrognosticSolution.IceVolume; ++ ++%backward ++md=md2; ++md.autodiff.isautodiff=false; ++md.geometry.thickness(index)=h2; ++md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; ++md.geometry.surface=md.geometry.bed+md.geometry.thickness; ++md=SetIceShelfBC(md); ++ ++md=solve(md,PrognosticSolutionEnum); ++V2=md.results.PrognosticSolution.IceVolume; ++ ++%compute resulting derivative ++dVdh_an=(V2-V0)/deltaH; ++ ++%evaluate derivative using ADOLC ++md=md2; ++md.autodiff.isautodiff=true; ++md.geometry.thickness(index)=h1; ++md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness; ++md.geometry.surface=md.geometry.bed+md.geometry.thickness; ++md=SetIceShelfBC(md); ++ ++md=solve(md,PrognosticSolutionEnum); ++%retrieve directly ++dVdh_ad=md.results.PrognosticSolution.AutodiffJacobian; ++ ++disp(sprintf('dV/dh: analytical: %16.16g\n using adolc: %16.16g\n',dVdh_an,dVdh_ad)); ++ ++%Fields and tolerances to track changes ++field_names ={'dV/dh-dV/dh0'}; ++field_tolerances={1e-1}; ++field_values={dVdh_ad-dVdh_an}; +Index: ../trunk-jpl/test/Archives/Archive3015.nc +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive3015.nc +=================================================================== +--- ../trunk-jpl/test/Archives/Archive3015.nc (revision 13437) ++++ ../trunk-jpl/test/Archives/Archive3015.nc (revision 13438) + +Property changes on: ../trunk-jpl/test/Archives/Archive3015.nc +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/c/solutions/prognostic_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/prognostic_core.cpp (revision 13437) ++++ ../trunk-jpl/src/c/solutions/prognostic_core.cpp (revision 13438) +@@ -17,6 +17,8 @@ + bool save_results; + bool issmbgradients,ispdd,isdelta18o; + int solution_type; ++ int *requested_outputs = NULL; ++ int numoutputs=0; + + /*activate formulation: */ + femmodel->SetCurrentConfiguration(PrognosticAnalysisEnum); +@@ -27,6 +29,8 @@ + femmodel->parameters->FindParam(&ispdd,SurfaceforcingsIspddEnum); + femmodel->parameters->FindParam(&isdelta18o,SurfaceforcingsIsdelta18oEnum); + femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); ++ femmodel->parameters->FindParam(&numoutputs,PrognosticNumRequestedOutputsEnum); ++ if(numoutputs) femmodel->parameters->FindParam(&requested_outputs,&numoutputs,PrognosticRequestedOutputsEnum); + + if(issmbgradients){ + _printf_(VerboseSolution()," call smb gradients module\n"); +@@ -46,8 +50,11 @@ + if(save_results){ + if(VerboseSolution()) _pprintLine_(" saving results"); + InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,ThicknessEnum); ++ RequestedOutputsx(femmodel->results,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,requested_outputs,numoutputs); + } + ++ if(solution_type==PrognosticSolutionEnum)RequestedDependentsx(femmodel->results,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + +- if(solution_type==PrognosticSolutionEnum)RequestedDependentsx(femmodel->results,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); ++ /*Free ressources:*/ ++ xDelete(requested_outputs); + } +Index: ../trunk-jpl/src/c/solutions/diagnostic_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/diagnostic_core.cpp (revision 13437) ++++ ../trunk-jpl/src/c/solutions/diagnostic_core.cpp (revision 13438) +@@ -104,6 +104,8 @@ + if(dim==3) InputToResultx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,VzEnum); + RequestedOutputsx(femmodel->results,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,requested_outputs,numoutputs); + } ++ ++ if(solution_type==DiagnosticSolutionEnum)RequestedDependentsx(femmodel->results,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + + /*Free ressources:*/ + xDelete(requested_outputs); +Index: ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13437) ++++ ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13438) +@@ -151,6 +151,8 @@ + PrognosticSpcthicknessEnum, + PrognosticStabilizationEnum, + PrognosticVertexPairingEnum, ++ PrognosticNumRequestedOutputsEnum, ++ PrognosticRequestedOutputsEnum, + QmuIsdakotaEnum, + QmuMassFluxSegmentsEnum, + QmuNumberofpartitionsEnum, +Index: ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13437) ++++ ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13438) +@@ -160,6 +160,8 @@ + else if (strcmp(name,"PrognosticSpcthickness")==0) return PrognosticSpcthicknessEnum; + else if (strcmp(name,"PrognosticStabilization")==0) return PrognosticStabilizationEnum; + else if (strcmp(name,"PrognosticVertexPairing")==0) return PrognosticVertexPairingEnum; ++ else if (strcmp(name,"PrognosticNumRequestedOutputs")==0) return PrognosticNumRequestedOutputsEnum; ++ else if (strcmp(name,"PrognosticRequestedOutputs")==0) return PrognosticRequestedOutputsEnum; + else if (strcmp(name,"QmuIsdakota")==0) return QmuIsdakotaEnum; + else if (strcmp(name,"QmuMassFluxSegments")==0) return QmuMassFluxSegmentsEnum; + else if (strcmp(name,"QmuNumberofpartitions")==0) return QmuNumberofpartitionsEnum; +@@ -258,12 +260,12 @@ + else if (strcmp(name,"TransientSolution")==0) return TransientSolutionEnum; + else if (strcmp(name,"Approximation")==0) return ApproximationEnum; + else if (strcmp(name,"NoneApproximation")==0) return NoneApproximationEnum; +- else if (strcmp(name,"HutterApproximation")==0) return HutterApproximationEnum; +- else if (strcmp(name,"MacAyealApproximation")==0) return MacAyealApproximationEnum; + else stage=3; + } + if(stage==3){ +- if (strcmp(name,"MacAyealPattynApproximation")==0) return MacAyealPattynApproximationEnum; ++ if (strcmp(name,"HutterApproximation")==0) return HutterApproximationEnum; ++ else if (strcmp(name,"MacAyealApproximation")==0) return MacAyealApproximationEnum; ++ else if (strcmp(name,"MacAyealPattynApproximation")==0) return MacAyealPattynApproximationEnum; + else if (strcmp(name,"MacAyealStokesApproximation")==0) return MacAyealStokesApproximationEnum; + else if (strcmp(name,"L1L2Approximation")==0) return L1L2ApproximationEnum; + else if (strcmp(name,"PattynApproximation")==0) return PattynApproximationEnum; +@@ -381,12 +383,12 @@ + else if (strcmp(name,"TemperatureOld")==0) return TemperatureOldEnum; + else if (strcmp(name,"TemperaturePicard")==0) return TemperaturePicardEnum; + else if (strcmp(name,"TemperatureSurface")==0) return TemperatureSurfaceEnum; +- else if (strcmp(name,"TemperatureBasal")==0) return TemperatureBasalEnum; +- else if (strcmp(name,"ThicknessAbsMisfit")==0) return ThicknessAbsMisfitEnum; + else stage=4; + } + if(stage==4){ +- if (strcmp(name,"Type")==0) return TypeEnum; ++ if (strcmp(name,"TemperatureBasal")==0) return TemperatureBasalEnum; ++ else if (strcmp(name,"ThicknessAbsMisfit")==0) return ThicknessAbsMisfitEnum; ++ else if (strcmp(name,"Type")==0) return TypeEnum; + else if (strcmp(name,"Vel")==0) return VelEnum; + else if (strcmp(name,"Velocity")==0) return VelocityEnum; + else if (strcmp(name,"VxAverage")==0) return VxAverageEnum; +@@ -504,12 +506,12 @@ + else if (strcmp(name,"Option")==0) return OptionEnum; + else if (strcmp(name,"GenericOption")==0) return GenericOptionEnum; + else if (strcmp(name,"OptionCell")==0) return OptionCellEnum; +- else if (strcmp(name,"OptionChar")==0) return OptionCharEnum; +- else if (strcmp(name,"OptionStruct")==0) return OptionStructEnum; + else stage=5; + } + if(stage==5){ +- if (strcmp(name,"OptionDouble")==0) return OptionDoubleEnum; ++ if (strcmp(name,"OptionChar")==0) return OptionCharEnum; ++ else if (strcmp(name,"OptionStruct")==0) return OptionStructEnum; ++ else if (strcmp(name,"OptionDouble")==0) return OptionDoubleEnum; + else if (strcmp(name,"OptionLogical")==0) return OptionLogicalEnum; + else if (strcmp(name,"Paterson")==0) return PatersonEnum; + else if (strcmp(name,"Arrhenius")==0) return ArrheniusEnum; +Index: ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13437) ++++ ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13438) +@@ -156,6 +156,8 @@ + case PrognosticSpcthicknessEnum : return "PrognosticSpcthickness"; + case PrognosticStabilizationEnum : return "PrognosticStabilization"; + case PrognosticVertexPairingEnum : return "PrognosticVertexPairing"; ++ case PrognosticNumRequestedOutputsEnum : return "PrognosticNumRequestedOutputs"; ++ case PrognosticRequestedOutputsEnum : return "PrognosticRequestedOutputs"; + case QmuIsdakotaEnum : return "QmuIsdakota"; + case QmuMassFluxSegmentsEnum : return "QmuMassFluxSegments"; + case QmuNumberofpartitionsEnum : return "QmuNumberofpartitions"; +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 13437) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 13438) +@@ -126,15 +126,22 @@ + parameters->AddObject(new IntParam(DiagnosticNumRequestedOutputsEnum,numoutputs)); + if(numoutputs)parameters->AddObject(new IntVecParam(DiagnosticRequestedOutputsEnum,requestedoutputs,numoutputs)); + iomodel->DeleteData(requestedoutputs,DiagnosticRequestedOutputsEnum); ++ + iomodel->FetchData(&requestedoutputs,&numoutputs,NULL,TransientRequestedOutputsEnum); + parameters->AddObject(new IntParam(TransientNumRequestedOutputsEnum,numoutputs)); + if(numoutputs)parameters->AddObject(new IntVecParam(TransientRequestedOutputsEnum,requestedoutputs,numoutputs)); + iomodel->DeleteData(requestedoutputs,TransientRequestedOutputsEnum); ++ + iomodel->FetchData(&requestedoutputs,&numoutputs,NULL,SteadystateRequestedOutputsEnum); + parameters->AddObject(new IntParam(SteadystateNumRequestedOutputsEnum,numoutputs)); + if(numoutputs)parameters->AddObject(new IntVecParam(SteadystateRequestedOutputsEnum,requestedoutputs,numoutputs)); + iomodel->DeleteData(requestedoutputs,SteadystateRequestedOutputsEnum); + ++ iomodel->FetchData(&requestedoutputs,&numoutputs,NULL,PrognosticRequestedOutputsEnum); ++ parameters->AddObject(new IntParam(PrognosticNumRequestedOutputsEnum,numoutputs)); ++ if(numoutputs)parameters->AddObject(new IntVecParam(PrognosticRequestedOutputsEnum,requestedoutputs,numoutputs)); ++ iomodel->DeleteData(requestedoutputs,PrognosticRequestedOutputsEnum); ++ + /*Before returning, create parameters in case we are running Qmu or control types runs: */ + #ifdef _HAVE_CONTROL_ + CreateParametersControl(¶meters,iomodel,solution_type,analysis_type); +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13437) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13438) +@@ -91,7 +91,7 @@ + + xDelete(this->data); + xDelete(this->independents); +- delete this->independent_objects; ++ if(this->independent_objects)delete this->independent_objects; + xDelete(this->my_elements); + xDelete(this->my_nodes); + xDelete(this->my_vertices); +@@ -251,7 +251,9 @@ + _error_("Cannot carry out AD mode computations without support of ADOLC compiled in!"); + #endif + } ++ else this->independent_objects=NULL; + ++ + } + /*}}}*/ + /*FUNCTION IoModel::DeleteData(int num,...){{{*/ +Index: ../trunk-jpl/src/m/classes/prognostic.m +=================================================================== +--- ../trunk-jpl/src/m/classes/prognostic.m (revision 13437) ++++ ../trunk-jpl/src/m/classes/prognostic.m (revision 13438) +@@ -11,6 +11,7 @@ + stabilization = 0; + vertex_pairing = NaN; + penalty_factor = 0; ++ requested_outputs = NaN; + end + methods + function obj = prognostic(varargin) % {{{ +@@ -44,7 +45,11 @@ + md = checkfield(md,'prognostic.hydrostatic_adjustment','values',{'Absolute' 'Incremental'}); + md = checkfield(md,'prognostic.stabilization','values',[0 1 2 3]); + md = checkfield(md,'prognostic.min_thickness','>',0); ++ if ~isempty(md.prognostic.requested_outputs), ++ md = checkfield(md,'prognostic.requested_outputs','size',[NaN 1]); ++ end + ++ + end % }}} + function disp(obj) % {{{ + disp(sprintf(' Prognostic solution parameters:')); +@@ -56,6 +61,7 @@ + disp(sprintf('\n %s','Penalty options:')); + fielddisplay(obj,'penalty_factor','offset used by penalties: penalty = Kmax*10^offset'); + fielddisplay(obj,'vertex_pairing','pairs of vertices that are penalized'); ++ fielddisplay(obj,'requested_outputs','additional outputs requested'); + + end % }}} + function marshall(obj,fid) % {{{ +@@ -65,6 +71,7 @@ + WriteData(fid,'object',obj,'fieldname','stabilization','format','Integer'); + WriteData(fid,'object',obj,'fieldname','vertex_pairing','format','DoubleMat','mattype',3); + WriteData(fid,'object',obj,'fieldname','penalty_factor','format','Double'); ++ WriteData(fid,'object',obj,'fieldname','requested_outputs','format','DoubleMat','mattype',3); + end % }}} + end + end +Index: ../trunk-jpl/src/m/enum/PrognosticNumRequestedOutputsEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/PrognosticNumRequestedOutputsEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/PrognosticNumRequestedOutputsEnum.m (revision 13438) +@@ -0,0 +1,11 @@ ++function macro=PrognosticNumRequestedOutputsEnum() ++%PROGNOSTICNUMREQUESTEDOUTPUTSENUM - Enum of PrognosticNumRequestedOutputs ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=PrognosticNumRequestedOutputsEnum() ++ ++macro=StringToEnum('PrognosticNumRequestedOutputs'); +Index: ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13437) ++++ ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13438) +@@ -8,4 +8,4 @@ + % Usage: + % macro=MaximumNumberOfEnums() + +-macro=484; ++macro=486; +Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py +=================================================================== +--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13437) ++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13438) +@@ -1408,6 +1408,26 @@ + + return StringToEnum('PrognosticVertexPairing')[0] + ++def PrognosticNumRequestedOutputsEnum(): ++ """ ++ PROGNOSTICNUMREQUESTEDOUTPUTSENUM - Enum of PrognosticNumRequestedOutputs ++ ++ Usage: ++ macro=PrognosticNumRequestedOutputsEnum() ++ """ ++ ++ return StringToEnum('PrognosticNumRequestedOutputs')[0] ++ ++def PrognosticRequestedOutputsEnum(): ++ """ ++ PROGNOSTICREQUESTEDOUTPUTSENUM - Enum of PrognosticRequestedOutputs ++ ++ Usage: ++ macro=PrognosticRequestedOutputsEnum() ++ """ ++ ++ return StringToEnum('PrognosticRequestedOutputs')[0] ++ + def QmuIsdakotaEnum(): + """ + QMUISDAKOTAENUM - Enum of QmuIsdakota +@@ -4856,5 +4876,5 @@ + macro=MaximumNumberOfEnums() + """ + +- return 484 ++ return 486 + +Index: ../trunk-jpl/src/m/enum/PrognosticRequestedOutputsEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/PrognosticRequestedOutputsEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/PrognosticRequestedOutputsEnum.m (revision 13438) +@@ -0,0 +1,11 @@ ++function macro=PrognosticRequestedOutputsEnum() ++%PROGNOSTICREQUESTEDOUTPUTSENUM - Enum of PrognosticRequestedOutputs ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=PrognosticRequestedOutputsEnum() ++ ++macro=StringToEnum('PrognosticRequestedOutputs'); Index: /issm/oecreview/Archive/13393-13976/ISSM-13438-13439.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13438-13439.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13438-13439.diff (revision 13980) @@ -0,0 +1,33 @@ +Index: ../trunk-jpl/src/m/classes/thermal.py +=================================================================== +--- ../trunk-jpl/src/m/classes/thermal.py (revision 13438) ++++ ../trunk-jpl/src/m/classes/thermal.py (revision 13439) +@@ -70,9 +70,12 @@ + md = checkfield(md,'thermal.stabilization','numel',[1],'values',[0,1,2]) + md = checkfield(md,'thermal.spctemperature','forcing',1) + if EnthalpyAnalysisEnum() in analyses and (md.thermal.isenthalpy or solution==EnthalpySolutionEnum()) and md.mesh.dimension==3: +- pos=numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices,:]))) +- replicate=numpy.tile(md.geometry.surface-md.mesh.z,(1,numpy.size(md.thermal.spctemperature,axis=1))) +- md = checkfield(md,'thermal.spctemperature(numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices,:]))))','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") ++ pos=numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices]))) ++# need to know if md.thermal.spctemperature can have multiple columns? ++# replicate=numpy.tile(md.geometry.surface-md.mesh.z,(1,numpy.size(md.thermal.spctemperature,axis=1))) ++# md = checkfield(md,'thermal.spctemperature[numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices,:])))]','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") ++ replicate=numpy.tile(md.geometry.surface-md.mesh.z,(1)) ++ md = checkfield(md,'thermal.spctemperature[numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices])))]','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") + md = checkfield(md,'thermal.isenthalpy','numel',[1],'values',[0,1]) + + return md +Index: ../trunk-jpl/src/m/classes/matice.py +=================================================================== +--- ../trunk-jpl/src/m/classes/matice.py (revision 13438) ++++ ../trunk-jpl/src/m/classes/matice.py (revision 13439) +@@ -7,7 +7,7 @@ + + class matice(object): + """ +- MATERIALS class definition ++ MATICE class definition + + Usage: + matice=matice(); Index: /issm/oecreview/Archive/13393-13976/ISSM-13439-13440.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13439-13440.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13439-13440.diff (revision 13980) @@ -0,0 +1,334 @@ +Index: ../trunk-jpl/src/m/plot/plot_manager.py +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_manager.py (revision 13439) ++++ ../trunk-jpl/src/m/plot/plot_manager.py (revision 13440) +@@ -1,7 +1,11 @@ + from pairoptions import * + import pylab as p +-from checkplotoptions import * +-from plot_mesh import * ++from checkplotoptions import checkplotoptions ++from plot_mesh import plot_mesh ++from processmesh import processmesh ++from processdata import processdata ++from plot_unit import plot_unit ++from applyoptions import applyoptions + + def plot_manager(md,options,subplotwidth,nlines,ncols,i): + ''' +@@ -24,12 +28,35 @@ + if isinstance(data,(str,unicode)): + + # convert string to lower case for a case-insensitive comparison +- if data.lower()=='mesh': plot_mesh(md,options,nlines,ncols,i) ++ if data.lower()=='mesh': ++ plot_mesh(md,options,nlines,ncols,i) ++ return + else: + print "WARNING: '%s' is not implemented or is not a valid string for option 'data'" % data + + #elif data in vars(md): +- else: +- print "'data' not a string, plotting model properties yet to be implemented..." ++ #else: ++ #print "'data' not a string, plotting model properties yet to be implemented..." + +- ++ #Overlay plot ++ ++ #Gridded plot ++ ++ #Section plot ++ ++ #Profile plot ++ ++ #process data and model ++ x,y,z,elements,is2d,isplanet=processmesh(md,data,options) ++ data2,datatype=processdata(md,data,options) ++ ++ #standard plot ++ p.subplot(nlines,ncols,i) ++ ++ #plot unit ++ plot_unit(x,y,z,elements,data2,is2d,isplanet,datatype,options) ++ ++ #apply all options ++ applyoptions(md,data2,options) ++ ++ #ground overlay on kml plot_unit +Index: ../trunk-jpl/src/m/plot/plot_mesh.py +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_mesh.py (revision 13439) ++++ ../trunk-jpl/src/m/plot/plot_mesh.py (revision 13440) +@@ -12,7 +12,7 @@ + See also: PLOTMODEL + ''' + +- x,y,z,elements,is2d=processmesh(md,[],options) ++ x,y,z,elements,is2d,isplanet=processmesh(md,[],options) + + if is2d: + p.subplot(nlines,ncols,i) +Index: ../trunk-jpl/src/m/plot/processmesh.py +=================================================================== +--- ../trunk-jpl/src/m/plot/processmesh.py (revision 13439) ++++ ../trunk-jpl/src/m/plot/processmesh.py (revision 13440) +@@ -16,7 +16,7 @@ + if md.mesh.numberofvertices==md.mesh.numberofelements: + raise ValueError('processmesh error: the number of elements is the same as the number of nodes') + +- if not data or not isinstance(data,dict): ++ if len(data)==0 or not isinstance(data,dict): + + if 'latlon' not in options.getfieldvalue('coord','xy').lower(): #convert to lower case for comparison + x=md.mesh.x +@@ -51,20 +51,20 @@ + else: + is2d=0 + else: +- raise ValueError('processmesh error: dim = %d not supported') ++ raise ValueError('processmesh error: dim = %d not supported' % md.mesh.dimension) + + #layer projection? + if options.getfieldvalue('layer',0)>=1: + if 'latlon' in options.getfieldvalue('coord','xy').lower(): + raise ValueError('processmesh error: cannot work with 3D mesh in lat-lon coords') +- #we modify (w/c?) the mesh temporarily to a 2D mesh from which the 3D mesh was extruded ++ #we modify the mesh temporarily to a 2D mesh from which the 3D mesh was extruded + x=x2d + y=y2d + z=zeros(size(x2d)) + elements=elements2d + + else: +- #Process mesh for plotting (triangulation for 2D, polycollection for 3D?) ++ #Process mesh for plotting + if md.mesh.dimension==2: + is2d=1 + else: +@@ -78,9 +78,10 @@ + y=y*unit + z=z*unit + +- ##is model a member of planet class? (won't work until planet class defined) +- #if isinstance(md,planet): +- # isplanet=1 +- #else: +- # isplanet=0 +- return x,y,z,elements,is2d ++ #is model a member of planet class? (workaround until planet class defined) ++ if md.__class__.__name__!='model': ++ isplanet=1 ++ else: ++ isplanet=0 ++ ++ return x,y,z,elements,is2d,isplanet +Index: ../trunk-jpl/src/m/plot/processdata.py +=================================================================== +--- ../trunk-jpl/src/m/plot/processdata.py (revision 0) ++++ ../trunk-jpl/src/m/plot/processdata.py (revision 13440) +@@ -0,0 +1,75 @@ ++from math import isnan ++import numpy as npy ++ ++def processdata(md,data,options): ++ """ ++ PROCESSDATA - process data to be plotted ++ ++ datatype = 1 -> elements ++ datatype = 2 -> nodes ++ datatype = 3 -> node quivers ++ datatype = 4 -> patch ++ ++ Usage: ++ data,datatype=processdata(md,data,options); ++ ++ See also: PLOTMODEL, PROCESSMESH ++ """ ++ ++ #check format ++ if (len(data)==0 or (len(data)==1 and not isinstance(data,dict) and isnan(data).all())): ++ raise ValueError("processdata error message: 'data' provided is empty") ++ ++ #needed later on ++ if md.mesh.numberofvertices2d: ++ numberofvertices2d=md.mesh.numberofvertices2d ++ numberofelements2d=md.mesh.numberofelements2d ++ else: ++ numberofvertices2d=npy.nan ++ numberofelements2d=npy.nan ++ ++ #process patch ++ ++ #initialize datatype ++ datatype=0 ++ ++ #get datasize ++ if npy.ndim(data)==1: ++ datasize=npy.array([len(data),1]) ++ else: ++ datasize=shape(data) ++ ++ #process NaN's if any ++ if options.exist('nan'): ++ data[npy.isnan(data)]=options.getfieldvalue('nan',0) ++ ++ #non-patch processing ++ ++ #element data ++ if datasize[0]==md.mesh.numberofelements and datasize[1]==1: ++ ++ #initialize datatype if non patch ++ if datatype!=4 and datatype!=5: ++ datatype=1 ++ ++ #mask? ++ ++ #log? ++ ++ #node data ++ if datasize[0]==md.mesh.numberofvertices and datasize[1]==1: ++ datatype=2 ++ ++ #mask? ++ ++ #log? ++ ++ #layer projection? ++ ++ #control arrow density if quiver plot ++ ++ #if datatype is still zero, error out ++ if datatype==0: ++ raise ValueError("processdata error: data provided not recognized or not supported") ++ else: ++ return data, datatype +Index: ../trunk-jpl/src/m/plot/plotmodel.py +=================================================================== +--- ../trunk-jpl/src/m/plot/plotmodel.py (revision 13439) ++++ ../trunk-jpl/src/m/plot/plotmodel.py (revision 13440) +@@ -40,7 +40,7 @@ + + #Go through plots + if numberofplots: +- ++ + #Create figure + #plots will be visible by default if ipython is run in interactive mode (invoked by ipython --pylab) + #handling the 'visible' option will need some check on whether ipython is currently in interactive or non-interactive mode +@@ -51,8 +51,7 @@ + p.figure(figurenumber,figsize=figsize) + else: + p.figure(figurenumber) +- +- ++ + #try: + for i in xrange(numberofplots): + plot_manager(options.list[i].getfieldvalue('model',md),options.list[i],subplotwidth,nlines,ncols,i) +Index: ../trunk-jpl/src/m/plot/applyoptions.py +=================================================================== +--- ../trunk-jpl/src/m/plot/applyoptions.py (revision 13439) ++++ ../trunk-jpl/src/m/plot/applyoptions.py (revision 13440) +@@ -138,14 +138,18 @@ + + #grid {{{ + if options.exist('grid'): +- p.grid() ++ if 'on' in options.getfieldvalue('grid','on'): ++ p.grid() + #}}} + + #colormap + + #wrapping + +- #colorbar ++ #colorbar {{{ ++ if 'on' in options.getfieldvalue('colorbar','on'): ++ p.colorbar() ++ #}}} + + #area + +@@ -161,9 +165,6 @@ + + #contours + +- +- +- + #axis positions + + #figure position +Index: ../trunk-jpl/src/m/plot/processdata.m +=================================================================== +--- ../trunk-jpl/src/m/plot/processdata.m (revision 13439) ++++ ../trunk-jpl/src/m/plot/processdata.m (revision 13440) +@@ -47,10 +47,10 @@ + datatype=0; + end + +-%get datatype ++%get datasize + datasize=size(data); + +-%Process NaN if any (do not now before mask is applied) ++%Process NaN if any (do not know before mask is applied) + if exist(options,'nan') + data(find(isnan(data)))=getfieldvalue(options,'nan',0); + end +Index: ../trunk-jpl/src/m/plot/plot_unit.py +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_unit.py (revision 0) ++++ ../trunk-jpl/src/m/plot/plot_unit.py (revision 13440) +@@ -0,0 +1,49 @@ ++import pylab as p ++ ++def plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options): ++ """ ++ PLOT_UNIT - unit plot, display data ++ ++ Usage: ++ plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) ++ ++ See also: PLOTMODEL, PLOT_MANAGER ++ """ ++ ++ #edgecolor ++ edgecolor=options.getfieldvalue('edgecolor','None') ++ ++ #number of colorlevels for plots ++ colorlevels=options.getfieldvalue('colorlevels',256) ++ ++ if datatype==1: ++ #element plot ++ if is2d: ++ p.tripcolor(x,y,elements,data,colorlevels) ++ else: ++ raise ValueError('plot_unit error: 3D element plot not supported yet') ++ return ++ ++ elif datatype==2: ++ #node plot ++ if is2d: ++ p.tricontourf(x,y,elements,data,colorlevels) ++ else: ++ raise ValueError('plot_unit error: 3D node plot not supported yet') ++ return ++ ++ elif datatype==3: ++ print 'plot_unit message: quiver plot not implemented yet' ++ return ++ ++ elif datatype==4: ++ #P1 patch plot ++ print 'plot_unit message: P1 patch plot not implemented yet' ++ return ++ ++ elif datatype==5: ++ print 'plot_unit message: P0 patch plot not implemented yet' ++ return ++ ++ else: ++ raise ValueError('datatype=%d not supported' % datatype) Index: /issm/oecreview/Archive/13393-13976/ISSM-13440-13441.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13440-13441.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13440-13441.diff (revision 13980) @@ -0,0 +1,23 @@ +Index: ../trunk-jpl/src/modules/python/Makefile.am +=================================================================== +--- ../trunk-jpl/src/modules/python/Makefile.am (revision 13440) ++++ ../trunk-jpl/src/modules/python/Makefile.am (revision 13441) +@@ -6,6 +6,7 @@ + if MODULES + lib_LTLIBRARIES = BamgConvertMesh.la\ + BamgMesher.la\ ++ ContourToMesh.la\ + ContourToNodes.la\ + ElementConnectivity.la\ + EnumToString.la\ +@@ -64,6 +65,10 @@ + ../BamgMesher/BamgMesher.h + BamgMesher_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) + ++ContourToMesh_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp\ ++ ../ContourToMesh/ContourToMesh.h ++ContourToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) ++ + ContourToNodes_la_SOURCES = ../ContourToNodes/ContourToNodes.cpp\ + ../ContourToNodes/ContourToNodes.h + ContourToNodes_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) Index: /issm/oecreview/Archive/13393-13976/ISSM-13441-13442.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13441-13442.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13441-13442.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/scripts/report.sh +=================================================================== +--- ../trunk-jpl/scripts/report.sh (revision 13441) ++++ ../trunk-jpl/scripts/report.sh (revision 13442) +@@ -214,7 +214,7 @@ + Test name + Field checked + +- $(cat matlab_short.log | while read line ++ $(cat python_short.log | while read line + do + echo "" + STATUS=`echo $line | awk '{print $1}'` Index: /issm/oecreview/Archive/13393-13976/ISSM-13442-13443.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13442-13443.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13442-13443.diff (revision 13980) @@ -0,0 +1,48 @@ +Index: ../trunk-jpl/src/m/classes/prognostic.m +=================================================================== +--- ../trunk-jpl/src/m/classes/prognostic.m (revision 13442) ++++ ../trunk-jpl/src/m/classes/prognostic.m (revision 13443) +@@ -11,7 +11,7 @@ + stabilization = 0; + vertex_pairing = NaN; + penalty_factor = 0; +- requested_outputs = NaN; ++ requested_outputs = NaN; + end + methods + function obj = prognostic(varargin) % {{{ +Index: ../trunk-jpl/src/m/classes/prognostic.py +=================================================================== +--- ../trunk-jpl/src/m/classes/prognostic.py (revision 13442) ++++ ../trunk-jpl/src/m/classes/prognostic.py (revision 13443) +@@ -22,6 +22,7 @@ + self.stabilization = 0 + self.vertex_pairing = float('NaN') + self.penalty_factor = 0 ++ self.requested_outputs = float('NaN') + + #set defaults + self.setdefaultparameters() +@@ -34,6 +35,7 @@ + string="%s\n%s"%(string,fielddisplay(self,'min_thickness','minimum ice thickness allowed')) + string="%s\n%s"%(string,fielddisplay(self,'hydrostatic_adjustment','adjustment of ice shelves surface and bed elevations: ''Incremental'' or ''Absolute'' ')) + string="%s\n%s"%(string,fielddisplay(self,'stabilization','0->no, 1->artificial_diffusivity, 2->streamline upwinding, 3->discontinuous Galerkin')) ++ string="%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested')) + + return string + #}}} +@@ -66,6 +68,7 @@ + md = checkfield(md,'prognostic.hydrostatic_adjustment','values',['Absolute','Incremental']) + md = checkfield(md,'prognostic.stabilization','values',[0,1,2,3]) + md = checkfield(md,'prognostic.min_thickness','>',0) ++ md = checkfield(md,'prognostic.requested_output','size',[float('NaN'),1]) + + return md + # }}} +@@ -77,5 +80,6 @@ + WriteData(fid,'object',self,'fieldname','stabilization','format','Integer') + WriteData(fid,'object',self,'fieldname','vertex_pairing','format','DoubleMat','mattype',3) + WriteData(fid,'object',self,'fieldname','penalty_factor','format','Double') ++ WriteData(fid,'object',self,'fieldname','requested_outputs','format','DoubleMat','mattype',3); + # }}} + Index: /issm/oecreview/Archive/13393-13976/ISSM-13443-13444.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13443-13444.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13443-13444.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/m/classes/prognostic.py +=================================================================== +--- ../trunk-jpl/src/m/classes/prognostic.py (revision 13443) ++++ ../trunk-jpl/src/m/classes/prognostic.py (revision 13444) +@@ -68,7 +68,7 @@ + md = checkfield(md,'prognostic.hydrostatic_adjustment','values',['Absolute','Incremental']) + md = checkfield(md,'prognostic.stabilization','values',[0,1,2,3]) + md = checkfield(md,'prognostic.min_thickness','>',0) +- md = checkfield(md,'prognostic.requested_output','size',[float('NaN'),1]) ++ md = checkfield(md,'prognostic.requested_outputs','size',[float('NaN'),1]) + + return md + # }}} Index: /issm/oecreview/Archive/13393-13976/ISSM-13444-13445.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13444-13445.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13444-13445.diff (revision 13980) @@ -0,0 +1,45 @@ +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13444) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13445) +@@ -80,11 +80,6 @@ + /*out of solution_type, figure out types of analyses needed in the femmodel: */ + AnalysisConfiguration(&analyses,&numanalyses,solution_type); + +- /*before we create the model, start the trace on for AD mode: */ +- #ifdef _HAVE_ADOLC_ +- trace_on(1); +- #endif +- + /*Create femmodel, using input file: */ + #ifdef _HAVE_MPI_ + MPI_Barrier(MPI_COMM_WORLD); start_init=MPI_Wtime(); +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13444) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13445) +@@ -52,7 +52,7 @@ + this->data=xNew(MaximumNumberOfEnums); + for(int i=0;idata[i]=NULL; + +- /*If we are running in AD mode, we need to declare our independent variables now, ++ /*If we are running in AD mode, we need to start the trace and declare our independent variables now, + *and prevent them from being erased during successive calls to iomodel->FetchConstants, iomodel->FetchData and + iomodel->DeleteData:*/ + this->DeclareIndependents(); +@@ -219,10 +219,14 @@ + + this->FetchData(&autodiff,AutodiffIsautodiffEnum); + if(autodiff){ +- ++ + this->FetchData(&numberofvertices,MeshNumberofverticesEnum); + + #ifdef _HAVE_ADOLC_ ++ ++ /*Start the trace: */ ++ trace_on(1); ++ + /*build dataset made of independent objects: */ + this->independent_objects=new DataSet(); + this->FetchData(&num_independent_objects,AutodiffNumIndependentObjectsEnum); Index: /issm/oecreview/Archive/13393-13976/ISSM-13445-13446.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13445-13446.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13445-13446.diff (revision 13980) @@ -0,0 +1,54 @@ +Index: ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13445) ++++ ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13446) +@@ -19,9 +19,6 @@ + int num_dependents; + int num_independents; + IssmDouble *axp = NULL; +- int configuration_type; +- int solveSize; +- int edf_n ,edf_m; + double *xp = NULL; + int anIndepNum; + +@@ -47,12 +44,6 @@ + xp[i]=reCast(axp[i]); + } + +- /* get the dimension for the solverx arguments*/ +- parameters->FindParam(&configuration_type,ConfigurationTypeEnum); +- solveSize=nodes->NumberOfDofs(configuration_type,FsetEnum); +- edf_n=solveSize*(solveSize+1); +- edf_m=solveSize; +- + /*get the EDF pointer:*/ + ext_diff_fct *anEDF_for_solverx_p=dynamic_cast * >(parameters->FindParamObject(AdolcParamEnum))->GetParameterValue().myEDF_for_solverx_p; + +@@ -64,16 +55,16 @@ + // anEDF_for_solverx_p->fov_reverse=EDF_fov_reverse_for_solverx; + + /*allocate the space for the parameters to invoke the forward methods:*/ +- anEDF_for_solverx_p->dp_x=xNew(edf_n); +- anEDF_for_solverx_p->dp_X=xNew(edf_n); +- anEDF_for_solverx_p->dpp_X=xNew(edf_n, num_independents); +- anEDF_for_solverx_p->dp_y=xNew(edf_m); +- anEDF_for_solverx_p->dp_Y=xNew(edf_m); +- anEDF_for_solverx_p->dpp_Y=xNew(edf_m, num_independents); +- anEDF_for_solverx_p->dp_U=xNew(edf_m); +- anEDF_for_solverx_p->dpp_U=xNew(num_dependents,edf_m); +- anEDF_for_solverx_p->dp_Z=xNew(edf_n); +- anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,edf_n); ++ anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dp_X=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dpp_X=xNew(anEDF_for_solverx_p->max_n, num_independents); ++ anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dp_Y=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dpp_Y=xNew(anEDF_for_solverx_p->max_m, num_independents); ++ anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dpp_U=xNew(num_dependents,anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,anEDF_for_solverx_p->max_n); + + /* Call AD driver:*/ + // single direction: Index: /issm/oecreview/Archive/13393-13976/ISSM-13446-13447.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13446-13447.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13446-13447.diff (revision 13980) @@ -0,0 +1,82 @@ +Index: ../trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp +=================================================================== +--- ../trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 13446) ++++ ../trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp (revision 13447) +@@ -113,7 +113,14 @@ + *pdataref=mxCreateString(string); + } + /*}}}*/ ++/*FUNCTION WriteData(mxArray** pdataref){{{*/ ++void WriteData(mxArray** pdataref){ + ++ ; ++ ++} ++/*}}}*/ ++ + /*ISSM objects*/ + /*FUNCTION WriteData(mxArray** pdataref,BamgGeom* bamggeom){{{*/ + void WriteData(mxArray** pdataref,BamgGeom* bamggeom){ +Index: ../trunk-jpl/src/c/matlab/io/matlabio.h +=================================================================== +--- ../trunk-jpl/src/c/matlab/io/matlabio.h (revision 13446) ++++ ../trunk-jpl/src/c/matlab/io/matlabio.h (revision 13447) +@@ -25,6 +25,7 @@ + void WriteData(mxArray** pdataref,bool boolean); + void WriteData(mxArray** pdataref,double scalar); + void WriteData(mxArray** pdataref,char* string); ++void WriteData(mxArray** pdataref); + void WriteData(mxArray** pdataref,BamgGeom* bamggeom); + void WriteData(mxArray** pdataref,BamgMesh* bamgmesh); + +Index: ../trunk-jpl/src/c/python/io/WritePythonData.cpp +=================================================================== +--- ../trunk-jpl/src/c/python/io/WritePythonData.cpp (revision 13446) ++++ ../trunk-jpl/src/c/python/io/WritePythonData.cpp (revision 13447) +@@ -45,7 +45,13 @@ + + PyTuple_SetItem(tuple, index, array); + }/*}}}*/ ++/*FUNCTION WriteData(PyObject* py_tuple,int index){{{*/ ++void WriteData(PyObject* py_tuple, int index){ ++ ++ PyTuple_SetItem(py_tuple, index, Py_None); + ++}/*}}}*/ ++ + /*ISSM objects*/ + /*FUNCTION WriteData(PyObject* py_tuple,int index,BamgGeom* bamggeom){{{*/ + void WriteData(PyObject* py_tuple,int index,BamgGeom* bamggeom){ +@@ -127,7 +133,7 @@ + + }/*}}}*/ + /*FUNCTION WriteData(PyObject* py_tuple,int index,SeqVec* vector){{{*/ +-void WriteData(PyObject* tuple,int index,SeqVec* vector){ ++void WriteData(PyObject* py_tuple,int index,SeqVec* vector){ + + int M; + double* buffer=NULL; +@@ -139,6 +145,6 @@ + dim=(npy_intp)M; + array=PyArray_SimpleNewFromData(1,&dim,NPY_DOUBLE,buffer); + +- PyTuple_SetItem(tuple, index, array); ++ PyTuple_SetItem(py_tuple, index, array); + } + /*}}}*/ +Index: ../trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp +=================================================================== +--- ../trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp (revision 13446) ++++ ../trunk-jpl/src/modules/ContourToMesh/ContourToMesh.cpp (revision 13447) +@@ -72,9 +72,11 @@ + /* output: */ + if (strcmp(interptype,"node")==0){ + WriteData(PLHS0,in_nod); ++ WriteData(PLHS1); + } + else if (strcmp(interptype,"element")==0){ + WriteData(PLHS0,in_elem); ++ WriteData(PLHS1); + } + else if (strcmp(interptype,"element and node")==0){ + WriteData(PLHS0,in_nod); Index: /issm/oecreview/Archive/13393-13976/ISSM-13447-13448.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13447-13448.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13447-13448.diff (revision 13980) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/c/python/io/pythonio.h +=================================================================== +--- ../trunk-jpl/src/c/python/io/pythonio.h (revision 13447) ++++ ../trunk-jpl/src/c/python/io/pythonio.h (revision 13448) +@@ -18,6 +18,7 @@ + void WriteData(PyObject* py_tuple,int index, double* matrix, int M,int N); + void WriteData(PyObject* py_tuple,int index, int integer); + void WriteData(PyObject* py_tuple,int index, char* string); ++void WriteData(PyObject* py_tuple,int index); + void WriteData(PyObject* py_tuple,int index, SeqMat* matrix); + void WriteData(PyObject* py_tuple,int index, SeqVec* vector); + void WriteData(PyObject* py_tuple,int index, BamgGeom* bamggeom); Index: /issm/oecreview/Archive/13393-13976/ISSM-13448-13449.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13448-13449.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13448-13449.diff (revision 13980) @@ -0,0 +1,122 @@ +Index: ../trunk-jpl/src/m/geometry/FlagElements.py +=================================================================== +--- ../trunk-jpl/src/m/geometry/FlagElements.py (revision 13448) ++++ ../trunk-jpl/src/m/geometry/FlagElements.py (revision 13449) +@@ -1,7 +1,7 @@ + import numpy + import os + #from basinzoom import * +-#from ContourToMesh import * ++from ContourToMesh import * + from MatlabFuncs import * + + def FlagElements(md,region): +@@ -40,12 +40,13 @@ + if not os.path.exists(region): + if len(region)>3 and not strcmp(region[-4:],'.exp'): + raise IOError("Error: File 'region' not found!" % region) ++ raise RuntimeError("FlagElements -- basinzoom not yet converted.") + xlim,ylim=basinzoom('basin',region) + flag_nodes=numpy.logical_and(numpy.logical_and(md.mesh.xxlim[0]),numpy.logical_and(md.mesh.yylim[0])).astype(float) + flag=numpy.prod(flag_nodes[md.mesh.elements],axis=1) + else: + #ok, flag elements +- flag=ContourToMesh(md.mesh.elements[:,0:3],md.mesh.x,md.mesh.y,region,'element',1) ++ [flag,fnone]=ContourToMesh(md.mesh.elements[:,0:3],md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),region,'element',1) + + if invert: + flag=numpy.logical_not(flag) +Index: ../trunk-jpl/src/m/parameterization/setmask.py +=================================================================== +--- ../trunk-jpl/src/m/parameterization/setmask.py (revision 13448) ++++ ../trunk-jpl/src/m/parameterization/setmask.py (revision 13449) +@@ -1,55 +1,51 @@ +-from numpy import * +-import FlagElements as fe ++import numpy ++from FlagElements import * + + def setmask(md, floatingicename, groundedicename): +- #SETMASK - establish boundaries between grounded and floating ice. +- # +- # By default, ice is considered grounded. The contour floatingicename defines nodes +- # for which ice is floating. The contour groundedicename defines nodes inside an floatingice, +- # that are grounded (ie: ice rises, islands, etc ...) +- # All input files are in the Argus format (extension .exp). +- # +- # Usage: +- # md=setmask(md,floatingicename,groundedicename) +- # +- # Examples: +- # md=setmask(md,'all',''); +- # md=setmask(md,'Iceshelves.exp','Islands.exp'); ++ """ ++ SETMASK - establish boundaries between grounded and floating ice. + +- #%Get assigned fields ++ By default, ice is considered grounded. The contour floatingicename defines nodes ++ for which ice is floating. The contour groundedicename defines nodes inside an floatingice, ++ that are grounded (ie: ice rises, islands, etc ...) ++ All input files are in the Argus format (extension .exp). ++ ++ Usage: ++ md=setmask(md,floatingicename,groundedicename) ++ ++ Examples: ++ md=setmask(md,'all',''); ++ md=setmask(md,'Iceshelves.exp','Islands.exp'); ++ """ ++ ++ #Get assigned fields + x = md.mesh.x + y = md.mesh.y + elements = md.mesh.elements + + #Assign elementonfloatingice, elementongroundedice, vertexongroundedice and vertexonfloatingice. Only change at your own peril! This is synchronized heavily with the GroundingLineMigration module. {{{ +- elementonfloatingice = fe.FlagElements(md, floatingicename) +- elementongroundedice = fe.FlagElements(md, groundedicename) ++ elementonfloatingice = FlagElements(md, floatingicename) ++ elementongroundedice = FlagElements(md, groundedicename) + + #Because groundedice nodes and elements can be included into an floatingice, we need to update. Remember, all the previous + #arrays come from domain outlines that can intersect one another: + +- elementonfloatingice = logical_and(elementonfloatingice,~elementongroundedice) +- elementongroundedice = ~elementonfloatingice ++ elementonfloatingice = numpy.logical_and(elementonfloatingice,numpy.logical_not(elementongroundedice)) ++ elementongroundedice = numpy.logical_not(elementonfloatingice) + + #the order here is important. we choose vertexongroundedice as default on the grounding line. +- vertexonfloatingice = zeros(md.mesh.numberofvertices,'bool') +- vertexongroundedice = zeros(md.mesh.numberofvertices,'bool') ++ vertexonfloatingice = numpy.zeros(md.mesh.numberofvertices,'bool') ++ vertexongroundedice = numpy.zeros(md.mesh.numberofvertices,'bool') ++ vertexongroundedice[md.mesh.elements[numpy.nonzero(elementongroundedice),:].astype(int)-1]=True ++ vertexonfloatingice[numpy.nonzero(numpy.logical_not(vertexongroundedice))]=True ++ #}}} + +- pos=argwhere(elementongroundedice==1) +- pos=md.mesh.elements[pos,:]-1 +- if pos.size: +- vertexongroundedice[pos]=True ++ #Return: ++ md.mask.elementonfloatingice = elementonfloatingice.astype(float) ++ md.mask.vertexonfloatingice = vertexonfloatingice.astype(float) ++ md.mask.elementongroundedice = elementongroundedice.astype(float) ++ md.mask.vertexongroundedice = vertexongroundedice.astype(float) ++ md.mask.vertexonwater = numpy.zeros(md.mesh.numberofvertices) ++ md.mask.elementonwater = numpy.zeros(md.mesh.numberofelements) + +- pos=argwhere(~vertexongroundedice) +- if pos.size: +- vertexonfloatingice[pos]=True; +- #%}}} +- +- #Return: +- md.mask.elementonfloatingice = double(elementonfloatingice) +- md.mask.vertexonfloatingice = double(vertexonfloatingice) +- md.mask.elementongroundedice = double(elementongroundedice) +- md.mask.vertexongroundedice = double(vertexongroundedice) +- md.mask.vertexonwater = zeros(md.mesh.numberofvertices) +- md.mask.elementonwater = zeros(md.mesh.numberofelements) + return md Index: /issm/oecreview/Archive/13393-13976/ISSM-13449-13450.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13449-13450.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13449-13450.diff (revision 13980) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/src/c/modules/RequestedOutputsx/RequestedOutputsx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/RequestedOutputsx/RequestedOutputsx.cpp (revision 13449) ++++ ../trunk-jpl/src/c/modules/RequestedOutputsx/RequestedOutputsx.cpp (revision 13450) +@@ -35,6 +35,10 @@ + Responsex(&output_value,elements,nodes,vertices,loads,materials,parameters,"TotalSmb",false,0); + results->AddObject(new GenericExternalResult(results->Size()+1,TotalSmbEnum,reCast(output_value),step,time)); + break; ++ case MaxVelEnum: ++ Responsex(&output_value,elements,nodes,vertices,loads,materials,parameters,"MaxVel",false,0); ++ results->AddObject(new GenericExternalResult(results->Size()+1,MaxVelEnum,reCast(output_value),step,time)); ++ break; + default: + /*create this output in the element inputs, and then transfer to results:*/ + for(int j=0;jSize();j++){ Index: /issm/oecreview/Archive/13393-13976/ISSM-13450-13451.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13450-13451.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13450-13451.diff (revision 13980) @@ -0,0 +1,40 @@ +Index: ../trunk-jpl/src/c/shared/Alloc/xNewDelete.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Alloc/xNewDelete.h (revision 13450) ++++ ../trunk-jpl/src/c/shared/Alloc/xNewDelete.h (revision 13451) +@@ -12,7 +12,7 @@ + // T with non-trivial constructors require + // C++ style memory management + #define USE_CXX_MEMORY_MANAGMENT_FOR_NON_POD_TYPES +-// but for speed on may alternatively use C memory managment ++// but for speed on may alternatively use C memory management + // but can do so safely only for T that are at most + // plain old data structures (POD) + #ifndef USE_CXX_MEMORY_MANAGMENT_FOR_NON_POD_TYPES +@@ -72,6 +72,26 @@ + } + + template ++T** xNewZeroInit(unsigned int dim1, unsigned int dim2) { ++#ifdef USE_CXX_MEMORY_MANAGMENT_FOR_NON_POD_TYPES ++ T** aT_pp=xNew(dim1,dim2); ++ for (unsigned int i=0; i + void xDelete(T**& aT_pp) { + if (aT_pp) { + #ifdef USE_CXX_MEMORY_MANAGMENT_FOR_NON_POD_TYPES Index: /issm/oecreview/Archive/13393-13976/ISSM-13451-13452.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13451-13452.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13451-13452.diff (revision 13980) @@ -0,0 +1,128 @@ +Index: ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13451) ++++ ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13452) +@@ -1,7 +1,7 @@ + /*!\file AutodiffDriversx + * \brief: compute outputs from the AD mode, using our dependents and independents, and drivers available in Adolc. + */ +- ++#include + #include "../../modules/modules.h" + #include "../../shared/shared.h" + #include "../../include/include.h" +@@ -20,7 +20,9 @@ + int num_independents; + IssmDouble *axp = NULL; + double *xp = NULL; +- int anIndepNum; ++ int anIndepIndex; ++ unsigned int * indepIndices = NULL; ++ int tangentDirNum = 1; // <----------- set this via config + + + /*AD mode on?: */ +@@ -35,6 +37,10 @@ + + if(!(num_dependents*num_independents)) return; + ++ if (tangentDirNum<1 || tangentDirNum>num_independents) { ++ _error_("tangentDirNum should be in [1,num_dependents]"); // <------------ fix this error message to relate to config ++ } ++ + /*retrieve state variable: */ + parameters->FindParam(&axp,&dummy,AutodiffXpEnum); + +@@ -57,33 +63,75 @@ + /*allocate the space for the parameters to invoke the forward methods:*/ + anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); + anEDF_for_solverx_p->dp_X=xNew(anEDF_for_solverx_p->max_n); +- anEDF_for_solverx_p->dpp_X=xNew(anEDF_for_solverx_p->max_n, num_independents); ++ anEDF_for_solverx_p->dpp_X=xNew(anEDF_for_solverx_p->max_n, tangentDirNum); + anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); + anEDF_for_solverx_p->dp_Y=xNew(anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dpp_Y=xNew(anEDF_for_solverx_p->max_m, num_independents); ++ anEDF_for_solverx_p->dpp_Y=xNew(anEDF_for_solverx_p->max_m, tangentDirNum); ++ /*allocate the space for the parameters to invoke the reverse methods:*/ + anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); + anEDF_for_solverx_p->dpp_U=xNew(num_dependents,anEDF_for_solverx_p->max_m); + anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); + anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,anEDF_for_solverx_p->max_n); + + /* Call AD driver:*/ +- // single direction: +- double *tangentDir=xNewZeroInit(num_independents); +- parameters->FindParam(&anIndepNum,AutodiffFosForwardIndexEnum); +- tangentDir[anIndepNum]=1.0; +- double *theJacVecProduct=xNew(num_dependents); +- double *theOutput=xNew(num_dependents); +- if (fos_forward(1,num_dependents,num_independents, 0, xp, tangentDir, theOutput, theJacVecProduct )) +- _error_("fos_forward returned non-zero error code"); ++ if (tangentDirNum==1) { ++ // single direction: ++ double *tangentDir=xNewZeroInit(num_independents); ++ parameters->FindParam(&anIndepIndex,AutodiffFosForwardIndexEnum); ++ tangentDir[anIndepIndex]=1.0; ++ double *jacTimesTangentDir=xNew(num_dependents); ++ double *theOutput=xNew(num_dependents); ++ if (fos_forward(1,num_dependents,num_independents, 0, xp, tangentDir, theOutput, jacTimesTangentDir )) ++ _error_("fos_forward returned non-zero error code"); ++ results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,jacTimesTangentDir,num_dependents,1,1,0.0)); ++ xDelete(theOutput); ++ xDelete(jacTimesTangentDir); ++ xDelete(tangentDir); ++ } ++ else { ++ // full Jacobian or Jacobian projection: ++ double **jacTimesSeed=xNew(num_dependents,tangentDirNum); ++ if (tangentDirNum>1 && tangentDirNum(num_independents,tangentDirNum); + +- results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,theJacVecProduct,num_dependents,1,1,0.0)); ++ // <<<<<<< from here <<<<<<<<<<<< ++ unsigned int * indepIndices=xNew(tangentDirNum); ++ for(int i =0; i< tangentDirNum;++i) { ++ indepIndices[i]=i; ++ } ++ // <<<<<<<< to here << get this vector of independent indices from the config - should be 0 based and ideally also unsigned + +-#if 0 +- double **J=xNew(num_dependents,num_independents); +- jacobian(1,num_dependents,num_independents,xp,J); +- results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,*J,num_independents,num_dependents,1,1,0.0)); +- xDelete(J); +-#endif ++ // collect indices in a set to prevent accidental duplicates as long as we don't do compression: ++ std::set anIndexSet; ++ for (int i=0; inum_independents) { ++ _error_("indepIndices values must be in [0,num_independents-1]"); ++ } ++ if (anIndexSet.find(indepIndices[i])!=anIndexSet.end()) { ++ _error_("duplicate indepIndices values are not allowed until we implement Jacobian decompression"); ++ } ++ anIndexSet.insert(indepIndices[i]); ++ // now populate the seed matrix from the set of independent indices; ++ // simple setup with a single 1.0 per column and at most a single 1.0 per row ++ seed[indepIndices[i]][i]=1.0; ++ } ++ double *theOutput=xNew(num_dependents); ++ if (fov_forward(1,num_dependents,num_independents, tangentDirNum, xp, seed, theOutput, jacTimesSeed )) { ++ _error_("fov_forward returned non-zero error code"); ++ } ++ xDelete(theOutput); ++ xDelete(indepIndices); ++ xDelete(seed); ++ } ++ else { ++ if (jacobian(1,num_dependents,num_independents,xp,jacTimesSeed)) { ++ _error_("jacobian returned non-zero error code"); ++ } ++ } ++ results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,*jacTimesSeed,num_dependents*tangentDirNum,1,1,0.0)); ++ xDelete(jacTimesSeed); ++ } + + /* delete the allocated space for the parameters:*/ + xDelete(anEDF_for_solverx_p->dp_x); Index: /issm/oecreview/Archive/13393-13976/ISSM-13452-13453.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13452-13453.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13452-13453.diff (revision 13980) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13452) ++++ ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13453) +@@ -38,7 +38,7 @@ + if(!(num_dependents*num_independents)) return; + + if (tangentDirNum<1 || tangentDirNum>num_independents) { +- _error_("tangentDirNum should be in [1,num_dependents]"); // <------------ fix this error message to relate to config ++ _error_("tangentDirNum should be in [1,num_independents]"); // <------------ fix this error message to relate to config + } + + /*retrieve state variable: */ +@@ -91,7 +91,7 @@ + else { + // full Jacobian or Jacobian projection: + double **jacTimesSeed=xNew(num_dependents,tangentDirNum); +- if (tangentDirNum>1 && tangentDirNum(num_independents,tangentDirNum); + + // <<<<<<< from here <<<<<<<<<<<< Index: /issm/oecreview/Archive/13393-13976/ISSM-13453-13454.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13453-13454.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13453-13454.diff (revision 13980) @@ -0,0 +1,10 @@ +Index: ../trunk-jpl/test +=================================================================== +--- ../trunk-jpl/test (revision 13453) ++++ ../trunk-jpl/test (revision 13454) + +Property changes on: ../trunk-jpl/test +___________________________________________________________________ +Added: svn:ignore +## -0,0 +1 ## ++AdTests Index: /issm/oecreview/Archive/13393-13976/ISSM-13454-13455.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13454-13455.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13454-13455.diff (revision 13980) @@ -0,0 +1,1016 @@ +Index: ../trunk-jpl/test/Par/SquareShelf.py +=================================================================== +--- ../trunk-jpl/test/Par/SquareShelf.py (revision 0) ++++ ../trunk-jpl/test/Par/SquareShelf.py (revision 13455) +@@ -0,0 +1,89 @@ ++import os.path ++import inspect ++import netCDF4 ++from numpy import * ++from verbose import * ++from InterpFromMeshToMesh2d import InterpFromMeshToMesh2d ++from paterson import * ++from SetIceShelfBC import * ++ ++#Start defining model parameters here ++#Geometry ++hmin=300. ++hmax=1000. ++ymin=min(md.mesh.y) ++ymax=max(md.mesh.y) ++ ++md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin) ++md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness ++md.geometry.surface=md.geometry.bed+md.geometry.thickness ++ ++#Initial velocity and pressure ++iVelF = netCDF4.Dataset('../Data/SquareShelf.nc','r') ++ ++x=reshape(iVelF.variables['x'][:],(-1)) ++y=reshape(iVelF.variables['y'][:],(-1)) ++vx=iVelF.variables['vx'][:] ++vy=iVelF.variables['vy'][:] ++index=iVelF.variables['index'][:].astype(float) ++index=reshape(index.T,(len(index),3),order='F') ++ ++#dbg - begin ++# #print 'vars in SquareShelf.nc:' ++# #for v in iVelF.variables: ++# # print v ++#dbg - end ++ ++iVelF.close() ++ ++[md.initialization.vx]=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y) ++[md.initialization.vy]=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y) ++md.initialization.vz=zeros(md.mesh.numberofvertices) ++md.initialization.pressure=zeros(md.mesh.numberofvertices) ++ ++#dbg - begin ++#print '...vx:' ++#print md.initialization.vx ++#print '...vy:' ++#print md.initialization.vy ++##print '...vz:' ++##print md.initialization.vz ++##print '...pressure:' ++##print md.initialization.pressure ++#dbg - end ++ ++ ++#Materials ++md.initialization.temperature = (273.-20.)*ones(md.mesh.numberofvertices) ++md.materials.rheology_B = paterson(md.initialization.temperature) ++md.materials.rheology_n = 3.*ones(md.mesh.numberofelements) ++ ++#Friction ++pos=nonzero(md.mask.elementonfloatingice) ++md.friction.coefficient = 20.*ones(md.mesh.numberofvertices) ++md.friction.coefficient[md.mesh.elements[pos,:].astype(int)-1] = 0. ++md.friction.p = ones(md.mesh.numberofelements) ++md.friction.q = ones(md.mesh.numberofelements) ++ ++#Numerical parameters ++md.diagnostic.viscosity_overshoot = 0.3 ++md.prognostic.stabilization = 1. ++md.thermal.stabilization = 1. ++md.settings.waitonlock = 30. ++md.verbose=verbose() ++md.diagnostic.restol = 0.10 ++md.steadystate.reltol = 0.02 ++md.diagnostic.reltol = 0.02 ++md.diagnostic.abstol = nan ++md.timestepping.time_step = 1. ++md.timestepping.final_time = 3. ++ ++#Boundary conditions: ++# #md=SetIceShelfBC(md) ++print '...calling seticeshelfbc:' ++md=SetIceShelfBC(md,'../Exp/SquareFront.exp') ++print '...called seticeshelfbc:' ++ ++#Change name so that no test have the same name ++if len(inspect.stack()) > 2: ++ md.miscellaneous.name=os.path.basename(inspect.stack()[2][1]).split('.')[0] +Index: ../trunk-jpl/test/NightlyRun/test3007.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3007.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3007.py (revision 13455) +@@ -0,0 +1,39 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3007.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md=setflowequation(md,'macayeal','all') ++md.extrude(5,3) ++md.cluster=generic('name',oshostname(),'np',3) ++md.autodiff.isautodiff=true ++md=solve(md,PrognosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Thickness'] ++field_tolerances=[1e-13] ++field_values=[\ ++ md.results['PrognosticSolution'][1]['Thickness'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test3002.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3002.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3002.py (revision 13455) +@@ -0,0 +1,43 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3002.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md.extrude(3,2) ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.autodiff.isautodiff=true ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vz'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test3005.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3005.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3005.py (revision 13455) +@@ -0,0 +1,38 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3005.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.autodiff.isautodiff=true ++md=solve(md,PrognosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Thickness'] ++field_tolerances=[1e-13] ++field_values=[\ ++ md.results['PrognosticSolution'][1]['Thickness'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test3008.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3008.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3008.py (revision 13455) +@@ -0,0 +1,41 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3008.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md.extrude(3,1) ++md=setflowequation(md,'macayeal','all') ++md.timestepping.time_step=0 ++md.cluster=generic('name',oshostname(),'np',3) ++md.autodiff.isautodiff=true ++md=solve(md,ThermalSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Temperature','BasalforcingsMeltingRate'] ++field_tolerances=[1e-13,1e-13] ++field_values=[\ ++ md.results['ThermalSolution'][1]['Temperature'],\ ++ md.results['ThermalSolution'][1]['BasalforcingsMeltingRate'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test3003.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3003.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3003.py (revision 13455) +@@ -0,0 +1,52 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3003.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md.extrude(3,2) ++md=setflowequation(md,'pattyn','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.diagnostic.requested_outputs=StressTensorEnum() ++md.autodiff.isautodiff=true ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure',\ ++ 'StressTensorxx','StressTensoryy','StressTensorzz','StressTensorxy','StressTensorxz','StressTensoryz'] ++field_tolerances=[1e-09,1e-09,1e-09,1e-09,1e-09,\ ++ 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vz'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorxx'],\ ++ md.results['DiagnosticSolution'][1]['StressTensoryy'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorzz'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorxy'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorxz'],\ ++ md.results['DiagnosticSolution'][1]['StressTensoryz'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test201.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test201.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test201.py (revision 13455) +@@ -0,0 +1,26 @@ ++from model import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from EnumDefinitions import * ++from solve import * ++from MatlabFuncs import * ++from ContourToMesh import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++#Fields and tolerances to track changes ++field_names =['Vx','Vy','Vel','Pressure'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test3006.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3006.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3006.py (revision 13455) +@@ -0,0 +1,42 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3006.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from meshconvert import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=meshconvert(md) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.prognostic.stabilization=3 ++md.prognostic.spcthickness=md.geometry.thickness ++md.autodiff.isautodiff=true ++md=solve(md,PrognosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Thickness'] ++field_tolerances=[1e-13] ++field_values=[\ ++ md.results['PrognosticSolution'][1]['Thickness'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test3001.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3001.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3001.py (revision 13455) +@@ -0,0 +1,47 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3001.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',50000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.diagnostic.requested_outputs=StressTensorEnum() ++md.autodiff.isautodiff=true ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vel','Pressure',\ ++ 'StressTensorxx','StressTensoryy','StressTensorxy'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,\ ++ 1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorxx'],\ ++ md.results['DiagnosticSolution'][1]['StressTensoryy'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorxy'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test3009.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3009.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3009.py (revision 13455) +@@ -0,0 +1,44 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3009.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md.extrude(3,1) ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.transient.isdiagnostic=0 ++md.transient.isprognostic=0 ++md.transient.isthermal=1 ++md.transient.isgroundingline=0 ++md.autodiff.isautodiff=true ++md=solve(md,TransientSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Temperature','BasalforcingsMeltingRate'] ++field_tolerances=[1e-13,1e-13] ++field_values=[\ ++ md.results['TransientSolution'][1]['Temperature'],\ ++ md.results['TransientSolution'][1]['BasalforcingsMeltingRate'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test3010.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3010.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3010.py (revision 13455) +@@ -0,0 +1,66 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3010.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.transient.requested_outputs=IceVolumeEnum() ++ ++ ++md.autodiff.isautodiff=true ++md=solve(md,TransientSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Volume1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Volume2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Volume3'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['TransientSolution'][1]['Vx'],\ ++ md.results['TransientSolution'][1]['Vy'],\ ++ md.results['TransientSolution'][1]['Vel'],\ ++ md.results['TransientSolution'][1]['Pressure'],\ ++ md.results['TransientSolution'][1]['Bed'],\ ++ md.results['TransientSolution'][1]['Surface'],\ ++ md.results['TransientSolution'][1]['Thickness'],\ ++ md.results['TransientSolution'][1]['IceVolume'],\ ++ md.results['TransientSolution'][2]['Vx'],\ ++ md.results['TransientSolution'][2]['Vy'],\ ++ md.results['TransientSolution'][2]['Vel'],\ ++ md.results['TransientSolution'][2]['Pressure'],\ ++ md.results['TransientSolution'][2]['Bed'],\ ++ md.results['TransientSolution'][2]['Surface'],\ ++ md.results['TransientSolution'][2]['Thickness'],\ ++ md.results['TransientSolution'][2]['IceVolume'],\ ++ md.results['TransientSolution'][3]['Vx'],\ ++ md.results['TransientSolution'][3]['Vy'],\ ++ md.results['TransientSolution'][3]['Vel'],\ ++ md.results['TransientSolution'][3]['Pressure'],\ ++ md.results['TransientSolution'][3]['Bed'],\ ++ md.results['TransientSolution'][3]['Surface'],\ ++ md.results['TransientSolution'][3]['Thickness'],\ ++ md.results['TransientSolution'][3]['IceVolume'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test3004.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3004.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3004.py (revision 13455) +@@ -0,0 +1,43 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3004.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md.extrude(3,2) ++md=setflowequation(md,'stokes','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.autodiff.isautodiff=true ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure'] ++field_tolerances=[1e-08,1e-08,1e-07,1e-08,1e-08] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vz'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ ] +Index: ../trunk-jpl/src/modules/python/Makefile.am +=================================================================== +--- ../trunk-jpl/src/modules/python/Makefile.am (revision 13454) ++++ ../trunk-jpl/src/modules/python/Makefile.am (revision 13455) +@@ -13,6 +13,7 @@ + InterpFromMeshToMesh2d.la\ + NodeConnectivity.la\ + StringToEnum.la\ ++ ContourToMesh.la\ + TriMesh.la + endif + #}}} +@@ -93,6 +94,10 @@ + ../StringToEnum/StringToEnum.h + StringToEnum_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) + ++ContourToMesh_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp\ ++ ../ContourToMesh/ContourToMesh.h ++ContourToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) ++ + TriMesh_la_SOURCES = ../TriMesh/TriMesh.cpp\ + ../TriMesh/TriMesh.h + TriMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB) +Index: ../trunk-jpl/src/m/classes/flowequation.py +=================================================================== +--- ../trunk-jpl/src/m/classes/flowequation.py (revision 13454) ++++ ../trunk-jpl/src/m/classes/flowequation.py (revision 13455) +@@ -1,4 +1,5 @@ + #module imports ++import copy + import numpy + from fielddisplay import fielddisplay + from EnumDefinitions import * +@@ -80,6 +81,8 @@ + # }}} + + def marshall(self,fid): # {{{ ++ #print "marshalling flowequation-1" ++ #print self.vertex_equation + WriteData(fid,'object',self,'fieldname','ismacayealpattyn','format','Boolean') + WriteData(fid,'object',self,'fieldname','ishutter','format','Boolean') + WriteData(fid,'object',self,'fieldname','isl1l2','format','Boolean') +@@ -88,7 +91,8 @@ + WriteData(fid,'object',self,'fieldname','borderpattyn','format','DoubleMat','mattype',1) + WriteData(fid,'object',self,'fieldname','borderstokes','format','DoubleMat','mattype',1) + #convert approximations to enums +- data=self.vertex_equation ++ ## data=list(self.vertex_equation) ++ data=copy.deepcopy(self.vertex_equation) + data[numpy.nonzero(data==0)]=NoneApproximationEnum() + data[numpy.nonzero(data==1)]=HutterApproximationEnum() + data[numpy.nonzero(data==2)]=MacAyealApproximationEnum() +@@ -99,7 +103,8 @@ + data[numpy.nonzero(data==7)]=PattynStokesApproximationEnum() + data[numpy.nonzero(data==8)]=L1L2ApproximationEnum() + WriteData(fid,'data',data,'enum',FlowequationVertexEquationEnum(),'format','DoubleMat','mattype',1) +- data=self.element_equation ++ ########data=self.element_equation ++ data=copy.deepcopy(self.element_equation) + data[numpy.nonzero(data==0)]=NoneApproximationEnum() + data[numpy.nonzero(data==1)]=HutterApproximationEnum() + data[numpy.nonzero(data==2)]=MacAyealApproximationEnum() +@@ -110,5 +115,7 @@ + data[numpy.nonzero(data==7)]=PattynStokesApproximationEnum() + data[numpy.nonzero(data==8)]=L1L2ApproximationEnum() + WriteData(fid,'data',data,'enum',FlowequationElementEquationEnum(),'format','DoubleMat','mattype',2) ++ #print "marshalling flowequation-4" ++ #print self.vertex_equation + # }}} + +Index: ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py +=================================================================== +--- ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13454) ++++ ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13455) +@@ -1,5 +1,6 @@ + import os + import numpy ++from ContourToMesh import ContourToMesh + + def SetIceShelfBC(md,icefrontfile=''): + """ +@@ -23,8 +24,8 @@ + if icefrontfile: + if not os.path.exists(icefrontfile): + raise IOError("SetIceShelfBC error message: ice front file '%s' not found." % icefrontfile) +- nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,icefrontfile,'node',2) +- nodeonicefront=double(md.mesh.vertexonboundary and nodeinsideicefront) ++ nodeinsideicefront=ContourToMesh((md.mesh.elements).reshape(-1,1),(md.mesh.x).reshape(-1,1),(md.mesh.y).reshape(-1,1),icefrontfile,'node',2) ++ nodeonicefront= numpy.bitwise_and( map(int,md.mesh.vertexonboundary), map(int,nodeinsideicefront[0].ravel()) ) + else: + nodeonicefront=numpy.zeros(md.mesh.numberofvertices) + +Index: ../trunk-jpl/scripts/mToPy.py +=================================================================== +--- ../trunk-jpl/scripts/mToPy.py (revision 0) ++++ ../trunk-jpl/scripts/mToPy.py (revision 13455) +@@ -0,0 +1,52 @@ ++#!/usr/bin/env python ++#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++# ++program = 'mToPy.py' ++version = '1.0' ++versionReleaseDate = '09/24/12' ++origAuthor = 'Mike Pellegrin' ++desc = '\nMain control unit for converting an matlab script file to python' ++# ++# Note: Output will be put in the same (absolute) location as the input. ++#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++# History ++# Date Developer Modification ++#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++# 09/24/12 Michael Pellegrin Initial Release V1.0 ++# ++# ++#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++ ++import sys, os, shutil ++import translateToPy ++import mToPy # touch mToPy to assertain location of installation ++ ++def convert ( inputFile ): ++ try: ++ if os.path.exists( inputFile + '.m') and os.path.isfile( inputFile + '.m'): ++ checkBackupOutputFile( inputFile ) ++ convertMToPy( inputFile ) ++ else: ++ print 'Specified input file: ' + inputFile + '.m doesn\'t appear to exist' ++ finally: ++ print '' ++ ++def convertMToPy ( inputFileName ): ++ translateToPy.convertToPython ( inputFileName + '.m', inputFileName + '.py' ) ++ ++def checkBackupOutputFile ( inputFile ): ++ mFile = inputFile + '.m' ++ pyFile = inputFile + '.py' ++ if os.path.exists( pyFile ): ++ i=1 ++ bkupName = pyFile + str(i) ++ while os.path.exists( bkupName ): ++ i+=1 ++ bkupName = pyFile + str(i) ++ os.rename( pyFile, bkupName ) ++ ++ shutil.copyfile(mFile, pyFile) ++ ++if __name__ == "__main__": ++ convert( sys.argv[1]) ++ + +Property changes on: ../trunk-jpl/scripts/mToPy.py +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/scripts/translateToPy.py +=================================================================== +--- ../trunk-jpl/scripts/translateToPy.py (revision 0) ++++ ../trunk-jpl/scripts/translateToPy.py (revision 13455) +@@ -0,0 +1,220 @@ ++ ++#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++# ++program = 'translateToPy.py' ++version = '1.0' ++versionReleaseDate = '09/24/12' ++origAuthor = 'Mike Pellegrin' ++desc = '\nMatlab script conversion into python' ++# ++#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++# History ++# Date Developer Modification ++#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++# 09/24/12 Michael Pellegrin Initial Release V1.0 ++# ++#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++ ++import codecs, unicodedata ++import sys, re, datetime, os ++import decimal, operator ++ ++ ++outputLocation = sys.stdout ++inputFile = "" ++ ++# other global vars ++indentLevel = 0 ++ ++ ++def setupOutputLocation ( outFile ): ++ if outFile != sys.stdout: ++ globals()['outputLocation'] = open( outFile, 'w' ) # clobber ++ ++def translateFile ( inputFile ): ++ f = codecs.open( inputFile, encoding='utf-8' ) ++ try: ++ for line in f: ++ # print "in: " +line ++ ++ asciiLine = unicodedata.normalize('NFKD', line).encode('ascii','ignore') ++ line = asciiLine ++ ++ translateLine( line ) ++ ++ finally: ++ f.close() ++ ++def translateLine ( line ): ++ ++ if len(line) == 1: # blank line ++ output( line ) ++ ++ elif line.split()[0][0] == '%': # comment line ++ output("# " + line.replace('%','') ) ++ ++ else: # needs cleanup. this is a real-quick-n-dirty implimentation ++ #print line ++ res = line.replace('{','[') ++ res = res.replace('}',']') ++ res = res.replace('model','model()') ++ res = res.replace('SolutionEnum','SolutionEnum()') ++ res = res.replace('StressTensorEnum','StressTensorEnum()') ++ res = res.replace('.par','.py') ++ res = res.replace('=extrude(md,','.extrude(') ++ ++ res = res.replace('thickness(pos)','thickness[pos]') ++ res = res.replace('find(md.','numpy.nonzero(md.') ++ ++ res = res.replace('...','\\') ++ res = res.replace(';','') ++ res = res.replace('\n','') ++ ++ res = convertFieldValues( res ) ++ ++ output(res) ++ ++def convertFieldValues ( currentLine ): ++ # before utilizing regex's {starting w/ eg. \([0-9]\) } for special case: ...(#)... ++ # i noticed what i'm looking for is only TransientSolution(*). So, ... ++ ++ res = currentLine ++ if 'md.results' in currentLine: ++ res = res.replace('(md.results.','md.results[\'') ++ ++ if 'TransientSolution(' in currentLine: # got a TransientSolution([0-9..]) case ++ res = res.replace('TransientSolution(','TransientSolution\'][') ++ parts = res.split(')') ++ res = parts[0] + '][\'' + parts[1].replace('.','') + '\']' + parts[2] ++ ++ else: # handle the other cases for md.results ++ ++ res = res.replace('Solution.Vx)','Solution\'][1][\'Vx\']') ++ res = res.replace('Solution.Vy)','Solution\'][1][\'Vy\']') ++ res = res.replace('Solution.Vz)','Solution\'][1][\'Vz\']') ++ res = res.replace('Solution.Vel)','Solution\'][1][\'Vel\']') ++ ++ res = res.replace('Solution.Pressure)','Solution\'][1][\'Pressure\']') ++ ++ res = res.replace('Solution.StressTensorxx)','Solution\'][1][\'StressTensorxx\']') ++ res = res.replace('Solution.StressTensorxy)','Solution\'][1][\'StressTensorxy\']') ++ res = res.replace('Solution.StressTensoryy)','Solution\'][1][\'StressTensoryy\']') ++ res = res.replace('Solution.StressTensorzz)','Solution\'][1][\'StressTensorzz\']') ++ res = res.replace('Solution.StressTensorxz)','Solution\'][1][\'StressTensorxz\']') ++ res = res.replace('Solution.StressTensoryz)','Solution\'][1][\'StressTensoryz\']') ++ ++ res = res.replace('Solution.Thickness)','Solution\'][1][\'Thickness\']') ++ ++ res = res.replace('Solution.Temperature)','Solution\'][1][\'Temperature\']') ++ ++ res = res.replace('Solution.BasalforcingsMeltingRate)','Solution\'][1][\'BasalforcingsMeltingRate\']') ++ ++ res = res.replace('Solution.SurfaceSlopeX)','Solution\'][1][\'SurfaceSlopeX\']') ++ res = res.replace('Solution.SurfaceSlopeY)','Solution\'][1][\'SurfaceSlopeY\']') ++ res = res.replace('Solution.SurfaceSlopeZ)','Solution\'][1][\'SurfaceSlopeZ\']') ++ ++ res = res.replace('Solution.BedSlopeX)','Solution\'][1][\'BedSlopeX\']') ++ res = res.replace('Solution.BedSlopeY)','Solution\'][1][\'BedSlopeY\']') ++ res = res.replace('Solution.BedSlopeZ)','Solution\'][1][\'BedSlopeZ\']') ++ ++ res = res.replace('Solution.Enthalpy)','Solution\'][1][\'Enthalpy\']') ++ res = res.replace('Solution.Waterfraction)','Solution\'][1][\'Waterfraction\']') ++ res = res.replace('Solution.Temperature)','Solution\'][1][\'Temperature\']') ++ return res ++ ++def output ( line ): ++ numTabs = indentLevel ++ while numTabs: ++ numTabs -= 1 ++ print >> outputLocation, '\t', ++ print >> outputLocation, line ++ ++def outputTopOfSript( inputFile ): ++ ++ global indentLevel ++ ++ output("\"\"\"") ++ output("== == == == == == == == == == == == == == == == == == ==") ++ output("Auto generated python script for ISSM: %s" % (inputFile) ) ++ output("Created on %s via %s Ver %s by %s" % ( datetime.date.today(), program, version, os.getlogin())) ++ output("== == == == == == == == == == == == == == == == == == ==") ++ #output("") ++ output(desc) ++ output("%s Author: Michael Pellegrin" % (program)) ++ output("%s Date: %s" % (program, versionReleaseDate)) ++ output("== == == == == == == == == == == == == == == == == == ==") ++ output("\"\"\"") ++ output("") ++ ++def outputBottomOfScript(): ++ ++ global indentLevel ++ ++ output("") ++ ++def genericImports (): ++ output("from MatlabFuncs import *") ++ output("from model import *") ++ output("from EnumDefinitions import *") ++ output("from numpy import *") ++ ++def createImports ( inputFile ): ++ genericImports() ++ ++ # cycle through eachline to assertain import needs ++ f = codecs.open( inputFile, encoding='utf-8' ) ++ try: ++ for line in f: ++ # print "in: " +line ++ ++ # toss blank lines ++ if len(line) == 1: ++ continue ++ ++ asciiLine = unicodedata.normalize('NFKD', line).encode('ascii','ignore') ++ line = asciiLine ++ ++ for il in importList: ++ if line.find(il) != -1: ++ output( "from %s import *" % (il) ) ++ importList.remove(il) # already got it ++ ++ finally: ++ output("") ++ f.close() ++ ++ ++def initImportList (): ++ global importList ++ ++ importList = [ \ ++ 'triangle' ,\ ++ 'setmask' ,\ ++ 'parameterize' ,\ ++ 'setflowequation' ,\ ++ 'meshconvert' ,\ ++ 'solve' ,\ ++ #'zeros' # -> numpy ++ ] ++ ++ ++ ++def convertToPython ( inFile, outFile = sys.stdout ): ++ #print ' in cnvrt to python w/ file:' + inFile ++ initImportList() ++ setupOutputLocation( outFile ) ++ outputTopOfSript( inFile ) ++ createImports( inFile ) ++ translateFile( inFile ) ++ # outputBottomOfScript() ++ ++ ++if __name__ == "__main__": ++ #print ' in main w/ arg:' + sys.argv[1]+' '+sys.argv[2] ++ if len(sys.argv)==2: ++ convertToPython( sys.argv[1], sys.argv[2] ) ++ else: ++ convertToPython( sys.argv[1] ) ++ ++ ++ + +Property changes on: ../trunk-jpl/scripts/translateToPy.py +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* Index: /issm/oecreview/Archive/13393-13976/ISSM-13455-13456.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13455-13456.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13455-13456.diff (revision 13980) @@ -0,0 +1,20 @@ +Index: ../trunk-jpl/test/NightlyRun/runme.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/runme.py (revision 13455) ++++ ../trunk-jpl/test/NightlyRun/runme.py (revision 13456) +@@ -214,13 +214,13 @@ + directory=os.getcwd().split('/') # not used? + message=me + if strcmpi(output,'nightly'): +- fid=open(os.path.join(ISSM_DIR+'nightlylog','pythonerror.log'), 'a') ++ fid=open(os.path.join(ISSM_DIR+'/nightlylog','pythonerror.log'), 'a') + fid.write('%s' % message) + fid.write('\n------------------------------------------------------------------\n') + fid.close() + print 'FAILURE difference: N/A test id: %i test name: %s field: %s' % (id,id_string,'N/A') + elif strcmpi(output,'daily'): +- fid=open(os.path.join(ISSM_DIR+'dailylog','pythonerror.log'), 'a') ++ fid=open(os.path.join(ISSM_DIR+'/dailylog','pythonerror.log'), 'a') + fid.write('%s' % message) + fid.write('\n------------------------------------------------------------------\n') + fid.close() Index: /issm/oecreview/Archive/13393-13976/ISSM-13456-13457.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13456-13457.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13456-13457.diff (revision 13980) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13456) ++++ ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13457) +@@ -22,7 +22,7 @@ + double *xp = NULL; + int anIndepIndex; + unsigned int * indepIndices = NULL; +- int tangentDirNum = 1; // <----------- set this via config ++ int tangentDirNum = 2; // <----------- set this via config + + + /*AD mode on?: */ +@@ -67,7 +67,7 @@ + anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); + anEDF_for_solverx_p->dp_Y=xNew(anEDF_for_solverx_p->max_m); + anEDF_for_solverx_p->dpp_Y=xNew(anEDF_for_solverx_p->max_m, tangentDirNum); +- /*allocate the space for the parameters to invoke the reverse methods:*/ ++ /*allocate the space for the parameters to invoke the reverse methods:*/ + anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); + anEDF_for_solverx_p->dpp_U=xNew(num_dependents,anEDF_for_solverx_p->max_m); + anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); Index: /issm/oecreview/Archive/13393-13976/ISSM-13457-13458.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13457-13458.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13457-13458.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13457) ++++ ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13458) +@@ -91,7 +91,7 @@ + else { + // full Jacobian or Jacobian projection: + double **jacTimesSeed=xNew(num_dependents,tangentDirNum); +- if (tangentDirNum(num_independents,tangentDirNum); + + // <<<<<<< from here <<<<<<<<<<<< Index: /issm/oecreview/Archive/13393-13976/ISSM-13458-13459.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13458-13459.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13458-13459.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/shared/Alloc/xNewDelete.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Alloc/xNewDelete.h (revision 13458) ++++ ../trunk-jpl/src/c/shared/Alloc/xNewDelete.h (revision 13459) +@@ -76,7 +76,7 @@ + #ifdef USE_CXX_MEMORY_MANAGMENT_FOR_NON_POD_TYPES + T** aT_pp=xNew(dim1,dim2); + for (unsigned int i=0; iFindParam(&isautodiff,AutodiffIsautodiffEnum); + +@@ -32,15 +33,13 @@ + + #ifdef _HAVE_ADOLC_ + ++ if(VerboseAutodiff())_pprintLine_(" start AD driver"); ++ ++ /*preliminary checks: */ + parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); + parameters->FindParam(&num_independents,AutodiffNumIndependentsEnum); +- + if(!(num_dependents*num_independents)) return; +- +- if (tangentDirNum<1 || tangentDirNum>num_independents) { +- _error_("tangentDirNum should be in [1,num_independents]"); // <------------ fix this error message to relate to config +- } +- ++ + /*retrieve state variable: */ + parameters->FindParam(&axp,&dummy,AutodiffXpEnum); + +@@ -53,85 +52,143 @@ + /*get the EDF pointer:*/ + ext_diff_fct *anEDF_for_solverx_p=dynamic_cast * >(parameters->FindParamObject(AdolcParamEnum))->GetParameterValue().myEDF_for_solverx_p; + +- /*set the forward method function pointers: */ +- anEDF_for_solverx_p->zos_forward=EDF_for_solverx; +- anEDF_for_solverx_p->fos_forward=EDF_fos_forward_for_solverx; +- anEDF_for_solverx_p->fov_forward=EDF_fov_forward_for_solverx; +- anEDF_for_solverx_p->fos_reverse=EDF_fos_reverse_for_solverx; +- // anEDF_for_solverx_p->fov_reverse=EDF_fov_reverse_for_solverx; ++ /*Branch according to AD driver: */ ++ parameters->FindParam(&driver,AutodiffDriverEnum); ++ ++ if (strcmp(driver,"fos_forward")==0){ ++ ++ int anIndepIndex; ++ double *tangentDir=NULL; ++ double *jacTimesTangentDir=NULL; ++ double *theOutput=NULL; ++ ++ /*retrieve direction index: */ ++ parameters->FindParam(&anIndepIndex,AutodiffFosForwardIndexEnum); ++ ++ tangentDir=xNewZeroInit(num_independents); ++ tangentDir[anIndepIndex]=1.0; + +- /*allocate the space for the parameters to invoke the forward methods:*/ +- anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); +- anEDF_for_solverx_p->dp_X=xNew(anEDF_for_solverx_p->max_n); +- anEDF_for_solverx_p->dpp_X=xNew(anEDF_for_solverx_p->max_n, tangentDirNum); +- anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dp_Y=xNew(anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dpp_Y=xNew(anEDF_for_solverx_p->max_m, tangentDirNum); +- /*allocate the space for the parameters to invoke the reverse methods:*/ +- anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dpp_U=xNew(num_dependents,anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); +- anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,anEDF_for_solverx_p->max_n); ++ jacTimesTangentDir=xNew(num_dependents); ++ theOutput=xNew(num_dependents); ++ ++ /*set the forward method function pointers: */ ++ anEDF_for_solverx_p->zos_forward=EDF_for_solverx; ++ anEDF_for_solverx_p->fos_forward=EDF_fos_forward_for_solverx; ++ anEDF_for_solverx_p->fos_reverse=EDF_fos_reverse_for_solverx; + +- /* Call AD driver:*/ +- if (tangentDirNum==1) { +- // single direction: +- double *tangentDir=xNewZeroInit(num_independents); +- parameters->FindParam(&anIndepIndex,AutodiffFosForwardIndexEnum); +- tangentDir[anIndepIndex]=1.0; +- double *jacTimesTangentDir=xNew(num_dependents); +- double *theOutput=xNew(num_dependents); +- if (fos_forward(1,num_dependents,num_independents, 0, xp, tangentDir, theOutput, jacTimesTangentDir )) +- _error_("fos_forward returned non-zero error code"); +- results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,jacTimesTangentDir,num_dependents,1,1,0.0)); +- xDelete(theOutput); +- xDelete(jacTimesTangentDir); +- xDelete(tangentDir); ++ /*allocate the space for the parameters to invoke the forward methods:*/ ++ anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dp_X=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dpp_X=xNew(anEDF_for_solverx_p->max_n, 1); ++ anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dp_Y=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dpp_Y=xNew(anEDF_for_solverx_p->max_m, 1); ++ ++ /*allocate the space for the parameters to invoke the reverse methods:*/ ++ anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dpp_U=xNew(num_dependents,anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,anEDF_for_solverx_p->max_n); ++ ++ /*call driver: */ ++ if (fos_forward(1,num_dependents,num_independents, 0, xp, tangentDir, theOutput, jacTimesTangentDir )) _error_("fos_forward returned non-zero error code"); ++ ++ /*add to results*/ ++ results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,jacTimesTangentDir,num_dependents,1,1,0.0)); ++ ++ /*free ressources :*/ ++ xDelete(theOutput); ++ xDelete(jacTimesTangentDir); ++ xDelete(tangentDir); + } +- else { +- // full Jacobian or Jacobian projection: +- double **jacTimesSeed=xNew(num_dependents,tangentDirNum); +- if (tangentDirNum(num_independents,tangentDirNum); ++ else if ((strcmp(driver,"fov_forward")==0) || (strcmp(driver,"fov_forward")==0)){ ++ ++ int* indepIndices=NULL; ++ int tangentDirNum; ++ int dummy; ++ double **jacTimesSeed=NULL; ++ double **seed=NULL; ++ double *theOutput=NULL; ++ std::set anIndexSet; + +- // <<<<<<< from here <<<<<<<<<<<< +- unsigned int * indepIndices=xNew(tangentDirNum); +- for(int i =0; i< tangentDirNum;++i) { +- indepIndices[i]=i; +- } +- // <<<<<<<< to here << get this vector of independent indices from the config - should be 0 based and ideally also unsigned ++ ++ /*retrieve directions:*/ ++ if (strcmp(driver,"jacobian")==0){ ++ tangentDirNum=num_independents; ++ indepIndices=xNewZeroInit(tangentDirNum); ++ for(i=0;iFindParam(&indepIndices,&tangentDirNum,&dummy,AutodiffFovForwardIndicesEnum); ++ } + +- // collect indices in a set to prevent accidental duplicates as long as we don't do compression: +- std::set anIndexSet; +- for (int i=0; inum_independents) { +- _error_("indepIndices values must be in [0,num_independents-1]"); +- } +- if (anIndexSet.find(indepIndices[i])!=anIndexSet.end()) { +- _error_("duplicate indepIndices values are not allowed until we implement Jacobian decompression"); +- } +- anIndexSet.insert(indepIndices[i]); +- // now populate the seed matrix from the set of independent indices; +- // simple setup with a single 1.0 per column and at most a single 1.0 per row +- seed[indepIndices[i]][i]=1.0; +- } +- double *theOutput=xNew(num_dependents); +- if (fov_forward(1,num_dependents,num_independents, tangentDirNum, xp, seed, theOutput, jacTimesSeed )) { +- _error_("fov_forward returned non-zero error code"); +- } +- xDelete(theOutput); +- xDelete(indepIndices); +- xDelete(seed); +- } +- else { +- if (jacobian(1,num_dependents,num_independents,xp,jacTimesSeed)) { +- _error_("jacobian returned non-zero error code"); +- } +- } +- results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,*jacTimesSeed,num_dependents*tangentDirNum,1,1,0.0)); +- xDelete(jacTimesSeed); ++ /*Some checks: */ ++ if (tangentDirNum<1 || tangentDirNum>num_independents) _error_("tangentDirNum should be in [1,num_independents]"); ++ ++ /* full Jacobian or Jacobian projection:*/ ++ jacTimesSeed=xNew(num_dependents,tangentDirNum); ++ ++ /*set the forward method function pointers: */ ++ anEDF_for_solverx_p->zos_forward=EDF_for_solverx; ++ anEDF_for_solverx_p->fov_forward=EDF_fov_forward_for_solverx; ++ // anEDF_for_solverx_p->fov_reverse=EDF_fov_reverse_for_solverx; ++ ++ /*allocate the space for the parameters to invoke the forward methods:*/ ++ anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dp_X=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dpp_X=xNew(anEDF_for_solverx_p->max_n, tangentDirNum); ++ anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dp_Y=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dpp_Y=xNew(anEDF_for_solverx_p->max_m, tangentDirNum); ++ ++ /*allocate the space for the parameters to invoke the reverse methods:*/ ++ anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dpp_U=xNew(num_dependents,anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,anEDF_for_solverx_p->max_n); ++ ++ /*seed matrix: */ ++ seed=xNewZeroInit(num_independents,tangentDirNum); ++ ++ /*collect indices in a set to prevent accidental duplicates as long as we don't do compression:*/ ++ for (int i=0; inum_independents) { ++ _error_("indepIndices values must be in [0,num_independents-1]"); ++ } ++ if (anIndexSet.find(indepIndices[i])!=anIndexSet.end()) { ++ _error_("duplicate indepIndices values are not allowed until we implement Jacobian decompression"); ++ } ++ anIndexSet.insert(indepIndices[i]); ++ /* now populate the seed matrix from the set of independent indices; ++ * simple setup with a single 1.0 per column and at most a single 1.0 per row*/ ++ seed[indepIndices[i]][i]=1.0; ++ } ++ ++ /*allocate output: */ ++ theOutput=xNew(num_dependents); ++ ++ /*call driver: */ ++ if (strcmp(driver,"fov_forward")==0){ ++ if (fov_forward(1,num_dependents,num_independents, tangentDirNum, xp, seed, theOutput, jacTimesSeed )) _error_("fov_forward returned non-zero error code"); ++ } ++ else{ ++ if (jacobian(1,num_dependents,num_independents,xp,jacTimesSeed)) _error_("jacobian returned non-zero error code"); ++ } ++ ++ /*Free ressources: */ ++ xDelete(theOutput); ++ xDelete(indepIndices); ++ xDelete(seed); ++ ++ /*add to results: */ ++ results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,*jacTimesSeed,num_dependents*tangentDirNum,1,1,0.0)); ++ ++ /*Free ressources: */ ++ xDelete(jacTimesSeed); ++ xDelete(indepIndices); + } ++ else _error_("driver: " << driver << " not yet supported!"); + + /* delete the allocated space for the parameters:*/ + xDelete(anEDF_for_solverx_p->dp_x); +@@ -148,6 +205,8 @@ + /*Free ressources: */ + xDelete(xp); + xDelete(axp); ++ ++ if(VerboseAutodiff())_pprintLine_(" end AD driver"); + + #else + _error_("Should not be requesting AD drivers when an AD library is not available!"); +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13460) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13461) +@@ -21,6 +21,9 @@ + int* names=NULL; + int* types=NULL; + int dummy; ++ char* autodiff_driver=NULL; ++ int* indices=NULL; ++ int num_indices; + + IssmDouble* xp=NULL; + IssmDouble* xp_backup=NULL; +@@ -36,8 +39,18 @@ + if(autodiff_analysis){ + + /*retrieve driver: */ ++ iomodel->Constant(&autodiff_driver,AutodiffDriverEnum); + parameters->AddObject(iomodel->CopyConstantObject(AutodiffDriverEnum)); +- parameters->AddObject(iomodel->CopyConstantObject(AutodiffFosForwardIndexEnum)); ++ ++ if(strcmp(autodiff_driver,"fos_forward")==0){ ++ parameters->AddObject(iomodel->CopyConstantObject(AutodiffFosForwardIndexEnum)); ++ } ++ else if(strcmp(autodiff_driver,"fov_forward")==0){ ++ /*Retrieve list of indices: */ ++ iomodel->FetchData(&indices,&num_indices,&dummy,AutodiffFovForwardIndicesEnum); ++ parameters->AddObject(new IntMatParam(AutodiffFovForwardIndicesEnum,indices,num_indices,1)); ++ xDelete(indices); ++ } + + /*Deal with dependents first: {{{*/ + iomodel->Constant(&num_dependent_objects,AutodiffNumDependentObjectsEnum); +@@ -91,5 +104,6 @@ + + /*Assign output pointer: */ + *pparameters=parameters; ++ + } + } +Index: ../trunk-jpl/src/m/classes/autodiff.m +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.m (revision 13460) ++++ ../trunk-jpl/src/m/classes/autodiff.m (revision 13461) +@@ -28,15 +28,26 @@ + if ~obj.isautodiff, return; end + + %Driver value: +- md = checkfield(md,'autodiff.driver','values',{'fos_forward'}); ++ md = checkfield(md,'autodiff.driver','values',{'fos_forward','fov_forward'}); + ++ %go through our dependents and independents and check consistency: ++ for i=1:numel(obj.dependents), ++ dep=obj.dependents{i}; ++ md=checkconsistency(dep,md,solution,analyses); ++ end ++ for i=1:numel(obj.independents), ++ indep=obj.independents{i}; ++ md=checkconsistency(indep,md,i,solution,analyses,obj.driver); ++ end ++ ++ + end % }}} + function disp(obj) % {{{ + disp(sprintf(' automatic differentiation parameters:')); + fielddisplay(obj,'isautodiff','indicates if the automatic differentiation is activated'); + fielddisplay(obj,'dependents','list of dependent variables'); + fielddisplay(obj,'independents','list of independent variables'); +- fielddisplay(obj,'driver','ADOLC driver'); ++ fielddisplay(obj,'driver','ADOLC driver (''fos_forward'' or ''fov_forward'''); + end % }}} + function marshall(obj,fid) % {{{ + +@@ -100,8 +111,31 @@ + end + end + end +- WriteData(fid,'data',index-1,'enum',AutodiffFosForwardIndexEnum(),'format','Integer'); %c-index numbering. ++ index=index-1; %get c-index numbering going ++ WriteData(fid,'data',index,'enum',AutodiffFosForwardIndexEnum(),'format','Integer'); + end ++ %if driver is fov_forward, build indices: ++ if strcmpi(obj.driver,'fov_forward'), ++ indices=0; ++ ++ for i=1:num_independent_objects, ++ indep=obj.independents{i}; ++ if ~isempty(indep.fos_forward_index), ++ indices=indices+indep.fov_forward_indices; ++ break; ++ else ++ if strcmpi(indep.type,'scalar'), ++ indices=indices+1; ++ else ++ indices=indices+indep.nods; ++ end ++ end ++ end ++ indices=indices-1; %get c-indices numbering going ++ ++ WriteData(fid,'data',indices,'enum',AutodiffFovForwardIndicesEnum,'format','IntMat','mattype',3); ++ end ++ + end % }}} + end + end +Index: ../trunk-jpl/src/m/classes/independent.m +=================================================================== +--- ../trunk-jpl/src/m/classes/independent.m (revision 13460) ++++ ../trunk-jpl/src/m/classes/independent.m (revision 13461) +@@ -8,6 +8,7 @@ + name = ''; + type = ''; + fos_forward_index = NaN; ++ fov_forward_indices = []; + nods = 0; + end + methods +@@ -25,14 +26,29 @@ + %do nothing + + end % }}} +- function md = checkconsistency(obj,md,solution,analyses) % {{{ ++ function md = checkconsistency(obj,md,i,solution,analyses,driver) % {{{ + %do nothing for now + if ~isnan(obj.fos_forward_index), ++ if ~strcmpi(driver,'fos_forward'), ++ error('cannot declare an independent with a fos_forward_index when the driver is not fos_forward!'); ++ end + if obj.nods==0, + error('independent checkconsistency error: nods should be set to the size of the independent variable'); + end + end + ++ if ~isempty(obj.fov_forward_indices), ++ if ~strcmpi(driver,'fov_forward'), ++ error('cannot declare an independent with fov_forward_indices when the driver is not fov_forward!'); ++ end ++ ++ if obj.nods==0, ++ error('independent checkconsistency error: nods should be set to the size of the independent variable'); ++ end ++ md = checkfield(md,['autodiff.independents{' num2str(i) '}.fov_forward_indices'],'>=',1,'<=',obj.nods,'size',[NaN 1]); ++ end ++ ++ + end % }}} + function disp(obj) % {{{ + disp(sprintf(' independent variable :')); +@@ -42,7 +58,9 @@ + if ~isnan(obj.fos_forward_index), + fielddisplay(obj,'fos_forward_index','index for fos_foward driver of ADOLC'); + end +- ++ if ~isnan(obj.fov_forward_indices), ++ fielddisplay(obj,'fov_forward_indices','indices for fov_foward driver of ADOLC'); ++ end + end % }}} + function scalar=typetoscalar(obj) % {{{ + if strcmpi(obj.type,'scalar'), +Index: ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13460) ++++ ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13461) +@@ -8,4 +8,4 @@ + % Usage: + % macro=MaximumNumberOfEnums() + +-macro=486; ++macro=487; +Index: ../trunk-jpl/src/m/enum/AutodiffFovForwardIndicesEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffFovForwardIndicesEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffFovForwardIndicesEnum.m (revision 13461) +@@ -0,0 +1,11 @@ ++function macro=AutodiffFovForwardIndicesEnum() ++%AUTODIFFFOVFORWARDINDICESENUM - Enum of AutodiffFovForwardIndices ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffFovForwardIndicesEnum() ++ ++macro=StringToEnum('AutodiffFovForwardIndices'); +Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py +=================================================================== +--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13460) ++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13461) +@@ -158,6 +158,16 @@ + + return StringToEnum('AutodiffFosForwardIndex')[0] + ++def AutodiffFovForwardIndicesEnum(): ++ """ ++ AUTODIFFFOVFORWARDINDICESENUM - Enum of AutodiffFovForwardIndices ++ ++ Usage: ++ macro=AutodiffFovForwardIndicesEnum() ++ """ ++ ++ return StringToEnum('AutodiffFovForwardIndices')[0] ++ + def BalancethicknessSpcthicknessEnum(): + """ + BALANCETHICKNESSSPCTHICKNESSENUM - Enum of BalancethicknessSpcthickness +@@ -4876,5 +4886,5 @@ + macro=MaximumNumberOfEnums() + """ + +- return 486 ++ return 487 + Index: /issm/oecreview/Archive/13393-13976/ISSM-13461-13462.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13461-13462.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13461-13462.diff (revision 13980) @@ -0,0 +1,287 @@ +Index: ../trunk-jpl/src/m/materials/paterson.py +=================================================================== +--- ../trunk-jpl/src/m/materials/paterson.py (revision 13461) ++++ ../trunk-jpl/src/m/materials/paterson.py (revision 13462) +@@ -1,24 +1,23 @@ +-from numpy import * ++import numpy + + def paterson(temperature): ++ """ ++ PATERSON - figure out the rigidity of ice for a given temperature + +- # Local Variables: pos11, pos5, pos10, temperature, pos, T, pos8, pos9, pos6, pos7, pos4, rigidity, pos2, pos3, pos1 +- # Function calls: length, zeros, argwhere, paterson, error +- #PATERSON - figure out the rigidity of ice for a given temperature +- # +- # rigidigty (in s^(1/3)Pa) is the flow law paramter in the flow law sigma=B*e(1/3) (Paterson, p97). +- # temperature is in Kelvin degrees +- # +- # Usage: +- # rigidity=paterson(temperature) +- +- pos=argwhere(temperature<0.) +- if len(pos): +- print 'input temperature should be in Kelvin (positive)' +- return [] +- ++ rigidity (in s^(1/3)Pa) is the flow law paramter in the flow law sigma=B*e(1/3) (Paterson, p97). ++ temperature is in Kelvin degrees ++ ++ Usage: ++ rigidity=paterson(temperature) ++ """ ++ ++ if numpy.any(temperature<0.): ++ raise RuntimeError("input temperature should be in Kelvin (positive)") ++ + T = temperature-273.15 ++ + #The routine below is equivalent to: ++ + # n=3; T=temperature-273; + # %From paterson, + # Temp=[0;-2;-5;-10;-15;-20;-25;-30;-35;-40;-45;-50]; +@@ -30,21 +29,33 @@ + # fittedmodel=fit(Temp,B,'cubicspline'); + # rigidity=fittedmodel(temperature); + +- rigidity=zeros(len(T)) +- pos1=argwhere(T<=-45); rigidity[pos1]=10**8*(-0.000292866376675*(T[pos1]+50)**3+ 0.011672640664130*(T[pos1]+50)**2 -0.325004442485481*(T[pos1]+50)+ 6.524779401948101) +- pos2=argwhere(logical_and(-45<=T,T<-40)); rigidity[pos2]=10**8*(-0.000292866376675*(T[pos2]+45)**3+ 0.007279645014004*(T[pos2]+45)**2 -0.230243014094813*(T[pos2]+45)+ 5.154964909039554) +- pos3=argwhere(logical_and(-40<=T,T<-35)); rigidity[pos3]=10**8*(0.000072737147457*(T[pos3]+40)**3+ 0.002886649363879*(T[pos3]+40)**2 -0.179411542205399*(T[pos3]+40)+ 4.149132666831214) +- pos4=argwhere(logical_and(-35<=T,T<-30)); rigidity[pos4]=10**8*(-0.000086144770023*(T[pos4]+35)**3+ 0.003977706575736*(T[pos4]+35)**2 -0.145089762507325*(T[pos4]+35)+ 3.333333333333331) +- pos5=argwhere(logical_and(-30<=T,T<-25)); rigidity[pos5]=10**8*(-0.000043984685769*(T[pos5]+30)**3+ 0.002685535025386*(T[pos5]+30)**2 -0.111773554501713*(T[pos5]+30)+ 2.696559088937191) +- pos6=argwhere(logical_and(-25<=T,T<-20)); rigidity[pos6]=10**8*(-0.000029799523463*(T[pos6]+25)**3+ 0.002025764738854*(T[pos6]+25)**2 -0.088217055680511*(T[pos6]+25)+ 2.199331606342181) +- pos7=argwhere(logical_and(-20<=T,T<-15)); rigidity[pos7]=10**8*(0.000136920904777*(T[pos7]+20)**3+ 0.001578771886910*(T[pos7]+20)**2 -0.070194372551690*(T[pos7]+20)+ 1.805165505978111) +- pos8=argwhere(logical_and(-15<=T,T<-10)); rigidity[pos8]=10**8*(-0.000899763781026*(T[pos8]+15)**3+ 0.003632585458564*(T[pos8]+15)**2 -0.044137585824322*(T[pos8]+15)+ 1.510778053489523) +- pos9=argwhere(logical_and(-10<=T,T<-5)); rigidity[pos9]=10**8*(0.001676964325070*(T[pos9]+10)**3- 0.009863871256831*(T[pos9]+10)**2 -0.075294014815659*(T[pos9]+10)+ 1.268434288203714) +- pos10=argwhere(logical_and(-5<=T,T<-2)); rigidity[pos10]=10**8*(-0.003748937622487*(T[pos10]+5)**3+0.015290593619213*(T[pos10]+5)**2 -0.048160403003748*(T[pos10]+5)+ 0.854987973338348) +- pos11=argwhere(-2<=T); rigidity[pos11]=10**8*(-0.003748937622488*(T[pos11]+2)**3-0.018449844983174*(T[pos11]+2)**2 -0.057638157095631*(T[pos11]+2)+ 0.746900791092860) ++ rigidity=numpy.zeros((numpy.size(T,axis=0),1)) ++ pos1=numpy.nonzero(T<=-45) ++ rigidity[pos1]=10**8*(-0.000292866376675*(T[pos1]+50)**3+ 0.011672640664130*(T[pos1]+50)**2 -0.325004442485481*(T[pos1]+50)+ 6.524779401948101) ++ pos2=numpy.nonzero(numpy.logical_and(-45<=T,T<-40)) ++ rigidity[pos2]=10**8*(-0.000292866376675*(T[pos2]+45)**3+ 0.007279645014004*(T[pos2]+45)**2 -0.230243014094813*(T[pos2]+45)+ 5.154964909039554) ++ pos3=numpy.nonzero(numpy.logical_and(-40<=T,T<-35)) ++ rigidity[pos3]=10**8*(0.000072737147457*(T[pos3]+40)**3+ 0.002886649363879*(T[pos3]+40)**2 -0.179411542205399*(T[pos3]+40)+ 4.149132666831214) ++ pos4=numpy.nonzero(numpy.logical_and(-35<=T,T<-30)) ++ rigidity[pos4]=10**8*(-0.000086144770023*(T[pos4]+35)**3+ 0.003977706575736*(T[pos4]+35)**2 -0.145089762507325*(T[pos4]+35)+ 3.333333333333331) ++ pos5=numpy.nonzero(numpy.logical_and(-30<=T,T<-25)) ++ rigidity[pos5]=10**8*(-0.000043984685769*(T[pos5]+30)**3+ 0.002685535025386*(T[pos5]+30)**2 -0.111773554501713*(T[pos5]+30)+ 2.696559088937191) ++ pos6=numpy.nonzero(numpy.logical_and(-25<=T,T<-20)) ++ rigidity[pos6]=10**8*(-0.000029799523463*(T[pos6]+25)**3+ 0.002025764738854*(T[pos6]+25)**2 -0.088217055680511*(T[pos6]+25)+ 2.199331606342181) ++ pos7=numpy.nonzero(numpy.logical_and(-20<=T,T<-15)) ++ rigidity[pos7]=10**8*(0.000136920904777*(T[pos7]+20)**3+ 0.001578771886910*(T[pos7]+20)**2 -0.070194372551690*(T[pos7]+20)+ 1.805165505978111) ++ pos8=numpy.nonzero(numpy.logical_and(-15<=T,T<-10)) ++ rigidity[pos8]=10**8*(-0.000899763781026*(T[pos8]+15)**3+ 0.003632585458564*(T[pos8]+15)**2 -0.044137585824322*(T[pos8]+15)+ 1.510778053489523) ++ pos9=numpy.nonzero(numpy.logical_and(-10<=T,T<-5)) ++ rigidity[pos9]=10**8*(0.001676964325070*(T[pos9]+10)**3- 0.009863871256831*(T[pos9]+10)**2 -0.075294014815659*(T[pos9]+10)+ 1.268434288203714) ++ pos10=numpy.nonzero(numpy.logical_and(-5<=T,T<-2)) ++ rigidity[pos10]=10**8*(-0.003748937622487*(T[pos10]+5)**3+0.015290593619213*(T[pos10]+5)**2 -0.048160403003748*(T[pos10]+5)+ 0.854987973338348) ++ pos11=numpy.nonzero(-2<=T) ++ rigidity[pos11]=10**8*(-0.003748937622488*(T[pos11]+2)**3-0.018449844983174*(T[pos11]+2)**2 -0.057638157095631*(T[pos11]+2)+ 0.746900791092860) + + #Now make sure that rigidity is positive +- pos=argwhere(rigidity<0); rigidity[pos]=1**6 ++ pos=numpy.nonzero(rigidity<0) ++ rigidity[pos]=1**6 + + return rigidity + +Index: ../trunk-jpl/src/m/materials/paterson.m +=================================================================== +--- ../trunk-jpl/src/m/materials/paterson.m (revision 13461) ++++ ../trunk-jpl/src/m/materials/paterson.m (revision 13462) +@@ -1,7 +1,7 @@ + function rigidity=paterson(temperature) + %PATERSON - figure out the rigidity of ice for a given temperature + % +-% rigidigty (in s^(1/3)Pa) is the flow law paramter in the flow law sigma=B*e(1/3) (Paterson, p97). ++% rigidity (in s^(1/3)Pa) is the flow law paramter in the flow law sigma=B*e(1/3) (Paterson, p97). + % temperature is in Kelvin degrees + % + % Usage: +Index: ../trunk-jpl/src/m/solve/parseresultsfromdisk.py +=================================================================== +--- ../trunk-jpl/src/m/solve/parseresultsfromdisk.py (revision 13461) ++++ ../trunk-jpl/src/m/solve/parseresultsfromdisk.py (revision 13462) +@@ -51,7 +51,7 @@ + if result['step'] in results and \ + result['fieldname'] in results[result['step']] and \ + not strcmp(result['fieldname'],'SolutionType'): +- results[result['step']][result['fieldname']]=numpy.concatenate((results[result['step']][result['fieldname']],result['field']),axis=0) ++ results[result['step']][result['fieldname']]=numpy.vstack((results[result['step']][result['fieldname']],result['field'])) + else: + results[result['step']][result['fieldname']]=result['field'] + +Index: ../trunk-jpl/src/m/classes/thermal.py +=================================================================== +--- ../trunk-jpl/src/m/classes/thermal.py (revision 13461) ++++ ../trunk-jpl/src/m/classes/thermal.py (revision 13462) +@@ -71,11 +71,8 @@ + md = checkfield(md,'thermal.spctemperature','forcing',1) + if EnthalpyAnalysisEnum() in analyses and (md.thermal.isenthalpy or solution==EnthalpySolutionEnum()) and md.mesh.dimension==3: + pos=numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices]))) +-# need to know if md.thermal.spctemperature can have multiple columns? +-# replicate=numpy.tile(md.geometry.surface-md.mesh.z,(1,numpy.size(md.thermal.spctemperature,axis=1))) +-# md = checkfield(md,'thermal.spctemperature[numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices,:])))]','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") +- replicate=numpy.tile(md.geometry.surface-md.mesh.z,(1)) +- md = checkfield(md,'thermal.spctemperature[numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices])))]','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") ++ replicate=numpy.tile(md.geometry.surface-md.mesh.z,(1,numpy.size(md.thermal.spctemperature,axis=1))) ++ md = checkfield(md,'thermal.spctemperature[numpy.nonzero(numpy.logical_not(numpy.isnan(md.thermal.spctemperature[0:md.mesh.numberofvertices,:])))]','<',md.materials.meltingpoint-md.materials.beta*md.materials.rho_ice*md.constants.g*replicate[pos],'message',"spctemperature should be below the adjusted melting point") + md = checkfield(md,'thermal.isenthalpy','numel',[1],'values',[0,1]) + + return md +Index: ../trunk-jpl/src/m/classes/model/model.py +=================================================================== +--- ../trunk-jpl/src/m/classes/model/model.py (revision 13461) ++++ ../trunk-jpl/src/m/classes/model/model.py (revision 13462) +@@ -241,7 +241,7 @@ + x3d=numpy.concatenate((x3d,md.mesh.x)) + y3d=numpy.concatenate((y3d,md.mesh.y)) + #nodes are distributed between bed and surface accordingly to the given exponent +- z3d=numpy.concatenate((z3d,bed3d+thickness3d*extrusionlist[i])) ++ z3d=numpy.concatenate((z3d,(bed3d+thickness3d*extrusionlist[i]).reshape(-1))) + number_nodes3d=numpy.size(x3d) #number of 3d nodes for the non extruded part of the mesh + + #Extrude elements +@@ -401,7 +401,7 @@ + + #Put lithostatic pressure if there is an existing pressure + if not numpy.any(numpy.isnan(md.initialization.pressure)): +- md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.z) ++ md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.z.reshape(-1,1)) + + #special for thermal modeling: + md.basalforcings.melting_rate=project3d(md,'vector',md.basalforcings.melting_rate,'type','node','layer',1) +Index: ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py +=================================================================== +--- ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13461) ++++ ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13462) +@@ -1,12 +1,12 @@ + import os + import numpy +-from ContourToMesh import ContourToMesh ++from ContourToMesh import * + + def SetIceShelfBC(md,icefrontfile=''): + """ + SETICESHELFBC - Create the boundary conditions for diagnostic and thermal models for a Ice Shelf with Ice Front + +- Neumann BC are used on the ice front (an ANRGUS contour around the ice front ++ Neumann BC are used on the ice front (an ARGUS contour around the ice front + must be given in input) + Dirichlet BC are used elsewhere for diagnostic + +@@ -24,23 +24,23 @@ + if icefrontfile: + if not os.path.exists(icefrontfile): + raise IOError("SetIceShelfBC error message: ice front file '%s' not found." % icefrontfile) +- nodeinsideicefront=ContourToMesh((md.mesh.elements).reshape(-1,1),(md.mesh.x).reshape(-1,1),(md.mesh.y).reshape(-1,1),icefrontfile,'node',2) ++ nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),icefrontfile,'node',2) + nodeonicefront= numpy.bitwise_and( map(int,md.mesh.vertexonboundary), map(int,nodeinsideicefront[0].ravel()) ) + else: +- nodeonicefront=numpy.zeros(md.mesh.numberofvertices) ++ nodeonicefront=numpy.zeros((md.mesh.numberofvertices,1)) + + # pos=find(md.mesh.vertexonboundary & ~nodeonicefront); + pos=[i for i,(vob,noif) in enumerate(zip(md.mesh.vertexonboundary,nodeonicefront)) if vob and not noif] +- md.diagnostic.spcvx=float('NaN')*numpy.ones(md.mesh.numberofvertices) +- md.diagnostic.spcvy=float('NaN')*numpy.ones(md.mesh.numberofvertices) +- md.diagnostic.spcvz=float('NaN')*numpy.ones(md.mesh.numberofvertices) ++ md.diagnostic.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) ++ md.diagnostic.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) ++ md.diagnostic.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvx[pos]=0 + md.diagnostic.spcvy[pos]=0 + md.diagnostic.spcvz[pos]=0 + md.diagnostic.referential=float('NaN')*numpy.ones((md.mesh.numberofvertices,6)) + + #Dirichlet Values +- if numpy.size(md.inversion.vx_obs)==md.mesh.numberofvertices and numpy.size(md.inversion.vy_obs)==md.mesh.numberofvertices: ++ if isinstance(md.inversion.vx_obs,numpy.ndarray) and numpy.size(md.inversion.vx_obs,axis=0)==md.mesh.numberofvertices and isinstance(md.inversion.vy_obs,numpy.ndarray) and numpy.size(md.inversion.vy_obs,axis=0)==md.mesh.numberofvertices: + print ' boundary conditions for diagnostic model: spc set as observed velocities' + md.diagnostic.spcvx[pos]=md.inversion.vx_obs[pos] + md.diagnostic.spcvy[pos]=md.inversion.vy_obs[pos] +@@ -55,43 +55,43 @@ + pressureload=md.mesh.segments[pos,:] + elif md.mesh.dimension==3: + # pressureload_layer1=[md.mesh.segments(pos,1:2) md.mesh.segments(pos,2)+md.mesh.numberofvertices2d md.mesh.segments(pos,1)+md.mesh.numberofvertices2d md.mesh.segments(pos,3)]; +- pressureload_layer1=numpy.concatenate((md.mesh.segments[pos,0:2],md.mesh.segments[pos,1]+md.mesh.numberofvertices2d,md.mesh.segments[pos,0]+md.mesh.numberofvertices2d,md.mesh.segments[pos,2]),axis=1) ++ pressureload_layer1=numpy.hstack((md.mesh.segments[pos,0:2],md.mesh.segments[pos,1]+md.mesh.numberofvertices2d,md.mesh.segments[pos,0]+md.mesh.numberofvertices2d,md.mesh.segments[pos,2])) + pressureload=numpy.zeros((0,5)) + for i in xrange(1,md.mesh.numberoflayers): + # pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.mesh.numberofvertices2d pressureload_layer1(:,5)+(i-1)*md.mesh.numberofelements2d ]; +- pressureload=numpy.concatenate((pressureload,numpy.concatenate((pressureload_layer1[:,0:3]+(i-1)*md.mesh.numberofvertices2d,pressureload_layer1[:,4]+(i-1)*md.mesh.numberofelements2d),axis=1)),axis=0) ++ pressureload=numpy.vstack((pressureload,numpy.hstack((pressureload_layer1[:,0:3]+(i-1)*md.mesh.numberofvertices2d,pressureload_layer1[:,4]+(i-1)*md.mesh.numberofelements2d)))) + + #Add water or air enum depending on the element + # pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))]; +- pressureload=numpy.concatenate((pressureload,1*md.mask.elementonfloatingice[pressureload[:,-1].astype('int')-1].reshape((-1,1))),axis=1) ++ pressureload=numpy.hstack((pressureload,1*md.mask.elementonfloatingice[pressureload[:,-1].astype('int')-1].reshape((-1,1)))) + + #plug onto model + md.diagnostic.icefront=pressureload + + #Create zeros basalforcings and surfaceforcings + if numpy.all(numpy.isnan(md.surfaceforcings.precipitation)) and (md.surfaceforcings.ispdd==1): +- md.surfaceforcings.precipitation=numpy.zeros(md.mesh.numberofvertices) ++ md.surfaceforcings.precipitation=numpy.zeros((md.mesh.numberofvertices,1)) + print ' no surfaceforcings.precipitation specified: values set as zero' + if numpy.all(numpy.isnan(md.surfaceforcings.mass_balance)) and (md.surfaceforcings.ispdd==0): +- md.surfaceforcings.mass_balance=numpy.zeros(md.mesh.numberofvertices) ++ md.surfaceforcings.mass_balance=numpy.zeros((md.mesh.numberofvertices,1)) + print ' no surfaceforcings.mass_balance specified: values set as zero' + if numpy.all(numpy.isnan(md.basalforcings.melting_rate)): +- md.basalforcings.melting_rate=numpy.zeros(md.mesh.numberofvertices) ++ md.basalforcings.melting_rate=numpy.zeros((md.mesh.numberofvertices,1)) + print ' no basalforcings.melting_rate specified: values set as zero' + if numpy.all(numpy.isnan(md.balancethickness.thickening_rate)): +- md.balancethickness.thickening_rate=numpy.zeros(md.mesh.numberofvertices) ++ md.balancethickness.thickening_rate=numpy.zeros((md.mesh.numberofvertices,1)) + print ' no balancethickness.thickening_rate specified: values set as zero' + +- md.prognostic.spcthickness=float('NaN')*numpy.ones(md.mesh.numberofvertices) +- md.balancethickness.spcthickness=float('NaN')*numpy.ones(md.mesh.numberofvertices) ++ md.prognostic.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) ++ md.balancethickness.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + + if numpy.size(md.initialization.temperature)==md.mesh.numberofvertices: +- md.thermal.spctemperature=float('NaN')*numpy.ones(md.mesh.numberofvertices) ++ md.thermal.spctemperature=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) + # pos=find(md.mesh.vertexonsurface); md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface + pos=[i for i,vos in enumerate(md.mesh.vertexonsurface) if vos] + md.thermal.spctemperature[pos]=md.initialization.temperature[pos] # impose observed temperature on surface + if not numpy.size(md.basalforcings.geothermalflux)==md.mesh.numberofvertices: +- md.basalforcings.geothermalflux=numpy.zeros(md.mesh.numberofvertices) ++ md.basalforcings.geothermalflux=numpy.zeros((md.mesh.numberofvertices,1)) + else: + print ' no thermal boundary conditions created: no observed temperature found' + +Index: ../trunk-jpl/src/m/parameterization/setflowequation.py +=================================================================== +--- ../trunk-jpl/src/m/parameterization/setflowequation.py (revision 13461) ++++ ../trunk-jpl/src/m/parameterization/setflowequation.py (revision 13462) +@@ -93,10 +93,10 @@ + fullspcnodes=numpy.logical_or(numpy.logical_not(numpy.isnan(md.diagnostic.spcvx)).astype(int)+ \ + numpy.logical_not(numpy.isnan(md.diagnostic.spcvy)).astype(int)+ \ + numpy.logical_not(numpy.isnan(md.diagnostic.spcvz)).astype(int)==3, \ +- numpy.logical_and(nodeonpattyn,nodeonstokes)).astype(int) #find all the nodes on the boundary of the domain without icefront ++ numpy.logical_and(nodeonpattyn,nodeonstokes).reshape(-1,1)).astype(int) #find all the nodes on the boundary of the domain without icefront + # fullspcelems=double(sum(fullspcnodes(md.mesh.elements),2)==6); %find all the nodes on the boundary of the domain without icefront + fullspcelems=(numpy.sum(fullspcnodes[md.mesh.elements.astype(int)-1],axis=1)==6).astype(int) #find all the nodes on the boundary of the domain without icefront +- stokesflag[numpy.nonzero(fullspcelems)]=0 ++ stokesflag[numpy.nonzero(fullspcelems.reshape(-1))]=0 + nodeonstokes[md.mesh.elements[numpy.nonzero(stokesflag),:].astype(int)-1]=1 + + #Then complete with NoneApproximation or the other model used if there is no stokes +@@ -128,7 +128,7 @@ + if numpy.all(numpy.logical_not(numpy.isnan(bordernodes2d))): + penalties=numpy.zeros((0,2)) + for i in xrange(1,numlayers): +- penalties=numpy.concatenate((penalties,numpy.concatenate((bordernodes2d,bordernodes2d+md.mesh.numberofvertices2d*(i)),axis=1)),axis=0) ++ penalties=numpy.vstack((penalties,numpy.hstack((bordernodes2d,bordernodes2d+md.mesh.numberofvertices2d*(i))))) + md.diagnostic.vertex_pairing=penalties + + elif strcmpi(coupling_method,'tiling'): Index: /issm/oecreview/Archive/13393-13976/ISSM-13462-13463.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13462-13463.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13462-13463.diff (revision 13980) @@ -0,0 +1,161 @@ +Index: ../trunk-jpl/test/Par/SquareShelfConstrained.py +=================================================================== +--- ../trunk-jpl/test/Par/SquareShelfConstrained.py (revision 13462) ++++ ../trunk-jpl/test/Par/SquareShelfConstrained.py (revision 13463) +@@ -14,7 +14,7 @@ + ymin = min(md.mesh.y) + ymax = max(md.mesh.y) + +-md.geometry.thickness = hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin) ++md.geometry.thickness = hmax+(hmin-hmax)*(md.mesh.y.reshape(-1,1)-ymin)/(ymax-ymin) + md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness + md.geometry.surface = md.geometry.bed+md.geometry.thickness + +@@ -25,28 +25,26 @@ + y=reshape(f.variables['y'][:],(-1)) + vx=f.variables['vx'][:] + vy=f.variables['vy'][:] +-#deal with 'F' oriented matlab matrices! +-index=f.variables['index'][:].astype(float) +-index=reshape(index.T,(len(index),3),order='F') ++index=f.variables['index'][:] + f.close() + + [md.initialization.vx] = InterpFromMeshToMesh2d(index, x, y, vx, md.mesh.x, md.mesh.y) + [md.initialization.vy] = InterpFromMeshToMesh2d(index, x, y, vy, md.mesh.x, md.mesh.y) +-md.initialization.vz = zeros(md.mesh.numberofvertices) +-md.initialization.pressure = zeros(md.mesh.numberofvertices) ++md.initialization.vz = zeros((md.mesh.numberofvertices,1)) ++md.initialization.pressure = zeros((md.mesh.numberofvertices,1)) + #Materials +-md.initialization.temperature = (273.-20)*ones(md.mesh.numberofvertices) ++md.initialization.temperature = (273.-20.)*ones((md.mesh.numberofvertices,1)) + md.materials.rheology_B = paterson(md.initialization.temperature) +-md.materials.rheology_n = 3.*ones(md.mesh.numberofelements) ++md.materials.rheology_n = 3.*ones((md.mesh.numberofelements,1)) + #Surface mass balance and basal melting +-md.surfaceforcings.mass_balance = 10.*ones(md.mesh.numberofvertices) +-md.basalforcings.melting_rate = 5.*ones(md.mesh.numberofvertices) ++md.surfaceforcings.mass_balance = 10.*ones((md.mesh.numberofvertices,1)) ++md.basalforcings.melting_rate = 5.*ones((md.mesh.numberofvertices,1)) + #Friction + pos = nonzero(md.mask.elementonfloatingice) +-md.friction.coefficient = 20.*ones(md.mesh.numberofvertices) ++md.friction.coefficient = 20.*ones((md.mesh.numberofvertices,1)) + md.friction.coefficient[md.mesh.elements[pos,:].astype(int)-1] =0. +-md.friction.p = ones(md.mesh.numberofelements) +-md.friction.q = ones(md.mesh.numberofelements) ++md.friction.p = ones((md.mesh.numberofelements,1)) ++md.friction.q = ones((md.mesh.numberofelements,1)) + #Numerical parameters + md.diagnostic.viscosity_overshoot = 0.0 + md.prognostic.stabilization = 1. +@@ -56,7 +54,7 @@ + md.diagnostic.restol = 0.05 + md.diagnostic.reltol = 0.05 + md.steadystate.reltol = 0.05 +-md.diagnostic.abstol = nan ++md.diagnostic.abstol = float('nan') + md.timestepping.time_step = 1. + md.timestepping.final_time = 3. + #Deal with boundary conditions: +Index: ../trunk-jpl/test/Par/Pig.py +=================================================================== +--- ../trunk-jpl/test/Par/Pig.py (revision 0) ++++ ../trunk-jpl/test/Par/Pig.py (revision 13463) +@@ -0,0 +1,63 @@ ++import os.path ++import inspect ++import netCDF4 ++from numpy import * ++from verbose import * ++from InterpFromMeshToMesh2d import InterpFromMeshToMesh2d ++from paterson import * ++from SetIceShelfBC import * ++ ++#Start defining model parameters here ++ ++#Geometry and observation ++f = netCDF4.Dataset('../Data/Pig.nc','r') ++x = reshape(f.variables['x'][:],(-1)) ++y = reshape(f.variables['y'][:],(-1)) ++vx_obs = f.variables['vx_obs'][:] ++vy_obs = f.variables['vy_obs'][:] ++index = f.variables['index'][:] ++surface = f.variables['surface'][:] ++thickness = f.variables['thickness'][:] ++f.close() ++ ++[md.inversion.vx_obs] =InterpFromMeshToMesh2d(index,x,y,vx_obs,md.mesh.x,md.mesh.y) ++[md.inversion.vy_obs] =InterpFromMeshToMesh2d(index,x,y,vy_obs,md.mesh.x,md.mesh.y) ++[md.geometry.surface] =InterpFromMeshToMesh2d(index,x,y,surface,md.mesh.x,md.mesh.y) ++[md.geometry.thickness]=InterpFromMeshToMesh2d(index,x,y,thickness,md.mesh.x,md.mesh.y) ++md.geometry.bed=md.geometry.surface-md.geometry.thickness ++md.initialization.vx=md.inversion.vx_obs ++md.initialization.vy=md.inversion.vy_obs ++md.initialization.vz=zeros((md.mesh.numberofvertices,1)) ++md.initialization.pressure=zeros((md.mesh.numberofvertices,1)) ++ ++#Materials ++md.initialization.temperature=(273.-20.)*ones((md.mesh.numberofvertices,1)) ++md.materials.rheology_B=paterson(md.initialization.temperature) ++md.materials.rheology_n=3.*ones((md.mesh.numberofelements,1)) ++md.initialization.temperature=md.initialization.temperature ++ ++#Friction ++pos=numpy.nonzero(md.mask.elementonfloatingice) ++md.friction.coefficient=50.*ones((md.mesh.numberofvertices,1)) ++md.friction.coefficient[md.mesh.elements[pos].astype(int)-1]=0. ++md.friction.p=ones((md.mesh.numberofelements,1)) ++md.friction.q=ones((md.mesh.numberofelements,1)) ++ ++#Numerical parameters ++md.diagnostic.viscosity_overshoot=0.3 ++md.prognostic.stabilization=1. ++md.verbose=verbose(0) ++md.settings.waitonlock=30. ++md.timestepping.time_step=1. ++md.timestepping.final_time=2. ++md.diagnostic.restol=0.05 ++md.diagnostic.reltol=1. ++md.steadystate.reltol=1. ++md.diagnostic.abstol=float('nan') ++ ++#Boundary conditions: ++#md=SetMarineIceSheetBC(md) ++ ++#Change name so that no test have the same name ++if len(inspect.stack()) > 2: ++ md.miscellaneous.name = os.path.basename(inspect.stack()[2][1]).split('.')[0] + +Property changes on: ../trunk-jpl/test/Par/Pig.py +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/test/NightlyRun/test121.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test121.py (revision 13462) ++++ ../trunk-jpl/test/NightlyRun/test121.py (revision 13463) +@@ -13,7 +13,7 @@ + md.extrude(3,1) + md=setflowequation(md,'macayeal','all') + md.cluster=generic('name',oshostname(),'np',3); +-md.initialization.waterfraction=numpy.zeros(md.mesh.numberofvertices) ++md.initialization.waterfraction=numpy.zeros((md.mesh.numberofvertices,1)) + md.transient.isdiagnostic=0 + md.transient.isprognostic=0 + md.transient.isthermal=1 +Index: ../trunk-jpl/test/NightlyRun/test122.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test122.py (revision 13462) ++++ ../trunk-jpl/test/NightlyRun/test122.py (revision 13463) +@@ -12,7 +12,7 @@ + md=parameterize(md,'../Par/SquareShelfConstrained.py') + md.extrude(3,1) + md=setflowequation(md,'pattyn','all') +-md.initialization.waterfraction=numpy.zeros(md.mesh.numberofvertices) ++md.initialization.waterfraction=numpy.zeros((md.mesh.numberofvertices,1)) + md.thermal.isenthalpy=1 + md.thermal.stabilization=2 + md.cluster=generic('name',oshostname(),'np',3) Index: /issm/oecreview/Archive/13393-13976/ISSM-13463-13464.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13463-13464.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13463-13464.diff (revision 13980) @@ -0,0 +1,23 @@ +Index: ../trunk-jpl/src/modules/python/Makefile.am +=================================================================== +--- ../trunk-jpl/src/modules/python/Makefile.am (revision 13463) ++++ ../trunk-jpl/src/modules/python/Makefile.am (revision 13464) +@@ -13,7 +13,6 @@ + InterpFromMeshToMesh2d.la\ + NodeConnectivity.la\ + StringToEnum.la\ +- ContourToMesh.la\ + TriMesh.la + endif + #}}} +@@ -94,10 +93,6 @@ + ../StringToEnum/StringToEnum.h + StringToEnum_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) + +-ContourToMesh_la_SOURCES = ../ContourToMesh/ContourToMesh.cpp\ +- ../ContourToMesh/ContourToMesh.h +-ContourToMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) +- + TriMesh_la_SOURCES = ../TriMesh/TriMesh.cpp\ + ../TriMesh/TriMesh.h + TriMesh_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(TRIANGLELIB) Index: /issm/oecreview/Archive/13393-13976/ISSM-13464-13465.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13464-13465.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13464-13465.diff (revision 13980) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/Par/SquareShelf.py +=================================================================== +--- ../trunk-jpl/test/Par/SquareShelf.py (revision 13464) ++++ ../trunk-jpl/test/Par/SquareShelf.py (revision 13465) +@@ -80,9 +80,7 @@ + + #Boundary conditions: + # #md=SetIceShelfBC(md) +-print '...calling seticeshelfbc:' + md=SetIceShelfBC(md,'../Exp/SquareFront.exp') +-print '...called seticeshelfbc:' + + #Change name so that no test have the same name + if len(inspect.stack()) > 2: +Index: ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py +=================================================================== +--- ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13464) ++++ ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13465) +@@ -24,6 +24,7 @@ + if icefrontfile: + if not os.path.exists(icefrontfile): + raise IOError("SetIceShelfBC error message: ice front file '%s' not found." % icefrontfile) ++ #nodeonicefront= numpy.logical_and( md.mesh.vertexonboundary, nodeinsideicefront.astype(float)) ) + nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),icefrontfile,'node',2) + nodeonicefront= numpy.bitwise_and( map(int,md.mesh.vertexonboundary), map(int,nodeinsideicefront[0].ravel()) ) + else: Index: /issm/oecreview/Archive/13393-13976/ISSM-13465-13466.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13465-13466.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13465-13466.diff (revision 13980) @@ -0,0 +1,46 @@ +Index: ../trunk-jpl/test/Par/SquareShelf.py +=================================================================== +--- ../trunk-jpl/test/Par/SquareShelf.py (revision 13465) ++++ ../trunk-jpl/test/Par/SquareShelf.py (revision 13466) +@@ -14,7 +14,7 @@ + ymin=min(md.mesh.y) + ymax=max(md.mesh.y) + +-md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y-ymin)/(ymax-ymin) ++md.geometry.thickness=hmax+(hmin-hmax)*(md.mesh.y.reshape(-1,1)-ymin)/(ymax-ymin) + md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness + md.geometry.surface=md.geometry.bed+md.geometry.thickness + +@@ -38,8 +38,8 @@ + + [md.initialization.vx]=InterpFromMeshToMesh2d(index,x,y,vx,md.mesh.x,md.mesh.y) + [md.initialization.vy]=InterpFromMeshToMesh2d(index,x,y,vy,md.mesh.x,md.mesh.y) +-md.initialization.vz=zeros(md.mesh.numberofvertices) +-md.initialization.pressure=zeros(md.mesh.numberofvertices) ++md.initialization.vz=zeros((md.mesh.numberofvertices,1)) ++md.initialization.pressure=zeros((md.mesh.numberofvertices,1)) + + #dbg - begin + #print '...vx:' +@@ -54,16 +54,16 @@ + + + #Materials +-md.initialization.temperature = (273.-20.)*ones(md.mesh.numberofvertices) ++md.initialization.temperature = (273.-20.)*ones((md.mesh.numberofvertices,1)) + md.materials.rheology_B = paterson(md.initialization.temperature) +-md.materials.rheology_n = 3.*ones(md.mesh.numberofelements) ++md.materials.rheology_n = 3.*ones((md.mesh.numberofelements,1)) + + #Friction + pos=nonzero(md.mask.elementonfloatingice) +-md.friction.coefficient = 20.*ones(md.mesh.numberofvertices) ++md.friction.coefficient = 20.*ones((md.mesh.numberofvertices,1)) + md.friction.coefficient[md.mesh.elements[pos,:].astype(int)-1] = 0. +-md.friction.p = ones(md.mesh.numberofelements) +-md.friction.q = ones(md.mesh.numberofelements) ++md.friction.p = ones((md.mesh.numberofelements,1)) ++md.friction.q = ones((md.mesh.numberofelements,1)) + + #Numerical parameters + md.diagnostic.viscosity_overshoot = 0.3 Index: /issm/oecreview/Archive/13393-13976/ISSM-13466-13467.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13466-13467.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13466-13467.diff (revision 13980) @@ -0,0 +1,16 @@ +Index: ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py +=================================================================== +--- ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13466) ++++ ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13467) +@@ -24,9 +24,8 @@ + if icefrontfile: + if not os.path.exists(icefrontfile): + raise IOError("SetIceShelfBC error message: ice front file '%s' not found." % icefrontfile) +- #nodeonicefront= numpy.logical_and( md.mesh.vertexonboundary, nodeinsideicefront.astype(float)) ) +- nodeinsideicefront=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),icefrontfile,'node',2) +- nodeonicefront= numpy.bitwise_and( map(int,md.mesh.vertexonboundary), map(int,nodeinsideicefront[0].ravel()) ) ++ [nodeinsideicefront,dum]=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),icefrontfile,'node',2) ++ nodeonicefront=numpy.logical_and(md.mesh.vertexonboundary,nodeinsideicefront).astype(float) + else: + nodeonicefront=numpy.zeros((md.mesh.numberofvertices,1)) + Index: /issm/oecreview/Archive/13393-13976/ISSM-13467-13468.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13467-13468.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13467-13468.diff (revision 13980) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13467) ++++ ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13468) +@@ -91,7 +91,7 @@ + anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,anEDF_for_solverx_p->max_n); + + /*call driver: */ +- if (fos_forward(1,num_dependents,num_independents, 0, xp, tangentDir, theOutput, jacTimesTangentDir )) _error_("fos_forward returned non-zero error code"); ++ fos_forward(1,num_dependents,num_independents, 0, xp, tangentDir, theOutput, jacTimesTangentDir ); + + /*add to results*/ + results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,jacTimesTangentDir,num_dependents,1,1,0.0)); +@@ -170,10 +170,10 @@ + + /*call driver: */ + if (strcmp(driver,"fov_forward")==0){ +- if (fov_forward(1,num_dependents,num_independents, tangentDirNum, xp, seed, theOutput, jacTimesSeed )) _error_("fov_forward returned non-zero error code"); ++ fov_forward(1,num_dependents,num_independents, tangentDirNum, xp, seed, theOutput, jacTimesSeed ); + } + else{ +- if (jacobian(1,num_dependents,num_independents,xp,jacTimesSeed)) _error_("jacobian returned non-zero error code"); ++ jacobian(1,num_dependents,num_independents,xp,jacTimesSeed); + } + + /*Free ressources: */ Index: /issm/oecreview/Archive/13393-13976/ISSM-13468-13469.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13468-13469.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13468-13469.diff (revision 13980) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/src/m/classes/prognostic.py +=================================================================== +--- ../trunk-jpl/src/m/classes/prognostic.py (revision 13468) ++++ ../trunk-jpl/src/m/classes/prognostic.py (revision 13469) +@@ -68,7 +68,8 @@ + md = checkfield(md,'prognostic.hydrostatic_adjustment','values',['Absolute','Incremental']) + md = checkfield(md,'prognostic.stabilization','values',[0,1,2,3]) + md = checkfield(md,'prognostic.min_thickness','>',0) +- md = checkfield(md,'prognostic.requested_outputs','size',[float('NaN'),1]) ++ if not md.prognostic.requested_outputs: ++ md = checkfield(md,'prognostic.requested_outputs','size',[float('NaN'),1]) + + return md + # }}} Index: /issm/oecreview/Archive/13393-13976/ISSM-13469-13470.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13469-13470.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13469-13470.diff (revision 13980) @@ -0,0 +1,295 @@ +Index: ../trunk-jpl/src/m/geometry/FlagElements.py +=================================================================== +--- ../trunk-jpl/src/m/geometry/FlagElements.py (revision 13469) ++++ ../trunk-jpl/src/m/geometry/FlagElements.py (revision 13470) +@@ -40,13 +40,13 @@ + if not os.path.exists(region): + if len(region)>3 and not strcmp(region[-4:],'.exp'): + raise IOError("Error: File 'region' not found!" % region) +- raise RuntimeError("FlagElements -- basinzoom not yet converted.") ++ raise RuntimeError("FlagElements.py calling basinzoom.py is not complete.") + xlim,ylim=basinzoom('basin',region) + flag_nodes=numpy.logical_and(numpy.logical_and(md.mesh.xxlim[0]),numpy.logical_and(md.mesh.yylim[0])).astype(float) + flag=numpy.prod(flag_nodes[md.mesh.elements],axis=1) + else: + #ok, flag elements +- [flag,fnone]=ContourToMesh(md.mesh.elements[:,0:3],md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),region,'element',1) ++ [flag,dum]=ContourToMesh(md.mesh.elements[:,0:3],md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),region,'element',1) + + if invert: + flag=numpy.logical_not(flag) +Index: ../trunk-jpl/src/m/mesh/bamg.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.py (revision 13469) ++++ ../trunk-jpl/src/m/mesh/bamg.py (revision 13470) +@@ -120,7 +120,7 @@ + raise RuntimeError("one rift has all its points outside of the domain outline") + + elif numpy.any(numpy.logical_not(flags)): +- raise RuntimeError("bamg.m for rifts is not complete.") ++ raise RuntimeError("bamg.py for rifts is not complete.") + #We LOTS of work to do + print("Rift tip outside of or on the domain has been detected and is being processed...") + """ +@@ -346,7 +346,7 @@ + + def processgeometry(geom,tol,outline): # {{{ + +- raise RuntimeError("bamg.m/processgeometry is not complete.") ++ raise RuntimeError("bamg.py/processgeometry is not complete.") + #Deal with edges + print("Checking Edge crossing...") + i=0 +Index: ../trunk-jpl/src/m/classes/model/model.py +=================================================================== +--- ../trunk-jpl/src/m/classes/model/model.py (revision 13469) ++++ ../trunk-jpl/src/m/classes/model/model.py (revision 13470) +@@ -166,6 +166,7 @@ + def checkmessage(self,string): # {{{ + print ("model not consistent: %s" % string) + self.private.isconsistent=False ++ return self + # }}} + + def extrude(md,*args): # {{{ +Index: ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.m +=================================================================== +--- ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.m (revision 13469) ++++ ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.m (revision 13470) +@@ -52,7 +52,7 @@ + end + + md.hydrology.spcwatercolumn=zeros(md.mesh.numberofvertices,2); +-pos=find(md.mesh.vertexonboundary); ++pos=find(md.mesh.vertexonboundary); + md.hydrology.spcwatercolumn(pos,1)=1; + + %segment on Neumann (Ice Front) +@@ -100,7 +100,7 @@ + pos=find(md.mesh.vertexonsurface); md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface + if (length(md.basalforcings.geothermalflux)~=md.mesh.numberofvertices), + md.basalforcings.geothermalflux=zeros(md.mesh.numberofvertices,1); +- md.basalforcings.geothermalflux(find(md.mask.vertexongroundedice))=50*10^-3; %50mW/m2 ++ md.basalforcings.geothermalflux(find(md.mask.vertexongroundedice))=50.*10.^-3; %50mW/m2 + end + else + disp(' no thermal boundary conditions created: no observed temperature found'); +Index: ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py +=================================================================== +--- ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13469) ++++ ../trunk-jpl/src/m/boundaryconditions/SetIceShelfBC.py (revision 13470) +@@ -25,32 +25,32 @@ + if not os.path.exists(icefrontfile): + raise IOError("SetIceShelfBC error message: ice front file '%s' not found." % icefrontfile) + [nodeinsideicefront,dum]=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),icefrontfile,'node',2) +- nodeonicefront=numpy.logical_and(md.mesh.vertexonboundary,nodeinsideicefront).astype(float) ++ nodeonicefront=numpy.logical_and(md.mesh.vertexonboundary,nodeinsideicefront.reshape(-1)).astype(float) + else: +- nodeonicefront=numpy.zeros((md.mesh.numberofvertices,1)) ++ nodeonicefront=numpy.zeros((md.mesh.numberofvertices)) + + # pos=find(md.mesh.vertexonboundary & ~nodeonicefront); +- pos=[i for i,(vob,noif) in enumerate(zip(md.mesh.vertexonboundary,nodeonicefront)) if vob and not noif] +- md.diagnostic.spcvx=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +- md.diagnostic.spcvy=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +- md.diagnostic.spcvz=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) ++ pos=numpy.nonzero(numpy.logical_and(md.mesh.vertexonboundary,numpy.logical_not(nodeonicefront)))[0] ++ md.diagnostic.spcvx=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) ++ md.diagnostic.spcvy=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) ++ md.diagnostic.spcvz=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvx[pos]=0 + md.diagnostic.spcvy[pos]=0 + md.diagnostic.spcvz[pos]=0 +- md.diagnostic.referential=float('NaN')*numpy.ones((md.mesh.numberofvertices,6)) ++ md.diagnostic.referential=float('nan')*numpy.ones((md.mesh.numberofvertices,6)) + + #Dirichlet Values + if isinstance(md.inversion.vx_obs,numpy.ndarray) and numpy.size(md.inversion.vx_obs,axis=0)==md.mesh.numberofvertices and isinstance(md.inversion.vy_obs,numpy.ndarray) and numpy.size(md.inversion.vy_obs,axis=0)==md.mesh.numberofvertices: +- print ' boundary conditions for diagnostic model: spc set as observed velocities' ++ print " boundary conditions for diagnostic model: spc set as observed velocities" + md.diagnostic.spcvx[pos]=md.inversion.vx_obs[pos] + md.diagnostic.spcvy[pos]=md.inversion.vy_obs[pos] + else: +- print ' boundary conditions for diagnostic model: spc set as zero' ++ print " boundary conditions for diagnostic model: spc set as zero" + + #segment on Ice Front + #segment on Neumann (Ice Front) + # pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); +- pos=[i for i,(noif1,noif2) in enumerate(zip(nodeonicefront[md.mesh.segments[:,0].astype('int')-1],nodeonicefront[md.mesh.segments[:,1].astype('int')-1])) if noif1 or noif2] ++ pos=numpy.nonzero(numpy.logical_or(nodeonicefront[md.mesh.segments[:,0].astype(int)-1],nodeonicefront[md.mesh.segments[:,1].astype(int)-1]))[0] + if md.mesh.dimension==2: + pressureload=md.mesh.segments[pos,:] + elif md.mesh.dimension==3: +@@ -59,11 +59,11 @@ + pressureload=numpy.zeros((0,5)) + for i in xrange(1,md.mesh.numberoflayers): + # pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.mesh.numberofvertices2d pressureload_layer1(:,5)+(i-1)*md.mesh.numberofelements2d ]; +- pressureload=numpy.vstack((pressureload,numpy.hstack((pressureload_layer1[:,0:3]+(i-1)*md.mesh.numberofvertices2d,pressureload_layer1[:,4]+(i-1)*md.mesh.numberofelements2d)))) ++ pressureload=numpy.vstack((pressureload,numpy.hstack((pressureload_layer1[:,0:4]+(i-1)*md.mesh.numberofvertices2d,pressureload_layer1[:,4]+(i-1)*md.mesh.numberofelements2d)))) + + #Add water or air enum depending on the element + # pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))]; +- pressureload=numpy.hstack((pressureload,1*md.mask.elementonfloatingice[pressureload[:,-1].astype('int')-1].reshape((-1,1)))) ++ pressureload=numpy.hstack((pressureload,1.*md.mask.elementonfloatingice[pressureload[:,-1].astype('int')-1].reshape(-1,1))) + + #plug onto model + md.diagnostic.icefront=pressureload +@@ -71,29 +71,29 @@ + #Create zeros basalforcings and surfaceforcings + if numpy.all(numpy.isnan(md.surfaceforcings.precipitation)) and (md.surfaceforcings.ispdd==1): + md.surfaceforcings.precipitation=numpy.zeros((md.mesh.numberofvertices,1)) +- print ' no surfaceforcings.precipitation specified: values set as zero' ++ print " no surfaceforcings.precipitation specified: values set as zero" + if numpy.all(numpy.isnan(md.surfaceforcings.mass_balance)) and (md.surfaceforcings.ispdd==0): + md.surfaceforcings.mass_balance=numpy.zeros((md.mesh.numberofvertices,1)) +- print ' no surfaceforcings.mass_balance specified: values set as zero' ++ print " no surfaceforcings.mass_balance specified: values set as zero" + if numpy.all(numpy.isnan(md.basalforcings.melting_rate)): + md.basalforcings.melting_rate=numpy.zeros((md.mesh.numberofvertices,1)) +- print ' no basalforcings.melting_rate specified: values set as zero' ++ print " no basalforcings.melting_rate specified: values set as zero" + if numpy.all(numpy.isnan(md.balancethickness.thickening_rate)): + md.balancethickness.thickening_rate=numpy.zeros((md.mesh.numberofvertices,1)) +- print ' no balancethickness.thickening_rate specified: values set as zero' ++ print " no balancethickness.thickening_rate specified: values set as zero" + +- md.prognostic.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) +- md.balancethickness.spcthickness=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) ++ md.prognostic.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) ++ md.balancethickness.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) + +- if numpy.size(md.initialization.temperature)==md.mesh.numberofvertices: +- md.thermal.spctemperature=float('NaN')*numpy.ones((md.mesh.numberofvertices,1)) ++ if isinstance(md.initialization.temperature,numpy.ndarray) and numpy.size(md.initialization.temperature,axis=0)==md.mesh.numberofvertices: ++ md.thermal.spctemperature=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) + # pos=find(md.mesh.vertexonsurface); md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface +- pos=[i for i,vos in enumerate(md.mesh.vertexonsurface) if vos] +- md.thermal.spctemperature[pos]=md.initialization.temperature[pos] # impose observed temperature on surface +- if not numpy.size(md.basalforcings.geothermalflux)==md.mesh.numberofvertices: ++ pos=numpy.nonzero(md.mesh.vertexonsurface)[0] ++ md.thermal.spctemperature[pos]=md.initialization.temperature[pos] #impose observed temperature on surface ++ if not isinstance(md.basalforcings.geothermalflux,numpy.ndarray) or not numpy.size(md.basalforcings.geothermalflux,axis=0)==md.mesh.numberofvertices: + md.basalforcings.geothermalflux=numpy.zeros((md.mesh.numberofvertices,1)) + else: +- print ' no thermal boundary conditions created: no observed temperature found' ++ print " no thermal boundary conditions created: no observed temperature found" + + return md + +Index: ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.py +=================================================================== +--- ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.py (revision 0) ++++ ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.py (revision 13470) +@@ -0,0 +1,111 @@ ++import os ++import numpy ++from ContourToMesh import * ++ ++def SetMarineIceSheetBC(md,icefrontfile=''): ++ """ ++ SETICEMARINESHEETBC - Create the boundary conditions for diagnostic and thermal models for a Marine Ice Sheet with Ice Front ++ ++ Neumann BC are used on the ice front (an ARGUS contour around the ice front ++ can be given in input, or it will be deduced as onfloatingice & onboundary) ++ Dirichlet BC are used elsewhere for diagnostic ++ ++ Usage: ++ md=SetMarineIceSheetBC(md,icefrontfile) ++ md=SetMarineIceSheetBC(md) ++ ++ Example: ++ md=SetMarineIceSheetBC(md,'Front.exp') ++ md=SetMarineIceSheetBC(md) ++ ++ See also: SETICESHELFBC, SETMARINEICESHEETBC ++ """ ++ ++ #node on Dirichlet (boundary and ~icefront) ++ if icefrontfile: ++ #User provided Front.exp, use it ++ if not os.path.exists(icefrontfile): ++ raise IOError("SetMarineIceSheetBC error message: ice front file '%s' not found." % icefrontfile) ++ [nodeinsideicefront,dum]=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),icefrontfile,'node',2) ++ vertexonicefront=numpy.logical_and(md.mesh.vertexonboundary,nodeinsideicefront.reshape(-1)).astype(float) ++ else: ++ #Guess where the ice front is ++ vertexonfloatingice=numpy.zeros((md.mesh.numberofvertices)) ++ vertexonfloatingice[md.mesh.elements[numpy.nonzero(md.mask.elementonfloatingice),:].astype(int)-1]=1 ++ vertexonicefront=numpy.logical_and(md.mesh.vertexonboundary,vertexonfloatingice).astype(float) ++ ++# pos=find(md.mesh.vertexonboundary & ~vertexonicefront); ++ pos=numpy.nonzero(numpy.logical_and(md.mesh.vertexonboundary,numpy.logical_not(vertexonicefront)))[0] ++ if not numpy.size(pos): ++ print("SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet found. Dirichlet must be added manually.") ++ ++ md.diagnostic.spcvx=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) ++ md.diagnostic.spcvy=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) ++ md.diagnostic.spcvz=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) ++ md.diagnostic.spcvx[pos]=0 ++ md.diagnostic.spcvy[pos]=0 ++ md.diagnostic.spcvz[pos]=0 ++ md.diagnostic.referential=float('nan')*numpy.ones((md.mesh.numberofvertices,6)) ++ ++ #Dirichlet Values ++ if isinstance(md.inversion.vx_obs,numpy.ndarray) and numpy.size(md.inversion.vx_obs,axis=0)==md.mesh.numberofvertices and isinstance(md.inversion.vy_obs,numpy.ndarray) and numpy.size(md.inversion.vy_obs,axis=0)==md.mesh.numberofvertices: ++ print(" boundary conditions for diagnostic model: spc set as observed velocities") ++ md.diagnostic.spcvx[pos]=md.inversion.vx_obs[pos] ++ md.diagnostic.spcvy[pos]=md.inversion.vy_obs[pos] ++ else: ++ print(" boundary conditions for diagnostic model: spc set as zero") ++ ++ md.hydrology.spcwatercolumn=numpy.zeros((md.mesh.numberofvertices,2)) ++ pos=numpy.nonzero(md.mesh.vertexonboundary)[0] ++ md.hydrology.spcwatercolumn[pos,0]=1 ++ ++ #segment on Neumann (Ice Front) ++# pos=find(vertexonicefront(md.mesh.segments(:,1)) | vertexonicefront(md.mesh.segments(:,2))); ++ pos=numpy.nonzero(numpy.logical_or(vertexonicefront[md.mesh.segments[:,0].astype(int)-1],vertexonicefront[md.mesh.segments[:,1].astype(int)-1]))[0] ++ if md.mesh.dimension==2: ++ pressureload=md.mesh.segments[pos,:] ++ elif md.mesh.dimension==3: ++# pressureload_layer1=[md.mesh.segments(pos,1:2) md.mesh.segments(pos,2)+md.mesh.numberofvertices2d md.mesh.segments(pos,1)+md.mesh.numberofvertices2d md.mesh.segments(pos,3)]; ++ pressureload_layer1=numpy.hstack((md.mesh.segments[pos,0:2],md.mesh.segments[pos,1]+md.mesh.numberofvertices2d,md.mesh.segments[pos,0]+md.mesh.numberofvertices2d,md.mesh.segments[pos,2])) ++ pressureload=numpy.zeros((0,5)) ++ for i in xrange(1,md.mesh.numberoflayers): ++# pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.mesh.numberofvertices2d pressureload_layer1(:,5)+(i-1)*md.mesh.numberofelements2d ]; ++ pressureload=numpy.vstack((pressureload,numpy.hstack((pressureload_layer1[:,0:4]+(i-1)*md.mesh.numberofvertices2d,pressureload_layer1[:,4]+(i-1)*md.mesh.numberofelements2d)))) ++ ++ #Add water or air enum depending on the element ++# pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end))+ 0*md.mask.elementongroundedice(pressureload(:,end))]; ++ pressureload=numpy.hstack((pressureload,1.*md.mask.elementonfloatingice[pressureload[:,-1].astype('int')-1].reshape(-1,1)+0.*md.mask.elementongroundedice[pressureload[:,-1].astype('int')-1].reshape(-1,1))) ++ ++ #plug onto model ++ md.diagnostic.icefront=pressureload ++ ++ #Create zeros basalforcings and surfaceforcings ++ if numpy.all(numpy.isnan(md.surfaceforcings.precipitation)) and (md.surfaceforcings.ispdd==1): ++ md.surfaceforcings.precipitation=numpy.zeros((md.mesh.numberofvertices,1)) ++ print(" no surfaceforcings.precipitation specified: values set as zero") ++ if numpy.all(numpy.isnan(md.surfaceforcings.mass_balance)) and (md.surfaceforcings.ispdd==0): ++ md.surfaceforcings.mass_balance=numpy.zeros((md.mesh.numberofvertices,1)) ++ print(" no surfaceforcings.mass_balance specified: values set as zero") ++ if numpy.all(numpy.isnan(md.basalforcings.melting_rate)): ++ md.basalforcings.melting_rate=numpy.zeros((md.mesh.numberofvertices,1)) ++ print(" no basalforcings.melting_rate specified: values set as zero") ++ if numpy.all(numpy.isnan(md.balancethickness.thickening_rate)): ++ md.balancethickness.thickening_rate=numpy.zeros((md.mesh.numberofvertices,1)) ++ print(" no balancethickness.thickening_rate specified: values set as zero") ++ ++ md.prognostic.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) ++ md.balancethickness.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) ++ ++ if isinstance(md.initialization.temperature,numpy.ndarray) and numpy.size(md.initialization.temperature,axis=0)==md.mesh.numberofvertices: ++ md.thermal.spctemperature=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) ++# pos=find(md.mesh.vertexonsurface); md.thermal.spctemperature(pos)=md.initialization.temperature(pos); %impose observed temperature on surface ++ pos=numpy.nonzero(md.mesh.vertexonsurface)[0] ++ md.thermal.spctemperature[pos]=md.initialization.temperature[pos] #impose observed temperature on surface ++ if not isinstance(md.basalforcings.geothermalflux,numpy.ndarray) or not numpy.size(md.basalforcings.geothermalflux,axis=0)==md.mesh.numberofvertices: ++ md.basalforcings.geothermalflux=numpy.zeros((md.mesh.numberofvertices,1)) ++ md.basalforcings.geothermalflux[numpy.nonzero(md.mask.vertexongroundedice)]=50.*10.**-3; #50mW/m2 ++ else: ++ print(" no thermal boundary conditions created: no observed temperature found"); ++ ++ return md ++ Index: /issm/oecreview/Archive/13393-13976/ISSM-13470-13471.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13470-13471.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13470-13471.diff (revision 13980) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/test/Par/Pig.py +=================================================================== +--- ../trunk-jpl/test/Par/Pig.py (revision 13470) ++++ ../trunk-jpl/test/Par/Pig.py (revision 13471) +@@ -5,7 +5,7 @@ + from verbose import * + from InterpFromMeshToMesh2d import InterpFromMeshToMesh2d + from paterson import * +-from SetIceShelfBC import * ++from SetMarineIceSheetBC import * + + #Start defining model parameters here + +@@ -56,7 +56,7 @@ + md.diagnostic.abstol=float('nan') + + #Boundary conditions: +-#md=SetMarineIceSheetBC(md) ++md=SetMarineIceSheetBC(md) + + #Change name so that no test have the same name + if len(inspect.stack()) > 2: Index: /issm/oecreview/Archive/13393-13976/ISSM-13471-13472.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13471-13472.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13471-13472.diff (revision 13980) @@ -0,0 +1,120 @@ +Index: ../trunk-jpl/src/m/geometry/GetAreas.py +=================================================================== +--- ../trunk-jpl/src/m/geometry/GetAreas.py (revision 0) ++++ ../trunk-jpl/src/m/geometry/GetAreas.py (revision 13472) +@@ -0,0 +1,52 @@ ++import numpy ++ ++def GetAreas(index,x,y,z=numpy.array([])): ++ """ ++ GETAREAS - compute areas or volumes of elements ++ ++ compute areas of triangular elements or volumes ++ of pentahedrons ++ ++ Usage: ++ areas =GetAreas(index,x,y); ++ volumes=GetAreas(index,x,y,z); ++ ++ Examples: ++ areas =GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y); ++ volumes=GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y,md.z); ++ """ ++ ++ #get number of elements and number of nodes ++ nels=numpy.size(index,axis=0) ++ nods=numpy.size(x) ++ ++ #some checks ++ if numpy.size(y)!=nods or (z and numpy.size(z)!=nods): ++ raise TypeError("GetAreas error message: x,y and z do not have the same length.") ++ if numpy.max(index)>nods: ++ raise TypeError("GetAreas error message: index should not have values above %d." % nods) ++ if (not z and numpy.size(index,axis=1)!=3): ++ raise TypeError("GetAreas error message: index should have 3 columns for 2d meshes.") ++ if (z and numpy.size(index,axis=1)!=6): ++ raise TypeError("GetAreas error message: index should have 6 columns for 3d meshes.") ++ ++ #initialization ++ areas=numpy.zeros(nels) ++ x1=x[index[:,0].astype(int)-1] ++ x2=x[index[:,1].astype(int)-1] ++ x3=x[index[:,2].astype(int)-1] ++ y1=y[index[:,0].astype(int)-1] ++ y2=y[index[:,1].astype(int)-1] ++ y3=y[index[:,2].astype(int)-1] ++ ++ #compute the volume of each element ++ if not z: ++ #compute the surface of the triangle ++ areas=(0.5*((x2-x1)*(y3-y1)-(y2-y1)*(x3-x1))) ++ else: ++ #V=area(triangle)*1/3(z1+z2+z3) ++ thickness=numpy.mean(z[index[:,3:6].astype(int)-1])-numpy.mean(z[index[:,0:3].astype(int)-1]) ++ areas=(0.5*((x2-x1)*(y3-y1)-(y2-y1)*(x3-x1)))*thickness ++ ++ return areas ++ +Index: ../trunk-jpl/src/m/mesh/GetNodalFunctionsCoeff.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/GetNodalFunctionsCoeff.py (revision 0) ++++ ../trunk-jpl/src/m/mesh/GetNodalFunctionsCoeff.py (revision 13472) +@@ -0,0 +1,58 @@ ++import numpy ++ ++def GetNodalFunctionsCoeff(index,x,y): ++ """ ++ GETNODELFUNCTIONSCOEFF - compute nodal functions coefficients ++ ++ Compute the coefficients alpha beta and optionaly gamma of ++ 2d triangular elements. For each element, the nodal function ++ is defined as: ++ N(x,y)=sum(i=1:3) alpha_i * x + beta_i * y + gamma_i ++ ++ Usage: ++ [alpha beta]=GetNodalFunctionsCoeff(index,x,y); ++ [alpha beta gamma]=GetNodalFunctionsCoeff(index,x,y); ++ ++ Example: ++ [alpha beta gamma]=GetNodalFunctionsCoeff(md.mesh.elements,md.mesh.x,md.mesh.y); ++ """ ++ ++ #make columns out of x and y ++ x=x.rshape(-1) ++ y=y.rshape(-1) ++ ++ #get nels and nods ++ nels=numpy.size(index,axis=0) ++ nods=numpy.size(x) ++ ++ #some checks ++ if numpy.size(y)!=nods: ++ raise TypeError("GetNodalFunctionsCoeff error message: x and y do not have the same length.") ++ if numpy.max(index)>nods: ++ raise TypeError("GetNodalFunctionsCoeff error message: index should not have values above %d." % nods) ++ if numpy.size(index,axis=1)!=3: ++ raise TypeError("GetNodalFunctionsCoeff error message: only 2d meshes supported. index should have 3 columns.") ++ ++ #initialize output ++ alpha=numpy.zeros((nels,3)) ++ beta=numpy.zeros((nels,3)) ++ ++ #compute nodal functions coefficients N(x,y)=alpha x + beta y +gamma ++ x1=x[index[:,0].astype(int)-1] ++ x2=x[index[:,1].astype(int)-1] ++ x3=x[index[:,2].astype(int)-1] ++ y1=y[index[:,0].astype(int)-1] ++ y2=y[index[:,1].astype(int)-1] ++ y3=y[index[:,2].astype(int)-1] ++ invdet=1./(x1*(y2-y3)-x2*(y1-y3)+x3*(y1-y2)) ++ ++ #get alpha and beta ++ alpha=numpy.hstack((invdet*(y2-y3),invdet*(y3-y1),invdet*(y1-y2))) ++ beta =numpy.hstack((invdet*(x3-x2),invdet*(x1-x3),invdet*(x2-x1))) ++ ++ #get gamma if requested ++ gamma=numpy.zeros((nels,3)) ++ gamma=numpy.hstack((invdet*(x2*y3-x3*y2),invdet*(y1*x3-y3*x1),invdet*(x1*y2-x2*y1))) ++ ++ return alpha,beta,gamma ++ Index: /issm/oecreview/Archive/13393-13976/ISSM-13472-13473.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13472-13473.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13472-13473.diff (revision 13980) @@ -0,0 +1,16 @@ +Index: ../trunk-jpl/test/NightlyRun/ad.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/ad.m (revision 13472) ++++ ../trunk-jpl/test/NightlyRun/ad.m (revision 13473) +@@ -6,10 +6,9 @@ + + md.autodiff.isautodiff=true; + md.verbose.autodiff=true; +-index=1; + md.autodiff.independents={... + independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fov_forward_indices',(1:md.mesh.numberofvertices)') +- %independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',index) ++ %independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',1) + }; + + md.autodiff.dependents={... Index: /issm/oecreview/Archive/13393-13976/ISSM-13473-13474.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13473-13474.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13473-13474.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/externalpackages/adolc +=================================================================== +--- ../trunk-jpl/externalpackages/adolc (revision 13473) ++++ ../trunk-jpl/externalpackages/adolc (revision 13474) + +Property changes on: ../trunk-jpl/externalpackages/adolc +___________________________________________________________________ +Modified: svn:ignore +## -1,3 +1,4 ## ++adolc_issm + adolc_v220_issm + trunk + *.gz Index: /issm/oecreview/Archive/13393-13976/ISSM-13474-13475.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13474-13475.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13474-13475.diff (revision 13980) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/execution +=================================================================== +--- ../trunk-jpl/execution (revision 13474) ++++ ../trunk-jpl/execution (revision 13475) + +Property changes on: ../trunk-jpl/execution +___________________________________________________________________ +Modified: svn:ignore +## -1,2 +1,3 ## + test* ++pig* + ad* Index: /issm/oecreview/Archive/13393-13976/ISSM-13475-13476.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13475-13476.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13475-13476.diff (revision 13980) @@ -0,0 +1,67 @@ +Index: ../trunk-jpl/src/m/mech/mechanicalproperties.m +=================================================================== +--- ../trunk-jpl/src/m/mech/mechanicalproperties.m (revision 13475) ++++ ../trunk-jpl/src/m/mech/mechanicalproperties.m (revision 13476) +@@ -75,9 +75,18 @@ + + %eigen values and vectors + [directions,value]=eig(stress); ++ %sort by absolute value of eigenvalue in descending order ++ [val,idx]=sort(abs(diag(value)),'descend'); ++ %re-order eigenvalues and associated vectors ++ value=value(idx,idx); ++ directions=directions(:,idx); + valuesstress(i,:)=[value(1,1) value(2,2)]; + directionsstress(i,:)=directions(:)'; + [directions,value]=eig(strain); ++ %same for strainrate ++ [val,idx]=sort(abs(diag(value)),'descend'); ++ value=value(idx,idx); ++ directions=directions(:,idx); + valuesstrain(i,:)=[value(1,1) value(2,2)]; + directionsstrain(i,:)=directions(:)'; + end +@@ -88,10 +97,10 @@ + stress.xx=tau_xx; + stress.yy=tau_yy; + stress.xy=tau_xy; +-stress.principalvalue2=valuesstress(:,1); +-stress.principalaxis2=directionsstress(:,1:2); +-stress.principalvalue1=valuesstress(:,2); +-stress.principalaxis1=directionsstress(:,3:4); ++stress.principalvalue1=valuesstress(:,1); ++stress.principalaxis1=directionsstress(:,1:2); ++stress.principalvalue2=valuesstress(:,2); ++stress.principalaxis2=directionsstress(:,3:4); + stress.effectivevalue=1/sqrt(2)*sqrt(stress.xx.^2+stress.yy.^2+2*stress.xy.^2); + md.results.stress=stress; + +@@ -99,10 +108,10 @@ + strainrate.xx=ux; + strainrate.yy=vy; + strainrate.xy=uyvx; +-strainrate.principalvalue2=valuesstrain(:,1)*(365.25*24*3600); %strain rate in 1/a instead of 1/s +-strainrate.principalaxis2=directionsstrain(:,1:2); +-strainrate.principalvalue1=valuesstrain(:,2)*(365.25*24*3600); %strain rate in 1/a instead of 1/s +-strainrate.principalaxis1=directionsstrain(:,3:4); ++strainrate.principalvalue1=valuesstrain(:,1)*(365.25*24*3600); %strain rate in 1/a instead of 1/s ++strainrate.principalaxis1=directionsstrain(:,1:2); ++strainrate.principalvalue2=valuesstrain(:,2)*(365.25*24*3600); %strain rate in 1/a instead of 1/s ++strainrate.principalaxis2=directionsstrain(:,3:4); + strainrate.effectivevalue=1/sqrt(2)*sqrt(strainrate.xx.^2+strainrate.yy.^2+2*strainrate.xy.^2); + md.results.strainrate=strainrate; + +@@ -110,9 +119,9 @@ + deviatoricstress.xx=tau_xx; + deviatoricstress.yy=tau_yy; + deviatoricstress.xy=tau_xy; +-deviatoricstress.principalvalue2=valuesstress(:,1); +-deviatoricstress.principalaxis2=directionsstress(:,1:2); +-deviatoricstress.principalvalue1=valuesstress(:,2); +-deviatoricstress.principalaxis1=directionsstress(:,3:4); ++deviatoricstress.principalvalue1=valuesstress(:,1); ++deviatoricstress.principalaxis1=directionsstress(:,1:2); ++deviatoricstress.principalvalue2=valuesstress(:,2); ++deviatoricstress.principalaxis2=directionsstress(:,3:4); + deviatoricstress.effectivevalue=1/sqrt(2)*sqrt(stress.xx.^2+stress.yy.^2+2*stress.xy.^2); + md.results.deviatoricstress=deviatoricstress; Index: /issm/oecreview/Archive/13393-13976/ISSM-13476-13477.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13476-13477.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13476-13477.diff (revision 13980) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/m4/issm_options.m4 +=================================================================== +--- ../trunk-jpl/m4/issm_options.m4 (revision 13476) ++++ ../trunk-jpl/m4/issm_options.m4 (revision 13477) +@@ -167,6 +167,9 @@ + R2012a) + MATLAB_MAJOR=7 + MATLAB_MINOR=14 ++ R2012b) ++ MATLAB_MAJOR=7 ++ MATLAB_MINOR=15 + ;; + *) + AC_MSG_ERROR([can not determine Matlab version number]) Index: /issm/oecreview/Archive/13393-13976/ISSM-13477-13478.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13477-13478.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13477-13478.diff (revision 13980) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/m4/issm_options.m4 +=================================================================== +--- ../trunk-jpl/m4/issm_options.m4 (revision 13477) ++++ ../trunk-jpl/m4/issm_options.m4 (revision 13478) +@@ -167,6 +167,7 @@ + R2012a) + MATLAB_MAJOR=7 + MATLAB_MINOR=14 ++ ;; + R2012b) + MATLAB_MAJOR=7 + MATLAB_MINOR=15 Index: /issm/oecreview/Archive/13393-13976/ISSM-13478-13479.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13478-13479.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13478-13479.diff (revision 13980) @@ -0,0 +1,35 @@ +Index: ../trunk-jpl/src/m/mech/mechanicalproperties.m +=================================================================== +--- ../trunk-jpl/src/m/mech/mechanicalproperties.m (revision 13478) ++++ ../trunk-jpl/src/m/mech/mechanicalproperties.m (revision 13479) +@@ -50,13 +50,26 @@ + B_bar=md.materials.rheology_B(index)*summation/3; + power=(md.materials.rheology_n-1)./(2*md.materials.rheology_n); + second_inv=(ux.^2+vy.^2+((uy+vx).^2)/4+ux.*vy); ++ + %some corrections +-location=find(second_inv~=0); +-nu(location)=B_bar(location)./(second_inv(location).^power(location)); + location=find(second_inv==0 & power~=0); + nu(location)=10^18; %arbitrary maximum viscosity to apply where there is no effective shear +-location=find(second_inv==0 & power==0); +-nu(location)=B_bar(location); ++ ++if isa(md.materials,'matice') ++ location=find(second_inv~=0); ++ nu(location)=B_bar(location)./(second_inv(location).^power(location)); ++ location=find(second_inv==0 & power==0); ++ nu(location)=B_bar(location); ++elseif isa(md.materials,'matdamageice') ++ Zinv=md.materials.rheology_Z(index)*summation/3; ++ location=find(second_inv~=0); ++ nu(location)=Zinv(location).*B_bar(location)./(second_inv(location).^power(location)); ++ location=find(second_inv==0 & power==0); ++ nu(location)=Zinv(location).*B_bar(location); ++ clear Zinv ++else ++ error(['class of md.materials (' class(md.materials) ') not recognized or not supported']); ++end + clear B_bar location second_inv power + + %compute stress Index: /issm/oecreview/Archive/13393-13976/ISSM-13479-13480.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13479-13480.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13479-13480.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/modules/matlab/Makefile.am +=================================================================== +--- ../trunk-jpl/src/modules/matlab/Makefile.am (revision 13479) ++++ ../trunk-jpl/src/modules/matlab/Makefile.am (revision 13480) +@@ -62,7 +62,7 @@ + AM_CXXFLAGS = -DTRILIBRARY -DANSI_DECLARATORS -DNO_TIMER + + #Matlab part +-AM_LDFLAGS = $(MEXLINK) -shrext ${EXEEXT} -module ++AM_LDFLAGS = -module $(MEXLINK) -shrext ${EXEEXT} + if VERSION + AM_LDFLAGS += + else Index: /issm/oecreview/Archive/13393-13976/ISSM-13480-13481.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13480-13481.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13480-13481.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13480) ++++ ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13481) +@@ -159,7 +159,7 @@ + return 0; + } + /*}}}*/ +-int EDF_fos_reverse_for_solverx(int m, double *dp_U, int n, double *dp_Z) { /*{{{*/ ++int EDF_fos_reverse_for_solverx(int m, double *dp_U, int n, double *dp_Z, double* dp_x, double* dp_y) { /*{{{*/ + return 0; + } + /*}}}*/ Index: /issm/oecreview/Archive/13393-13976/ISSM-13481-13482.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13481-13482.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13481-13482.diff (revision 13980) @@ -0,0 +1,325 @@ +Index: ../trunk-jpl/src/m/mesh/GetNodalFunctionsCoeff.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/GetNodalFunctionsCoeff.py (revision 13481) ++++ ../trunk-jpl/src/m/mesh/GetNodalFunctionsCoeff.py (revision 13482) +@@ -18,8 +18,8 @@ + """ + + #make columns out of x and y +- x=x.rshape(-1) +- y=y.rshape(-1) ++ x=x.reshape(-1) ++ y=y.reshape(-1) + + #get nels and nods + nels=numpy.size(index,axis=0) +@@ -47,12 +47,12 @@ + invdet=1./(x1*(y2-y3)-x2*(y1-y3)+x3*(y1-y2)) + + #get alpha and beta +- alpha=numpy.hstack((invdet*(y2-y3),invdet*(y3-y1),invdet*(y1-y2))) +- beta =numpy.hstack((invdet*(x3-x2),invdet*(x1-x3),invdet*(x2-x1))) ++ alpha=numpy.hstack(((invdet*(y2-y3)).reshape(-1,1),(invdet*(y3-y1)).reshape(-1,1),(invdet*(y1-y2)).reshape(-1,1))) ++ beta =numpy.hstack(((invdet*(x3-x2)).reshape(-1,1),(invdet*(x1-x3)).reshape(-1,1),(invdet*(x2-x1)).reshape(-1,1))) + + #get gamma if requested + gamma=numpy.zeros((nels,3)) +- gamma=numpy.hstack((invdet*(x2*y3-x3*y2),invdet*(y1*x3-y3*x1),invdet*(x1*y2-x2*y1))) ++ gamma=numpy.hstack(((invdet*(x2*y3-x3*y2)).reshape(-1,1),(invdet*(y1*x3-y3*x1)).reshape(-1,1),(invdet*(x1*y2-x2*y1)).reshape(-1,1))) + + return alpha,beta,gamma + +Index: ../trunk-jpl/src/m/mesh/ComputeHessian.m +=================================================================== +--- ../trunk-jpl/src/m/mesh/ComputeHessian.m (revision 13481) ++++ ../trunk-jpl/src/m/mesh/ComputeHessian.m (revision 13482) +@@ -19,7 +19,7 @@ + if length(field)~=numberofnodes & length(field)~=numberofelements, + error('ComputeHessian error message: the given field size not supported yet'); + end +-if strcmpi(type,'node') & strcmpi(type,'element'), ++if ~strcmpi(type,'node') & ~strcmpi(type,'element'), + error('ComputeHessian error message: only ''node'' or ''element'' type supported yet'); + end + +@@ -27,11 +27,11 @@ + line=index(:); + linesize=3*numberofelements; + +-%get areas and nodal functions coefficients N(x,y)=alpha x + beta y + gamma ++%get areas and nodal functions coefficients N(x,y)=alpha x + beta y + gamma + [alpha beta]=GetNodalFunctionsCoeff(index,x,y); + areas=GetAreas(index,x,y); + +-%comput weights that holds the volume of all the element holding the node i ++%compute weights that hold the volume of all the element holding the node i + weights=sparse(line,ones(linesize,1),repmat(areas,3,1),numberofnodes,1); + + %compute field on nodes if on elements +Index: ../trunk-jpl/src/m/mesh/bamg.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.py (revision 13481) ++++ ../trunk-jpl/src/m/mesh/bamg.py (revision 13482) +@@ -261,7 +261,7 @@ + #bamg_geometry=processgeometry(bamg_geometry,options.getfieldvalue('tol',float(nan)),domain[0]) + + elif isinstance(md.private.bamg,dict) and 'geometry' in md.private.bamg: +- bamg_geometry=bamggeom(md.private.bamg['geometry']) ++ bamg_geometry=bamggeom(md.private.bamg['geometry'].__dict__) + else: + #do nothing... + pass +@@ -309,7 +309,7 @@ + #}}} + + #call Bamg +- bamgmesh_out,bamggeom_out=BamgMesher(bamg_mesh.__dict__,bamg_geometry.__dict__,bamg_options) ++ [bamgmesh_out,bamggeom_out]=BamgMesher(bamg_mesh.__dict__,bamg_geometry.__dict__,bamg_options) + + # plug results onto model + md.private.bamg=OrderedDict() +Index: ../trunk-jpl/src/m/mesh/ComputeMetric.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/ComputeMetric.py (revision 0) ++++ ../trunk-jpl/src/m/mesh/ComputeMetric.py (revision 13482) +@@ -0,0 +1,74 @@ ++import numpy ++ ++def ComputeMetric(hessian,scale,epsilon,hmin,hmax,pos): ++ """ ++ COMPUTEMETRIC - compute metric from an Hessian ++ ++ Usage: ++ metric=ComputeMetric(hessian,scale,epsilon,hmin,hmax,pos) ++ pos is contains the positions where the metric is wished to be maximized (water?) ++ ++ Example: ++ metric=ComputeMetric(hessian,2/9,10^-1,100,10^5,find(md.nodeonwater) ++ """ ++ ++ #first, find the eigen values of each line of H=[hessian(i,1) hessian(i,2); hessian(i,2) hessian(i,3)] ++ a=hessian[:,0] ++ b=hessian[:,1] ++ d=hessian[:,2] ++ lambda1=0.5*((a+d)+numpy.sqrt(4.*b**2+(a-d)**2)) ++ lambda2=0.5*((a+d)-numpy.sqrt(4.*b**2+(a-d)**2)) ++ pos1=numpy.nonzero(lambda1==0)[0] ++ pos2=numpy.nonzero(lambda2==0)[0] ++ pos3=numpy.nonzero(numpy.logical_and(b==0,lambda1==lambda2))[0] ++ ++ #Modify the eigen values to control the shape of the elements ++ lambda1=numpy.minimum(numpy.maximum(numpy.abs(lambda1)*scale/epsilon,1./hmax**2),1./hmin**2) ++ lambda2=numpy.minimum(numpy.maximum(numpy.abs(lambda2)*scale/epsilon,1./hmax**2),1./hmin**2) ++ ++ #compute eigen vectors ++ norm1=numpy.sqrt(8.*b**2+2.*(d-a)**2+2.*(d-a)*numpy.sqrt((a-d)**2+4.*b**2)) ++ v1x=2.*b/norm1 ++ v1y=((d-a)+numpy.sqrt((a-d)**2+4.*b**2))/norm1 ++ norm2=numpy.sqrt(8.*b**2+2.*(d-a)**2-2.*(d-a)*numpy.sqrt((a-d)**2+4.*b**2)) ++ v2x=2.*b/norm2 ++ v2y=((d-a)-numpy.sqrt((a-d)**2+4.*b**2))/norm2 ++ ++ v1x[pos3]=1. ++ v1y[pos3]=0. ++ v2x[pos3]=0. ++ v2y[pos3]=1. ++ ++ #Compute new metric (for each node M=V*Lambda*V^-1) ++ metric=numpy.hstack((((v1x*v2y-v1y*v2x)**(-1)*( lambda1*v2y*v1x-lambda2*v1y*v2x)).reshape(-1,1), \ ++ ((v1x*v2y-v1y*v2x)**(-1)*( lambda1*v1y*v2y-lambda2*v1y*v2y)).reshape(-1,1), \ ++ ((v1x*v2y-v1y*v2x)**(-1)*(-lambda1*v2x*v1y+lambda2*v1x*v2y)).reshape(-1,1))) ++ ++ #some corrections for 0 eigen values ++ metric[pos1,:]=numpy.tile(numpy.array([[1./hmax**2,0.,1./hmax**2]]),(numpy.size(pos1),1)) ++ metric[pos2,:]=numpy.tile(numpy.array([[1./hmax**2,0.,1./hmax**2]]),(numpy.size(pos2),1)) ++ ++ #take care of water elements ++ metric[pos ,:]=numpy.tile(numpy.array([[1./hmax**2,0.,1./hmax**2]]),(numpy.size(pos ),1)) ++ ++ #take care of NaNs if any (use Numpy eig in a loop) ++ pos=numpy.nonzero(numpy.isnan(metric))[0] ++ if pos: ++ print(" %i NaN found in the metric. Use Numpy routine..." % numpy.size(pos)) ++ for posi in pos: ++ H=numpy.array([[hessian[posi,0],hessian[posi,1]],[hessian[posi,1],hessian[posi,2]]]) ++ [v,u]=numpy.linalg.eig(H) ++ v=numpy.diag(v) ++ lambda1=v[0,0] ++ lambda2=v[1,1] ++ v[0,0]=numpy.minimum(numpy.maximum(numpy.abs(lambda1)*scale/epsilon,1./hmax**2),1./hmin**2) ++ v[1,1]=numpy.minimum(numpy.maximum(numpy.abs(lambda2)*scale/epsilon,1./hmax**2),1./hmin**2) ++ ++ metricTria=numpy.dot(numpy.dot(u,v),numpy.linalg.inv(u)) ++ metric[posi,:]=numpy.array([metricTria[0,0],metricTria[0,1],metricTria[1,1]]) ++ ++ if numpy.any(numpy.isnan(metric)): ++ raise RunTimeError("ComputeMetric error message: NaN in the metric despite our efforts...") ++ ++ return metric ++ +Index: ../trunk-jpl/src/m/mesh/ComputeMetric.m +=================================================================== +--- ../trunk-jpl/src/m/mesh/ComputeMetric.m (revision 13481) ++++ ../trunk-jpl/src/m/mesh/ComputeMetric.m (revision 13482) +@@ -8,28 +8,28 @@ + % Example: + % metric=ComputeMetric(hessian,2/9,10^-1,100,10^5,find(md.nodeonwater) + +-%first, find the eigen values of eah line of H=[hessian(i,1) hessian(i,2); hessian(i,2) hessian(i,3)] ++%first, find the eigen values of each line of H=[hessian(i,1) hessian(i,2); hessian(i,2) hessian(i,3)] + a=hessian(:,1); b=hessian(:,2); d=hessian(:,3); +-lambda1=0.5*((a+d)+sqrt(4*b.^2+(a-d).^2)); +-lambda2=0.5*((a+d)-sqrt(4*b.^2+(a-d).^2)); ++lambda1=0.5*((a+d)+sqrt(4.*b.^2+(a-d).^2)); ++lambda2=0.5*((a+d)-sqrt(4.*b.^2+(a-d).^2)); + pos1=find(lambda1==0); + pos2=find(lambda2==0); + pos3=find(b==0 & lambda1==lambda2); + + %Modify the eigen values to control the shape of the elements +-lambda1=min(max(abs(lambda1)*scale/epsilon,1/hmax^2),1/hmin^2); +-lambda2=min(max(abs(lambda2)*scale/epsilon,1/hmax^2),1/hmin^2); ++lambda1=min(max(abs(lambda1)*scale/epsilon,1./hmax^2),1./hmin^2); ++lambda2=min(max(abs(lambda2)*scale/epsilon,1./hmax^2),1./hmin^2); + + %compute eigen vectors +-norm1=sqrt(8*b.^2+2*(d-a).^2+2*(d-a).*sqrt((a-d).^2+4*b.^2)); +-v1x=2*b./norm1; +-v1y=((d-a)+sqrt((a-d).^2+4*b.^2))./norm1; +-norm2=sqrt(8*b.^2+2*(d-a).^2-2*(d-a).*sqrt((a-d).^2+4*b.^2)); +-v2x=2*b./norm2; +-v2y=((d-a)-sqrt((a-d).^2+4*b.^2))./norm2; ++norm1=sqrt(8.*b.^2+2.*(d-a).^2+2.*(d-a).*sqrt((a-d).^2+4.*b.^2)); ++v1x=2.*b./norm1; ++v1y=((d-a)+sqrt((a-d).^2+4.*b.^2))./norm1; ++norm2=sqrt(8.*b.^2+2.*(d-a).^2-2.*(d-a).*sqrt((a-d).^2+4.*b.^2)); ++v2x=2.*b./norm2; ++v2y=((d-a)-sqrt((a-d).^2+4.*b.^2))./norm2; + +-v1x(pos3)=1; v1y(pos3)=0; +-v2x(pos3)=0; v2y(pos3)=1; ++v1x(pos3)=1.; v1y(pos3)=0.; ++v2x(pos3)=0.; v2y(pos3)=1.; + + %Compute new metric (for each node M=V*Lambda*V^-1) + metric=full([(v1x.*v2y-v1y.*v2x).^(-1).*(lambda1.*v2y.*v1x-lambda2.*v1y.*v2x) ... +@@ -37,11 +37,11 @@ + (v1x.*v2y-v1y.*v2x).^(-1).*(-lambda1.*v2x.*v1y+lambda2.*v1x.*v2y)]); + + %some corrections for 0 eigen values +-metric(pos1,:)=repmat([1/hmax^2 0 1/hmax^2],length(pos1),1); +-metric(pos2,:)=repmat([1/hmax^2 0 1/hmax^2],length(pos2),1); ++metric(pos1,:)=repmat([1./hmax^2 0. 1./hmax^2],length(pos1),1); ++metric(pos2,:)=repmat([1./hmax^2 0. 1./hmax^2],length(pos2),1); + + %take care of water elements +-metric(pos,:)=repmat([1/hmax^2 0 1/hmax^2],length(pos),1); ++metric(pos,:)=repmat([1./hmax^2 0. 1./hmax^2],length(pos),1); + + %take care of NaNs if any (use Matlab eig in a loop) + [pos posj]=find(isnan(metric)); clear posj; +@@ -53,8 +53,8 @@ + [u,v]=eig(full(H)); + lambda1=v(1,1); + lambda2=v(2,2); +- v(1,1)=min(max(abs(lambda1)*scale/epsilon,1/hmax^2),1/hmin^2); +- v(2,2)=min(max(abs(lambda2)*scale/epsilon,1/hmax^2),1/hmin^2); ++ v(1,1)=min(max(abs(lambda1)*scale/epsilon,1./hmax^2),1./hmin^2); ++ v(2,2)=min(max(abs(lambda2)*scale/epsilon,1./hmax^2),1./hmin^2); + + metricTria=u*v*u^(-1); + metric(pos(i),:)=[metricTria(1,1) metricTria(1,2) metricTria(2,2)]; +Index: ../trunk-jpl/src/m/mesh/ComputeHessian.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/ComputeHessian.py (revision 0) ++++ ../trunk-jpl/src/m/mesh/ComputeHessian.py (revision 13482) +@@ -0,0 +1,66 @@ ++import numpy ++from GetNodalFunctionsCoeff import * ++from GetAreas import * ++from MatlabFuncs import * ++ ++def ComputeHessian(index,x,y,field,type): ++ """ ++ COMPUTEHESSIAN - compute hessian matrix from a field ++ ++ Compute the hessian matrix of a given field ++ return the three components Hxx Hxy Hyy ++ for each element or each node ++ ++ Usage: ++ hessian=ComputeHessian(index,x,y,field,type) ++ ++ Example: ++ hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,md.inversion.vel_obs,'node') ++ """ ++ ++ #some variables ++ numberofnodes=numpy.size(x) ++ numberofelements=numpy.size(index,axis=0) ++ ++ #some checks ++ if numpy.size(field)!=numberofnodes and numpy.size(field)!=numberofelements: ++ raise TypeError("ComputeHessian error message: the given field size not supported yet") ++ if not strcmpi(type,'node') and not strcmpi(type,'element'): ++ raise TypeError("ComputeHessian error message: only 'node' or 'element' type supported yet") ++ ++ #initialization ++ line=index.reshape(-1,order='F') ++ linesize=3*numberofelements ++ ++ #get areas and nodal functions coefficients N(x,y)=alpha x + beta y + gamma ++ [alpha,beta,dum]=GetNodalFunctionsCoeff(index,x,y) ++ areas=GetAreas(index,x,y) ++ ++ #compute weights that hold the volume of all the element holding the node i ++ weights=sparse(line,numpy.ones((linesize,1)),numpy.tile(areas.reshape(-1,1),(3,1)),numberofnodes,1) ++ ++ #compute field on nodes if on elements ++ if numpy.size(field,axis=0)==numberofelements: ++ field=sparse(line,numpy.ones((linesize,1)),numpy.tile(areas*field,(3,1)),numberofnodes,1)/weights ++ ++ #Compute gradient for each element ++ grad_elx=numpy.sum(field[index.astype(int)-1,0]*alpha,axis=1) ++ grad_ely=numpy.sum(field[index.astype(int)-1,0]*beta,axis=1) ++ ++ #Compute gradient for each node (average of the elements around) ++ gradx=sparse(line,numpy.ones((linesize,1)),numpy.tile((areas*grad_elx).reshape(-1,1),(3,1)),numberofnodes,1) ++ grady=sparse(line,numpy.ones((linesize,1)),numpy.tile((areas*grad_ely).reshape(-1,1),(3,1)),numberofnodes,1) ++ gradx=gradx/weights ++ grady=grady/weights ++ ++ #Compute hessian for each element ++ hessian=numpy.hstack((numpy.sum(gradx[index.astype(int)-1,0]*alpha,axis=1).reshape(-1,1),numpy.sum(grady[index.astype(int)-1,0]*alpha,axis=1).reshape(-1,1),numpy.sum(grady[index.astype(int)-1,0]*beta,axis=1).reshape(-1,1))) ++ ++ if strcmpi(type,'node'): ++ #Compute Hessian on the nodes (average of the elements around) ++ hessian=numpy.hstack((sparse(line,numpy.ones((linesize,1)),numpy.tile((areas*hessian[:,0]).reshape(-1,1),(3,1)),numberofnodes,1)/weights, \ ++ sparse(line,numpy.ones((linesize,1)),numpy.tile((areas*hessian[:,1]).reshape(-1,1),(3,1)),numberofnodes,1)/weights, \ ++ sparse(line,numpy.ones((linesize,1)),numpy.tile((areas*hessian[:,2]).reshape(-1,1),(3,1)),numberofnodes,1)/weights )) ++ ++ return hessian ++ +Index: ../trunk-jpl/src/m/miscellaneous/MatlabFuncs.py +=================================================================== +--- ../trunk-jpl/src/m/miscellaneous/MatlabFuncs.py (revision 13481) ++++ ../trunk-jpl/src/m/miscellaneous/MatlabFuncs.py (revision 13482) +@@ -73,3 +73,18 @@ + else: + raise TypeError("MatlabFunc.det only implemented for shape (2, 2), not for shape %s." % str(a.shape)) + ++def sparse(ivec,jvec,svec,m=0,n=0,nzmax=0): ++ import numpy ++ ++ if not m: ++ m=numpy.max(ivec) ++ if not n: ++ n=numpy.max(jvec) ++ ++ a=numpy.zeros((m,n)) ++ ++ for i,j,s in zip(ivec.reshape(-1,order='F'),jvec.reshape(-1,order='F'),svec.reshape(-1,order='F')): ++ a[i-1,j-1]+=s ++ ++ return a ++ Index: /issm/oecreview/Archive/13393-13976/ISSM-13482-13483.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13482-13483.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13482-13483.diff (revision 13980) @@ -0,0 +1,814 @@ +Index: ../trunk-jpl/test/NightlyRun/ad.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/ad.m (revision 13482) ++++ ../trunk-jpl/test/NightlyRun/ad.m (revision 13483) +@@ -1,4 +1,4 @@ +-md=triangle(model,'../Exp/Square.exp',50000); ++md=triangle(model,'../Exp/Square.exp',100000); + md=setmask(md,'all',''); + md=parameterize(md,'../Par/SquareShelfConstrained.par'); + md=setflowequation(md,'macayeal','all'); +@@ -14,8 +14,16 @@ + md.autodiff.dependents={... + dependent('name','IceVolume','type','scalar')... + dependent('name','MaxVel','type','scalar')... ++ dependent('name','MassFlux','type','scalar','exp','../Exp/MassFlux1.exp','mesh',md.mesh,'index',1)... ++ dependent('name','MassFlux','type','scalar','exp','../Exp/MassFlux2.exp','mesh',md.mesh,'index',2)... + }; ++ + %md.autodiff.driver='fos_forward'; + md.autodiff.driver='fov_forward'; + + md=solve(md,TransientSolutionEnum); ++ ++%plot ++nods=md.mesh.numberofvertices; ++jac=md.results.TransientSolution(1).AutodiffJacobian; ++plotmodel(md,'data',jac(1:nods),'data',jac(nods+1:2*nods),'data',jac(2*nods+1:3*nods),'data',jac(3*nods+1:4*nods)); +Index: ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13482) ++++ ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13483) +@@ -16,6 +16,7 @@ + AutodiffNumDependentObjectsEnum, + AutodiffDependentObjectNamesEnum, + AutodiffDependentObjectTypesEnum, ++ AutodiffDependentObjectIndicesEnum, + AutodiffDependentObjectsEnum, + AutodiffNumIndependentsEnum, + AutodiffNumIndependentObjectsEnum, +@@ -155,7 +156,8 @@ + PrognosticNumRequestedOutputsEnum, + PrognosticRequestedOutputsEnum, + QmuIsdakotaEnum, +- QmuMassFluxSegmentsEnum, ++ MassFluxSegmentsEnum, ++ MassFluxSegmentsPresentEnum, + QmuNumberofpartitionsEnum, + QmuNumberofresponsesEnum, + QmuPartitionEnum, +Index: ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13482) ++++ ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13483) +@@ -22,6 +22,7 @@ + else if (strcmp(name,"AutodiffNumDependentObjects")==0) return AutodiffNumDependentObjectsEnum; + else if (strcmp(name,"AutodiffDependentObjectNames")==0) return AutodiffDependentObjectNamesEnum; + else if (strcmp(name,"AutodiffDependentObjectTypes")==0) return AutodiffDependentObjectTypesEnum; ++ else if (strcmp(name,"AutodiffDependentObjectIndices")==0) return AutodiffDependentObjectIndicesEnum; + else if (strcmp(name,"AutodiffDependentObjects")==0) return AutodiffDependentObjectsEnum; + else if (strcmp(name,"AutodiffNumIndependents")==0) return AutodiffNumIndependentsEnum; + else if (strcmp(name,"AutodiffNumIndependentObjects")==0) return AutodiffNumIndependentObjectsEnum; +@@ -136,11 +137,11 @@ + else if (strcmp(name,"MeshElementconnectivity")==0) return MeshElementconnectivityEnum; + else if (strcmp(name,"MeshElementonbed")==0) return MeshElementonbedEnum; + else if (strcmp(name,"MeshElementonsurface")==0) return MeshElementonsurfaceEnum; +- else if (strcmp(name,"MeshElements2d")==0) return MeshElements2dEnum; + else stage=2; + } + if(stage==2){ +- if (strcmp(name,"MeshElements")==0) return MeshElementsEnum; ++ if (strcmp(name,"MeshElements2d")==0) return MeshElements2dEnum; ++ else if (strcmp(name,"MeshElements")==0) return MeshElementsEnum; + else if (strcmp(name,"MeshLowerelements")==0) return MeshLowerelementsEnum; + else if (strcmp(name,"MeshNumberofedges")==0) return MeshNumberofedgesEnum; + else if (strcmp(name,"MeshNumberofelements2d")==0) return MeshNumberofelements2dEnum; +@@ -164,7 +165,8 @@ + else if (strcmp(name,"PrognosticNumRequestedOutputs")==0) return PrognosticNumRequestedOutputsEnum; + else if (strcmp(name,"PrognosticRequestedOutputs")==0) return PrognosticRequestedOutputsEnum; + else if (strcmp(name,"QmuIsdakota")==0) return QmuIsdakotaEnum; +- else if (strcmp(name,"QmuMassFluxSegments")==0) return QmuMassFluxSegmentsEnum; ++ else if (strcmp(name,"MassFluxSegments")==0) return MassFluxSegmentsEnum; ++ else if (strcmp(name,"MassFluxSegmentsPresent")==0) return MassFluxSegmentsPresentEnum; + else if (strcmp(name,"QmuNumberofpartitions")==0) return QmuNumberofpartitionsEnum; + else if (strcmp(name,"QmuNumberofresponses")==0) return QmuNumberofresponsesEnum; + else if (strcmp(name,"QmuPartition")==0) return QmuPartitionEnum; +@@ -258,12 +260,12 @@ + else if (strcmp(name,"SurfaceSlopeYAnalysis")==0) return SurfaceSlopeYAnalysisEnum; + else if (strcmp(name,"ThermalAnalysis")==0) return ThermalAnalysisEnum; + else if (strcmp(name,"ThermalSolution")==0) return ThermalSolutionEnum; +- else if (strcmp(name,"TransientSolution")==0) return TransientSolutionEnum; +- else if (strcmp(name,"Approximation")==0) return ApproximationEnum; + else stage=3; + } + if(stage==3){ +- if (strcmp(name,"NoneApproximation")==0) return NoneApproximationEnum; ++ if (strcmp(name,"TransientSolution")==0) return TransientSolutionEnum; ++ else if (strcmp(name,"Approximation")==0) return ApproximationEnum; ++ else if (strcmp(name,"NoneApproximation")==0) return NoneApproximationEnum; + else if (strcmp(name,"HutterApproximation")==0) return HutterApproximationEnum; + else if (strcmp(name,"MacAyealApproximation")==0) return MacAyealApproximationEnum; + else if (strcmp(name,"MacAyealPattynApproximation")==0) return MacAyealPattynApproximationEnum; +@@ -381,12 +383,12 @@ + else if (strcmp(name,"SurfaceSlopeX")==0) return SurfaceSlopeXEnum; + else if (strcmp(name,"SurfaceSlopeY")==0) return SurfaceSlopeYEnum; + else if (strcmp(name,"Temperature")==0) return TemperatureEnum; +- else if (strcmp(name,"TemperatureOld")==0) return TemperatureOldEnum; +- else if (strcmp(name,"TemperaturePicard")==0) return TemperaturePicardEnum; + else stage=4; + } + if(stage==4){ +- if (strcmp(name,"TemperatureSurface")==0) return TemperatureSurfaceEnum; ++ if (strcmp(name,"TemperatureOld")==0) return TemperatureOldEnum; ++ else if (strcmp(name,"TemperaturePicard")==0) return TemperaturePicardEnum; ++ else if (strcmp(name,"TemperatureSurface")==0) return TemperatureSurfaceEnum; + else if (strcmp(name,"TemperatureBasal")==0) return TemperatureBasalEnum; + else if (strcmp(name,"ThicknessAbsMisfit")==0) return ThicknessAbsMisfitEnum; + else if (strcmp(name,"Type")==0) return TypeEnum; +@@ -504,12 +506,12 @@ + else if (strcmp(name,"NearestInterp")==0) return NearestInterpEnum; + else if (strcmp(name,"XY")==0) return XYEnum; + else if (strcmp(name,"XYZP")==0) return XYZPEnum; +- else if (strcmp(name,"Option")==0) return OptionEnum; +- else if (strcmp(name,"GenericOption")==0) return GenericOptionEnum; + else stage=5; + } + if(stage==5){ +- if (strcmp(name,"OptionCell")==0) return OptionCellEnum; ++ if (strcmp(name,"Option")==0) return OptionEnum; ++ else if (strcmp(name,"GenericOption")==0) return GenericOptionEnum; ++ else if (strcmp(name,"OptionCell")==0) return OptionCellEnum; + else if (strcmp(name,"OptionChar")==0) return OptionCharEnum; + else if (strcmp(name,"OptionStruct")==0) return OptionStructEnum; + else if (strcmp(name,"OptionDouble")==0) return OptionDoubleEnum; +Index: ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13482) ++++ ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13483) +@@ -21,6 +21,7 @@ + case AutodiffNumDependentObjectsEnum : return "AutodiffNumDependentObjects"; + case AutodiffDependentObjectNamesEnum : return "AutodiffDependentObjectNames"; + case AutodiffDependentObjectTypesEnum : return "AutodiffDependentObjectTypes"; ++ case AutodiffDependentObjectIndicesEnum : return "AutodiffDependentObjectIndices"; + case AutodiffDependentObjectsEnum : return "AutodiffDependentObjects"; + case AutodiffNumIndependentsEnum : return "AutodiffNumIndependents"; + case AutodiffNumIndependentObjectsEnum : return "AutodiffNumIndependentObjects"; +@@ -160,7 +161,8 @@ + case PrognosticNumRequestedOutputsEnum : return "PrognosticNumRequestedOutputs"; + case PrognosticRequestedOutputsEnum : return "PrognosticRequestedOutputs"; + case QmuIsdakotaEnum : return "QmuIsdakota"; +- case QmuMassFluxSegmentsEnum : return "QmuMassFluxSegments"; ++ case MassFluxSegmentsEnum : return "MassFluxSegments"; ++ case MassFluxSegmentsPresentEnum : return "MassFluxSegmentsPresent"; + case QmuNumberofpartitionsEnum : return "QmuNumberofpartitions"; + case QmuNumberofresponsesEnum : return "QmuNumberofresponses"; + case QmuPartitionEnum : return "QmuPartition"; +Index: ../trunk-jpl/src/c/modules/RequestedDependentsx/RequestedDependentsx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/RequestedDependentsx/RequestedDependentsx.cpp (revision 13482) ++++ ../trunk-jpl/src/c/modules/RequestedDependentsx/RequestedDependentsx.cpp (revision 13483) +@@ -33,7 +33,7 @@ + /*Go through our dependent variables, and compute the response:*/ + for(i=0;iSize();i++){ + DependentObject* dep=(DependentObject*)dependent_objects->GetObjectByOffset(i); +- Responsex(&output_value,elements,nodes,vertices,loads,materials,parameters,dep->name,false,0); ++ dep->Responsex(&output_value,elements,nodes,vertices,loads,materials,parameters); + output_value>>=dependents[i]; + } + } +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13482) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13483) +@@ -60,9 +60,10 @@ + if(num_dependent_objects){ + iomodel->FetchData(&names,&dummy,&dummy,AutodiffDependentObjectNamesEnum); + iomodel->FetchData(&types,&dummy,&dummy,AutodiffDependentObjectTypesEnum); ++ iomodel->FetchData(&indices,&dummy,&dummy,AutodiffDependentObjectIndicesEnum); + + for(i=0;iAddObject(dep); + num_dep+=dep->NumDependents(); + } +@@ -76,7 +77,6 @@ + + delete dependent_objects; + /*}}}*/ +- + /*Deal with independents: {{{*/ + + /*Independents have already been recovered in iomodel->DeclareIndependents. Just do some more processing. +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp (revision 13482) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp (revision 13483) +@@ -38,19 +38,9 @@ + //descriptors: + char tag[50]; + +- /*parameters for mass flux: */ +- bool qmu_mass_flux_present=false; +- int qmu_mass_flux_num_profiles=0; +- double** array=NULL; +- int* mdims_array=NULL; +- int* ndims_array=NULL; +- +- double* matrix=NULL; +- double* temp_matrix=NULL; ++ + int M; +- int temp_m,temp_n; + int m,n; +- int count; + bool dakota_analysis=false; + char* name=NULL; + int numberofresponses; +@@ -139,67 +129,6 @@ + } + } + /*}}}*/ +- /*Deal with data needed to compute qmu responses: {{{*/ +- for(i=0;iFetchData(&array,&mdims_array,&ndims_array,&qmu_mass_flux_num_profiles,QmuMassFluxSegmentsEnum); +- if(qmu_mass_flux_num_profiles==0)_error_("qmu_mass_flux_num_profiles is 0, when MassFlux computations were requested!"); +- +- /*Go through segments, and extract those that belong to this cpu: */ +- for(i=0;imy_elements[(int)(*(temp_matrix+5*j+4))-1])m++; +- } +- if(m){ +- matrix=xNewZeroInit(5*m); +- count=0; +- for(j=0;jmy_elements[(int)*(temp_matrix+5*j+4)-1]){ +- for(k=0;k<5;k++)*(matrix+5*count+k)=*(temp_matrix+5*j+k); +- count++; +- } +- } +- } +- else{ +- matrix=NULL; +- } +- +- /*Assign: */ +- array[i]=matrix; +- mdims_array[i]=m; +- ndims_array[i]=5; +- +- /*Free temporary matrix: */ +- xDelete(temp_matrix); +- } +- +- /*Ok, we have an array of segments, different on every cpu. Create a DoubleMatArrayParam object with it: */ +- parameters->AddObject(new DoubleMatArrayParam(QmuMassFluxSegmentsEnum,array,qmu_mass_flux_num_profiles,mdims_array,ndims_array)); +- +- /*Free data: */ +- for(i=0;i(matrix); +- } +- xDelete(mdims_array); +- xDelete(ndims_array); +- xDelete(array); +- } +- /*}}}*/ + /*Free data: {{{*/ + for(i=0;iAddObject(new IntParam(PrognosticNumRequestedOutputsEnum,numoutputs)); + if(numoutputs)parameters->AddObject(new IntVecParam(PrognosticRequestedOutputsEnum,requestedoutputs,numoutputs)); + iomodel->DeleteData(requestedoutputs,PrognosticRequestedOutputsEnum); ++ ++ ++ /*Deal with mass flux segments: {{{*/ ++ iomodel->FetchData(&mass_flux_present,MassFluxSegmentsPresentEnum); ++ parameters->AddObject(new BoolParam(MassFluxSegmentsPresentEnum,mass_flux_present)); + ++ if(mass_flux_present){ ++ ++ /*Fetch the mass flux segments necessary to compute the mass fluxes. Build a DoubleMatArrayParam object out of them: */ ++ iomodel->FetchData(&array,&mdims_array,&ndims_array,&mass_flux_num_profiles,MassFluxSegmentsEnum); ++ if(mass_flux_num_profiles==0)_error_("mass_flux_num_profiles is 0, when MassFlux computations were requested!"); ++ ++ /*Go through segments, and extract those that belong to this cpu: */ ++ for(i=0;imy_elements[reCast(*(temp_matrix+5*j+4))-1] )m++; ++ } ++ if(m){ ++ matrix=xNewZeroInit(5*m); ++ count=0; ++ for(j=0;jmy_elements[reCast(*(temp_matrix+5*j+4))-1]){ ++ for(k=0;k<5;k++)*(matrix+5*count+k)=*(temp_matrix+5*j+k); ++ count++; ++ } ++ } ++ } ++ else{ ++ matrix=NULL; ++ } ++ ++ /*Assign: */ ++ array[i]=matrix; ++ mdims_array[i]=m; ++ ndims_array[i]=5; ++ ++ /*Free temporary matrix: */ ++ xDelete(temp_matrix); ++ } ++ ++ /*Ok, we have an array of segments, different on every cpu. Create a DoubleMatArrayParam object with it: */ ++ parameters->AddObject(new DoubleMatArrayParam(MassFluxSegmentsEnum,array,mass_flux_num_profiles,mdims_array,ndims_array)); ++ ++ /*Free data: */ ++ for(i=0;i(matrix); ++ } ++ xDelete(mdims_array); ++ xDelete(ndims_array); ++ xDelete(array); ++ } ++ /*}}}*/ ++ + /*Before returning, create parameters in case we are running Qmu or control types runs: */ + #ifdef _HAVE_CONTROL_ + CreateParametersControl(¶meters,iomodel,solution_type,analysis_type); +Index: ../trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp (revision 13482) ++++ ../trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp (revision 13483) +@@ -14,6 +14,7 @@ + int i,j; + Element *element = NULL; + int element_id; ++ bool ispresent=false; + + /*output: */ + IssmDouble mass_flux=0; +@@ -31,15 +32,18 @@ + int num_segments; + + /*First, figure out which segment to compute our mass flux on. Start with retrieving qmu_mass_flux_segments: */ +- parameters->FindParam(&array,&M,&mdims_array,&ndims_array,QmuMassFluxSegmentsEnum); ++ parameters->FindParam(&ispresent,MassFluxSegmentsPresentEnum); ++ if(!ispresent)_error_("no mass flux segments available!"); + ++ parameters->FindParam(&array,&M,&mdims_array,&ndims_array,MassFluxSegmentsEnum); ++ + /*Retrieve index of segments being used for MassFlux computation: */ + parameters->FindParam(&counter,IndexEnum); + + /*retrieve segments from array: */ + segments=array[counter-1]; //matlab to "C" indexing + num_segments=mdims_array[counter-1]; +- ++ + /*Go through segments, and then elements, and figure out which elements belong to a segment. + * When we find one, use the element to compute the mass flux on the segment: */ + for(i=0;iname=NoneEnum; + this->type=0; ++ this->index=-1; + } + /*}}}*/ +-/*FUNCTION DependentObject::DependentObject(int in_name, int in_type){{{*/ +-DependentObject::DependentObject(int in_name, int in_type){ ++/*FUNCTION DependentObject::DependentObject(int in_name, int in_type, int in_index){{{*/ ++DependentObject::DependentObject(int in_name, int in_type,int in_index){ + + this->name=in_name; + this->type=in_type; ++ this->index=in_index; + if(in_type!=0 && in_type!=1)_error_("cannot create an DependentObject of type " << in_type); + if(in_type==1)_error_("not implemented yet!"); + +@@ -51,6 +54,7 @@ + _printLine_(" type: vertex"); + else + _error_(" unknown type: " << this->type); ++ if(this->index>=0) _printLine_(" index: " << this->index); + } + /*}}}*/ + /*FUNCTION DependentObject::DeepEcho{{{*/ +@@ -77,7 +81,7 @@ + /*}}}*/ + /*FUNCTION DependentObject::copy{{{*/ + Object* DependentObject::copy(void) { +- return new DependentObject(name,type); ++ return new DependentObject(name,type,index); + } /*}}}*/ + + /*DependentObject methods: */ +@@ -94,3 +98,16 @@ + else _error_("should not have a type of " << type); + } + /*}}}*/ ++/*FUNCTION DependentObject::Responsex{{{*/ ++void DependentObject::Responsex(IssmDouble* poutput_value,Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters){ ++ ++ if(this->name==MassFluxEnum){ ++ ++ /*to identify the mass flux that will be computed, we need the index of the profile: */ ++ parameters->SetParam(this->index,IndexEnum); ++ } ++ ++ ::Responsex(poutput_value,elements,nodes,vertices,loads,materials,parameters,this->name,false,0); ++ ++} ++/*}}}*/ +Index: ../trunk-jpl/src/m/classes/autodiff.m +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.m (revision 13482) ++++ ../trunk-jpl/src/m/classes/autodiff.m (revision 13483) +@@ -57,26 +57,28 @@ + %early return + if ~obj.isautodiff, return; end + +- %process dependent variables ++ %process dependent variables {{{ + num_dependent_objects=numel(obj.dependents); + WriteData(fid,'data',num_dependent_objects,'enum',AutodiffNumDependentObjectsEnum(),'format','Integer'); + + if(num_dependent_objects), + names=zeros(num_dependent_objects,1); + types=zeros(num_dependent_objects,1); ++ indices=zeros(num_dependent_objects,1); + + for i=1:num_dependent_objects, + dep=obj.dependents{i}; + + names(i)=StringToEnum(dep.name); + types(i)=dep.typetoscalar(); ++ indices(i)=dep.index; + end + WriteData(fid,'data',names,'enum',AutodiffDependentObjectNamesEnum(),'format','IntMat','mattype',3); + WriteData(fid,'data',types,'enum',AutodiffDependentObjectTypesEnum(),'format','IntMat','mattype',3); ++ WriteData(fid,'data',indices,'enum',AutodiffDependentObjectIndicesEnum(),'format','IntMat','mattype',3); + end +- +- +- %process independent variables ++ %}}} ++ %process independent variables {{{ + num_independent_objects=numel(obj.independents); + WriteData(fid,'data',num_independent_objects,'enum',AutodiffNumIndependentObjectsEnum(),'format','Integer'); + +@@ -93,8 +95,8 @@ + WriteData(fid,'data',names,'enum',AutodiffIndependentObjectNamesEnum(),'format','IntMat','mattype',3); + WriteData(fid,'data',types,'enum',AutodiffIndependentObjectTypesEnum(),'format','IntMat','mattype',3); + end +- +- %if driver is fos_forward, build index: ++ %}}} ++ %if driver is fos_forward, build index: {{{ + if strcmpi(obj.driver,'fos_forward'), + index=0; + +@@ -114,7 +116,8 @@ + index=index-1; %get c-index numbering going + WriteData(fid,'data',index,'enum',AutodiffFosForwardIndexEnum(),'format','Integer'); + end +- %if driver is fov_forward, build indices: ++ %}}} ++ %if driver is fov_forward, build indices: {{{ + if strcmpi(obj.driver,'fov_forward'), + indices=0; + +@@ -135,6 +138,21 @@ + + WriteData(fid,'data',indices,'enum',AutodiffFovForwardIndicesEnum,'format','IntMat','mattype',3); + end ++ %}}} ++ %deal with mass fluxes: {{{ ++ mass_flux_segments=cell(0,1); ++ for i=1:num_dependent_objects, ++ dep=obj.dependents{i}; ++ if strcmpi(dep.name,'MassFlux'), ++ mass_flux_segments{end+1,1}=dep.segments; ++ end ++ end ++ if ~isempty(mass_flux_segments), ++ WriteData(fid,'data',mass_flux_segments,'enum',MassFluxSegmentsEnum,'format','MatArray'); ++ flag=true; ++ WriteData(fid,'data',flag,'enum',MassFluxSegmentsPresentEnum,'format','Boolean'); ++ end ++ %}}} + + end % }}} + end +Index: ../trunk-jpl/src/m/classes/qmu.m +=================================================================== +--- ../trunk-jpl/src/m/classes/qmu.m (revision 13482) ++++ ../trunk-jpl/src/m/classes/qmu.m (revision 13483) +@@ -147,7 +147,11 @@ + WriteData(fid,'object',obj,'fieldname','numberofresponses','format','Integer'); + WriteData(fid,'object',obj,'fieldname','variabledescriptors','format','StringArray'); + WriteData(fid,'object',obj,'fieldname','responsedescriptors','format','StringArray'); +- WriteData(fid,'object',obj,'fieldname','mass_flux_segments','format','MatArray'); ++ WriteData(fid,'data',obj.mass_flux_segments,'enum',MassFluxSegmentsEnum,'format','MatArray'); ++ if ~isempty(mass_flux_segments), ++ flag=true; ++ WriteData(fid,'data',flag,'enum',MassFluxSegmentsPrsentEnum,'format','Boolean'); ++ end + end % }}} + end + end +Index: ../trunk-jpl/src/m/classes/dependent.m +=================================================================== +--- ../trunk-jpl/src/m/classes/dependent.m (revision 13482) ++++ ../trunk-jpl/src/m/classes/dependent.m (revision 13483) +@@ -7,24 +7,47 @@ + properties (SetAccess=public) + name = ''; + type = ''; ++ exp = ''; ++ segments = []; ++ index = -1; + end + methods + function obj= dependent(varargin) % {{{ + + %use provided options to change fields + options=pairoptions(varargin{:}); ++ ++ obj.name=getfieldvalue(options,'name',''); ++ obj.type=getfieldvalue(options,'type',''); ++ obj.exp=getfieldvalue(options,'exp',''); ++ obj.segments=getfieldvalue(options,'segments',[]); ++ obj.index=getfieldvalue(options,'index',-1); + +- %OK get other fields +- obj=AssignObjectFields(pairoptions(varargin{:}),obj); +- ++ %if name is mass flux: ++ if strcmpi(obj.name,'MassFlux'), ++ %make sure that we supplied a file and that it exists! ++ if exist(obj.exp)~=2, ++ error('dependent checkconsistency: specified ''exp'' file does not exist!'); ++ end ++ %process the file and retrieve segments ++ mesh=getfieldvalue(options,'mesh'); ++ obj.segments=MeshProfileIntersection(mesh.elements,mesh.x,mesh.y,obj.exp); ++ end + end + %}}} + function obj = setdefaultparameters(obj) % {{{ +- %do nothing +- ++ %do nothing + end % }}} + function md = checkconsistency(obj,md,solution,analyses) % {{{ + %do nothing for now ++ if strcmpi(obj.name,'MassFlux'), ++ if isempty(obj.segments), ++ error('dependent checkconsistency error: need segments to compute this dependent response'); ++ end ++ if obj.index<=0, ++ error('dependent checkconsistency error: index for segments should be >=1'); ++ end ++ end + + end % }}} + function disp(obj) % {{{ +@@ -32,6 +55,10 @@ + + fielddisplay(obj,'name','variable name (must match corresponding Enum)'); + fielddisplay(obj,'type','type of variable (''vertex'' or ''scalar'')'); ++ if ~isempty(obj.exp), ++ fielddisplay(obj,'exp','file needed to compute dependent variable'); ++ fielddisplay(obj,'segments','mass flux segments'); ++ end + + end % }}} + function scalar=typetoscalar(obj) % {{{ +Index: ../trunk-jpl/src/m/enum/QmuMassFluxSegmentsEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/QmuMassFluxSegmentsEnum.m (revision 13482) ++++ ../trunk-jpl/src/m/enum/QmuMassFluxSegmentsEnum.m (revision 13483) +@@ -1,11 +0,0 @@ +-function macro=QmuMassFluxSegmentsEnum() +-%QMUMASSFLUXSEGMENTSENUM - Enum of QmuMassFluxSegments +-% +-% WARNING: DO NOT MODIFY THIS FILE +-% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh +-% Please read src/c/EnumDefinitions/README for more information +-% +-% Usage: +-% macro=QmuMassFluxSegmentsEnum() +- +-macro=StringToEnum('QmuMassFluxSegments'); +Index: ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13482) ++++ ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13483) +@@ -8,4 +8,4 @@ + % Usage: + % macro=MaximumNumberOfEnums() + +-macro=487; ++macro=489; +Index: ../trunk-jpl/src/m/enum/MassFluxSegmentsPresentEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MassFluxSegmentsPresentEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/MassFluxSegmentsPresentEnum.m (revision 13483) +@@ -0,0 +1,11 @@ ++function macro=MassFluxSegmentsPresentEnum() ++%MASSFLUXSEGMENTSPRESENTENUM - Enum of MassFluxSegmentsPresent ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=MassFluxSegmentsPresentEnum() ++ ++macro=StringToEnum('MassFluxSegmentsPresent'); +Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py +=================================================================== +--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13482) ++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13483) +@@ -58,6 +58,16 @@ + + return StringToEnum('AutodiffDependentObjectTypes')[0] + ++def AutodiffDependentObjectIndicesEnum(): ++ """ ++ AUTODIFFDEPENDENTOBJECTINDICESENUM - Enum of AutodiffDependentObjectIndices ++ ++ Usage: ++ macro=AutodiffDependentObjectIndicesEnum() ++ """ ++ ++ return StringToEnum('AutodiffDependentObjectIndices')[0] ++ + def AutodiffDependentObjectsEnum(): + """ + AUTODIFFDEPENDENTOBJECTSENUM - Enum of AutodiffDependentObjects +@@ -1448,16 +1458,26 @@ + + return StringToEnum('QmuIsdakota')[0] + +-def QmuMassFluxSegmentsEnum(): ++def MassFluxSegmentsEnum(): + """ +- QMUMASSFLUXSEGMENTSENUM - Enum of QmuMassFluxSegments ++ MASSFLUXSEGMENTSENUM - Enum of MassFluxSegments + + Usage: +- macro=QmuMassFluxSegmentsEnum() ++ macro=MassFluxSegmentsEnum() + """ + +- return StringToEnum('QmuMassFluxSegments')[0] ++ return StringToEnum('MassFluxSegments')[0] + ++def MassFluxSegmentsPresentEnum(): ++ """ ++ MASSFLUXSEGMENTSPRESENTENUM - Enum of MassFluxSegmentsPresent ++ ++ Usage: ++ macro=MassFluxSegmentsPresentEnum() ++ """ ++ ++ return StringToEnum('MassFluxSegmentsPresent')[0] ++ + def QmuNumberofpartitionsEnum(): + """ + QMUNUMBEROFPARTITIONSENUM - Enum of QmuNumberofpartitions +@@ -4886,5 +4906,5 @@ + macro=MaximumNumberOfEnums() + """ + +- return 487 ++ return 489 + +Index: ../trunk-jpl/src/m/enum/AutodiffDependentObjectIndicesEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffDependentObjectIndicesEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffDependentObjectIndicesEnum.m (revision 13483) +@@ -0,0 +1,11 @@ ++function macro=AutodiffDependentObjectIndicesEnum() ++%AUTODIFFDEPENDENTOBJECTINDICESENUM - Enum of AutodiffDependentObjectIndices ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffDependentObjectIndicesEnum() ++ ++macro=StringToEnum('AutodiffDependentObjectIndices'); +Index: ../trunk-jpl/src/m/enum/MassFluxSegmentsEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MassFluxSegmentsEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/MassFluxSegmentsEnum.m (revision 13483) +@@ -0,0 +1,11 @@ ++function macro=MassFluxSegmentsEnum() ++%MASSFLUXSEGMENTSENUM - Enum of MassFluxSegments ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=MassFluxSegmentsEnum() ++ ++macro=StringToEnum('MassFluxSegments'); Index: /issm/oecreview/Archive/13393-13976/ISSM-13483-13484.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13483-13484.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13483-13484.diff (revision 13980) @@ -0,0 +1,83 @@ +Index: ../trunk-jpl/src/c/python/io/FetchPythonData.cpp +=================================================================== +--- ../trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 13483) ++++ ../trunk-jpl/src/c/python/io/FetchPythonData.cpp (revision 13484) +@@ -74,12 +74,16 @@ + dims=PyArray_DIMS((PyArrayObject*)py_matrix); + M=dims[0]; N=dims[1]; + +- /*retrieve internal value: */ +- dmatrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix); ++ if (M && N) { ++ /*retrieve internal value: */ ++ dmatrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix); + +- /*copy matrix: */ +- matrix=xNew(M*N); +- memcpy(matrix,dmatrix,(M*N)*sizeof(double)); ++ /*copy matrix: */ ++ matrix=xNew(M*N); ++ memcpy(matrix,dmatrix,(M*N)*sizeof(double)); ++ } ++ else ++ matrix=NULL; + + /*output: */ + if(pM)*pM=M; +@@ -106,12 +110,16 @@ + dims=PyArray_DIMS((PyArrayObject*)py_matrix); + M=dims[0]; N=dims[1]; + +- /*retrieve internal value: */ +- dmatrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix); ++ if (M && N) { ++ /*retrieve internal value: */ ++ dmatrix=(double*)PyArray_DATA((PyArrayObject*)py_matrix); + +- /*transform into integer matrix: */ +- matrix=xNew(M*N); +- for(i=0;i(M*N); ++ for(i=0;i(M); +- memcpy(vector,dvector,(M)*sizeof(double)); ++ /*copy vector: */ ++ vector=xNew(M); ++ memcpy(vector,dvector,(M)*sizeof(double)); ++ } ++ else ++ vector=NULL; + + /*output: */ + if(pM)*pM=M; +Index: ../trunk-jpl/src/m/classes/bamggeom.py +=================================================================== +--- ../trunk-jpl/src/m/classes/bamggeom.py (revision 13483) ++++ ../trunk-jpl/src/m/classes/bamggeom.py (revision 13484) +@@ -11,7 +11,7 @@ + def __init__(self,*args): # {{{ + self.Vertices=numpy.empty((0,3)) + self.Edges=numpy.empty((0,3)) +- self.TangentAtEdges=numpy.empty((0,0)) ++ self.TangentAtEdges=numpy.empty((0,4)) + self.Corners=numpy.empty((0,1)) + self.RequiredVertices=numpy.empty((0,1)) + self.RequiredEdges=numpy.empty((0,1)) Index: /issm/oecreview/Archive/13393-13976/ISSM-13484-13485.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13484-13485.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13484-13485.diff (revision 13980) @@ -0,0 +1,122 @@ +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 13484) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 13485) +@@ -24,7 +24,7 @@ + int numoutputs; + Parameters *parameters = NULL; + IssmDouble *requestedoutputs = NULL; +- bool isdelta18o; ++ bool isdelta18o,isautodiff; + + /*parameters for mass flux: {{{*/ + int mass_flux_num_profiles=0; +@@ -155,62 +155,65 @@ + iomodel->DeleteData(requestedoutputs,PrognosticRequestedOutputsEnum); + + +- /*Deal with mass flux segments: {{{*/ +- iomodel->FetchData(&mass_flux_present,MassFluxSegmentsPresentEnum); +- parameters->AddObject(new BoolParam(MassFluxSegmentsPresentEnum,mass_flux_present)); ++ if(isautodiff){ ++ /*Deal with mass flux segments: {{{*/ ++ iomodel->Constant(&isautodiff,AutodiffIsautodiffEnum); ++ iomodel->FetchData(&mass_flux_present,MassFluxSegmentsPresentEnum); ++ parameters->AddObject(new BoolParam(MassFluxSegmentsPresentEnum,mass_flux_present)); + +- if(mass_flux_present){ ++ if(mass_flux_present){ + +- /*Fetch the mass flux segments necessary to compute the mass fluxes. Build a DoubleMatArrayParam object out of them: */ +- iomodel->FetchData(&array,&mdims_array,&ndims_array,&mass_flux_num_profiles,MassFluxSegmentsEnum); +- if(mass_flux_num_profiles==0)_error_("mass_flux_num_profiles is 0, when MassFlux computations were requested!"); ++ /*Fetch the mass flux segments necessary to compute the mass fluxes. Build a DoubleMatArrayParam object out of them: */ ++ iomodel->FetchData(&array,&mdims_array,&ndims_array,&mass_flux_num_profiles,MassFluxSegmentsEnum); ++ if(mass_flux_num_profiles==0)_error_("mass_flux_num_profiles is 0, when MassFlux computations were requested!"); + +- /*Go through segments, and extract those that belong to this cpu: */ +- for(i=0;imy_elements[reCast(*(temp_matrix+5*j+4))-1] )m++; +- } +- if(m){ +- matrix=xNewZeroInit(5*m); +- count=0; ++ m=0; + for(j=0;jmy_elements[reCast(*(temp_matrix+5*j+4))-1]){ +- for(k=0;k<5;k++)*(matrix+5*count+k)=*(temp_matrix+5*j+k); +- count++; ++ if ( iomodel->my_elements[reCast(*(temp_matrix+5*j+4))-1] )m++; ++ } ++ if(m){ ++ matrix=xNewZeroInit(5*m); ++ count=0; ++ for(j=0;jmy_elements[reCast(*(temp_matrix+5*j+4))-1]){ ++ for(k=0;k<5;k++)*(matrix+5*count+k)=*(temp_matrix+5*j+k); ++ count++; ++ } + } + } +- } +- else{ +- matrix=NULL; +- } ++ else{ ++ matrix=NULL; ++ } + +- /*Assign: */ +- array[i]=matrix; +- mdims_array[i]=m; +- ndims_array[i]=5; ++ /*Assign: */ ++ array[i]=matrix; ++ mdims_array[i]=m; ++ ndims_array[i]=5; + +- /*Free temporary matrix: */ +- xDelete(temp_matrix); +- } ++ /*Free temporary matrix: */ ++ xDelete(temp_matrix); ++ } + +- /*Ok, we have an array of segments, different on every cpu. Create a DoubleMatArrayParam object with it: */ +- parameters->AddObject(new DoubleMatArrayParam(MassFluxSegmentsEnum,array,mass_flux_num_profiles,mdims_array,ndims_array)); ++ /*Ok, we have an array of segments, different on every cpu. Create a DoubleMatArrayParam object with it: */ ++ parameters->AddObject(new DoubleMatArrayParam(MassFluxSegmentsEnum,array,mass_flux_num_profiles,mdims_array,ndims_array)); + +- /*Free data: */ +- for(i=0;i(matrix); ++ /*Free data: */ ++ for(i=0;i(matrix); ++ } ++ xDelete(mdims_array); ++ xDelete(ndims_array); ++ xDelete(array); + } +- xDelete(mdims_array); +- xDelete(ndims_array); +- xDelete(array); ++ /*}}}*/ + } +- /*}}}*/ + + /*Before returning, create parameters in case we are running Qmu or control types runs: */ + #ifdef _HAVE_CONTROL_ Index: /issm/oecreview/Archive/13393-13976/ISSM-13485-13486.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13485-13486.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13485-13486.diff (revision 13980) @@ -0,0 +1,417 @@ +Index: ../trunk-jpl/test/NightlyRun/test223.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test223.m (revision 13485) ++++ ../trunk-jpl/test/NightlyRun/test223.m (revision 13486) +@@ -3,7 +3,7 @@ + md=parameterize(md,'../Par/SquareShelf.par'); + md=setflowequation(md,'macayeal','all'); + md.geometry.bed=md.geometry.bed+50; md.geometry.surface=md.geometry.surface+50; +-md.cluster=generic('name',oshostname(),'np',3); ++md.cluster=generic('name',oshostname(),'np',1); + md.prognostic.hydrostatic_adjustment='Incremental'; + md=solve(md,TransientSolutionEnum); + +Index: ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13485) ++++ ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13486) +@@ -28,6 +28,7 @@ + AutodiffDriverEnum, + AutodiffFosForwardIndexEnum, + AutodiffFovForwardIndicesEnum, ++ AutodiffMassFluxSegmentsPresentEnum, + BalancethicknessSpcthicknessEnum, + BalancethicknessStabilizationEnum, + BalancethicknessThickeningRateEnum, +@@ -158,6 +159,7 @@ + QmuIsdakotaEnum, + MassFluxSegmentsEnum, + MassFluxSegmentsPresentEnum, ++ QmuMassFluxSegmentsPresentEnum, + QmuNumberofpartitionsEnum, + QmuNumberofresponsesEnum, + QmuPartitionEnum, +Index: ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13485) ++++ ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13486) +@@ -34,6 +34,7 @@ + else if (strcmp(name,"AutodiffDriver")==0) return AutodiffDriverEnum; + else if (strcmp(name,"AutodiffFosForwardIndex")==0) return AutodiffFosForwardIndexEnum; + else if (strcmp(name,"AutodiffFovForwardIndices")==0) return AutodiffFovForwardIndicesEnum; ++ else if (strcmp(name,"AutodiffMassFluxSegmentsPresent")==0) return AutodiffMassFluxSegmentsPresentEnum; + else if (strcmp(name,"BalancethicknessSpcthickness")==0) return BalancethicknessSpcthicknessEnum; + else if (strcmp(name,"BalancethicknessStabilization")==0) return BalancethicknessStabilizationEnum; + else if (strcmp(name,"BalancethicknessThickeningRate")==0) return BalancethicknessThickeningRateEnum; +@@ -136,11 +137,11 @@ + else if (strcmp(name,"MeshEdges")==0) return MeshEdgesEnum; + else if (strcmp(name,"MeshElementconnectivity")==0) return MeshElementconnectivityEnum; + else if (strcmp(name,"MeshElementonbed")==0) return MeshElementonbedEnum; +- else if (strcmp(name,"MeshElementonsurface")==0) return MeshElementonsurfaceEnum; + else stage=2; + } + if(stage==2){ +- if (strcmp(name,"MeshElements2d")==0) return MeshElements2dEnum; ++ if (strcmp(name,"MeshElementonsurface")==0) return MeshElementonsurfaceEnum; ++ else if (strcmp(name,"MeshElements2d")==0) return MeshElements2dEnum; + else if (strcmp(name,"MeshElements")==0) return MeshElementsEnum; + else if (strcmp(name,"MeshLowerelements")==0) return MeshLowerelementsEnum; + else if (strcmp(name,"MeshNumberofedges")==0) return MeshNumberofedgesEnum; +@@ -167,6 +168,7 @@ + else if (strcmp(name,"QmuIsdakota")==0) return QmuIsdakotaEnum; + else if (strcmp(name,"MassFluxSegments")==0) return MassFluxSegmentsEnum; + else if (strcmp(name,"MassFluxSegmentsPresent")==0) return MassFluxSegmentsPresentEnum; ++ else if (strcmp(name,"QmuMassFluxSegmentsPresent")==0) return QmuMassFluxSegmentsPresentEnum; + else if (strcmp(name,"QmuNumberofpartitions")==0) return QmuNumberofpartitionsEnum; + else if (strcmp(name,"QmuNumberofresponses")==0) return QmuNumberofresponsesEnum; + else if (strcmp(name,"QmuPartition")==0) return QmuPartitionEnum; +@@ -258,12 +260,12 @@ + else if (strcmp(name,"SurfaceSlopeSolution")==0) return SurfaceSlopeSolutionEnum; + else if (strcmp(name,"SurfaceSlopeXAnalysis")==0) return SurfaceSlopeXAnalysisEnum; + else if (strcmp(name,"SurfaceSlopeYAnalysis")==0) return SurfaceSlopeYAnalysisEnum; +- else if (strcmp(name,"ThermalAnalysis")==0) return ThermalAnalysisEnum; +- else if (strcmp(name,"ThermalSolution")==0) return ThermalSolutionEnum; + else stage=3; + } + if(stage==3){ +- if (strcmp(name,"TransientSolution")==0) return TransientSolutionEnum; ++ if (strcmp(name,"ThermalAnalysis")==0) return ThermalAnalysisEnum; ++ else if (strcmp(name,"ThermalSolution")==0) return ThermalSolutionEnum; ++ else if (strcmp(name,"TransientSolution")==0) return TransientSolutionEnum; + else if (strcmp(name,"Approximation")==0) return ApproximationEnum; + else if (strcmp(name,"NoneApproximation")==0) return NoneApproximationEnum; + else if (strcmp(name,"HutterApproximation")==0) return HutterApproximationEnum; +@@ -381,12 +383,12 @@ + else if (strcmp(name,"SurfaceLogVxVyMisfit")==0) return SurfaceLogVxVyMisfitEnum; + else if (strcmp(name,"SurfaceRelVelMisfit")==0) return SurfaceRelVelMisfitEnum; + else if (strcmp(name,"SurfaceSlopeX")==0) return SurfaceSlopeXEnum; +- else if (strcmp(name,"SurfaceSlopeY")==0) return SurfaceSlopeYEnum; +- else if (strcmp(name,"Temperature")==0) return TemperatureEnum; + else stage=4; + } + if(stage==4){ +- if (strcmp(name,"TemperatureOld")==0) return TemperatureOldEnum; ++ if (strcmp(name,"SurfaceSlopeY")==0) return SurfaceSlopeYEnum; ++ else if (strcmp(name,"Temperature")==0) return TemperatureEnum; ++ else if (strcmp(name,"TemperatureOld")==0) return TemperatureOldEnum; + else if (strcmp(name,"TemperaturePicard")==0) return TemperaturePicardEnum; + else if (strcmp(name,"TemperatureSurface")==0) return TemperatureSurfaceEnum; + else if (strcmp(name,"TemperatureBasal")==0) return TemperatureBasalEnum; +@@ -504,12 +506,12 @@ + else if (strcmp(name,"TriangleInterp")==0) return TriangleInterpEnum; + else if (strcmp(name,"BilinearInterp")==0) return BilinearInterpEnum; + else if (strcmp(name,"NearestInterp")==0) return NearestInterpEnum; +- else if (strcmp(name,"XY")==0) return XYEnum; +- else if (strcmp(name,"XYZP")==0) return XYZPEnum; + else stage=5; + } + if(stage==5){ +- if (strcmp(name,"Option")==0) return OptionEnum; ++ if (strcmp(name,"XY")==0) return XYEnum; ++ else if (strcmp(name,"XYZP")==0) return XYZPEnum; ++ else if (strcmp(name,"Option")==0) return OptionEnum; + else if (strcmp(name,"GenericOption")==0) return GenericOptionEnum; + else if (strcmp(name,"OptionCell")==0) return OptionCellEnum; + else if (strcmp(name,"OptionChar")==0) return OptionCharEnum; +Index: ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13485) ++++ ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13486) +@@ -33,6 +33,7 @@ + case AutodiffDriverEnum : return "AutodiffDriver"; + case AutodiffFosForwardIndexEnum : return "AutodiffFosForwardIndex"; + case AutodiffFovForwardIndicesEnum : return "AutodiffFovForwardIndices"; ++ case AutodiffMassFluxSegmentsPresentEnum : return "AutodiffMassFluxSegmentsPresent"; + case BalancethicknessSpcthicknessEnum : return "BalancethicknessSpcthickness"; + case BalancethicknessStabilizationEnum : return "BalancethicknessStabilization"; + case BalancethicknessThickeningRateEnum : return "BalancethicknessThickeningRate"; +@@ -163,6 +164,7 @@ + case QmuIsdakotaEnum : return "QmuIsdakota"; + case MassFluxSegmentsEnum : return "MassFluxSegments"; + case MassFluxSegmentsPresentEnum : return "MassFluxSegmentsPresent"; ++ case QmuMassFluxSegmentsPresentEnum : return "QmuMassFluxSegmentsPresent"; + case QmuNumberofpartitionsEnum : return "QmuNumberofpartitions"; + case QmuNumberofresponsesEnum : return "QmuNumberofresponses"; + case QmuPartitionEnum : return "QmuPartition"; +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 13485) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 13486) +@@ -24,10 +24,12 @@ + int numoutputs; + Parameters *parameters = NULL; + IssmDouble *requestedoutputs = NULL; +- bool isdelta18o,isautodiff; ++ bool isdelta18o; + + /*parameters for mass flux: {{{*/ + int mass_flux_num_profiles=0; ++ bool qmu_mass_flux_present=false; ++ bool autodiff_mass_flux_present=false; + bool mass_flux_present=false; + IssmDouble** array=NULL; + int* mdims_array=NULL; +@@ -155,65 +157,66 @@ + iomodel->DeleteData(requestedoutputs,PrognosticRequestedOutputsEnum); + + +- if(isautodiff){ +- /*Deal with mass flux segments: {{{*/ +- iomodel->Constant(&isautodiff,AutodiffIsautodiffEnum); +- iomodel->FetchData(&mass_flux_present,MassFluxSegmentsPresentEnum); +- parameters->AddObject(new BoolParam(MassFluxSegmentsPresentEnum,mass_flux_present)); ++ /*Deal with mass flux segments: {{{*/ ++ iomodel->FetchData(&qmu_mass_flux_present,QmuMassFluxSegmentsPresentEnum); ++ iomodel->FetchData(&autodiff_mass_flux_present,AutodiffMassFluxSegmentsPresentEnum); + +- if(mass_flux_present){ ++ if(qmu_mass_flux_present || autodiff_mass_flux_present)mass_flux_present=true; ++ else mass_flux_present=false; ++ parameters->AddObject(new BoolParam(MassFluxSegmentsPresentEnum,mass_flux_present)); + +- /*Fetch the mass flux segments necessary to compute the mass fluxes. Build a DoubleMatArrayParam object out of them: */ +- iomodel->FetchData(&array,&mdims_array,&ndims_array,&mass_flux_num_profiles,MassFluxSegmentsEnum); +- if(mass_flux_num_profiles==0)_error_("mass_flux_num_profiles is 0, when MassFlux computations were requested!"); ++ if(mass_flux_present){ + +- /*Go through segments, and extract those that belong to this cpu: */ +- for(i=0;iFetchData(&array,&mdims_array,&ndims_array,&mass_flux_num_profiles,MassFluxSegmentsEnum); ++ if(mass_flux_num_profiles==0)_error_("mass_flux_num_profiles is 0, when MassFlux computations were requested!"); + +- m=0; ++ /*Go through segments, and extract those that belong to this cpu: */ ++ for(i=0;imy_elements[reCast(*(temp_matrix+5*j+4))-1] )m++; ++ } ++ if(m){ ++ matrix=xNewZeroInit(5*m); ++ count=0; + for(j=0;jmy_elements[reCast(*(temp_matrix+5*j+4))-1] )m++; +- } +- if(m){ +- matrix=xNewZeroInit(5*m); +- count=0; +- for(j=0;jmy_elements[reCast(*(temp_matrix+5*j+4))-1]){ +- for(k=0;k<5;k++)*(matrix+5*count+k)=*(temp_matrix+5*j+k); +- count++; +- } ++ if (iomodel->my_elements[reCast(*(temp_matrix+5*j+4))-1]){ ++ for(k=0;k<5;k++)*(matrix+5*count+k)=*(temp_matrix+5*j+k); ++ count++; + } + } +- else{ +- matrix=NULL; +- } ++ } ++ else{ ++ matrix=NULL; ++ } + +- /*Assign: */ +- array[i]=matrix; +- mdims_array[i]=m; +- ndims_array[i]=5; ++ /*Assign: */ ++ array[i]=matrix; ++ mdims_array[i]=m; ++ ndims_array[i]=5; + +- /*Free temporary matrix: */ +- xDelete(temp_matrix); +- } ++ /*Free temporary matrix: */ ++ xDelete(temp_matrix); ++ } + +- /*Ok, we have an array of segments, different on every cpu. Create a DoubleMatArrayParam object with it: */ +- parameters->AddObject(new DoubleMatArrayParam(MassFluxSegmentsEnum,array,mass_flux_num_profiles,mdims_array,ndims_array)); ++ /*Ok, we have an array of segments, different on every cpu. Create a DoubleMatArrayParam object with it: */ ++ parameters->AddObject(new DoubleMatArrayParam(MassFluxSegmentsEnum,array,mass_flux_num_profiles,mdims_array,ndims_array)); + +- /*Free data: */ +- for(i=0;i(matrix); +- } +- xDelete(mdims_array); +- xDelete(ndims_array); +- xDelete(array); ++ /*Free data: */ ++ for(i=0;i(matrix); + } +- /*}}}*/ ++ xDelete(mdims_array); ++ xDelete(ndims_array); ++ xDelete(array); + } ++ /*}}}*/ + + /*Before returning, create parameters in case we are running Qmu or control types runs: */ + #ifdef _HAVE_CONTROL_ +Index: ../trunk-jpl/src/m/classes/autodiff.m +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.m (revision 13485) ++++ ../trunk-jpl/src/m/classes/autodiff.m (revision 13486) +@@ -55,7 +55,10 @@ + WriteData(fid,'object',obj,'fieldname','driver','format','String'); + + %early return +- if ~obj.isautodiff, return; end ++ if ~obj.isautodiff, ++ WriteData(fid,'data',false,'enum',AutodiffMassFluxSegmentsPresentEnum,'format','Boolean'); ++ return; ++ end + + %process dependent variables {{{ + num_dependent_objects=numel(obj.dependents); +@@ -147,11 +150,13 @@ + mass_flux_segments{end+1,1}=dep.segments; + end + end +- if ~isempty(mass_flux_segments), ++ if ~isempty(mass_flux_segments), + WriteData(fid,'data',mass_flux_segments,'enum',MassFluxSegmentsEnum,'format','MatArray'); + flag=true; +- WriteData(fid,'data',flag,'enum',MassFluxSegmentsPresentEnum,'format','Boolean'); ++ else ++ flag=false; + end ++ WriteData(fid,'data',flag,'enum',AutodiffMassFluxSegmentsPresentEnum,'format','Boolean'); + %}}} + + end % }}} +Index: ../trunk-jpl/src/m/classes/qmu.m +=================================================================== +--- ../trunk-jpl/src/m/classes/qmu.m (revision 13485) ++++ ../trunk-jpl/src/m/classes/qmu.m (revision 13486) +@@ -141,17 +141,22 @@ + end % }}} + function marshall(obj,fid) % {{{ + WriteData(fid,'object',obj,'fieldname','isdakota','format','Boolean'); +- if ~obj.isdakota, return; end ++ if ~obj.isdakota, ++ WriteData(fid,'data',false,'enum',QmuMassFluxSegmentsPresentEnum,'format','Boolean'); ++ return; ++ end + WriteData(fid,'object',obj,'fieldname','partition','format','DoubleMat','mattype',2); + WriteData(fid,'object',obj,'fieldname','numberofpartitions','format','Integer'); + WriteData(fid,'object',obj,'fieldname','numberofresponses','format','Integer'); + WriteData(fid,'object',obj,'fieldname','variabledescriptors','format','StringArray'); + WriteData(fid,'object',obj,'fieldname','responsedescriptors','format','StringArray'); +- WriteData(fid,'data',obj.mass_flux_segments,'enum',MassFluxSegmentsEnum,'format','MatArray'); +- if ~isempty(mass_flux_segments), +- flag=true; +- WriteData(fid,'data',flag,'enum',MassFluxSegmentsPrsentEnum,'format','Boolean'); ++ if ~isempty(obj.mass_flux_segments), ++ WriteData(fid,'data',obj.mass_flux_segments,'enum',MassFluxSegmentsEnum,'format','MatArray'); ++ flag=true; ++ else ++ flag=false; + end ++ WriteData(fid,'data',flag,'enum',QmuMassFluxSegmentsPresentEnum,'format','Boolean'); + end % }}} + end + end +Index: ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13485) ++++ ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13486) +@@ -8,4 +8,4 @@ + % Usage: + % macro=MaximumNumberOfEnums() + +-macro=489; ++macro=491; +Index: ../trunk-jpl/src/m/enum/AutodiffMassFluxSegmentsPresentEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffMassFluxSegmentsPresentEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffMassFluxSegmentsPresentEnum.m (revision 13486) +@@ -0,0 +1,11 @@ ++function macro=AutodiffMassFluxSegmentsPresentEnum() ++%AUTODIFFMASSFLUXSEGMENTSPRESENTENUM - Enum of AutodiffMassFluxSegmentsPresent ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffMassFluxSegmentsPresentEnum() ++ ++macro=StringToEnum('AutodiffMassFluxSegmentsPresent'); +Index: ../trunk-jpl/src/m/enum/QmuMassFluxSegmentsPresentEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/QmuMassFluxSegmentsPresentEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/QmuMassFluxSegmentsPresentEnum.m (revision 13486) +@@ -0,0 +1,11 @@ ++function macro=QmuMassFluxSegmentsPresentEnum() ++%QMUMASSFLUXSEGMENTSPRESENTENUM - Enum of QmuMassFluxSegmentsPresent ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=QmuMassFluxSegmentsPresentEnum() ++ ++macro=StringToEnum('QmuMassFluxSegmentsPresent'); +Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py +=================================================================== +--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13485) ++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13486) +@@ -178,6 +178,16 @@ + + return StringToEnum('AutodiffFovForwardIndices')[0] + ++def AutodiffMassFluxSegmentsPresentEnum(): ++ """ ++ AUTODIFFMASSFLUXSEGMENTSPRESENTENUM - Enum of AutodiffMassFluxSegmentsPresent ++ ++ Usage: ++ macro=AutodiffMassFluxSegmentsPresentEnum() ++ """ ++ ++ return StringToEnum('AutodiffMassFluxSegmentsPresent')[0] ++ + def BalancethicknessSpcthicknessEnum(): + """ + BALANCETHICKNESSSPCTHICKNESSENUM - Enum of BalancethicknessSpcthickness +@@ -1478,6 +1488,16 @@ + + return StringToEnum('MassFluxSegmentsPresent')[0] + ++def QmuMassFluxSegmentsPresentEnum(): ++ """ ++ QMUMASSFLUXSEGMENTSPRESENTENUM - Enum of QmuMassFluxSegmentsPresent ++ ++ Usage: ++ macro=QmuMassFluxSegmentsPresentEnum() ++ """ ++ ++ return StringToEnum('QmuMassFluxSegmentsPresent')[0] ++ + def QmuNumberofpartitionsEnum(): + """ + QMUNUMBEROFPARTITIONSENUM - Enum of QmuNumberofpartitions +@@ -4906,5 +4926,5 @@ + macro=MaximumNumberOfEnums() + """ + +- return 489 ++ return 491 + Index: /issm/oecreview/Archive/13393-13976/ISSM-13486-13487.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13486-13487.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13486-13487.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/etc/environment.sh +=================================================================== +--- ../trunk-jpl/etc/environment.sh (revision 13486) ++++ ../trunk-jpl/etc/environment.sh (revision 13487) +@@ -211,7 +211,7 @@ + pathappend "$MODELE_DIR/src/exec" + + GIT_DIR="$ISSM_DIR/externalpackages/git/install" +-pathappend "$GIT_DIR/bin" ++pathprepend "$GIT_DIR/bin" + + NCVIEW_DIR="$ISSM_DIR/externalpackages/ncview/install" + pathappend "$NCVIEW_DIR" Index: /issm/oecreview/Archive/13393-13976/ISSM-13487-13488.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13487-13488.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13487-13488.diff (revision 13980) @@ -0,0 +1,104 @@ +Index: ../trunk-jpl/configs/config-linux64-murdo-ad.sh +=================================================================== +--- ../trunk-jpl/configs/config-linux64-murdo-ad.sh (revision 13487) ++++ ../trunk-jpl/configs/config-linux64-murdo-ad.sh (revision 13488) +@@ -1,37 +1,10 @@ + #!/bin/sh + + ./configure \ +- --prefix=$ISSM_DIR \ +- --with-serial=no\ +- --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ +- --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ +- --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +- --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +- --with-hypre-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +- --with-ml-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +- --with-graphics-lib=/usr/lib64/libX11.so \ +- --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ +- --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/ -lg2c /usr/lib/gcc/x86_64-redhat-linux/4.1.1/libgfortran.a" \ +- --with-adic2-dir=$ISSM_DIR/externalpackages/adic/install/ \ +---with-numthreads=24 \ +- --without-thermal \ +- --without-control \ +- --without-hydrology \ +- --without-diagnostic \ +- --without-balanced \ +- --without-responses \ +- --without-slope \ +- --without-rifts \ +- --without-steadystate \ +- --without-transient \ +- --without-3d \ +- --without-groundingline +- +-#--without-prognostic \ ++ --prefix=$ISSM_DIR \ ++ --without-kriging \ ++ --without-kml \ ++ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ ++ --with-adolc-dir=$ISSM_DIR/externalpackages/adolc/install \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install +Index: ../trunk-jpl/configs/config-linux64-murdo.sh +=================================================================== +--- ../trunk-jpl/configs/config-linux64-murdo.sh (revision 13487) ++++ ../trunk-jpl/configs/config-linux64-murdo.sh (revision 13488) +@@ -1,26 +1,27 @@ + #!/bin/sh + ++#petsc 3.2 ++#mpich 1.4 ++ + ./configure \ +- --prefix=$ISSM_DIR \ +- --with-matlab-dir=$MATLAB_DIR \ +- --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ +- --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ +- --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ +- --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ +- --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ +- --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ +- --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +- --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +- --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" \ +- --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ +- --with-graphics-lib=/usr/lib64/libX11.so \ +- --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ +- --with-numthreads=18 \ +- --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ +- --enable-debugging +- +- ++ --prefix=$ISSM_DIR \ ++ --with-matlab-dir=$MATLAB_DIR \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ ++ --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" \ ++ --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-plapack-lib="-L$ISSM_DIR/externalpackages/petsc/install/ -lPLAPACK" \ ++ --with-plapack-include="-I$ISSM_DIR/externalpackages/petsc/install/externalpackages/PLAPACKR32-hg/INCLUDE" \ ++ --with-petsc-arch=$ISSM_ARCH \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ ++ --with-graphics-lib=/usr/lib64/libX11.so \ ++ --with-cxxoptflags="-mtune=barcelona -ffast-math -O3 -msse4.2 -Wno-write-strings "\ ++ --with-numthreads=18 \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ ++ --enable-debugging \ ++ --with-scotch-dir="$ISSM_DIR/externalpackages/scotch/install" Index: /issm/oecreview/Archive/13393-13976/ISSM-13488-13489.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13488-13489.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13488-13489.diff (revision 13980) @@ -0,0 +1,25 @@ +Index: ../trunk-jpl/externalpackages/adolc/update.sh +=================================================================== +--- ../trunk-jpl/externalpackages/adolc/update.sh (revision 0) ++++ ../trunk-jpl/externalpackages/adolc/update.sh (revision 13489) +@@ -0,0 +1,14 @@ ++#!/bin/bash ++ ++cd adolc_issm ++git pull ++ ++autoreconf -f -i ++./configure --prefix=$ISSM_DIR/externalpackages/adolc/install ++ ++if [ $# -eq 0 ]; then ++ make ++else ++ make -j $1 ++fi ++make install + +Property changes on: ../trunk-jpl/externalpackages/adolc/update.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* Index: /issm/oecreview/Archive/13393-13976/ISSM-13489-13490.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13489-13490.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13489-13490.diff (revision 13980) @@ -0,0 +1,55 @@ +Index: ../trunk-jpl/src/m/classes/autodiff.py +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.py (revision 13489) ++++ ../trunk-jpl/src/m/classes/autodiff.py (revision 13490) +@@ -38,5 +38,6 @@ + + def marshall(self,fid): # {{{ + WriteData(fid,'object',self,'fieldname','isautodiff','format','Boolean') ++ WriteData(fid,'data',False,'enum',AutodiffMassFluxSegmentsPresentEnum(),'format','Boolean'); + # }}} + +Index: ../trunk-jpl/src/m/classes/qmu.py +=================================================================== +--- ../trunk-jpl/src/m/classes/qmu.py (revision 13489) ++++ ../trunk-jpl/src/m/classes/qmu.py (revision 13490) +@@ -44,7 +44,6 @@ + # {{{setdefaultparameters + return self + #}}} +- + def checkconsistency(self,md,solution,analyses): # {{{ + + #Early return +@@ -67,7 +66,6 @@ + + return md + # }}} +- + def __repr__(self): # {{{ + s =' qmu parameters:\n' + +@@ -140,16 +138,21 @@ + + return s + # }}} +- + def marshall(self,fid): # {{{ + WriteData(fid,'object',self,'fieldname','isdakota','format','Boolean') + if not self.isdakota: ++ WriteData(fid,'data',False,'enum',QmuMassFluxSegmentsPresentEnum(),'format','Boolean'); + return + WriteData(fid,'object',self,'fieldname','partition','format','DoubleMat','mattype',2) + WriteData(fid,'object',self,'fieldname','numberofpartitions','format','Integer') + WriteData(fid,'object',self,'fieldname','numberofresponses','format','Integer') + WriteData(fid,'object',self,'fieldname','variabledescriptors','format','StringArray') + WriteData(fid,'object',self,'fieldname','responsedescriptors','format','StringArray') +- WriteData(fid,'object',self,'fieldname','mass_flux_segments','format','MatArray') ++ if not self.mass_flux_segments: ++ WriteData(fid,'data',self.mass_flux_segments,'enum',MassFluxSegmentsEnum(),'format','MatArray'); ++ flag=True; ++ else: ++ flag=False; ++ WriteData(fid,'data',flag,'enum',QmuMassFluxSegmentsPresentEnum(),'format','Boolean'); + # }}} + Index: /issm/oecreview/Archive/13393-13976/ISSM-13490-13491.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13490-13491.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13490-13491.diff (revision 13980) @@ -0,0 +1,602 @@ +Index: ../trunk-jpl/test/NightlyRun/test202.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test202.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test202.py (revision 13491) +@@ -0,0 +1,42 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test202.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,2) ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vz'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test211.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test211.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test211.py (revision 13491) +@@ -0,0 +1,74 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test211.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',200000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,1) ++md=setflowequation(md,'stokes','all') ++md.diagnostic.reltol=NaN ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,TransientSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names=[\ ++ 'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', \ ++ 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', \ ++ 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'] ++field_tolerances=[\ ++ 1e-08,1e-08,1e-06,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,\ ++ 1e-08,1e-08,1e-06,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06,\ ++ 1e-07,1e-07,1e-06,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-06] ++field_values=[\ ++ md.results['TransientSolution'][1]['Vx'],\ ++ md.results['TransientSolution'][1]['Vy'],\ ++ md.results['TransientSolution'][1]['Vz'],\ ++ md.results['TransientSolution'][1]['Vel'],\ ++ md.results['TransientSolution'][1]['Pressure'],\ ++ md.results['TransientSolution'][1]['Bed'],\ ++ md.results['TransientSolution'][1]['Surface'],\ ++ md.results['TransientSolution'][1]['Thickness'],\ ++ md.results['TransientSolution'][1]['Temperature'],\ ++ md.results['TransientSolution'][1]['BasalforcingsMeltingRate'],\ ++ md.results['TransientSolution'][2]['Vx'],\ ++ md.results['TransientSolution'][2]['Vy'],\ ++ md.results['TransientSolution'][2]['Vz'],\ ++ md.results['TransientSolution'][2]['Vel'],\ ++ md.results['TransientSolution'][2]['Pressure'],\ ++ md.results['TransientSolution'][2]['Bed'],\ ++ md.results['TransientSolution'][2]['Surface'],\ ++ md.results['TransientSolution'][2]['Thickness'],\ ++ md.results['TransientSolution'][2]['Temperature'],\ ++ md.results['TransientSolution'][2]['BasalforcingsMeltingRate'],\ ++ md.results['TransientSolution'][3]['Vx'],\ ++ md.results['TransientSolution'][3]['Vy'],\ ++ md.results['TransientSolution'][3]['Vz'],\ ++ md.results['TransientSolution'][3]['Vel'],\ ++ md.results['TransientSolution'][3]['Pressure'],\ ++ md.results['TransientSolution'][3]['Bed'],\ ++ md.results['TransientSolution'][3]['Surface'],\ ++ md.results['TransientSolution'][3]['Thickness'],\ ++ md.results['TransientSolution'][3]['Temperature'],\ ++ md.results['TransientSolution'][3]['BasalforcingsMeltingRate'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test208.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test208.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test208.py (revision 13491) +@@ -0,0 +1,57 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test208.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,TransientSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['TransientSolution'][1]['Vx'],\ ++ md.results['TransientSolution'][1]['Vy'],\ ++ md.results['TransientSolution'][1]['Vel'],\ ++ md.results['TransientSolution'][1]['Pressure'],\ ++ md.results['TransientSolution'][1]['Bed'],\ ++ md.results['TransientSolution'][1]['Surface'],\ ++ md.results['TransientSolution'][1]['Thickness'],\ ++ md.results['TransientSolution'][2]['Vx'],\ ++ md.results['TransientSolution'][2]['Vy'],\ ++ md.results['TransientSolution'][2]['Vel'],\ ++ md.results['TransientSolution'][2]['Pressure'],\ ++ md.results['TransientSolution'][2]['Bed'],\ ++ md.results['TransientSolution'][2]['Surface'],\ ++ md.results['TransientSolution'][2]['Thickness'],\ ++ md.results['TransientSolution'][3]['Vx'],\ ++ md.results['TransientSolution'][3]['Vy'],\ ++ md.results['TransientSolution'][3]['Vel'],\ ++ md.results['TransientSolution'][3]['Pressure'],\ ++ md.results['TransientSolution'][3]['Bed'],\ ++ md.results['TransientSolution'][3]['Surface'],\ ++ md.results['TransientSolution'][3]['Thickness'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test203.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test203.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test203.py (revision 13491) +@@ -0,0 +1,42 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test203.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,2) ++md=setflowequation(md,'pattyn','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure'] ++field_tolerances=[1e-09,1e-09,1e-09,1e-09,1e-09] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vz'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test206.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test206.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test206.py (revision 13491) +@@ -0,0 +1,40 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test206.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,1) ++md=setflowequation(md,'macayeal','all') ++md.timestepping.time_step=0 ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,ThermalSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Temperature','BasalforcingsMeltingRate'] ++field_tolerances=[1e-13,1e-13] ++field_values=[\ ++ md.results['ThermalSolution'][1]['Temperature'],\ ++ md.results['ThermalSolution'][1]['BasalforcingsMeltingRate'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test209.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test209.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test209.py (revision 13491) +@@ -0,0 +1,72 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test209.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,1) ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,TransientSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', \ ++ 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', \ ++ 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'] ++field_tolerances=[\ ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-8,\ ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-8,\ ++ 1e-13,1e-13,1e-08,1e-13,1e-13,1e-10,1e-10,1e-10,1e-13,1e-8] ++field_values=[\ ++ md.results['TransientSolution'][1]['Vx'],\ ++ md.results['TransientSolution'][1]['Vy'],\ ++ md.results['TransientSolution'][1]['Vz'],\ ++ md.results['TransientSolution'][1]['Vel'],\ ++ md.results['TransientSolution'][1]['Pressure'],\ ++ md.results['TransientSolution'][1]['Bed'],\ ++ md.results['TransientSolution'][1]['Surface'],\ ++ md.results['TransientSolution'][1]['Thickness'],\ ++ md.results['TransientSolution'][1]['Temperature'],\ ++ md.results['TransientSolution'][1]['BasalforcingsMeltingRate'],\ ++ md.results['TransientSolution'][2]['Vx'],\ ++ md.results['TransientSolution'][2]['Vy'],\ ++ md.results['TransientSolution'][2]['Vz'],\ ++ md.results['TransientSolution'][2]['Vel'],\ ++ md.results['TransientSolution'][2]['Pressure'],\ ++ md.results['TransientSolution'][2]['Bed'],\ ++ md.results['TransientSolution'][2]['Surface'],\ ++ md.results['TransientSolution'][2]['Thickness'],\ ++ md.results['TransientSolution'][2]['Temperature'],\ ++ md.results['TransientSolution'][2]['BasalforcingsMeltingRate'],\ ++ md.results['TransientSolution'][3]['Vx'],\ ++ md.results['TransientSolution'][3]['Vy'],\ ++ md.results['TransientSolution'][3]['Vz'],\ ++ md.results['TransientSolution'][3]['Vel'],\ ++ md.results['TransientSolution'][3]['Pressure'],\ ++ md.results['TransientSolution'][3]['Bed'],\ ++ md.results['TransientSolution'][3]['Surface'],\ ++ md.results['TransientSolution'][3]['Thickness'],\ ++ md.results['TransientSolution'][3]['Temperature'],\ ++ md.results['TransientSolution'][3]['BasalforcingsMeltingRate'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test210.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test210.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test210.py (revision 13491) +@@ -0,0 +1,72 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test210.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',200000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,1) ++md=setflowequation(md,'pattyn','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,TransientSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsMeltingRate1', \ ++ 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsMeltingRate2', \ ++ 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsMeltingRate3'] ++field_tolerances=[\ ++ 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,\ ++ 1e-09,1e-09,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-06,\ ++ 1e-09,1e-09,1e-08,1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-05] ++field_values=[\ ++ md.results['TransientSolution'][1]['Vx'],\ ++ md.results['TransientSolution'][1]['Vy'],\ ++ md.results['TransientSolution'][1]['Vz'],\ ++ md.results['TransientSolution'][1]['Vel'],\ ++ md.results['TransientSolution'][1]['Pressure'],\ ++ md.results['TransientSolution'][1]['Bed'],\ ++ md.results['TransientSolution'][1]['Surface'],\ ++ md.results['TransientSolution'][1]['Thickness'],\ ++ md.results['TransientSolution'][1]['Temperature'],\ ++ md.results['TransientSolution'][1]['BasalforcingsMeltingRate'],\ ++ md.results['TransientSolution'][2]['Vx'],\ ++ md.results['TransientSolution'][2]['Vy'],\ ++ md.results['TransientSolution'][2]['Vz'],\ ++ md.results['TransientSolution'][2]['Vel'],\ ++ md.results['TransientSolution'][2]['Pressure'],\ ++ md.results['TransientSolution'][2]['Bed'],\ ++ md.results['TransientSolution'][2]['Surface'],\ ++ md.results['TransientSolution'][2]['Thickness'],\ ++ md.results['TransientSolution'][2]['Temperature'],\ ++ md.results['TransientSolution'][2]['BasalforcingsMeltingRate'],\ ++ md.results['TransientSolution'][3]['Vx'],\ ++ md.results['TransientSolution'][3]['Vy'],\ ++ md.results['TransientSolution'][3]['Vz'],\ ++ md.results['TransientSolution'][3]['Vel'],\ ++ md.results['TransientSolution'][3]['Pressure'],\ ++ md.results['TransientSolution'][3]['Bed'],\ ++ md.results['TransientSolution'][3]['Surface'],\ ++ md.results['TransientSolution'][3]['Thickness'],\ ++ md.results['TransientSolution'][3]['Temperature'],\ ++ md.results['TransientSolution'][3]['BasalforcingsMeltingRate'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test204.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test204.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test204.py (revision 13491) +@@ -0,0 +1,42 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test204.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,2) ++md=setflowequation(md,'stokes','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure'] ++field_tolerances=[1e-08,1e-08,1e-07,1e-08,1e-08] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vz'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test207.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test207.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test207.py (revision 13491) +@@ -0,0 +1,47 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test207.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,1) ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.transient.isdiagnostic=0 ++md.transient.isprognostic=0 ++md.transient.isthermal=1 ++md.transient.isgroundingline=0 ++md=solve(md,TransientSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Temperature1','BasalforcingsMeltingRate1','Temperature2','BasalforcingsMeltingRate2','Temperature3','BasalforcingsMeltingRate3'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['TransientSolution'][1]['Temperature'],\ ++ md.results['TransientSolution'][1]['BasalforcingsMeltingRate'],\ ++ md.results['TransientSolution'][2]['Temperature'],\ ++ md.results['TransientSolution'][2]['BasalforcingsMeltingRate'],\ ++ md.results['TransientSolution'][3]['Temperature'],\ ++ md.results['TransientSolution'][3]['BasalforcingsMeltingRate'],\ ++ ] +Index: ../trunk-jpl/scripts/translateToPy.py +=================================================================== +--- ../trunk-jpl/scripts/translateToPy.py (revision 13490) ++++ ../trunk-jpl/scripts/translateToPy.py (revision 13491) +@@ -66,12 +66,31 @@ + res = res.replace('thickness(pos)','thickness[pos]') + res = res.replace('find(md.','numpy.nonzero(md.') + ++ res = res.replace('\n','') ++ ++ # handle inline comments ++ res = res.replace('%','#') ++ + res = res.replace('...','\\') ++ ++ # determine if the m file has mult. line cmd (real quick solution) ++ multCmds = res.split(';') ++ numLines = len( multCmds ) - 2 ++ allParts = '' ++ for part in multCmds: ++ allParts += part ++ #allParts += re.sub('^\s+','',part) ++ #allParts += part.strip() ++ if numLines > 0: ++ allParts += '\n' ++ numLines -= 1 ++ res = allParts ++ + res = res.replace(';','') +- res = res.replace('\n','') + ++ + res = convertFieldValues( res ) +- ++ #print 'resulting line:' + str(res) + '\n' + output(res) + + def convertFieldValues ( currentLine ): +@@ -103,6 +122,19 @@ + res = res.replace('Solution.StressTensorxz)','Solution\'][1][\'StressTensorxz\']') + res = res.replace('Solution.StressTensoryz)','Solution\'][1][\'StressTensoryz\']') + ++ res = res.replace('Solution.FrictionCoefficient)','Solution\'][1][\'FrictionCoefficient\']') ++ res = res.replace('Solution.SurfaceforcingsMasBalance)','Solution\'][1][\'SurfaceforcingsMasBalance\']') ++ res = res.replace('Solution.MaskElementonfloatingice)','Solution\'][1][\'MaskElementonfloatingice\']') ++ res = res.replace('Solution.J)','Solution\'][1][\'J\']') ++ res = res.replace('Solution.BalancethicknessThickeningRate)','Solution\'][1][\'BalancethicknessThickeningRate\']') ++ ++ res = res.replace('Solution.Gradient1)','Solution\'][1][\'Gradient1\']') ++ res = res.replace('Solution.Gradient2)','Solution\'][1][\'Gradient2\']') ++ ++ res = res.replace('Solution.MaterialsRheologyZbar)','Solution\'][1][\'MaterialsRheologyZbar\']') ++ res = res.replace('Solution.MaterialsRheologyBbar)','Solution\'][1][\'MaterialsRheologyBbar\']') ++ res = res.replace('Solution.MaterialsRheologyB)','Solution\'][1][\'MaterialsRheologyB\']') ++ + res = res.replace('Solution.Thickness)','Solution\'][1][\'Thickness\']') + + res = res.replace('Solution.Temperature)','Solution\'][1][\'Temperature\']') +@@ -120,6 +152,10 @@ + res = res.replace('Solution.Enthalpy)','Solution\'][1][\'Enthalpy\']') + res = res.replace('Solution.Waterfraction)','Solution\'][1][\'Waterfraction\']') + res = res.replace('Solution.Temperature)','Solution\'][1][\'Temperature\']') ++ ++ # special case ++ res = res.replace('.DiagnosticSolution.J','[\'DiagnosticSolution\'][1][\'J\']') ++ + return res + + def output ( line ): Index: /issm/oecreview/Archive/13393-13976/ISSM-13491-13492.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13491-13492.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13491-13492.diff (revision 13980) @@ -0,0 +1,2303 @@ +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3006.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3006.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3006.py (revision 13492) +@@ -0,0 +1,42 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3006.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from meshconvert import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=meshconvert(md) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.prognostic.stabilization=3 ++md.prognostic.spcthickness=md.geometry.thickness ++md.autodiff.isautodiff=true ++md=solve(md,PrognosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Thickness'] ++field_tolerances=[1e-13] ++field_values=[\ ++ md.results['PrognosticSolution'][1]['Thickness'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1602.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1602.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1602.py (revision 13492) +@@ -0,0 +1,62 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test1602.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'../Exp/SquareShelf.exp','') ++md=parameterize(md,'../Par/SquareSheetShelf.py') ++md.extrude(5,1) ++md=setflowequation(md,'pattyn','all') ++md.diagnostic.spcvx(numpy.nonzero(md.mesh.y>0))=NaN ++md.initialization.vx(:)=0 ++md.initialization.vy(:)=0 ++md.initialization.vel(:)=0 ++ ++ ++md.cluster=generic('name',oshostname,'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++vel0=md.results.DiagnosticSolution.Vel ++ ++ ++theta=30*pi/180 ++x=md.mesh.x ++y=md.mesh.y ++md.mesh.x=cos(theta)*x-sin(theta)*y ++md.mesh.y=sin(theta)*x+cos(theta)*y ++ ++ ++md.diagnostic.referential(:,1:3)=repmat([cos(theta),sin(theta),0],md.mesh.numberofvertices,1) ++md.diagnostic.referential(:,4:6)=repmat([0,0,1],md.mesh.numberofvertices,1) ++md=solve(md,DiagnosticSolutionEnum()) ++vel1=md.results.DiagnosticSolution.Vel ++ ++ ++plotmodel()(md,'data',vel0,'data',vel1,'data',vel1-vel0,'title','Cartesian CS','title','Rotated CS','title','difference','view#all',2) ++disp(['Error between Cartesian and rotated CS: ' num2str(max(abs(vel0-vel1))/(max(abs(vel0))+eps)) ]) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['vel1'] ++field_tolerances=[1e-9] ++field_values=[\ ++ vel1, \ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3007.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3007.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3007.py (revision 13492) +@@ -0,0 +1,39 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3007.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md=setflowequation(md,'macayeal','all') ++md.extrude(5,3) ++md.cluster=generic('name',oshostname(),'np',3) ++md.autodiff.isautodiff=true ++md=solve(md,PrognosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Thickness'] ++field_tolerances=[1e-13] ++field_values=[\ ++ md.results['PrognosticSolution'][1]['Thickness'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3008.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3008.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3008.py (revision 13492) +@@ -0,0 +1,41 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3008.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md.extrude(3,1) ++md=setflowequation(md,'macayeal','all') ++md.timestepping.time_step=0 ++md.cluster=generic('name',oshostname(),'np',3) ++md.autodiff.isautodiff=true ++md=solve(md,ThermalSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Temperature','BasalforcingsMeltingRate'] ++field_tolerances=[1e-13,1e-13] ++field_values=[\ ++ md.results['ThermalSolution'][1]['Temperature'],\ ++ md.results['ThermalSolution'][1]['BasalforcingsMeltingRate'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3009.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3009.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3009.py (revision 13492) +@@ -0,0 +1,44 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3009.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md.extrude(3,1) ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.transient.isdiagnostic=0 ++md.transient.isprognostic=0 ++md.transient.isthermal=1 ++md.transient.isgroundingline=0 ++md.autodiff.isautodiff=true ++md=solve(md,TransientSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Temperature','BasalforcingsMeltingRate'] ++field_tolerances=[1e-13,1e-13] ++field_values=[\ ++ md.results['TransientSolution'][1]['Temperature'],\ ++ md.results['TransientSolution'][1]['BasalforcingsMeltingRate'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test220.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test220.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test220.py (revision 13492) +@@ -0,0 +1,42 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test220.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',120000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(2,1) ++md=setflowequation(md,'stokes','../Exp/SquareHalfRight.exp','fill','pattyn') ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure'] ++field_tolerances=[1e-09,1e-09,1e-06,1e-09,1e-09] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vz'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test212.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test212.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test212.py (revision 13492) +@@ -0,0 +1,61 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test212.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',200000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md=setflowequation(md,'macayeal','all') ++ ++ ++# control parameters ++ ++md.inversion.iscontrol=1 ++md.inversion.control_parameters=['MaterialsRheologyBbar'] ++md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1) ++md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1) ++md.inversion.nsteps=2 ++md.inversion.cost_functions=101*ones(md.inversion.nsteps,1) ++md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1) ++md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1) ++md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1) ++md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1) ++md.inversion.vx_obs=md.initialization.vx ++md.inversion.vy_obs=md.initialization.vy ++ ++ ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++md.results['DiagnosticSolution'][1]['Gradient1'],\ ++md.results['DiagnosticSolution.J'],\ ++md.results['DiagnosticSolution'][1]['MaterialsRheologyBbar'],\ ++md.results['DiagnosticSolution'][1]['Pressure'],\ ++md.results['DiagnosticSolution'][1]['Vel'],\ ++md.results['DiagnosticSolution'][1]['Vx'],\ ++md.results['DiagnosticSolution'][1]['Vy'],\ ++] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test213.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test213.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test213.py (revision 13492) +@@ -0,0 +1,63 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test213.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',200000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,1) ++md=setflowequation(md,'macayeal','all') ++ ++ ++# control parameters ++ ++md.inversion.iscontrol=1 ++md.inversion.control_parameters=['MaterialsRheologyBbar'] ++md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1) ++md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1) ++md.inversion.nsteps=2 ++md.inversion.cost_functions=101*ones(md.inversion.nsteps,1) ++md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1) ++md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1) ++md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1) ++md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1) ++md.inversion.vx_obs=md.initialization.vx ++md.inversion.vy_obs=md.initialization.vy ++ ++ ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++#field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Gradient1'],\ ++ md.results['DiagnosticSolution'][1]['J'],\ ++ md.results['DiagnosticSolution'][1]['MaterialsRheologyB'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test205.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test205.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test205.py (revision 13492) +@@ -0,0 +1,42 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test205.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,2) ++md=setflowequation(md,'pattyn','../Exp/SquareHalfRight.exp','fill','macayeal','coupling','penalties') ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure'] ++field_tolerances=[1e-05,1e-05,1e-05,1e-05,1e-05] ++field_values=[\ ++md.results['DiagnosticSolution'][1]['Vx'],\ ++md.results['DiagnosticSolution'][1]['Vy'],\ ++md.results['DiagnosticSolution'][1]['Vz'],\ ++md.results['DiagnosticSolution'][1]['Vel'],\ ++md.results['DiagnosticSolution'][1]['Pressure'],\ ++] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test214.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test214.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test214.py (revision 13492) +@@ -0,0 +1,61 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test214.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',200000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,1) ++md=setflowequation(md,'pattyn','all') ++ ++ ++# control parameters ++ ++md.inversion.iscontrol=1 ++md.inversion.control_parameters=['MaterialsRheologyBbar'] ++md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1) ++md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1) ++md.inversion.nsteps=2 ++md.inversion.cost_functions=101*ones(md.inversion.nsteps,1) ++md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1) ++md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1) ++md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1) ++md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1) ++md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy ++ ++ ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'] ++field_tolerances=[1e-07,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08] ++field_values=[\ ++ md.results['DiagnosticSolution.Gradient1),\ ++ md.results.DiagnosticSolution.J,\ ++ md.results['DiagnosticSolution.MaterialsRheologyB),\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'] ++] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test215.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test215.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test215.py (revision 13492) +@@ -0,0 +1,61 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test215.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',200000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,1) ++md=setflowequation(md,'stokes','all') ++ ++ ++# control parameters ++ ++md.inversion.iscontrol=1 ++md.inversion.control_parameters=['MaterialsRheologyBbar'] ++md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1) ++md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1) ++md.inversion.nsteps=2 ++md.inversion.cost_functions=101*ones(md.inversion.nsteps,1) ++md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1) ++md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1) ++md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1) ++md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1) ++md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy ++ ++ ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'] ++field_tolerances=[1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09] ++field_values=[\ ++ md.results['DiagnosticSolution.Gradient1),\ ++ md.results.DiagnosticSolution.J,\ ++ md.results['DiagnosticSolution.MaterialsRheologyB),\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'] ++] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test216.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test216.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test216.py (revision 13492) +@@ -0,0 +1,50 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test216.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/SquareHole.exp','../Exp/Rifts.exp',50000) ++md=meshprocessrifts(md,'../Exp/Square.exp') ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++ ++ ++# rift settings ++ ++md.rifts.riftstruct.fill=MelangeEnum() ++md.rifts.riftstruct.fraction=0 ++md.diagnostic.rift_penalty_lock=2 ++md.diagnostic.rift_penalty_threshold=0 ++md.rifts.riftstruct.fractionincrement=.1 ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vel','Pressure'] ++field_tolerances=[1e-11,1e-11,1e-11,1e-11] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test217.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test217.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test217.py (revision 13492) +@@ -0,0 +1,121 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test217.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++ ++ ++# redo the parameter file for this special shelf. ++ ++# constant thickness, constrained (vy=0) flow into an icefront, ++ ++# from 0 m/yr at the grounding line. ++ ++ ++ ++# tighten ++ ++md.diagnostic.restol=10^-4 ++ ++ ++# needed later ++ ++ymin=min(md.mesh.y) ++ymax=max(md.mesh.y) ++xmin=min(md.mesh.x) ++xmax=max(md.mesh.x) ++ ++ ++di=md.materials.rho_ice/md.materials.rho_water ++ ++ ++h=1000 ++md.geometry.thickness=h*ones(md.mesh.numberofvertices,1) ++md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness ++md.geometry.surface=md.geometry.bed+md.geometry.thickness ++ ++ ++# Initial velocity and pressure ++ ++md.initialization.vx=zeros(md.mesh.numberofvertices,1) ++md.initialization.vy=zeros(md.mesh.numberofvertices,1) ++md.initialization.vz=zeros(md.mesh.numberofvertices,1) ++md.initialization.pressure=zeros(md.mesh.numberofvertices,1) ++ ++ ++# Materials ++ ++md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1) ++md.materials.rheology_B=paterson(md.initialization.temperature) ++md.materials.rheology_n=3*ones(md.mesh.numberofelements,1) ++ ++ ++# Boundary conditions: ++ ++md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1) ++md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1) ++md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1) ++ ++ ++# constrain flanks to 0 normal velocity ++ ++pos=numpy.nonzero(md.mesh.x==xmin | md.mesh.x==xmax) ++md.diagnostic.spcvx(pos)=0 ++md.diagnostic.spcvz(pos)=NaN ++ ++ ++# constrain grounding line to 0 velocity ++ ++pos=numpy.nonzero(md.mesh.y==ymin) ++md.diagnostic.spcvx(pos)=0 ++md.diagnostic.spcvy(pos)=0 ++ ++ ++# icefront ++ ++nodeonicefront=zeros(md.mesh.numberofvertices,1) ++pos=numpy.nonzero(md.mesh.y==ymax) ++nodeonicefront(pos)=1 ++pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))) diagnostic.icefront=md.mesh.segments(pos,:) ++diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))] ++md.diagnostic.icefront=diagnostic.icefront ++ ++ ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# create analytical solution: strain rate is constant = ((rho_ice*g*h)/4B)^3 (Paterson, 4th Edition, page 292. ++ ++# ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3; ++ ++# vy_c=ey_c.*md.mesh.y*md.constants.yts; ++ ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vy'] ++field_tolerances=[1e-13] ++field_values=[md.results['DiagnosticSolution'][1]['Vy']] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test218.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test218.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test218.py (revision 13492) +@@ -0,0 +1,152 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test218.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=squaremesh(model(),1000000,1000000,5,5) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++ ++ ++# redo the parameter file for this special shelf. ++ ++# constant thickness, constrained (vy=0) flow into an icefront, ++ ++# from 0 m/yr at the grounding line. ++ ++ ++ ++# needed later ++ ++ymin=min(md.mesh.y) ++ymax=max(md.mesh.y) ++xmin=min(md.mesh.x) ++xmax=max(md.mesh.x) ++ ++ ++di=md.materials.rho_ice/md.materials.rho_water ++ ++ ++h=1000 ++md.geometry.thickness=h*ones(md.mesh.numberofvertices,1) ++md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness ++md.geometry.surface=md.geometry.bed+md.geometry.thickness ++ ++ ++# Initial velocity and pressure ++ ++md.initialization.vx=zeros(md.mesh.numberofvertices,1) ++md.initialization.vy=zeros(md.mesh.numberofvertices,1) ++md.initialization.vz=zeros(md.mesh.numberofvertices,1) ++md.initialization.pressure=zeros(md.mesh.numberofvertices,1) ++ ++ ++# Materials ++ ++md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1) ++md.materials.rheology_B=paterson(md.initialization.temperature) ++md.materials.rheology_n=3*ones(md.mesh.numberofelements,1) ++ ++ ++# Boundary conditions: ++ ++md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1) ++md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1) ++md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1) ++ ++ ++# constrain flanks to 0 normal velocity ++ ++pos=numpy.nonzero(md.mesh.x==xmin | md.mesh.x==xmax) ++md.diagnostic.spcvx(pos)=0 ++md.diagnostic.spcvz(pos)=NaN ++ ++ ++# constrain grounding line to 0 velocity ++ ++pos=numpy.nonzero(md.mesh.y==ymin) ++md.diagnostic.spcvx(pos)=0 ++md.diagnostic.spcvy(pos)=0 ++ ++ ++# icefront ++ ++nodeonicefront=zeros(md.mesh.numberofvertices,1) ++pos=numpy.nonzero(md.mesh.y==ymax) ++nodeonicefront(pos)=1 ++pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))) ++diagnostic.icefront=md.mesh.segments(pos,:) ++diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))] ++md.diagnostic.icefront=diagnostic.icefront ++ ++ ++# partitioning ++ ++md.qmu.numberofpartitions=md.mesh.numberofvertices ++md=partitioner(md,'package','linear','npart',md.qmu.numberofpartitions) ++md.qmu.pytition=md.qmu.pytition-1 ++ ++ ++# Dakota options ++ ++# variables ++ ++md.qmu.variables.rheology_B=normal_uncertain('scaled_MaterialsRheologyB',1,.05) ++ ++ ++# responses ++ ++md.qmu.responses.MaxVel=response_function('MaxVel',[],[0.0001 0.001 0.01 0.25 0.5 0.75 0.99 0.999 0.9999]) ++ ++ ++# method ++ ++md.qmu.method =dakota_method('nond_l') ++ ++ ++# parameters ++ ++md.qmu.pyams.direct=true ++md.qmu.pyams.analysis_driver='diagnostic' ++md.qmu.pyams.evaluation_concurrency=1 ++md.qmu.pyams.interval_type='forward' ++ ++ ++# imperative! ++ ++md.diagnostic.reltol=10^-10#tighten for qmu analysese ++md.qmu.isdakota=1 ++ ++ ++# solve ++ ++md=solve(md,DiagnosticSolutionEnum(),'overwrite','y') ++ ++ ++# Fields and tolerances to track changes ++ ++md.qmu.results=md.results.dakota ++md.results.dakota.importancefactors=importancefactors(md,'scaled_MaterialsRheologyB','MaxVel') ++field_names =['importancefactors'] ++field_tolerances=[1e-10] ++field_values=[\ ++md.results.dakota.importancefactors,\ ++] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test219.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test219.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test219.py (revision 13492) +@@ -0,0 +1,42 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test219.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,2) ++md=setflowequation(md,'pattyn','../Exp/SquareHalfRight.exp','fill','macayeal') ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure'] ++field_tolerances=[1e-09,1e-09,1e-09,1e-09,1e-13] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vz'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3001.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3001.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3001.py (revision 13492) +@@ -0,0 +1,47 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3001.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',50000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.diagnostic.requested_outputs=StressTensorEnum() ++md.autodiff.isautodiff=true ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vel','Pressure',\ ++ 'StressTensorxx','StressTensoryy','StressTensorxy'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,\ ++ 1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorxx'],\ ++ md.results['DiagnosticSolution'][1]['StressTensoryy'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorxy'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3010.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3010.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3010.py (revision 13492) +@@ -0,0 +1,66 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3010.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.transient.requested_outputs=IceVolumeEnum() ++ ++ ++md.autodiff.isautodiff=true ++md=solve(md,TransientSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Volume1','Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Volume2','Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Volume3'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['TransientSolution'][1]['Vx'],\ ++ md.results['TransientSolution'][1]['Vy'],\ ++ md.results['TransientSolution'][1]['Vel'],\ ++ md.results['TransientSolution'][1]['Pressure'],\ ++ md.results['TransientSolution'][1]['Bed'],\ ++ md.results['TransientSolution'][1]['Surface'],\ ++ md.results['TransientSolution'][1]['Thickness'],\ ++ md.results['TransientSolution'][1]['IceVolume'],\ ++ md.results['TransientSolution'][2]['Vx'],\ ++ md.results['TransientSolution'][2]['Vy'],\ ++ md.results['TransientSolution'][2]['Vel'],\ ++ md.results['TransientSolution'][2]['Pressure'],\ ++ md.results['TransientSolution'][2]['Bed'],\ ++ md.results['TransientSolution'][2]['Surface'],\ ++ md.results['TransientSolution'][2]['Thickness'],\ ++ md.results['TransientSolution'][2]['IceVolume'],\ ++ md.results['TransientSolution'][3]['Vx'],\ ++ md.results['TransientSolution'][3]['Vy'],\ ++ md.results['TransientSolution'][3]['Vel'],\ ++ md.results['TransientSolution'][3]['Pressure'],\ ++ md.results['TransientSolution'][3]['Bed'],\ ++ md.results['TransientSolution'][3]['Surface'],\ ++ md.results['TransientSolution'][3]['Thickness'],\ ++ md.results['TransientSolution'][3]['IceVolume'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1301.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1301.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1301.py (revision 13492) +@@ -0,0 +1,87 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test1301.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++# This file can be run to check that the melting in simple conduction is correctly modeled. ++ ++# There is no velocity (no advection) the only thermal boundary conditions are an imposed temperature ++ ++# at upper surface and an impose flux at its base. The result must be a linear temperature from the upper to the lower ++ ++# surface with an imposed slope (Geothermal flux). if it is not the case, something is thermal modeling has been changed... ++ ++printingflag=false ++ ++ ++md=model() ++md=triangle(md,'../Exp/Square.exp',100000) ++md=setmask(md,'','') ++md=parameterize(md,'../Par/SquareThermal.py') ++md.extrude(3,2) ++md=setflowequation(md,'Pattyn','all') ++ ++ ++# Some conditions specific to melting test ++ ++md.initialization.pressure=zeros(md.mesh.numberofvertices,1) ++md.initialization.temperature=273.15*ones(md.mesh.numberofvertices,1) ++pos=numpy.nonzero(md.mesh.vertexonsurface) ++md.thermal.spctemperature(pos)=md.initialization.temperature(pos) ++md.materials.rheology_B=paterson(md.initialization.temperature) ++ ++ ++# analytical results ++ ++# melting heat = geothermal flux ++ ++# Mb*L*rho=G => Mb=G/L*rho ++ ++melting=md.basalforcings.geothermalflux/(md.materials.rho_ice*md.materials.latentheat)*md.constants.yts ++ ++ ++# modeled results ++ ++md.cluster=generic('name',oshostname(),'np',2) ++md=solve(md,ThermalSolutionEnum()) ++ ++ ++# plot results ++ ++comp_melting=md.results.ThermalSolution.BasalforcingsMeltingRate ++relative=abs((comp_melting-melting)./melting)*100 ++relative(find(comp_melting==melting))=0 ++plotmodel()(md,'data',comp_melting,'title','Modeled melting','data',melting,'title','Analytical melting',\ ++ 'data',comp_melting-melting,'title','Absolute error','data',relative,'title','Relative error [%]',\ ++ 'layer#all',1,'caxis#2',[1.02964 1.02966]*10^-4,'FontSize#all',20,'figposition','mathieu') ++if printingflag, ++ set(gcf,'Color','w') ++ printmodel()('thermalmelting','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off') ++ system(['mv thermalmelting.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']) ++end ++ ++ ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['BasalMelting'] ++field_tolerances=[1e-08] ++field_values =[comp_melting] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3002.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3002.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3002.py (revision 13492) +@@ -0,0 +1,43 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3002.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md.extrude(3,2) ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.autodiff.isautodiff=true ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vz'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1302.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1302.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1302.py (revision 13492) +@@ -0,0 +1,86 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test1302.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++# This file can be run to check that the advection-diffusion is correctly modeled. ++ ++# There is u=v=0 and w=cst everywhere the only thermal boundary conditions are an imposed temperature ++ ++# at upper surface and an impose flux at its base. ++ ++printingflag=false ++ ++ ++md=model() ++md=triangle(md,'../Exp/Square.exp',100000) ++md=setmask(md,'','') ++md=parameterize(md,'../Par/SquareThermal.py') ++md.extrude(30,1) %NB: the more one extrudes, the better (10-> relative~0.35%, 20->0.1%, 30->0.05%) ++md=setflowequation(md,'Pattyn','all') ++ ++ ++# Thermal boundary conditions ++ ++pos1=numpy.nonzero(md.mesh.elementonbed) md.thermal.spctemperature(md.mesh.elements(pos1,1:3))=10 ++pos2=numpy.nonzero(md.mesh.elementonsurface) md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0 ++md.initialization.vz=0.1*ones(md.mesh.numberofvertices,1) ++md.initialization.vel=sqrt( md.initialization.vx.^2+ md.initialization.vy.^2+ md.initialization.vz.^2) ++md.initialization.pressure=zeros(md.mesh.numberofvertices,1) ++ ++ ++md.thermal.stabilization=2 ++# analytical results ++ ++# d2T/dz2-w*rho_ice*c/k*dT/dz=0 T(surface)=0 T(bed)=10 => T=A exp(alpha z)+B ++ ++alpha=0.1/md.constants.yts*md.materials.rho_ice*md.materials.heatcapacity/md.materials.thermalconductivity %alpha=w rho_ice c /k and w=0.1m/an ++A=10/(exp(alpha*(-1000))-1) %A=T(bed)/(exp(alpha*bed)-1) with bed=-1000 T(bed)=10 ++B=-A ++md.initialization.temperature=A*exp(alpha*md.mesh.z)+B ++ ++ ++# modeled results ++ ++md.cluster=generic('name',oshostname(),'np',2) ++md=solve(md,ThermalSolutionEnum()) ++ ++ ++# plot results ++ ++comp_temp=md.results.ThermalSolution.Temperature ++relative=abs((comp_temp-md.initialization.temperature)./md.initialization.temperature)*100 ++relative(find(comp_temp==md.initialization.temperature))=0 ++plotmodel()(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,\ ++ 'title','Analytical temperature [K]','view',3,'data',comp_temp-md.initialization.temperature,\ ++ 'title','Absolute error [K]','view',3,'data',relative,'title','Relative error [%]','view',3,\ ++ 'figposition','mathieu','FontSize#all',20) ++if printingflag, ++ set(gcf,'Color','w') ++ printmodel()('thermaladvection','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off') ++ system(['mv thermaladvection.png ' ISSM_DIR '/website/doc_pdf/validation/Images/EISMINT ']) ++end ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['AdvectionTemperature'] ++field_tolerances=[1e-13] ++field_values =[comp_temp] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3003.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3003.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3003.py (revision 13492) +@@ -0,0 +1,52 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3003.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md.extrude(3,2) ++md=setflowequation(md,'pattyn','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.diagnostic.requested_outputs=StressTensorEnum() ++md.autodiff.isautodiff=true ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure',\ ++ 'StressTensorxx','StressTensoryy','StressTensorzz','StressTensorxy','StressTensorxz','StressTensoryz'] ++field_tolerances=[1e-09,1e-09,1e-09,1e-09,1e-09,\ ++ 1e-09,1e-09,1e-09,1e-09,1e-09,1e-09] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vz'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorxx'],\ ++ md.results['DiagnosticSolution'][1]['StressTensoryy'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorzz'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorxy'],\ ++ md.results['DiagnosticSolution'][1]['StressTensorxz'],\ ++ md.results['DiagnosticSolution'][1]['StressTensoryz'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1501.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1501.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1501.py (revision 13492) +@@ -0,0 +1,267 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test1501.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++printingflag = false ++ ++ ++md=triangle(model(),'../Exp/Square.exp',350000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.transient.isthermal=0 ++ ++ ++md.timestepping.time_step=1 ++md.settings.output_frequency=1 ++md.timestepping.final_time=2000 ++ ++ ++# Solve for thinning rate -> -1 * surface mass balance ++ ++smb= 2*ones(md.mesh.numberofvertices,1) ++md.surfaceforcings.mass_balance= smb ++md.basalforcings.melting_rate= smb ++ ++ ++md=solve(md,PrognosticSolutionEnum()) ++ ++ ++for i=1:10 ++ md=solve(md,PrognosticSolutionEnum()) ++ md.surfaceforcings.mass_balance= md.surfaceforcings.mass_balance - (md.results['PrognosticSolution'][1]['Thickness']-md.geometry.thickness) ++end ++ ++ ++# Set up transient ++ ++smb = md.surfaceforcings.mass_balance ++ ++ ++tooth= [ [ones(400,1)*(smb') - 10]' [ones(400,1)*(smb')]' ] ++smb=[ [ones(399,1)*(smb')]' smb tooth tooth] ++ ++ ++md.surfaceforcings.mass_balance= smb ++md.surfaceforcings.mass_balance(end+1,:)=[1:2000] ++ ++ ++md=solve(md,TransientSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names=['Vx1','Vy1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', \ ++ 'Vx2','Vy2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', \ ++ 'Vx3','Vy3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3', \ ++ 'Vx4','Vy4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceforcingsMassBalance4', \ ++ 'Vx5','Vy5','Vel5','Pressure5','Bed5','Surface5','Thickness5','SurfaceforcingsMassBalance5'] ++field_tolerances=[1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,\ ++ 1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,\ ++ 1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,\ ++ 1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10,\ ++ 1e-09,1e-09,1e-09,1e-10,1e-10,1e-10,1e-10,1e-10] ++field_values=[\ ++ md.results['TransientSolution'][400]['Vx'],\ ++ md.results['TransientSolution'][400]['Vy'],\ ++ md.results['TransientSolution'][400]['Vel'],\ ++ md.results['TransientSolution'][400]['Pressure'],\ ++ md.results['TransientSolution'][400]['Bed'],\ ++ md.results['TransientSolution'][400]['Surface'],\ ++ md.results['TransientSolution'][400]['Thickness'],\ ++ md.results['TransientSolution'][400]['SurfaceforcingsMassBalance'],\ ++ md.results['TransientSolution'][800]['Vx'],\ ++ md.results['TransientSolution'][800]['Vy'],\ ++ md.results['TransientSolution'][800]['Vel'],\ ++ md.results['TransientSolution'][800]['Pressure'],\ ++ md.results['TransientSolution'][800]['Bed'],\ ++ md.results['TransientSolution'][800]['Surface'],\ ++ md.results['TransientSolution'][800]['Thickness'],\ ++ md.results['TransientSolution'][800]['SurfaceforcingsMassBalance'],\ ++ md.results['TransientSolution'][1200]['Vx'],\ ++ md.results['TransientSolution'][1200]['Vy'],\ ++ md.results['TransientSolution'][1200]['Vel'],\ ++ md.results['TransientSolution'][1200]['Pressure'],\ ++ md.results['TransientSolution'][1200]['Bed'],\ ++ md.results['TransientSolution'][1200]['Surface'],\ ++ md.results['TransientSolution'][1200]['Thickness'],\ ++ md.results['TransientSolution'][1200]['SurfaceforcingsMassBalance'],\ ++ md.results['TransientSolution'][1600]['Vx'],\ ++ md.results['TransientSolution'][1600]['Vy'],\ ++ md.results['TransientSolution'][1600]['Vel'],\ ++ md.results['TransientSolution'][1600]['Pressure'],\ ++ md.results['TransientSolution'][1600]['Bed'],\ ++ md.results['TransientSolution'][1600]['Surface'],\ ++ md.results['TransientSolution'][1600]['Thickness'],\ ++ md.results['TransientSolution'][1600]['SurfaceforcingsMassBalance'],\ ++ md.results['TransientSolution'][2000]['Vx'],\ ++ md.results['TransientSolution'][2000]['Vy'],\ ++ md.results['TransientSolution'][2000]['Vel'],\ ++ md.results['TransientSolution'][2000]['Pressure'],\ ++ md.results['TransientSolution'][2000]['Bed'],\ ++ md.results['TransientSolution'][2000]['Surface'],\ ++ md.results['TransientSolution'][2000]['Thickness'],\ ++ md.results['TransientSolution'][2000]['SurfaceforcingsMassBalance'],\ ++ ] ++ ++ ++if printingflag, ++ ++ ++ starttime = 360 ++ endtime = 2000 ++ res = 40 ++ ts = [starttime:res:endtime] ++ ++ ++ index = md.mesh.elements ++ x1=md.mesh.x(index(:,1)) x2=md.mesh.x(index(:,2)) x3=md.mesh.x(index(:,3)) ++ y1=md.mesh.y(index(:,1)) y2=md.mesh.y(index(:,2)) y3=md.mesh.y(index(:,3)) ++ areas=(0.5*((x2-x1).*(y3-y1)-(y2-y1).*(x3-x1))) ++ ++ ++ thickness = [] ++ volume = [] ++ massbal = [] ++ velocity = [] ++ for t=starttime:endtime ++ thickness = [thickness md.results['TransientSolution'][t]['Thickness']] ++ volume = [volume meanmd.results['TransientSolution'][t]['Thicknessvalue,2'].*areas] ++ massbal = [massbal md.results['TransientSolution'][t]['SurfaceforcingsMassBalance']] ++ velocity = [velocity md.results['TransientSolution'][t]['Vel']] ++ end ++ ++ ++ figure('Position', [0 0 860 932]) ++ ++ ++ options = plotoptions('data','transient_movie','unit','km') ++ options = options.list[1] ++ options = checkplotoptions(md,options) ++ ++ ++# loop over the time steps ++ ++ results=md.results.TransientSolution ++ count = 1 ++ for i=ts ++ ++ ++ subplot(5,9,[28:31 37:40]) ++ set(gca,'pos',get(gca,'pos')+[-0.08 -0.08 0.07 0.08]) ++ field = 'Thickness' ++ ++ ++# process data ++ ++ [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options) ++ [data datatype]=processdata(md,results(i).(field),options) ++ ++ ++ titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year'] ++ plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) ++ options=changefieldvalue(options,'title',titlestring) ++ options=addfielddefault(options,'colorbar',1) ++ options=changefieldvalue(options,'caxis',[0 max(max(thickness))]) ++ applyoptions(md,[],options) ++ ++ ++ subplot(5,9,[33:36 42:45]) ++ set(gca,'pos',get(gca,'pos')+[-0.00 -0.08 0.07 0.08]) ++ field = 'Vel' ++ ++ ++# process data ++ ++ [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options) ++ [data datatype]=processdata(md,results(i).(field),options) ++ ++ ++ titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year'] ++ plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) ++ options=changefieldvalue(options,'title',titlestring) ++ options=addfielddefault(options,'colorbar',1) ++ options=changefieldvalue(options,'caxis',[0 max(max(velocity))]) ++ applyoptions(md,[],options) ++ ++ ++ subplot(5,4,1:4) ++ cla ++ set(gca,'pos',get(gca,'pos')+[-0.07 0.03 0.12 0.015]) ++ plot(starttime:endtime,mean(massbal),'k','LineWidth', 4) ++ hold on ++ ya = ylim ++ plot([i i], ya, 'r', 'LineWidth',6) ++ ylim(ya) xlim([starttime endtime]) ++ title('Surface Mass Balance','FontSize',14) ++ ylabel('m/year','FontSize',14) ++ ++ ++ subplot(5,4,5:8) ++ cla ++ set(gca,'pos',get(gca,'pos')+[-0.07 0.015 0.12 0.015]) ++ plot(starttime:endtime,sum(volume)/1000/1000/1000,'LineWidth',4) ++ hold on ++ ya = ylim ++ plot([i i], ya, 'r', 'LineWidth',6) ++ ylim(ya) xlim([starttime endtime]) ++ title('Ice Volume','FontSize',14) ++ ylabel('km^3','FontSize',14) ++ ++ ++ subplot(5,4,9:12) ++ cla ++ set(gca,'pos',get(gca,'pos')+[-0.07 0 0.12 0.015]) ++ plot(starttime:endtime,mean(velocity)/1000, 'LineWidth', 4) ++ hold on ++ ya = ylim ++ plot([i i], ya, 'r', 'LineWidth',6) ++ ylim(ya) xlim([starttime endtime]) ++ title('Mean Velocity','FontSize', 14) ++ ylabel('km/year','FontSize', 14) ++ xlabel('year','FontSize', 14) ++ ++ ++ set(gcf,'Renderer','zbuffer','color','white') %fixes a bug on Mac OS X (not needed in future Matlab version) ++ if i==starttime, ++# initialize images and frame ++ ++ frame=getframe(gcf) ++ [images,map]=rgb2ind(frame.cdata,256,'nodither') ++ images(1,1,1,length(ts))=0 ++ else ++ frame=getframe(gcf) ++ images(:,:,1,count) = rgb2ind(frame.cdata,map,'nodither') ++ end ++ ++ ++ count = count+1 ++ ++ ++ end ++ ++ ++ filename='transawtooth2d.gif' ++ imwrite(images,map,filename,'DelayTime',1.0,'LoopCount',inf) ++ ++ ++end %printingflag +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1303.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1303.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1303.py (revision 13492) +@@ -0,0 +1,80 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test1303.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++# This file can be run to check that the conduction is correctly modeled. ++ ++# There is no velocity (no advection) the only thermal boundary conditions are an imposed temperature ++ ++# at the lower and upper surface. The result must be a linear temperature from the upper to the lower ++ ++# surface. if it is not the case, something is thermal modeling has been changed... ++ ++printingflag=false ++ ++ ++md=model() ++md=triangle(md,'../Exp/Square.exp',100000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareThermal.py') ++md.extrude(11,2) ++md=setflowequation(md,'Pattyn','all') ++pos1=numpy.nonzero(md.mesh.elementonbed) md.thermal.spctemperature(md.mesh.elements(pos1,1:3))=10 ++pos2=numpy.nonzero(md.mesh.elementonsurface) md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0 ++md.initialization.pressure=zeros(md.mesh.numberofvertices,1) ++ ++ ++# analytical results ++ ++# d2T/dz2=0 T(bed)=10 T(surface)=0 => T=0*(z-bed)/thickness+10*(surface-z)/thickness ++ ++# each layer of the 3d mesh must have a constant value ++ ++md.initialization.temperature=10*(md.geometry.surface-md.mesh.z)./md.geometry.thickness ++ ++ ++# modeled results ++ ++md.cluster=generic('name',oshostname(),'np',2) ++md=solve(md,ThermalSolutionEnum()) ++ ++ ++# plot results ++ ++comp_temp=md.results.ThermalSolution.Temperature ++relative=abs((comp_temp-md.initialization.temperature)./md.initialization.temperature)*100 ++relative(find(comp_temp==md.initialization.temperature))=0 ++plotmodel()(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,\ ++ 'title','Analytical temperature [K]','view',3,'data',comp_temp-md.initialization.temperature,\ ++ 'title','Absolute error [K]','view',3,'data',relative,'title','Relative error [%]','view',3,\ ++ 'figposition','mathieu','FontSize#all',20) ++if printingflag, ++ set(gcf,'Color','w') ++ printmodel()('thermalconduction','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off') ++ system(['mv thermalconduction.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']) ++end ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['ConductionTemperature'] ++field_tolerances=[1e-13] ++field_values =[comp_temp] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3004.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3004.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3004.py (revision 13492) +@@ -0,0 +1,43 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3004.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',180000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md.extrude(3,2) ++md=setflowequation(md,'stokes','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.autodiff.isautodiff=true ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure'] ++field_tolerances=[1e-08,1e-08,1e-07,1e-08,1e-08] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++ md.results['DiagnosticSolution'][1]['Vz'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1601.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1601.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1601.py (revision 13492) +@@ -0,0 +1,76 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test1601.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md=setflowequation(md,'macayeal','all') ++md.diagnostic.spcvx(numpy.nonzero(md.mesh.y>0))=NaN ++md.initialization.vx(:)=0 ++md.initialization.vy(:)=0 ++md.initialization.vel(:)=0 ++ ++ ++md.cluster=generic('name',oshostname,'np',2) ++md=solve(md,DiagnosticSolutionEnum()) ++vel0=md.results.DiagnosticSolution.Vel ++ ++ ++theta=30*pi/180 ++x=md.mesh.x ++y=md.mesh.y ++md.mesh.x=cos(theta)*x-sin(theta)*y ++md.mesh.y=sin(theta)*x+cos(theta)*y ++ ++ ++md.diagnostic.referential(:,1:3)=repmat([cos(theta),sin(theta),0],md.mesh.numberofvertices,1) ++md.diagnostic.referential(:,4:6)=repmat([0,0,1],md.mesh.numberofvertices,1) ++md=solve(md,DiagnosticSolutionEnum()) ++vel1=md.results.DiagnosticSolution.Vel ++ ++ ++plotmodel()(md,'data',vel0,'data',vel1,'data',vel1-vel0,'title','Cartesian CS','title','Rotated CS','title','difference') ++disp(['Error between Cartesian and rotated CS: ' num2str(max(abs(vel0-vel1))/(max(abs(vel0))+eps)) ]) ++ ++ ++# Now, put CS back to normal except on the side where the spc are applied ++ ++pos=find(x==0 | x==1000000) ++md.diagnostic.referential(:)=NaN ++md.diagnostic.referential(pos,1:3)=repmat([cos(theta),sin(theta),0],size(pos,1),1) ++md.diagnostic.referential(pos,4:6)=repmat([0,0,1],size(pos,1),1) ++md=solve(md,DiagnosticSolutionEnum()) ++vel2=md.results.DiagnosticSolution.Vel ++ ++ ++plotmodel()(md,'data',vel0,'data',vel2,'data',vel2-vel0,'title','Cartesian CS','title','Rotated CS','title','difference') ++disp(['Error between Cartesian and rotated CS: ' num2str(max(abs(vel0-vel2))/(max(abs(vel0))+eps)) ]) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['vel1','vel2'] ++field_tolerances=[1e-11,1e-11] ++field_values=[\ ++ vel1, \ ++ vel2, \ ++ ] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1502.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1502.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1502.py (revision 13492) +@@ -0,0 +1,273 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test1502.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++printingflag = false ++ ++ ++md=triangle(model(),'../Exp/Square.exp',450000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md=setflowequation(md,'macayeal','all') ++md.extrude(3,1) ++md.cluster=generic('name',oshostname(),'np',2) ++md.transient.isthermal=0 ++ ++ ++md.timestepping.time_step=1 ++md.settings.output_frequency=1 ++md.timestepping.final_time=2000 ++ ++ ++# Solve for thinning rate -> -1 * surface mass balance ++ ++smb= 2*ones(md.mesh.numberofvertices,1) ++md.surfaceforcings.mass_balance= smb ++md.basalforcings.melting_rate= smb ++ ++ ++md=solve(md,PrognosticSolutionEnum()) ++ ++ ++for i=1:10 ++ md=solve(md,PrognosticSolutionEnum()) ++ md.surfaceforcings.mass_balance= md.surfaceforcings.mass_balance - (md.results['PrognosticSolution'][1]['Thickness']-md.geometry.thickness) ++end ++ ++ ++# Set up transient ++ ++smb = md.surfaceforcings.mass_balance ++ ++ ++tooth= [ [ones(400,1)*(smb') - 10]' [ones(400,1)*(smb')]' ] ++smb=[ [ones(399,1)*(smb')]' smb tooth tooth] ++ ++ ++md.surfaceforcings.mass_balance= smb ++md.surfaceforcings.mass_balance(end+1,:)=[1:2000] ++ ++ ++md=solve(md,TransientSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names=['Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','SurfaceforcingsMassBalance1', \ ++ 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','SurfaceforcingsMassBalance2', \ ++ 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','SurfaceforcingsMassBalance3', \ ++ 'Vx4','Vy4','Vz4','Vel4','Pressure4','Bed4','Surface4','Thickness4','SurfaceforcingsMassBalance4', \ ++ 'Vx5','Vy5','Vz5','Vel5','Pressure5','Bed5','Surface5','Thickness5','SurfaceforcingsMassBalance5'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,\ ++ 1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['TransientSolution'][400]['Vx'],\ ++ md.results['TransientSolution'][400]['Vy'],\ ++ md.results['TransientSolution'][400]['Vz'],\ ++ md.results['TransientSolution'][400]['Vel'],\ ++ md.results['TransientSolution'][400]['Pressure'],\ ++ md.results['TransientSolution'][400]['Bed'],\ ++ md.results['TransientSolution'][400]['Surface'],\ ++ md.results['TransientSolution'][400]['Thickness'],\ ++ md.results['TransientSolution'][400]['SurfaceforcingsMassBalance'],\ ++ md.results['TransientSolution'][800]['Vx'],\ ++ md.results['TransientSolution'][800]['Vy'],\ ++ md.results['TransientSolution'][800]['Vz'],\ ++ md.results['TransientSolution'][800]['Vel'],\ ++ md.results['TransientSolution'][800]['Pressure'],\ ++ md.results['TransientSolution'][800]['Bed'],\ ++ md.results['TransientSolution'][800]['Surface'],\ ++ md.results['TransientSolution'][800]['Thickness'],\ ++ md.results['TransientSolution'][800]['SurfaceforcingsMassBalance'],\ ++ md.results['TransientSolution'][1200]['Vx'],\ ++ md.results['TransientSolution'][1200]['Vy'],\ ++ md.results['TransientSolution'][1200]['Vz'],\ ++ md.results['TransientSolution'][1200]['Vel'],\ ++ md.results['TransientSolution'][1200]['Pressure'],\ ++ md.results['TransientSolution'][1200]['Bed'],\ ++ md.results['TransientSolution'][1200]['Surface'],\ ++ md.results['TransientSolution'][1200]['Thickness'],\ ++ md.results['TransientSolution'][1200]['SurfaceforcingsMassBalance'],\ ++ md.results['TransientSolution'][1600]['Vx'],\ ++ md.results['TransientSolution'][1600]['Vy'],\ ++ md.results['TransientSolution'][1600]['Vz'],\ ++ md.results['TransientSolution'][1600]['Vel'],\ ++ md.results['TransientSolution'][1600]['Pressure'],\ ++ md.results['TransientSolution'][1600]['Bed'],\ ++ md.results['TransientSolution'][1600]['Surface'],\ ++ md.results['TransientSolution'][1600]['Thickness'],\ ++ md.results['TransientSolution'][1600]['SurfaceforcingsMassBalance'],\ ++ md.results['TransientSolution'][2000]['Vx'],\ ++ md.results['TransientSolution'][2000]['Vy'],\ ++ md.results['TransientSolution'][2000]['Vz'],\ ++ md.results['TransientSolution'][2000]['Vel'],\ ++ md.results['TransientSolution'][2000]['Pressure'],\ ++ md.results['TransientSolution'][2000]['Bed'],\ ++ md.results['TransientSolution'][2000]['Surface'],\ ++ md.results['TransientSolution'][2000]['Thickness'],\ ++ md.results['TransientSolution'][2000]['SurfaceforcingsMassBalance'],\ ++ ] ++ ++ ++if printingflag, ++ ++ ++ starttime = 360 ++ endtime = 2000 ++ res = 40 ++ ts = [starttime:res:endtime] ++ ++ ++ index = md.mesh.elements ++ x1=md.mesh.x(index(:,1)) x2=md.mesh.x(index(:,2)) x3=md.mesh.x(index(:,3)) ++ y1=md.mesh.y(index(:,1)) y2=md.mesh.y(index(:,2)) y3=md.mesh.y(index(:,3)) ++ areas=(0.5*((x2-x1).*(y3-y1)-(y2-y1).*(x3-x1))) ++ ++ ++ thickness = [] ++ volume = [] ++ massbal = [] ++ velocity = [] ++ for t=starttime:endtime ++ thickness = [thickness md.results['TransientSolution'][t]['Thickness']] ++ volume = [volume meanmd.results['TransientSolution'][t]['Thicknessvalue,2'].*areas] ++ massbal = [massbal md.results['TransientSolution'][t]['SurfaceforcingsMassBalance']] ++ velocity = [velocity md.results['TransientSolution'][t]['Vel']] ++ end ++ ++ ++ figure('Position', [0 0 1060 1060]) ++ ++ ++ options = plotoptions('data','transient_movie','unit','km') ++ options = options.list[1] ++ options = checkplotoptions(md,options) ++ ++ ++# loop over the time steps ++ ++ results=md.results.TransientSolution ++ count = 1 ++ for i=ts ++ ++ ++ subplot(5,9,[28:31 37:40]) ++ set(gca,'pos',get(gca,'pos')+[-0.08 -0.08 0.07 0.08]) ++ field = 'Thickness' ++ ++ ++# process data ++ ++ [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options) ++ [data datatype]=processdata(md,results(i).(field),options) ++ ++ ++ titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year'] ++ plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) ++ options=changefieldvalue(options,'title',titlestring) ++ options=addfielddefault(options,'colorbar',1) ++ options=changefieldvalue(options,'caxis',[0 max(max(thickness))]) ++ applyoptions(md,[],options) ++ ++ ++ subplot(5,9,[33:36 42:45]) ++ set(gca,'pos',get(gca,'pos')+[-0.01 -0.08 0.07 0.08]) ++ field = 'Vel' ++ ++ ++# process data ++ ++ [x y z elements is2d isplanet]=processmesh(md,results(i).(field),options) ++ [data datatype]=processdata(md,results(i).(field),options) ++ ++ ++ titlestring=[field ' at time ' num2str(results(i).time/md.constants.yts) ' year'] ++ plot_unit(x,y,z,elements,data,is2d,isplanet,datatype,options) ++ options=changefieldvalue(options,'title',titlestring) ++ options=addfielddefault(options,'colorbar',1) ++ options=changefieldvalue(options,'caxis',[0 max(max(velocity))]) ++ applyoptions(md,[],options) ++ ++ ++ subplot(5,4,1:4) ++ cla ++ set(gca,'pos',get(gca,'pos')+[-0.07 0.03 0.12 0.015]) ++ plot(starttime:endtime,mean(massbal),'k','LineWidth', 4) ++ hold on ++ ya = ylim ++ plot([i i], ya, 'r', 'LineWidth',6) ++ ylim(ya) xlim([starttime endtime]) ++ title('Surface Mass Balance','FontSize',14) ++ ylabel('m/year','FontSize',14) ++ ++ ++ subplot(5,4,5:8) ++ cla ++ set(gca,'pos',get(gca,'pos')+[-0.07 0.015 0.12 0.015]) ++ plot(starttime:endtime,sum(volume)/1000/1000/1000,'LineWidth',4) ++ hold on ++ ya = ylim ++ plot([i i], ya, 'r', 'LineWidth',6) ++ ylim(ya) xlim([starttime endtime]) ++ title('Ice Volume','FontSize',14) ++ ylabel('km^3','FontSize',14) ++ ++ ++ subplot(5,4,9:12) ++ cla ++ set(gca,'pos',get(gca,'pos')+[-0.07 0 0.12 0.015]) ++ plot(starttime:endtime,mean(velocity)/1000, 'LineWidth', 4) ++ hold on ++ ya = ylim ++ plot([i i], ya, 'r', 'LineWidth',6) ++ ylim(ya) xlim([starttime endtime]) ++ title('Mean Velocity','FontSize', 14) ++ ylabel('km/year','FontSize', 14) ++ xlabel('year','FontSize', 14) ++ ++ ++ set(gcf,'Renderer','zbuffer','color','white') %fixes a bug on Mac OS X (not needed in future Matlab version) ++ if i==starttime, ++# initialize images and frame ++ ++ frame=getframe(gcf) ++ [images,map]=rgb2ind(frame.cdata,256,'nodither') ++ images(1,1,1,length(ts))=0 ++ else ++ frame=getframe(gcf) ++ images(:,:,1,count) = rgb2ind(frame.cdata,map,'nodither') ++ end ++ ++ ++ count = count+1 ++ ++ ++ end ++ ++ ++ filename='transawtooth3d.gif' ++ imwrite(images,map,filename,'DelayTime',1.0,'LoopCount',inf) ++ ++ ++end %printingflag +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1304.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1304.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test1304.py (revision 13492) +@@ -0,0 +1,82 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test1304.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++# This file can be run to check that the geothermal flux in simple conduction is correctly modeled. ++ ++# There is no velocity (no advection) the only thermal boundary conditions are an imposed temperature ++ ++# at upper surface and an impose flux at its base. The result must be a linear temperature from the upper to the lower ++ ++# surface with an imposed slope (Geothermal flux). if it is not the case, something is thermal modeling has been changed... ++ ++printingflag=false ++ ++ ++md=model() ++md=triangle(md,'../Exp/Square.exp',100000) ++md=setmask(md,'','') ++md=parameterize(md,'../Par/SquareThermal.py') ++md.extrude(11,1) ++md=setflowequation(md,'Pattyn','all') ++ ++ ++pos2=numpy.nonzero(md.mesh.elementonsurface) md.thermal.spctemperature(md.mesh.elements(pos2,4:6))=0 ++md.initialization.pressure=zeros(md.mesh.numberofvertices,1) ++md.basalforcings.geothermalflux(:)=0.1 %100mW/m^2 ++ ++ ++# analytical results ++ ++# the result is linear with depth and is equal to 0 on the upper surface (See BC) ++ ++# d2T/dz2=0 -k*dT/dz(bed)=G T(surface)=0 => T=-G/k*(z-surface) ++ ++md.initialization.temperature=-0.1/md.materials.thermalconductivity*(md.mesh.z-md.geometry.surface) %G=0.1 W/m2 ++ ++ ++# modeled results ++ ++md.cluster=generic('name',oshostname(),'np',2) ++md=solve(md,ThermalSolutionEnum()) ++ ++ ++# plot results ++ ++comp_temp=md.results.ThermalSolution.Temperature ++relative=abs((comp_temp-md.initialization.temperature)./md.initialization.temperature)*100 ++relative(find(comp_temp==md.initialization.temperature))=0 ++plotmodel()(md,'data',comp_temp,'title','Modeled temperature [K]','data',md.initialization.temperature,'view',3,\ ++ 'title','Analytical temperature','view',3,'data',comp_temp-md.initialization.temperature,\ ++ 'title','Absolute error [K]','view',3,'data',relative,'title','Relative error [%]','view',3,\ ++ 'figposition','mathieu','FontSize#all',20) ++if printingflag, ++ set(gcf,'Color','w') ++ printmodel()('thermalgeothermalflux','png','margin','on','marginsize',25,'frame','off','resolution',0.7,'hardcopy','off') ++ system(['mv thermalgeothermalflux.png ' ISSM_DIR '/website/doc_pdf/validation/Images/Thermal ']) ++end ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['GeothermalFluxTemperature'] ++field_tolerances=[1e-13] ++field_values =[comp_temp] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3005.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3005.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test3005.py (revision 13492) +@@ -0,0 +1,38 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test3005.m ++Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++import numpy ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelfConstrained.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++md.autodiff.isautodiff=true ++md=solve(md,PrognosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Thickness'] ++field_tolerances=[1e-13] ++field_values=[\ ++ md.results['PrognosticSolution'][1]['Thickness'],\ ++ ] Index: /issm/oecreview/Archive/13393-13976/ISSM-13492-13493.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13492-13493.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13492-13493.diff (revision 13980) @@ -0,0 +1,17 @@ +Index: ../trunk-jpl/src/m/mesh/bamg.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.py (revision 13492) ++++ ../trunk-jpl/src/m/mesh/bamg.py (revision 13493) +@@ -267,10 +267,10 @@ + pass + #}}} + # Bamg Mesh parameters {{{ +- if options.exist('domain') and md.mesh.numberofvertices and md.mesh.dimension==2: ++ if not options.exist('domain') and md.mesh.numberofvertices and md.mesh.dimension==2: + + if isinstance(md.private.bamg,dict) and 'mesh' in md.private.bamg: +- bamg_mesh=bamgmesh(md.private.bamg['mesh']) ++ bamg_mesh=bamgmesh(md.private.bamg['mesh'].__dict__) + else: + bamg_mesh.Vertices=numpy.hstack((md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),numpy.ones((md.mesh.numberofvertices,1)))) + bamg_mesh.Triangles=numpy.hstack((md.mesh.elements,numpy.ones((md.mesh.numberofelements,1)))) Index: /issm/oecreview/Archive/13393-13976/ISSM-13493-13494.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13493-13494.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13493-13494.diff (revision 13980) @@ -0,0 +1,130 @@ +Index: ../trunk-jpl/test/NightlyRun/test514.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test514.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test514.py (revision 13494) +@@ -0,0 +1,66 @@ ++import numpy ++import copy ++from model import * ++from bamg import * ++from setmask import * ++from parameterize import * ++from ComputeHessian import * ++from ComputeMetric import * ++from MatlabFuncs import * ++ ++#Simple mesh 1 ++hVertices=10000.*numpy.ones((27,1)) ++hVertices[0:5]=1000. ++md=bamg(model(),'domain','../Exp/Pig.exp','hmax',20000.,'hVertices',hVertices,'gradation',3.,'geometricalmetric',1) ++x1=md.mesh.x ++y1=md.mesh.y ++ ++#Simple mesh 2 ++md=bamg(model(),'domain','../Exp/Pig.exp','hmax',10000.) ++md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp') ++md=parameterize(md,'../Par/Pig.py') ++x2=md.mesh.x ++y2=md.mesh.y ++ ++#refine existing mesh 1 ++hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,md.inversion.vy_obs,'node') ++metric=ComputeMetric(hessian,2./9.,1.,1000.,25.*10.**3,[]) ++md.miscellaneous.dummy=metric ++md2=bamg(copy.deepcopy(md),'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1) ++x3=md2.mesh.x ++y3=md2.mesh.y ++ ++#refine existing mesh 2 ++md2=bamg(copy.deepcopy(md),'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'anisomax',1.) ++x4=md2.mesh.x ++y4=md2.mesh.y ++ ++#refine existing mesh 3 ++hVertices=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) ++hVertices[numpy.nonzero(md.mesh.vertexonboundary)]=500. ++md2=bamg(copy.deepcopy(md),'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'anisomax',1.,'hVertices',hVertices) ++x5=md2.mesh.x ++y5=md2.mesh.y ++ ++#refine existing mesh 4 ++md2=bamg(copy.deepcopy(md),'field',md.inversion.vy_obs,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',0,'err',numpy.array([[1.]])) ++x6=md2.mesh.x ++y6=md2.mesh.y ++ ++#refine existing mesh 5 ++md2=bamg(copy.deepcopy(md),'field',numpy.hstack((md.inversion.vy_obs,md.geometry.thickness)),'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',1,'err',numpy.array([[10.,100.]])) ++x7=md2.mesh.x ++y7=md2.mesh.y ++ ++#Fields and tolerances to track changes ++field_names =['x1','y1','x2','y2','x3','y3','x4','y4','x5','y5','x6','y6','x7','y7'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ x1, y1,\ ++ y2, y2,\ ++ y3, y3,\ ++ y4, y4,\ ++ y5, y5,\ ++ y6, y6,\ ++ y7, y7,\ ++ ] +Index: ../trunk-jpl/test/NightlyRun/test514.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test514.m (revision 13493) ++++ ../trunk-jpl/test/NightlyRun/test514.m (revision 13494) +@@ -1,12 +1,12 @@ + %Simple mesh 1 +-hVertices=10000*ones(27,1); +-hVertices(1:5)=1000; +-md=bamg(model,'domain','../Exp/Pig.exp','hmax',20000,'hVertices',hVertices,'gradation',3,'geometricalmetric',1); ++hVertices=10000.*ones(27,1); ++hVertices(1:5)=1000.; ++md=bamg(model,'domain','../Exp/Pig.exp','hmax',20000.,'hVertices',hVertices,'gradation',3.,'geometricalmetric',1); + x1=md.mesh.x; + y1=md.mesh.y; + + %Simple mesh 2 +-md=bamg(model,'domain','../Exp/Pig.exp','hmax',10000); ++md=bamg(model,'domain','../Exp/Pig.exp','hmax',10000.); + md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp'); + md=parameterize(md,'../Par/Pig.par'); + x2=md.mesh.x; +@@ -14,31 +14,31 @@ + + %refine existing mesh 1 + hessian=ComputeHessian(md.mesh.elements,md.mesh.x,md.mesh.y,md.inversion.vy_obs,'node'); +-metric=ComputeMetric(hessian,2/9,1,1000,25*10^3,[]); ++metric=ComputeMetric(hessian,2./9.,1.,1000.,25.*10.^3,[]); + md.miscellaneous.dummy=metric; +-md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1); ++md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1); + x3=md2.mesh.x; + y3=md2.mesh.y; + + %refine existing mesh 2 +-md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'anisomax',1); ++md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'anisomax',1.); + x4=md2.mesh.x; + y4=md2.mesh.y; + + %refine existing mesh 3 + hVertices=NaN*ones(md.mesh.numberofvertices,1); + hVertices(find(md.mesh.vertexonboundary))=500; +-md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'anisomax',1,'hVertices',hVertices); ++md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'anisomax',1.,'hVertices',hVertices); + x5=md2.mesh.x; + y5=md2.mesh.y; + + %refine existing mesh 4 +-md2=bamg(md,'field',md.inversion.vy_obs,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'Hessiantype',0,'err',1); ++md2=bamg(md,'field',md.inversion.vy_obs,'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',0,'err',1.); + x6=md2.mesh.x; + y6=md2.mesh.y; + + %refine existing mesh 5 +-md2=bamg(md,'field',[md.inversion.vy_obs md.geometry.thickness],'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'Hessiantype',1,'err',[10 100]); ++md2=bamg(md,'field',[md.inversion.vy_obs md.geometry.thickness],'hmin',1000.,'hmax',20000.,'gradation',3.,'geometricalmetric',1,'Hessiantype',1,'err',[10. 100.]); + x7=md2.mesh.x; + y7=md2.mesh.y; + Index: /issm/oecreview/Archive/13393-13976/ISSM-13494-13495.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13494-13495.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13494-13495.diff (revision 13980) @@ -0,0 +1,262 @@ +Index: ../trunk-jpl/src/m/mesh/bamg.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.py (revision 13494) ++++ ../trunk-jpl/src/m/mesh/bamg.py (revision 13495) +@@ -6,6 +6,7 @@ + from bamgmesh import * + from expread import * + from expwrite import * ++from SegIntersect import * + from MatlabFuncs import * + from BamgMesher import * + +@@ -120,93 +121,93 @@ + raise RuntimeError("one rift has all its points outside of the domain outline") + + elif numpy.any(numpy.logical_not(flags)): +- raise RuntimeError("bamg.py for rifts is not complete.") + #We LOTS of work to do + print("Rift tip outside of or on the domain has been detected and is being processed...") +- """ + +- %check that only one point is outside (for now) +- if sum(~flags)~=1, +- error('bamg error message: only one point outside of the domain is supported yet'); +- end ++ #check that only one point is outside (for now) ++ if numpy.sum(numpy.logical_not(flags).astype(int))!=1: ++ raise RuntimeError("bamg error message: only one point outside of the domain is supported yet") + +- %Move tip outside to the first position +- if flags(1)==0, +- %OK, first point is outside (do nothing), +- elseif (flags(end)==0), +- rift(i).x=flipud(rift(i).x); +- rift(i).y=flipud(rift(i).y); +- else +- error('bamg error message: only a rift tip can be outside of the domain'); +- end ++ #Move tip outside to the first position ++ if not flags[0]: ++ #OK, first point is outside (do nothing), ++ pass ++ elif not flags[-1]: ++ rifti['x']=numpy.flipud(rifti['x']) ++ rifti['y']=numpy.flipud(rifti['y']) ++ else: ++ raise RuntimeError("bamg error message: only a rift tip can be outside of the domain") + +- %Get cordinate of intersection point +- x1=rift(i).x(1); y1=rift(i).y(1); +- x2=rift(i).x(2); y2=rift(i).y(2); +- for j=1:length(domain[0]['x'])-1; +- if SegIntersect([x1 y1; x2 y2],[domain[0]['x'](j) domain[0]['y'](j); domain[0]['x'](j+1) domain[0]['y'](j+1)]), ++ #Get cordinate of intersection point ++ x1=rifti['x'][0] ++ y1=rifti['y'][0] ++ x2=rifti['x'][1] ++ y2=rifti['y'][1] ++ for j in xrange(0,numpy.size(domain[0]['x'])-1): ++ if SegIntersect(numpy.array([[x1,y1],[x2,y2]]),numpy.array([[domain[0]['x'][j],domain[0]['y'][j]],[domain[0]['x'][j+1],domain[0]['y'][j+1]]])): + +- %Get position of the two nodes of the edge in domain +- i1=j; +- i2=mod(j+1,domain[0]['nods']); ++ #Get position of the two nodes of the edge in domain ++ i1=j ++ i2=j+1 + +- %rift is crossing edge [i1 i2] of the domain +- %Get coordinate of intersection point (http://mathworld.wolfram.com/Line-LineIntersection.html) +- x3=domain[0]['x'](i1); y3=domain[0]['y'](i1); +- x4=domain[0]['x'](i2); y4=domain[0]['y'](i2); +- x=det([det([x1 y1; x2 y2]) x1-x2;det([x3 y3; x4 y4]) x3-x4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); +- y=det([det([x1 y1; x2 y2]) y1-y2;det([x3 y3; x4 y4]) y3-y4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); ++ #rift is crossing edge [i1 i2] of the domain ++ #Get coordinate of intersection point (http://mathworld.wolfram.com/Line-LineIntersection.html) ++ x3=domain[0]['x'][i1] ++ y3=domain[0]['y'][i1] ++ x4=domain[0]['x'][i2] ++ y4=domain[0]['y'][i2] ++# x=det([det([x1 y1; x2 y2]) x1-x2;det([x3 y3; x4 y4]) x3-x4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); ++# y=det([det([x1 y1; x2 y2]) y1-y2;det([x3 y3; x4 y4]) y3-y4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); ++ x=numpy.linalg.det(numpy.array([[numpy.linalg.det(numpy.array([[x1,y1],[x2,y2]])),x1-x2],[numpy.linalg.det(numpy.array([[x3,y3],[x4,y4]])),x3-x4]]))/numpy.linalg.det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]])); ++ y=numpy.linalg.det(numpy.array([[numpy.linalg.det(numpy.array([[x1,y1],[x2,y2]])),y1-y2],[numpy.linalg.det(numpy.array([[x3,y3],[x4,y4]])),y3-y4]]))/numpy.linalg.det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]])); + +- segdis= sqrt((x4-x3)**2+(y4-y3)**2); +- tipdis=[sqrt((x-x3)**2+(y-y3)**2) sqrt((x-x4)**2+(y-y4)**2)]; ++ segdis= sqrt((x4-x3)**2+(y4-y3)**2) ++ tipdis=numpy.array([sqrt((x-x3)**2+(y-y3)**2),sqrt((x-x4)**2+(y-y4)**2)]) + +- if (min(tipdis)/segdis) < getfieldvalue(options,'toltip',0), +- disp('moving tip-domain intersection point'); ++ if numpy.min(tipdis)/segdis < options.getfieldvalue('toltip',0): ++ print("moving tip-domain intersection point") + +- %Get position of the closest point +- if tipdis(1)>tipdis(2), +- pos=i2; +- else +- pos=i1; +- end ++ #Get position of the closer point ++ if tipdis[0]>tipdis[1]: ++ pos=i2 ++ else: ++ pos=i1 + +- %This point is only in Vertices (number pos). +- %OK, now we can add our own rift +- nods=rift(i).nods-1; +- bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(2:end) rift(i).y(2:end) ones(nods,1)]]; +- bamg_geometry.Edges=[bamg_geometry.Edges;... +- pos count+1 (1+i);... +- [transpose(count+1:count+nods-1) transpose([count+2:count+nods]) (1+i)*ones(nods-1,1)]]; +- count=count+nods; ++ #This point is only in Vertices (number pos). ++ #OK, now we can add our own rift ++ nods=rifti['nods']-1 ++ bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,numpy.hstack((rifti['x'][1:].reshape(-1,1),rifti['y'][1:].reshape(-1,1),numpy.ones((nods,1)))))) ++ bamg_geometry.Edges=numpy.vstack((bamg_geometry.Edges,\ ++ numpy.array([[pos,count+1,(1+i)]]),\ ++ numpy.hstack((numpy.arange(count+1,count+nods).reshape(-1,1),numpy.arange(count+2,count+nods+1).reshape(-1,1),(1+i)*numpy.ones((nods-1,1)))))) ++ count+=nods + +- break; ++ break + +- else +- %Add intersection point to Vertices +- bamg_geometry.Vertices=[bamg_geometry.Vertices; x y 1]; +- count=count+1; ++ else: ++ #Add intersection point to Vertices ++ bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,numpy.array([[x,y,1]]))) ++ count+=1 + +- %Decompose the crossing edge in 2 subedges +- pos=find(bamg_geometry.Edges(:,1)==i1 & bamg_geometry.Edges(:,2)==i2); +- if isempty(pos) error('bamg error message: a problem occured...'); end +- bamg_geometry.Edges=[bamg_geometry.Edges(1:pos-1,:);... +- bamg_geometry.Edges(pos,1) count bamg_geometry.Edges(pos,3);... +- count bamg_geometry.Edges(pos,2) bamg_geometry.Edges(pos,3);... +- bamg_geometry.Edges(pos+1:end,:)]; ++ #Decompose the crossing edge into 2 subedges ++ pos=numpy.nonzero(numpy.logical_and(bamg_geometry.Edges[:,0]==i1,bamg_geometry.Edges[:,1]==i2))[0] ++ if not pos: ++ raise RuntimeError("bamg error message: a problem occurred...") ++ bamg_geometry.Edges=numpy.vstack((bamg_geometry.Edges[0:pos-1,:],\ ++ numpy.array([[bamg_geometry.Edges[pos,0],count ,bamg_geometry.Edges[pos,2]]]),\ ++ numpy.array([[count ,bamg_geometry.Edges[pos,1],bamg_geometry.Edges[pos,2]]]),\ ++ bamg_geometry.Edges[pos+1:,:])) + +- %OK, now we can add our own rift +- nods=rift(i).nods-1; +- bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(2:end) rift(i).y(2:end) ones(nods,1)]]; +- bamg_geometry.Edges=[bamg_geometry.Edges;... +- count count+1 2 ;... +- [transpose(count+1:count+nods-1) transpose([count+2:count+nods]) (1+i)*ones(nods-1,1)]]; ++ #OK, now we can add our own rift ++ nods=rifti['nods']-1 ++ bamg_geometry.Vertices=numpy.vstack((bamg_geometry.Vertices,numpy.hstack((rifti['x'][1:].reshape(-1,1),rifti['y'][1:].reshape(-1,1),numpy.ones((nods,1)))))) ++ bamg_geometry.Edges=numpy.vstack((bamg_geometry.Edges,\ ++ numpy.array([[count,count+1,2]]),\ ++ numpy.hstack((numpy.arange(count+1,count+nods).reshape(-1,1),numpy.arange(count+2,count+nods+1).reshape(-1,1),(1+i)*numpy.ones((nods-1,1)))))) + count=count+nods; + +- break; +- end +- end +- end +- """ ++ break ++ + else: + nods=rifti['nods']-1 + bamg_geometry.Vertices=numpy.vstack(bamg_geometry.Vertices, numpy.hstack(rifti['x'][:],rifti['y'][:],numpy.ones((nods+1,1)))) +@@ -383,8 +384,8 @@ + if SegIntersect(numpy.array([[x1,y1],[x2,y2]]),numpy.array([[x3,y3],[x4,y4]])): + + #Get coordinate of intersection point (http://mathworld.wolfram.com/Line-LineIntersection.html) +- x=det(numpy.array([det(numpy.array([[x1,y1],[x2,y2]])),x1-x2],[det(numpy.array([[x3,y3],[x4,y4]])),x3-x4])/det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]]))) +- y=det(numpy.array([det(numpy.array([[x1,y1],[x2,y2]])),y1-y2],[det(numpy.array([[x3,y3],[x4,y4]])),y3-y4])/det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]]))) ++ x=numpy.linalg.det(numpy.array([numpy.linalg.det(numpy.array([[x1,y1],[x2,y2]])),x1-x2],[numpy.linalg.det(numpy.array([[x3,y3],[x4,y4]])),x3-x4])/numpy.linalg.det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]]))) ++ y=numpy.linalg.det(numpy.array([numpy.linalg.det(numpy.array([[x1,y1],[x2,y2]])),y1-y2],[numpy.linalg.det(numpy.array([[x3,y3],[x4,y4]])),y3-y4])/numpy.linalg.det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]]))) + + #Add vertex to the list of vertices + geom.Vertices=numpy.vstack((geom.Vertices,[x,y,min(color1,color2)])) +Index: ../trunk-jpl/src/m/mesh/bamg.m +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.m (revision 13494) ++++ ../trunk-jpl/src/m/mesh/bamg.m (revision 13495) +@@ -136,7 +136,7 @@ + + %Get position of the two nodes of the edge in domain + i1=j; +- i2=mod(j+1,domain(1).nods); ++ i2=j+1; + + %rift is crossing edge [i1 i2] of the domain + %Get coordinate of intersection point (http://mathworld.wolfram.com/Line-LineIntersection.html) +@@ -151,7 +151,7 @@ + if (min(tipdis)/segdis) < getfieldvalue(options,'toltip',0), + disp('moving tip-domain intersection point'); + +- %Get position of the closest point ++ %Get position of the closer point + if tipdis(1)>tipdis(2), + pos=i2; + else +@@ -164,7 +164,7 @@ + bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(2:end) rift(i).y(2:end) ones(nods,1)]]; + bamg_geometry.Edges=[bamg_geometry.Edges;... + pos count+1 (1+i);... +- [transpose(count+1:count+nods-1) transpose([count+2:count+nods]) (1+i)*ones(nods-1,1)]]; ++ [transpose(count+1:count+nods-1) transpose(count+2:count+nods) (1+i)*ones(nods-1,1)]]; + count=count+nods; + + break; +@@ -174,12 +174,12 @@ + bamg_geometry.Vertices=[bamg_geometry.Vertices; x y 1]; + count=count+1; + +- %Decompose the crossing edge in 2 subedges ++ %Decompose the crossing edge into 2 subedges + pos=find(bamg_geometry.Edges(:,1)==i1 & bamg_geometry.Edges(:,2)==i2); +- if isempty(pos) error('bamg error message: a problem occured...'); end ++ if isempty(pos) error('bamg error message: a problem occurred...'); end + bamg_geometry.Edges=[bamg_geometry.Edges(1:pos-1,:);... +- bamg_geometry.Edges(pos,1) count bamg_geometry.Edges(pos,3);... +- count bamg_geometry.Edges(pos,2) bamg_geometry.Edges(pos,3);... ++ bamg_geometry.Edges(pos,1) count bamg_geometry.Edges(pos,3);... ++ count bamg_geometry.Edges(pos,2) bamg_geometry.Edges(pos,3);... + bamg_geometry.Edges(pos+1:end,:)]; + + %OK, now we can add our own rift +@@ -187,7 +187,7 @@ + bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(2:end) rift(i).y(2:end) ones(nods,1)]]; + bamg_geometry.Edges=[bamg_geometry.Edges;... + count count+1 2 ;... +- [transpose(count+1:count+nods-1) transpose([count+2:count+nods]) (1+i)*ones(nods-1,1)]]; ++ [transpose(count+1:count+nods-1) transpose(count+2:count+nods) (1+i)*ones(nods-1,1)]]; + count=count+nods; + + break; +@@ -197,7 +197,7 @@ + else + nods=rift(i).nods-1; + bamg_geometry.Vertices=[bamg_geometry.Vertices; [rift(i).x(:) rift(i).y(:) ones(nods+1,1)]]; +- bamg_geometry.Edges=[bamg_geometry.Edges; [transpose(count+1:count+nods) transpose([count+2:count+nods+1]) (1+i)*ones(nods,1)]]; ++ bamg_geometry.Edges=[bamg_geometry.Edges; [transpose(count+1:count+nods) transpose(count+2:count+nods+1) (1+i)*ones(nods,1)]]; + count=count+nods+1; + end + end +@@ -223,7 +223,7 @@ + %Add all points to bamg_geometry + nods=size(track,1); + bamg_geometry.Vertices=[bamg_geometry.Vertices; track]; +- bamg_geometry.Edges=[bamg_geometry.Edges; [transpose(count+1:count+nods-1) transpose([count+2:count+nods]) 3.*ones(nods-1,1)]]; ++ bamg_geometry.Edges=[bamg_geometry.Edges; [transpose(count+1:count+nods-1) transpose(count+2:count+nods) 3.*ones(nods-1,1)]]; + + %update counter + count=count+nods; Index: /issm/oecreview/Archive/13393-13976/ISSM-13495-13496.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13495-13496.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13495-13496.diff (revision 13980) @@ -0,0 +1,33 @@ +Index: ../trunk-jpl/src/m/mesh/bamg.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.py (revision 13495) ++++ ../trunk-jpl/src/m/mesh/bamg.py (revision 13496) +@@ -158,8 +158,8 @@ + y4=domain[0]['y'][i2] + # x=det([det([x1 y1; x2 y2]) x1-x2;det([x3 y3; x4 y4]) x3-x4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); + # y=det([det([x1 y1; x2 y2]) y1-y2;det([x3 y3; x4 y4]) y3-y4])/det([x1-x2 y1-y2;x3-x4 y3-y4]); +- x=numpy.linalg.det(numpy.array([[numpy.linalg.det(numpy.array([[x1,y1],[x2,y2]])),x1-x2],[numpy.linalg.det(numpy.array([[x3,y3],[x4,y4]])),x3-x4]]))/numpy.linalg.det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]])); +- y=numpy.linalg.det(numpy.array([[numpy.linalg.det(numpy.array([[x1,y1],[x2,y2]])),y1-y2],[numpy.linalg.det(numpy.array([[x3,y3],[x4,y4]])),y3-y4]]))/numpy.linalg.det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]])); ++ x=numpy.linalg.det(numpy.array([[numpy.linalg.det(numpy.array([[x1,y1],[x2,y2]])),x1-x2],[numpy.linalg.det(numpy.array([[x3,y3],[x4,y4]])),x3-x4]]))/numpy.linalg.det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]])) ++ y=numpy.linalg.det(numpy.array([[numpy.linalg.det(numpy.array([[x1,y1],[x2,y2]])),y1-y2],[numpy.linalg.det(numpy.array([[x3,y3],[x4,y4]])),y3-y4]]))/numpy.linalg.det(numpy.array([[x1-x2,y1-y2],[x3-x4,y3-y4]])) + + segdis= sqrt((x4-x3)**2+(y4-y3)**2) + tipdis=numpy.array([sqrt((x-x3)**2+(y-y3)**2),sqrt((x-x4)**2+(y-y4)**2)]) +@@ -204,7 +204,7 @@ + bamg_geometry.Edges=numpy.vstack((bamg_geometry.Edges,\ + numpy.array([[count,count+1,2]]),\ + numpy.hstack((numpy.arange(count+1,count+nods).reshape(-1,1),numpy.arange(count+2,count+nods+1).reshape(-1,1),(1+i)*numpy.ones((nods-1,1)))))) +- count=count+nods; ++ count+=nods + + break + +@@ -326,7 +326,7 @@ + #Fill in rest of fields: + md.mesh.dimension=2 + md.mesh.numberofelements=numpy.size(md.mesh.elements,axis=0) +- md.mesh.numberofvertices=numpy.size(md.mesh.x); ++ md.mesh.numberofvertices=numpy.size(md.mesh.x) + md.mesh.numberofedges=numpy.size(md.mesh.edges,axis=0) + md.mesh.z=numpy.zeros(md.mesh.numberofvertices) + md.mesh.vertexonbed=numpy.ones(md.mesh.numberofvertices) Index: /issm/oecreview/Archive/13393-13976/ISSM-13496-13497.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13496-13497.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13496-13497.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/externalpackages/petsc/install-3.2-greenplanet.sh +=================================================================== +--- ../trunk-jpl/externalpackages/petsc/install-3.2-greenplanet.sh (revision 13496) ++++ ../trunk-jpl/externalpackages/petsc/install-3.2-greenplanet.sh (revision 13497) +@@ -21,7 +21,7 @@ + --PETSC_ARCH="$ISSM_ARCH" \ + --with-batch=1 \ + --with-debugging=0 \ +- --with-shared-libraries=0 \ ++ --with-shared-libraries=1 \ + --known-mpi-shared-libraries=1 \ + --with-mpi-dir=/sopt/mpi/openmpi-1.5.4_psm/intel/ \ + --with-blas-lapack-dir=/opt/intel/mkl/10.2.4.032/ \ Index: /issm/oecreview/Archive/13393-13976/ISSM-13497-13498.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13497-13498.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13497-13498.diff (revision 13980) @@ -0,0 +1,64 @@ +Index: ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13497) ++++ ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13498) +@@ -160,6 +160,22 @@ + } + /*}}}*/ + int EDF_fos_reverse_for_solverx(int m, double *dp_U, int n, double *dp_Z, double* dp_x, double* dp_y) { /*{{{*/ ++ // copy to transpose the matrix ++ double* transposed=xNew(m*m); ++ for (int i=0; iFetchData(&driver,AutodiffDriverEnum); ++ if (strlen(driver)<=3){ ++ /*there is no "_reverse" string within the driver string: */ ++ if(VerboseAutodiff())_pprintLine_(" trace activated with keep off"); ++ trace_on(1); ++ } ++ else{ ++ if (strcmp((const char*)(driver+3),"_reverse")==0){ ++ if(VerboseAutodiff())_pprintLine_(" trace activated with keep on"); ++ trace_on(1,1); ++ } ++ else{ ++ if(VerboseAutodiff())_pprintLine_(" trace activated with keep off"); ++ trace_on(1); ++ } ++ } ++ xDelete(driver); ++ /*}}}*/ ++ /*build dataset made of independent objects: {{{*/ + this->independent_objects=new DataSet(); + this->FetchData(&num_independent_objects,AutodiffNumIndependentObjectsEnum); + if(num_independent_objects){ +@@ -249,7 +276,8 @@ + } + xDelete(names); + xDelete(types); +- } ++ } /*}}}*/ ++ + #else + /*if we asked for AD computations, we have a problem!: */ + _error_("Cannot carry out AD mode computations without support of ADOLC compiled in!"); Index: /issm/oecreview/Archive/13393-13976/ISSM-13501-13502.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13501-13502.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13501-13502.diff (revision 13980) @@ -0,0 +1,18 @@ +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13501) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13502) +@@ -118,6 +118,13 @@ + #ifdef _HAVE_ADOLC_ + GenericParam *theAdolcEDF_p=new GenericParam(AdolcParamEnum); + theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p=reg_ext_fct(EDF_for_solverx); ++ // to save some space: ++ // we know we won't use adolc inside of the solver: ++ theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->nestedAdolc=false; ++ // the solution vector is just allocated and doesn't have a meaningfull prior value ++ theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->dp_y_priorRequired=false; ++ // the solver wrapper makes sure the matrix and the right hand side don't change ++ theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->dp_x_changes=false; + femmodel->parameters->AddObject(theAdolcEDF_p); + #else + if(autodiff) _error_("ISSM was not compiled with ADOLC support, cannot carry out autodiff analysis!"); Index: /issm/oecreview/Archive/13393-13976/ISSM-13502-13503.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13502-13503.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13502-13503.diff (revision 13980) @@ -0,0 +1,52 @@ +Index: ../trunk-jpl/src/m/geometry/SegIntersect.py +=================================================================== +--- ../trunk-jpl/src/m/geometry/SegIntersect.py (revision 13502) ++++ ../trunk-jpl/src/m/geometry/SegIntersect.py (revision 13503) +@@ -1,5 +1,4 @@ + import numpy +-from MatlabFuncs import * + + def SegIntersect(seg1,seg2): + """ +@@ -47,7 +46,7 @@ + return bval + + #if colinear +- if test1*test2==0 and test3*test4==0 and det(numpy.hstack((n1.reshape((-1,1)),n2.reshape(-1,1))))==0: ++ if test1*test2==0 and test3*test4==0 and numpy.linalg.det(numpy.hstack((n1.reshape((-1,1)),n2.reshape(-1,1))))==0: + + #projection on the axis O1O2 + O2O1=numpy.array([xA/2.+xB/2.,yB/2.+yA/2.])-numpy.array([xD/2.+xC/2.,yD/2.+yC/2.]) +Index: ../trunk-jpl/src/m/geometry/FlagElements.py +=================================================================== +--- ../trunk-jpl/src/m/geometry/FlagElements.py (revision 13502) ++++ ../trunk-jpl/src/m/geometry/FlagElements.py (revision 13503) +@@ -46,7 +46,7 @@ + flag=numpy.prod(flag_nodes[md.mesh.elements],axis=1) + else: + #ok, flag elements +- [flag,dum]=ContourToMesh(md.mesh.elements[:,0:3],md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),region,'element',1) ++ [flag,dum]=ContourToMesh(md.mesh.elements[:,0:3].copy(),md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),region,'element',1) + + if invert: + flag=numpy.logical_not(flag) +Index: ../trunk-jpl/src/m/parameterization/setflowequation.py +=================================================================== +--- ../trunk-jpl/src/m/parameterization/setflowequation.py (revision 13502) ++++ ../trunk-jpl/src/m/parameterization/setflowequation.py (revision 13503) +@@ -122,13 +122,13 @@ + #Create the border nodes between Pattyn and MacAyeal and extrude them + numnodes2d=md.mesh.numberofvertices2d + numlayers=md.mesh.numberoflayers +- bordernodes2d=numpy.nonzero(numpy.logical_and(nodeonpattyn[1:numnodes2d],nodeonmacayeal[1:numnodes2d])) #Nodes connected to two different types of elements ++ bordernodes2d=numpy.nonzero(numpy.logical_and(nodeonpattyn[0:numnodes2d],nodeonmacayeal[0:numnodes2d]))[0]+1 #Nodes connected to two different types of elements + + #initialize and fill in penalties structure + if numpy.all(numpy.logical_not(numpy.isnan(bordernodes2d))): + penalties=numpy.zeros((0,2)) + for i in xrange(1,numlayers): +- penalties=numpy.vstack((penalties,numpy.hstack((bordernodes2d,bordernodes2d+md.mesh.numberofvertices2d*(i))))) ++ penalties=numpy.vstack((penalties,numpy.hstack((bordernodes2d.reshape(-1,1),bordernodes2d.reshape(-1,1)+md.mesh.numberofvertices2d*(i))))) + md.diagnostic.vertex_pairing=penalties + + elif strcmpi(coupling_method,'tiling'): Index: /issm/oecreview/Archive/13393-13976/ISSM-13503-13504.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13503-13504.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13503-13504.diff (revision 13980) @@ -0,0 +1,94 @@ +Index: ../trunk-jpl/test/NightlyRun/test205.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test205.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test205.py (revision 13504) +@@ -0,0 +1,42 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test205.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,2) ++md=setflowequation(md,'pattyn','../Exp/SquareHalfRight.exp','fill','macayeal','coupling','penalties') ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Vx','Vy','Vz','Vel','Pressure'] ++field_tolerances=[1e-05,1e-05,1e-05,1e-05,1e-05] ++field_values=[\ ++md.results['DiagnosticSolution'][1]['Vx'],\ ++md.results['DiagnosticSolution'][1]['Vy'],\ ++md.results['DiagnosticSolution'][1]['Vz'],\ ++md.results['DiagnosticSolution'][1]['Vel'],\ ++md.results['DiagnosticSolution'][1]['Pressure'],\ ++] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test205.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test205.py (revision 13503) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test205.py (revision 13504) +@@ -1,42 +0,0 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test205.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- +-from MatlabFuncs import * +-from model import * +-from EnumDefinitions import * +-from numpy import * +-from triangle import * +-from setmask import * +-from parameterize import * +-from setflowequation import * +-from solve import * +- +-md=triangle(model(),'../Exp/Square.exp',150000) +-md=setmask(md,'all','') +-md=parameterize(md,'../Par/SquareShelf.py') +-md.extrude(3,2) +-md=setflowequation(md,'pattyn','../Exp/SquareHalfRight.exp','fill','macayeal','coupling','penalties') +-md.cluster=generic('name',oshostname(),'np',3) +-md=solve(md,DiagnosticSolutionEnum()) +- +- +-# Fields and tolerances to track changes +- +-field_names =['Vx','Vy','Vz','Vel','Pressure'] +-field_tolerances=[1e-05,1e-05,1e-05,1e-05,1e-05] +-field_values=[\ +-md.results['DiagnosticSolution'][1]['Vx'],\ +-md.results['DiagnosticSolution'][1]['Vy'],\ +-md.results['DiagnosticSolution'][1]['Vz'],\ +-md.results['DiagnosticSolution'][1]['Vel'],\ +-md.results['DiagnosticSolution'][1]['Pressure'],\ +-] Index: /issm/oecreview/Archive/13393-13976/ISSM-13504-13505.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13504-13505.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13504-13505.diff (revision 13980) @@ -0,0 +1,92 @@ +Index: ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13504) ++++ ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13505) +@@ -28,6 +28,7 @@ + AutodiffDriverEnum, + AutodiffFosForwardIndexEnum, + AutodiffFovForwardIndicesEnum, ++ AutodiffFosReverseIndexEnum, + AutodiffMassFluxSegmentsPresentEnum, + BalancethicknessSpcthicknessEnum, + BalancethicknessStabilizationEnum, +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13504) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13505) +@@ -243,7 +243,7 @@ + trace_on(1); + } + else{ +- if (strcmp((const char*)(driver+3),"_reverse")==0){ ++ if (strncmp((const char*)(driver+3),"_reverse",8)==0){ + if(VerboseAutodiff())_pprintLine_(" trace activated with keep on"); + trace_on(1,1); + } +Index: ../trunk-jpl/src/m/classes/autodiff.m +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.m (revision 13504) ++++ ../trunk-jpl/src/m/classes/autodiff.m (revision 13505) +@@ -28,7 +28,7 @@ + if ~obj.isautodiff, return; end + + %Driver value: +- md = checkfield(md,'autodiff.driver','values',{'fos_forward','fov_forward','fos_reverse','fov_reverse'}); ++ md = checkfield(md,'autodiff.driver','values',{'fos_forward','fov_forward','fov_forward_all','fos_reverse','fov_reverse','fov_reverse_all'}); + + %go through our dependents and independents and check consistency: + for i=1:numel(obj.dependents), +Index: ../trunk-jpl/src/m/enum/AutodiffFosReverseIndexEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffFosReverseIndexEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffFosReverseIndexEnum.m (revision 13505) +@@ -0,0 +1,11 @@ ++function macro=AutodiffFosReverseIndexEnum() ++%AUTODIFFFOSREVERSEINDEXENUM - Enum of AutodiffFosReverseIndex ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffFosReverseIndexEnum() ++ ++macro=StringToEnum('AutodiffFosReverseIndex'); +Index: ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13504) ++++ ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13505) +@@ -8,4 +8,4 @@ + % Usage: + % macro=MaximumNumberOfEnums() + +-macro=491; ++macro=492; +Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py +=================================================================== +--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13504) ++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13505) +@@ -178,6 +178,16 @@ + + return StringToEnum('AutodiffFovForwardIndices')[0] + ++def AutodiffFosReverseIndexEnum(): ++ """ ++ AUTODIFFFOSREVERSEINDEXENUM - Enum of AutodiffFosReverseIndex ++ ++ Usage: ++ macro=AutodiffFosReverseIndexEnum() ++ """ ++ ++ return StringToEnum('AutodiffFosReverseIndex')[0] ++ + def AutodiffMassFluxSegmentsPresentEnum(): + """ + AUTODIFFMASSFLUXSEGMENTSPRESENTENUM - Enum of AutodiffMassFluxSegmentsPresent +@@ -4926,5 +4936,5 @@ + macro=MaximumNumberOfEnums() + """ + +- return 491 ++ return 492 + Index: /issm/oecreview/Archive/13393-13976/ISSM-13505-13506.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13505-13506.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13505-13506.diff (revision 13980) @@ -0,0 +1,80 @@ +Index: ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13505) ++++ ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13506) +@@ -34,6 +34,7 @@ + else if (strcmp(name,"AutodiffDriver")==0) return AutodiffDriverEnum; + else if (strcmp(name,"AutodiffFosForwardIndex")==0) return AutodiffFosForwardIndexEnum; + else if (strcmp(name,"AutodiffFovForwardIndices")==0) return AutodiffFovForwardIndicesEnum; ++ else if (strcmp(name,"AutodiffFosReverseIndex")==0) return AutodiffFosReverseIndexEnum; + else if (strcmp(name,"AutodiffMassFluxSegmentsPresent")==0) return AutodiffMassFluxSegmentsPresentEnum; + else if (strcmp(name,"BalancethicknessSpcthickness")==0) return BalancethicknessSpcthicknessEnum; + else if (strcmp(name,"BalancethicknessStabilization")==0) return BalancethicknessStabilizationEnum; +@@ -136,11 +137,11 @@ + else if (strcmp(name,"MeshDimension")==0) return MeshDimensionEnum; + else if (strcmp(name,"MeshEdges")==0) return MeshEdgesEnum; + else if (strcmp(name,"MeshElementconnectivity")==0) return MeshElementconnectivityEnum; +- else if (strcmp(name,"MeshElementonbed")==0) return MeshElementonbedEnum; + else stage=2; + } + if(stage==2){ +- if (strcmp(name,"MeshElementonsurface")==0) return MeshElementonsurfaceEnum; ++ if (strcmp(name,"MeshElementonbed")==0) return MeshElementonbedEnum; ++ else if (strcmp(name,"MeshElementonsurface")==0) return MeshElementonsurfaceEnum; + else if (strcmp(name,"MeshElements2d")==0) return MeshElements2dEnum; + else if (strcmp(name,"MeshElements")==0) return MeshElementsEnum; + else if (strcmp(name,"MeshLowerelements")==0) return MeshLowerelementsEnum; +@@ -259,11 +260,11 @@ + else if (strcmp(name,"SurfaceSlopeAnalysis")==0) return SurfaceSlopeAnalysisEnum; + else if (strcmp(name,"SurfaceSlopeSolution")==0) return SurfaceSlopeSolutionEnum; + else if (strcmp(name,"SurfaceSlopeXAnalysis")==0) return SurfaceSlopeXAnalysisEnum; +- else if (strcmp(name,"SurfaceSlopeYAnalysis")==0) return SurfaceSlopeYAnalysisEnum; + else stage=3; + } + if(stage==3){ +- if (strcmp(name,"ThermalAnalysis")==0) return ThermalAnalysisEnum; ++ if (strcmp(name,"SurfaceSlopeYAnalysis")==0) return SurfaceSlopeYAnalysisEnum; ++ else if (strcmp(name,"ThermalAnalysis")==0) return ThermalAnalysisEnum; + else if (strcmp(name,"ThermalSolution")==0) return ThermalSolutionEnum; + else if (strcmp(name,"TransientSolution")==0) return TransientSolutionEnum; + else if (strcmp(name,"Approximation")==0) return ApproximationEnum; +@@ -382,11 +383,11 @@ + else if (strcmp(name,"SurfaceLogVelMisfit")==0) return SurfaceLogVelMisfitEnum; + else if (strcmp(name,"SurfaceLogVxVyMisfit")==0) return SurfaceLogVxVyMisfitEnum; + else if (strcmp(name,"SurfaceRelVelMisfit")==0) return SurfaceRelVelMisfitEnum; +- else if (strcmp(name,"SurfaceSlopeX")==0) return SurfaceSlopeXEnum; + else stage=4; + } + if(stage==4){ +- if (strcmp(name,"SurfaceSlopeY")==0) return SurfaceSlopeYEnum; ++ if (strcmp(name,"SurfaceSlopeX")==0) return SurfaceSlopeXEnum; ++ else if (strcmp(name,"SurfaceSlopeY")==0) return SurfaceSlopeYEnum; + else if (strcmp(name,"Temperature")==0) return TemperatureEnum; + else if (strcmp(name,"TemperatureOld")==0) return TemperatureOldEnum; + else if (strcmp(name,"TemperaturePicard")==0) return TemperaturePicardEnum; +@@ -505,11 +506,11 @@ + else if (strcmp(name,"Verbose")==0) return VerboseEnum; + else if (strcmp(name,"TriangleInterp")==0) return TriangleInterpEnum; + else if (strcmp(name,"BilinearInterp")==0) return BilinearInterpEnum; +- else if (strcmp(name,"NearestInterp")==0) return NearestInterpEnum; + else stage=5; + } + if(stage==5){ +- if (strcmp(name,"XY")==0) return XYEnum; ++ if (strcmp(name,"NearestInterp")==0) return NearestInterpEnum; ++ else if (strcmp(name,"XY")==0) return XYEnum; + else if (strcmp(name,"XYZP")==0) return XYZPEnum; + else if (strcmp(name,"Option")==0) return OptionEnum; + else if (strcmp(name,"GenericOption")==0) return GenericOptionEnum; +Index: ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13505) ++++ ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13506) +@@ -33,6 +33,7 @@ + case AutodiffDriverEnum : return "AutodiffDriver"; + case AutodiffFosForwardIndexEnum : return "AutodiffFosForwardIndex"; + case AutodiffFovForwardIndicesEnum : return "AutodiffFovForwardIndices"; ++ case AutodiffFosReverseIndexEnum : return "AutodiffFosReverseIndex"; + case AutodiffMassFluxSegmentsPresentEnum : return "AutodiffMassFluxSegmentsPresent"; + case BalancethicknessSpcthicknessEnum : return "BalancethicknessSpcthickness"; + case BalancethicknessStabilizationEnum : return "BalancethicknessStabilization"; Index: /issm/oecreview/Archive/13393-13976/ISSM-13506-13507.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13506-13507.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13506-13507.diff (revision 13980) @@ -0,0 +1,178 @@ +Index: ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13506) ++++ ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13507) +@@ -55,6 +55,10 @@ + /*Branch according to AD driver: */ + parameters->FindParam(&driver,AutodiffDriverEnum); + ++ /* these are always needed regardless of the interpreter */ ++ anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); ++ + if (strcmp(driver,"fos_forward")==0){ + + int anIndepIndex; +@@ -65,43 +69,33 @@ + /*retrieve direction index: */ + parameters->FindParam(&anIndepIndex,AutodiffFosForwardIndexEnum); + ++ if (anIndepIndex<0 || anIndepIndex>=num_independents) _error_("index value for AutodiffFosForwardIndexEnum should be in [0,num_independents-1]"); ++ + tangentDir=xNewZeroInit(num_independents); + tangentDir[anIndepIndex]=1.0; + + jacTimesTangentDir=xNew(num_dependents); + theOutput=xNew(num_dependents); + +- /*set the forward method function pointers: */ +- anEDF_for_solverx_p->zos_forward=EDF_for_solverx; ++ /*set the forward method function pointer: */ + anEDF_for_solverx_p->fos_forward=EDF_fos_forward_for_solverx; +- anEDF_for_solverx_p->fos_reverse=EDF_fos_reverse_for_solverx; + +- /*allocate the space for the parameters to invoke the forward methods:*/ +- anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); ++ /*allocate the space for the parameters to invoke the EDF fos_forward:*/ + anEDF_for_solverx_p->dp_X=xNew(anEDF_for_solverx_p->max_n); +- anEDF_for_solverx_p->dpp_X=xNew(anEDF_for_solverx_p->max_n, 1); +- anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); + anEDF_for_solverx_p->dp_Y=xNew(anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dpp_Y=xNew(anEDF_for_solverx_p->max_m, 1); + +- /*allocate the space for the parameters to invoke the reverse methods:*/ +- anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dpp_U=xNew(num_dependents,anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); +- anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,anEDF_for_solverx_p->max_n); +- + /*call driver: */ + fos_forward(1,num_dependents,num_independents, 0, xp, tangentDir, theOutput, jacTimesTangentDir ); + + /*add to results*/ + results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,jacTimesTangentDir,num_dependents,1,1,0.0)); + +- /*free ressources :*/ ++ /*free resources :*/ + xDelete(theOutput); + xDelete(jacTimesTangentDir); + xDelete(tangentDir); + } +- else if ((strcmp(driver,"fov_forward")==0) || (strcmp(driver,"jacobian")==0)){ ++ else if ((strcmp(driver,"fov_forward")==0) || (strcmp(driver,"fov_forward_all")==0)){ + + int* indepIndices=NULL; + int tangentDirNum; +@@ -113,7 +107,7 @@ + + + /*retrieve directions:*/ +- if (strcmp(driver,"jacobian")==0){ ++ if (strcmp(driver,"fov_forward_all")==0){ + tangentDirNum=num_independents; + indepIndices=xNewZeroInit(tangentDirNum); + for(i=0;i(num_dependents,tangentDirNum); + + /*set the forward method function pointers: */ +- anEDF_for_solverx_p->zos_forward=EDF_for_solverx; + anEDF_for_solverx_p->fov_forward=EDF_fov_forward_for_solverx; + // anEDF_for_solverx_p->fov_reverse=EDF_fov_reverse_for_solverx; + +- /*allocate the space for the parameters to invoke the forward methods:*/ +- anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); +- anEDF_for_solverx_p->dp_X=xNew(anEDF_for_solverx_p->max_n); ++ /*allocate the space for the parameters to invoke EDF fov_forward:*/ + anEDF_for_solverx_p->dpp_X=xNew(anEDF_for_solverx_p->max_n, tangentDirNum); +- anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dp_Y=xNew(anEDF_for_solverx_p->max_m); + anEDF_for_solverx_p->dpp_Y=xNew(anEDF_for_solverx_p->max_m, tangentDirNum); + +- /*allocate the space for the parameters to invoke the reverse methods:*/ +- anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dpp_U=xNew(num_dependents,anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); +- anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,anEDF_for_solverx_p->max_n); +- + /*seed matrix: */ + seed=xNewZeroInit(num_independents,tangentDirNum); + +@@ -169,14 +152,8 @@ + theOutput=xNew(num_dependents); + + /*call driver: */ +- if (strcmp(driver,"fov_forward")==0){ +- fov_forward(1,num_dependents,num_independents, tangentDirNum, xp, seed, theOutput, jacTimesSeed ); +- } +- else{ +- jacobian(1,num_dependents,num_independents,xp,jacTimesSeed); +- } +- +- /*Free ressources: */ ++ fov_forward(1,num_dependents,num_independents, tangentDirNum, xp, seed, theOutput, jacTimesSeed ); ++ /*Free resources: */ + xDelete(theOutput); + xDelete(indepIndices); + xDelete(seed); +@@ -184,10 +161,49 @@ + /*add to results: */ + results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,*jacTimesSeed,num_dependents*tangentDirNum,1,1,0.0)); + +- /*Free ressources: */ ++ /*Free resources: */ + xDelete(jacTimesSeed); +- xDelete(indepIndices); ++ xDelete(indepIndices); + } ++ else if (strcmp(driver,"fos_reverse")==0) { ++ ++ int aDepIndex=0; ++ double *aWeightVector=NULL; ++ double *weightVectorTimesJac=NULL; ++ ++ /*retrieve direction index: */ ++ parameters->FindParam(&aDepIndex,AutodiffFosReverseIndexEnum); ++ ++ if (aDepIndex<0 || aDepIndex>=num_dependents) _error_("index value for AutodiffFosReverseIndexEnum should be in [0,num_dependents-1]"); ++ ++ aWeightVector=xNewZeroInit(num_dependents); ++ aWeightVector[aDepIndex]=1.0; ++ ++ weightVectorTimesJac=xNew(num_independents); ++ ++ /*set the forward method function pointer: */ ++ anEDF_for_solverx_p->fos_reverse=EDF_fos_reverse_for_solverx; ++ ++ /*allocate the space for the parameters to invoke the EDF fos_reverse :*/ ++ anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); ++ ++ /*call driver: */ ++ fos_reverse(1,num_dependents,num_independents, aWeightVector, weightVectorTimesJac ); ++ ++ /*add to results*/ ++ results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,weightVectorTimesJac,num_independents,1,1,0.0)); ++ ++ /*free resources :*/ ++ xDelete(weightVectorTimesJac); ++ xDelete(aWeightVector); ++ } ++ else if (strcmp(driver,"fov_reverse")==0) { ++ /*allocate the space for the parameters to invoke the EDF fos_reverse :*/ ++ anEDF_for_solverx_p->dpp_U=xNew(num_dependents,anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,anEDF_for_solverx_p->max_n); ++ _error_("driver: " << driver << " not yet supported!"); ++ } + else _error_("driver: " << driver << " not yet supported!"); + + /* delete the allocated space for the parameters:*/ +@@ -202,7 +218,7 @@ + xDelete(anEDF_for_solverx_p->dp_Z); + xDelete(anEDF_for_solverx_p->dpp_Z); + +- /*Free ressources: */ ++ /*Free resources: */ + xDelete(xp); + xDelete(axp); + Index: /issm/oecreview/Archive/13393-13976/ISSM-13507-13508.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13507-13508.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13507-13508.diff (revision 13980) @@ -0,0 +1,85 @@ +Index: ../trunk-jpl/test/NightlyRun/ad.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/ad.m (revision 13507) ++++ ../trunk-jpl/test/NightlyRun/ad.m (revision 13508) +@@ -7,19 +7,20 @@ + md.autodiff.isautodiff=true; + md.verbose.autodiff=true; + md.autodiff.independents={... +- independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fov_forward_indices',(1:md.mesh.numberofvertices)') ++ independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices); ++ %independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fov_forward_indices',(1:md.mesh.numberofvertices)') + %independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',1) + }; + + md.autodiff.dependents={... +- dependent('name','IceVolume','type','scalar')... +- dependent('name','MaxVel','type','scalar')... +- dependent('name','MassFlux','type','scalar','exp','../Exp/MassFlux1.exp','mesh',md.mesh,'index',1)... +- dependent('name','MassFlux','type','scalar','exp','../Exp/MassFlux2.exp','mesh',md.mesh,'index',2)... ++ dependent('name','MaxVel','type','scalar','fos_reverse_index',1)... ++ %dependent('name','IceVolume','type','scalar')... ++ %dependent('name','MassFlux','type','scalar','exp','../Exp/MassFlux1.exp','mesh',md.mesh,'index',1)... ++ %dependent('name','MassFlux','type','scalar','exp','../Exp/MassFlux2.exp','mesh',md.mesh,'index',2)... + }; + + %md.autodiff.driver='fos_forward'; +-md.autodiff.driver='fov_forward'; ++md.autodiff.driver='fos_reverse'; + + md=solve(md,TransientSolutionEnum); + +Index: ../trunk-jpl/test/NightlyRun/test3019.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3019.m (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test3019.m (revision 13508) +@@ -0,0 +1,35 @@ ++md=triangle(model,'../Exp/Square.exp',100000); ++md=setmask(md,'all',''); ++md=parameterize(md,'../Par/SquareShelfConstrained.par'); ++md=setflowequation(md,'macayeal','all'); ++md.cluster=generic('name',oshostname(),'np',3); ++ ++md.autodiff.isautodiff=true; ++md.verbose.autodiff=true; ++ ++%first run scalar reverse mode: ++md.autodiff.independents={independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices)}; ++md.autodiff.dependents={dependent('name','MaxVel','type','scalar','fos_reverse_index',1)}; ++md.autodiff.driver='fos_reverse'; ++ ++md=solve(md,TransientSolutionEnum); ++ ++%recover jacobian: ++jac_reverse=md.results.TransientSolution(1).AutodiffJacobian; ++ ++ ++%now run vectorial forward mode ++md.autodiff.independents={independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fov_forward_indices',(1:md.mesh.numberofvertices)')}; ++md.autodiff.dependents={dependent('name','MaxVel','type','scalar')}; ++md.autodiff.driver='fov_forward'; ++ ++md=solve(md,TransientSolutionEnum); ++ ++%recover jacobian: ++jac_forward=md.results.TransientSolution(1).AutodiffJacobian; ++ ++ ++%Fields and tolerances to track changes ++field_names ={'Jac Forward','Jac Reverse','Jac Forward - Reverse'}; ++field_tolerances={1e-13,1e-13,1e-13}; ++field_values={jac_forward,jac_reverse,jac_forward-jac_reverse}; +Index: ../trunk-jpl/test/Archives/Archive3019.nc +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/test/Archives/Archive3019.nc +=================================================================== +--- ../trunk-jpl/test/Archives/Archive3019.nc (revision 13507) ++++ ../trunk-jpl/test/Archives/Archive3019.nc (revision 13508) + +Property changes on: ../trunk-jpl/test/Archives/Archive3019.nc +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream Index: /issm/oecreview/Archive/13393-13976/ISSM-13508-13509.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13508-13509.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13508-13509.diff (revision 13980) @@ -0,0 +1,97 @@ +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13508) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13509) +@@ -45,6 +45,9 @@ + if(strcmp(autodiff_driver,"fos_forward")==0){ + parameters->AddObject(iomodel->CopyConstantObject(AutodiffFosForwardIndexEnum)); + } ++ else if(strcmp(autodiff_driver,"fos_reverse")==0){ ++ parameters->AddObject(iomodel->CopyConstantObject(AutodiffFosReverseIndexEnum)); ++ } + else if(strcmp(autodiff_driver,"fov_forward")==0){ + /*Retrieve list of indices: */ + iomodel->FetchData(&indices,&num_indices,&dummy,AutodiffFovForwardIndicesEnum); +Index: ../trunk-jpl/src/m/classes/autodiff.m +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.m (revision 13508) ++++ ../trunk-jpl/src/m/classes/autodiff.m (revision 13509) +@@ -120,6 +120,27 @@ + WriteData(fid,'data',index,'enum',AutodiffFosForwardIndexEnum(),'format','Integer'); + end + %}}} ++ %if driver is fos_reverse, build index: {{{ ++ if strcmpi(obj.driver,'fos_reverse'), ++ index=0; ++ ++ for i=1:num_dependent_objects, ++ dep=obj.dependents{i}; ++ if ~isnan(dep.fos_reverse_index), ++ index=index+dep.fos_reverse_index; ++ break; ++ else ++ if strcmpi(dep.type,'scalar'), ++ index=index+1; ++ else ++ index=index+dep.nods; ++ end ++ end ++ end ++ index=index-1; %get c-index numbering going ++ WriteData(fid,'data',index,'enum',AutodiffFosReverseIndexEnum(),'format','Integer'); ++ end ++ %}}} + %if driver is fov_forward, build indices: {{{ + if strcmpi(obj.driver,'fov_forward'), + indices=0; +Index: ../trunk-jpl/src/m/classes/dependent.m +=================================================================== +--- ../trunk-jpl/src/m/classes/dependent.m (revision 13508) ++++ ../trunk-jpl/src/m/classes/dependent.m (revision 13509) +@@ -7,9 +7,11 @@ + properties (SetAccess=public) + name = ''; + type = ''; ++ fos_reverse_index = NaN; + exp = ''; + segments = []; + index = -1; ++ nods = 0; + end + methods + function obj= dependent(varargin) % {{{ +@@ -22,6 +24,7 @@ + obj.exp=getfieldvalue(options,'exp',''); + obj.segments=getfieldvalue(options,'segments',[]); + obj.index=getfieldvalue(options,'index',-1); ++ obj.nods=getfieldvalue(options,'nods',0); + + %if name is mass flux: + if strcmpi(obj.name,'MassFlux'), +@@ -48,13 +51,26 @@ + error('dependent checkconsistency error: index for segments should be >=1'); + end + end ++ if ~isnan(obj.fos_reverse_index), ++ if ~strcmpi(driver,'fos_reverse'), ++ error('cannot declare a dependent with a fos_reverse_index when the driver is not fos_reverse!'); ++ end ++ if obj.nods==0, ++ error('ependent checkconsistency error: nods should be set to the size of the independent variable'); ++ end + ++ end ++ + end % }}} + function disp(obj) % {{{ + disp(sprintf(' dependent variable :')); + + fielddisplay(obj,'name','variable name (must match corresponding Enum)'); + fielddisplay(obj,'type','type of variable (''vertex'' or ''scalar'')'); ++ ++ if ~isnan(obj.fos_reverse_index), ++ fielddisplay(obj,'fos_reverse_index','index for fos_reverse driver of ADOLC'); ++ end + if ~isempty(obj.exp), + fielddisplay(obj,'exp','file needed to compute dependent variable'); + fielddisplay(obj,'segments','mass flux segments'); Index: /issm/oecreview/Archive/13393-13976/ISSM-13509-13510.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13509-13510.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13509-13510.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/execution +=================================================================== +--- ../trunk-jpl/execution (revision 13509) ++++ ../trunk-jpl/execution (revision 13510) + +Property changes on: ../trunk-jpl/execution +___________________________________________________________________ +Modified: svn:ignore +## -1,3 +1,4 ## ++Pig + test* + pig* + ad* Index: /issm/oecreview/Archive/13393-13976/ISSM-13510-13511.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13510-13511.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13510-13511.diff (revision 13980) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/execution +=================================================================== +--- ../trunk-jpl/execution (revision 13510) ++++ ../trunk-jpl/execution (revision 13511) + +Property changes on: ../trunk-jpl/execution +___________________________________________________________________ +Modified: svn:ignore +## -1,4 +1,4 ## +-Pig ++Pig-* + test* + pig* + ad* Index: /issm/oecreview/Archive/13393-13976/ISSM-13511-13512.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13511-13512.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13511-13512.diff (revision 13980) @@ -0,0 +1,33 @@ +Index: ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13511) ++++ ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13512) +@@ -179,6 +179,28 @@ + return 0; + } + /*}}}*/ ++int EDF_fov_reverse_for_solverx(int m, int p, double **dpp_U, int n, double **dpp_Z, double* dp_x, double* dp_y) { /*{{{*/ ++ // copy to transpose the matrix ++ double* transposed=xNew(m*m); ++ for (int i=0; i anIndexSet; ++ ++ ++ /*retrieve directions:*/ ++ if (strcmp(driver,"fov_reverse_all")==0){ ++ weightNum=num_dependents; ++ depIndices=xNewZeroInit(weightNum); ++ for(i=0;iFindParam(&depIndices,&weightNum,&dummy,AutodiffFovForwardIndicesEnum); ++ } ++ ++ /*Some checks: */ ++ if (weightNum<1 || weightNum>num_dependents) _error_("tangentDirNum should be in [1,num_dependents]"); ++ ++ /* full Jacobian or Jacobian projection:*/ ++ weightsTimesJac=xNew(weightNum,num_independents); ++ ++ /*set the forward method function pointers: */ ++ anEDF_for_solverx_p->fov_reverse=EDF_fov_reverse_for_solverx; ++ + /*allocate the space for the parameters to invoke the EDF fos_reverse :*/ +- anEDF_for_solverx_p->dpp_U=xNew(num_dependents,anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dpp_Z=xNew(num_dependents,anEDF_for_solverx_p->max_n); +- _error_("driver: " << driver << " not yet supported!"); ++ anEDF_for_solverx_p->dpp_U=xNew(weightNum,anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dpp_Z=xNew(weightNum,anEDF_for_solverx_p->max_n); ++ ++ /*seed matrix: */ ++ weights=xNewZeroInit(weightNum,num_dependents); ++ ++ /*collect indices in a set to prevent accidental duplicates as long as we don't do compression:*/ ++ for (int i=0; inum_dependents) { ++ _error_("depIndices values must be in [0,num_dependents-1]"); ++ } ++ if (anIndexSet.find(depIndices[i])!=anIndexSet.end()) { ++ _error_("duplicate depIndices values are not allowed until we implement Jacobian decompression"); ++ } ++ anIndexSet.insert(depIndices[i]); ++ /* now populate the seed matrix from the set of independent indices; ++ * simple setup with a single 1.0 per column and at most a single 1.0 per row*/ ++ weights[depIndices[i]][i]=1.0; ++ } ++ ++ /*call driver: */ ++ fov_reverse(1,num_dependents,num_independents, weightNum, weights, weightsTimesJac ); ++ ++ /*add to results: */ ++ results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,*weightsTimesJac,weightNum*num_independents,1,1,0.0)); ++ ++ /*Free resources: */ ++ xDelete(weights); ++ xDelete(weightsTimesJac); ++ xDelete(depIndices); + } + else _error_("driver: " << driver << " not yet supported!"); + Index: /issm/oecreview/Archive/13393-13976/ISSM-13513-13514.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13513-13514.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13513-13514.diff (revision 13980) @@ -0,0 +1,216 @@ +Index: ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13513) ++++ ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13514) +@@ -70,113 +70,113 @@ + + #ifdef _HAVE_ADOLC_ + int EDF_for_solverx(int n, IssmPDouble *x, int m, IssmPDouble *y){ /*{{{*/ +- SolverxSeq(y,x, x+m*m, m); // x is where the matrix starts, x+m*m is where the right-hand side starts +- return 0; ++ SolverxSeq(y,x, x+m*m, m); // x is where the matrix starts, x+m*m is where the right-hand side starts ++ return 0; + } /*}}}*/ + int EDF_fos_forward_for_solverx(int n, IssmPDouble *inVal, IssmPDouble *inDeriv, int m, IssmPDouble *outVal, IssmPDouble *outDeriv) { /*{{{*/ + #ifdef _HAVE_GSL_ +-// for (int i=0; iConstant(&autodiff_analysis,AutodiffIsautodiffEnum); + + if(autodiff_analysis){ ++ ++ /*Copy some parameters from IoModel to parameters dataset: */ ++ parameters->AddObject(iomodel->CopyConstantObject(AutodiffKeepEnum)); + +- /*retrieve driver: */ ++ /*retrieve driver: {{{*/ + iomodel->Constant(&autodiff_driver,AutodiffDriverEnum); + parameters->AddObject(iomodel->CopyConstantObject(AutodiffDriverEnum)); + +@@ -54,7 +57,7 @@ + parameters->AddObject(new IntMatParam(AutodiffFovForwardIndicesEnum,indices,num_indices,1)); + xDelete(indices); + } +- ++ /*}}}*/ + /*Deal with dependents first: {{{*/ + iomodel->Constant(&num_dependent_objects,AutodiffNumDependentObjectsEnum); + dependent_objects=new DataSet(); +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13515) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 13516) +@@ -211,7 +211,7 @@ + + int numberofvertices; + int dummy; +- char* driver=NULL; ++ bool keep=false; + + + /*Initialize array detecting whether data[i] is an independent AD mode variable: */ +@@ -225,34 +225,11 @@ + + #ifdef _HAVE_ADOLC_ + +- /*Start the trace: {{{ +- * to do so, figure out what kind of driver we are running. Then, according to ADOLC documentation, +- * we'll need to activate keep. +- * +- * From ADOLC userdoc: +- * The optional integer argument keep of trace on determines whether the numerical values of all active variables are +- * recorded in a buffered temporary array or file called the taylor stack. This option takes effect if keep = 1 and +- * prepares the scene for an immediately following gradient evaluation by a call to a routine implementing the reverse +- * mode as described in the Section 4 and Section 5. +- * +- */ +- this->FetchData(&driver,AutodiffDriverEnum); +- if (strlen(driver)<=3){ +- /*there is no "_reverse" string within the driver string: */ +- if(VerboseAutodiff())_pprintLine_(" trace activated with keep off"); +- trace_on(1); +- } +- else{ +- if (strncmp((const char*)(driver+3),"_reverse",8)==0){ +- if(VerboseAutodiff())_pprintLine_(" trace activated with keep on"); +- trace_on(1,1); +- } +- else{ +- if(VerboseAutodiff())_pprintLine_(" trace activated with keep off"); +- trace_on(1); +- } +- } +- xDelete(driver); ++ /*Start trace: {{{*/ ++ this->FetchData(&keep,AutodiffKeepEnum); ++ if(keep)trace_on(1,1); ++ else trace_on(1); ++ + /*}}}*/ + /*build dataset made of independent objects: {{{*/ + this->independent_objects=new DataSet(); +Index: ../trunk-jpl/src/m/classes/autodiff.py +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.py (revision 13515) ++++ ../trunk-jpl/src/m/classes/autodiff.py (revision 13516) +@@ -39,5 +39,6 @@ + def marshall(self,fid): # {{{ + WriteData(fid,'object',self,'fieldname','isautodiff','format','Boolean') + WriteData(fid,'data',False,'enum',AutodiffMassFluxSegmentsPresentEnum(),'format','Boolean'); ++ WriteData(fid,'data',False,'enum',AutodiffKeepEnum(),'format','Boolean'); + # }}} + +Index: ../trunk-jpl/src/m/classes/autodiff.m +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.m (revision 13515) ++++ ../trunk-jpl/src/m/classes/autodiff.m (revision 13516) +@@ -57,6 +57,7 @@ + %early return + if ~obj.isautodiff, + WriteData(fid,'data',false,'enum',AutodiffMassFluxSegmentsPresentEnum,'format','Boolean'); ++ WriteData(fid,'data',false,'enum',AutodiffKeepEnum,'format','Boolean'); + return; + end + +@@ -179,7 +180,28 @@ + end + WriteData(fid,'data',flag,'enum',AutodiffMassFluxSegmentsPresentEnum,'format','Boolean'); + %}}} ++ %deal with trace keep on: {{{ ++ keep=false; + ++ %From ADOLC userdoc: ++ % The optional integer argument keep of trace on determines whether the numerical values of all active variables are ++ % recorded in a buffered temporary array or file called the taylor stack. This option takes effect if keep = 1 and ++ % prepares the scene for an immediately following gradient evaluation by a call to a routine implementing the reverse ++ % mode as described in the Section 4 and Section 5. ++ % ++ ++ if length(obj.driver)<=3, ++ keep=false; %there is no "_reverse" string within the driver string: ++ else ++ if strncmpi(obj.driver(4:end),'_reverse',8), ++ keep=true; ++ else ++ keep=false; ++ end ++ end ++ WriteData(fid,'data',keep,'enum',AutodiffKeepEnum,'format','Boolean'); ++ %}}} ++ + end % }}} + end + end +Index: ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13515) ++++ ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13516) +@@ -8,4 +8,4 @@ + % Usage: + % macro=MaximumNumberOfEnums() + +-macro=492; ++macro=493; +Index: ../trunk-jpl/src/m/enum/AutodiffKeepEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/AutodiffKeepEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/AutodiffKeepEnum.m (revision 13516) +@@ -0,0 +1,11 @@ ++function macro=AutodiffKeepEnum() ++%AUTODIFFKEEPENUM - Enum of AutodiffKeep ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=AutodiffKeepEnum() ++ ++macro=StringToEnum('AutodiffKeep'); +Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py +=================================================================== +--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13515) ++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13516) +@@ -198,6 +198,16 @@ + + return StringToEnum('AutodiffMassFluxSegmentsPresent')[0] + ++def AutodiffKeepEnum(): ++ """ ++ AUTODIFFKEEPENUM - Enum of AutodiffKeep ++ ++ Usage: ++ macro=AutodiffKeepEnum() ++ """ ++ ++ return StringToEnum('AutodiffKeep')[0] ++ + def BalancethicknessSpcthicknessEnum(): + """ + BALANCETHICKNESSSPCTHICKNESSENUM - Enum of BalancethicknessSpcthickness +@@ -4936,5 +4946,5 @@ + macro=MaximumNumberOfEnums() + """ + +- return 492 ++ return 493 + +Index: ../trunk-jpl/configs/config-macosx64-larour-bothapis.sh +=================================================================== +--- ../trunk-jpl/configs/config-macosx64-larour-bothapis.sh (revision 13515) ++++ ../trunk-jpl/configs/config-macosx64-larour-bothapis.sh (revision 13516) +@@ -11,7 +11,7 @@ + --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ Index: /issm/oecreview/Archive/13393-13976/ISSM-13516-13517.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13516-13517.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13516-13517.diff (revision 13980) @@ -0,0 +1,21 @@ +Index: ../trunk-jpl/src/m/classes/inversion.py +=================================================================== +--- ../trunk-jpl/src/m/classes/inversion.py (revision 13516) ++++ ../trunk-jpl/src/m/classes/inversion.py (revision 13517) +@@ -170,13 +170,13 @@ + WriteData(fid,'object',self,'fieldname','thickness_obs','format','DoubleMat','mattype',1) + + #process control parameters +- num_control_parameters=numpy.size(self.control_parameters) +- data=[StringToEnum(self.control_parameters[i])[0] for i in xrange(0,num_control_parameters)] ++ num_control_parameters=len(self.control_parameters) ++ data=numpy.array([StringToEnum(control_parameter)[0] for control_parameter in self.control_parameters]) + WriteData(fid,'data',data,'enum',InversionControlParametersEnum(),'format','DoubleMat','mattype',3) + WriteData(fid,'data',num_control_parameters,'enum',InversionNumControlParametersEnum(),'format','Integer') + + #process cost functions +- num_cost_functions=size(self.cost_functions,1) ++ num_cost_functions=numpy.size(self.cost_functions,1) + data=self.cost_functions + data[numpy.nonzero(data==101)]=SurfaceAbsVelMisfitEnum() + data[numpy.nonzero(data==102)]=SurfaceRelVelMisfitEnum() Index: /issm/oecreview/Archive/13393-13976/ISSM-13517-13518.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13517-13518.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13517-13518.diff (revision 13980) @@ -0,0 +1,145 @@ +Index: ../trunk-jpl/test/NightlyRun/test212.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test212.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test212.py (revision 13518) +@@ -0,0 +1,61 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test212.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',200000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md=setflowequation(md,'macayeal','all') ++ ++ ++# control parameters ++ ++md.inversion.iscontrol=1 ++md.inversion.control_parameters=['MaterialsRheologyBbar'] ++md.inversion.min_parameters=10**6*ones((md.mesh.numberofvertices,1)) ++md.inversion.max_parameters=2*10**9*ones((md.mesh.numberofvertices,1)) ++md.inversion.nsteps=2 ++md.inversion.cost_functions=101*ones((md.inversion.nsteps,1)) ++md.inversion.cost_functions_coefficients=ones((md.mesh.numberofvertices,1)) ++md.inversion.gradient_scaling=10**7*ones((md.inversion.nsteps,1)) ++md.inversion.maxiter_per_step=2*ones((md.inversion.nsteps,1)) ++md.inversion.step_threshold=0.3*ones((md.inversion.nsteps,1)) ++md.inversion.vx_obs=md.initialization.vx ++md.inversion.vy_obs=md.initialization.vy ++ ++ ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Gradient','Misfits','MaterialsRheologyBbar','Pressure','Vel','Vx','Vy'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++md.results['DiagnosticSolution'][1]['Gradient1'],\ ++md.results['DiagnosticSolution'][1]['J'],\ ++md.results['DiagnosticSolution'][1]['MaterialsRheologyBbar'],\ ++md.results['DiagnosticSolution'][1]['Pressure'],\ ++md.results['DiagnosticSolution'][1]['Vel'],\ ++md.results['DiagnosticSolution'][1]['Vx'],\ ++md.results['DiagnosticSolution'][1]['Vy'],\ ++] +Index: ../trunk-jpl/test/NightlyRun/test212.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test212.m (revision 13517) ++++ ../trunk-jpl/test/NightlyRun/test212.m (revision 13518) +@@ -24,7 +24,7 @@ + field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; + field_values={... + (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... ++ (md.results.DiagnosticSolution.J),... + (md.results.DiagnosticSolution.MaterialsRheologyBbar),... + (md.results.DiagnosticSolution.Pressure),... + (md.results.DiagnosticSolution.Vel),... +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test212.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test212.py (revision 13517) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test212.py (revision 13518) +@@ -1,61 +0,0 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test212.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- +-from MatlabFuncs import * +-from model import * +-from EnumDefinitions import * +-from numpy import * +-from triangle import * +-from setmask import * +-from parameterize import * +-from setflowequation import * +-from solve import * +- +-md=triangle(model(),'../Exp/Square.exp',200000) +-md=setmask(md,'all','') +-md=parameterize(md,'../Par/SquareShelf.py') +-md=setflowequation(md,'macayeal','all') +- +- +-# control parameters +- +-md.inversion.iscontrol=1 +-md.inversion.control_parameters=['MaterialsRheologyBbar'] +-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1) +-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1) +-md.inversion.nsteps=2 +-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1) +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1) +-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1) +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1) +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1) +-md.inversion.vx_obs=md.initialization.vx +-md.inversion.vy_obs=md.initialization.vy +- +- +-md.cluster=generic('name',oshostname(),'np',3) +-md=solve(md,DiagnosticSolutionEnum()) +- +- +-# Fields and tolerances to track changes +- +-field_names =['Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'] +-field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] +-field_values=[\ +-md.results['DiagnosticSolution'][1]['Gradient1'],\ +-md.results['DiagnosticSolution.J'],\ +-md.results['DiagnosticSolution'][1]['MaterialsRheologyBbar'],\ +-md.results['DiagnosticSolution'][1]['Pressure'],\ +-md.results['DiagnosticSolution'][1]['Vel'],\ +-md.results['DiagnosticSolution'][1]['Vx'],\ +-md.results['DiagnosticSolution'][1]['Vy'],\ +-] Index: /issm/oecreview/Archive/13393-13976/ISSM-13518-13519.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13518-13519.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13518-13519.diff (revision 13980) @@ -0,0 +1,448 @@ +Index: ../trunk-jpl/test/NightlyRun/test214.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test214.m (revision 13518) ++++ ../trunk-jpl/test/NightlyRun/test214.m (revision 13519) +@@ -25,7 +25,7 @@ + field_tolerances={1e-07,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08}; + field_values={... + (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... ++ (md.results.DiagnosticSolution.J),... + (md.results.DiagnosticSolution.MaterialsRheologyB),... + (md.results.DiagnosticSolution.Pressure),... + (md.results.DiagnosticSolution.Vel),... +Index: ../trunk-jpl/test/NightlyRun/test214.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test214.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test214.py (revision 13519) +@@ -0,0 +1,62 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test214.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',200000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,1) ++md=setflowequation(md,'pattyn','all') ++ ++ ++# control parameters ++ ++md.inversion.iscontrol=1 ++md.inversion.control_parameters=['MaterialsRheologyBbar'] ++md.inversion.min_parameters=10**6*ones((md.mesh.numberofvertices,1)) ++md.inversion.max_parameters=2.*10**9*ones((md.mesh.numberofvertices,1)) ++md.inversion.nsteps=2 ++md.inversion.cost_functions=101.*ones((md.inversion.nsteps,1)) ++md.inversion.cost_functions_coefficients=ones((md.mesh.numberofvertices,1)) ++md.inversion.gradient_scaling=10**7*ones((md.inversion.nsteps,1)) ++md.inversion.maxiter_per_step=2.*ones((md.inversion.nsteps,1)) ++md.inversion.step_threshold=0.3*ones((md.inversion.nsteps,1)) ++md.inversion.vx_obs=md.initialization.vx ++md.inversion.vy_obs=md.initialization.vy ++ ++ ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Gradient','Misfits','MaterialsRheologyBbar','Pressure','Vel','Vx','Vy'] ++field_tolerances=[1e-07,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Gradient1'],\ ++ md.results['DiagnosticSolution'][1]['J'],\ ++ md.results['DiagnosticSolution'][1]['MaterialsRheologyB'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'] ++] +Index: ../trunk-jpl/test/NightlyRun/test215.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test215.m (revision 13518) ++++ ../trunk-jpl/test/NightlyRun/test215.m (revision 13519) +@@ -25,7 +25,7 @@ + field_tolerances={1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09}; + field_values={... + (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... ++ (md.results.DiagnosticSolution.J),... + (md.results.DiagnosticSolution.MaterialsRheologyB),... + (md.results.DiagnosticSolution.Pressure),... + (md.results.DiagnosticSolution.Vel),... +Index: ../trunk-jpl/test/NightlyRun/test212.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test212.py (revision 13518) ++++ ../trunk-jpl/test/NightlyRun/test212.py (revision 13519) +@@ -31,12 +31,12 @@ + md.inversion.iscontrol=1 + md.inversion.control_parameters=['MaterialsRheologyBbar'] + md.inversion.min_parameters=10**6*ones((md.mesh.numberofvertices,1)) +-md.inversion.max_parameters=2*10**9*ones((md.mesh.numberofvertices,1)) ++md.inversion.max_parameters=2.*10**9*ones((md.mesh.numberofvertices,1)) + md.inversion.nsteps=2 +-md.inversion.cost_functions=101*ones((md.inversion.nsteps,1)) ++md.inversion.cost_functions=101.*ones((md.inversion.nsteps,1)) + md.inversion.cost_functions_coefficients=ones((md.mesh.numberofvertices,1)) + md.inversion.gradient_scaling=10**7*ones((md.inversion.nsteps,1)) +-md.inversion.maxiter_per_step=2*ones((md.inversion.nsteps,1)) ++md.inversion.maxiter_per_step=2.*ones((md.inversion.nsteps,1)) + md.inversion.step_threshold=0.3*ones((md.inversion.nsteps,1)) + md.inversion.vx_obs=md.initialization.vx + md.inversion.vy_obs=md.initialization.vy +Index: ../trunk-jpl/test/NightlyRun/test215.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test215.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test215.py (revision 13519) +@@ -0,0 +1,62 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test215.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',200000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,1) ++md=setflowequation(md,'stokes','all') ++ ++ ++# control parameters ++ ++md.inversion.iscontrol=1 ++md.inversion.control_parameters=['MaterialsRheologyBbar'] ++md.inversion.min_parameters=10**6*ones((md.mesh.numberofvertices,1)) ++md.inversion.max_parameters=2.*10**9*ones((md.mesh.numberofvertices,1)) ++md.inversion.nsteps=2 ++md.inversion.cost_functions=101.*ones((md.inversion.nsteps,1)) ++md.inversion.cost_functions_coefficients=ones((md.mesh.numberofvertices,1)) ++md.inversion.gradient_scaling=10**7*ones((md.inversion.nsteps,1)) ++md.inversion.maxiter_per_step=2.*ones((md.inversion.nsteps,1)) ++md.inversion.step_threshold=0.3*ones((md.inversion.nsteps,1)) ++md.inversion.vx_obs=md.initialization.vx ++md.inversion.vy_obs=md.initialization.vy ++ ++ ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Gradient','Misfits','MaterialsRheologyBbar','Pressure','Vel','Vx','Vy'] ++field_tolerances=[1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Gradient1'],\ ++ md.results['DiagnosticSolution'][1]['J'],\ ++ md.results['DiagnosticSolution'][1]['MaterialsRheologyB'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'] ++] +Index: ../trunk-jpl/test/NightlyRun/test213.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test213.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test213.py (revision 13519) +@@ -0,0 +1,63 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test213.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',200000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md.extrude(3,1) ++md=setflowequation(md,'macayeal','all') ++ ++ ++# control parameters ++ ++md.inversion.iscontrol=1 ++md.inversion.control_parameters=['MaterialsRheologyBbar'] ++md.inversion.min_parameters=10**6*ones((md.mesh.numberofvertices,1)) ++md.inversion.max_parameters=2.*10**9*ones((md.mesh.numberofvertices,1)) ++md.inversion.nsteps=2 ++md.inversion.cost_functions=101.*ones((md.inversion.nsteps,1)) ++md.inversion.cost_functions_coefficients=ones((md.mesh.numberofvertices,1)) ++md.inversion.gradient_scaling=10**7*ones((md.inversion.nsteps,1)) ++md.inversion.maxiter_per_step=2.*ones((md.inversion.nsteps,1)) ++md.inversion.step_threshold=0.3*ones((md.inversion.nsteps,1)) ++md.inversion.vx_obs=md.initialization.vx ++md.inversion.vy_obs=md.initialization.vy ++ ++ ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++ ++# Fields and tolerances to track changes ++ ++field_names =['Gradient','Misfits','MaterialsRheologyBbar','Pressure','Vel','Vx','Vy'] ++field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++#field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Gradient1'],\ ++ md.results['DiagnosticSolution'][1]['J'],\ ++ md.results['DiagnosticSolution'][1]['MaterialsRheologyB'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test213.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test213.py (revision 13518) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test213.py (revision 13519) +@@ -1,63 +0,0 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test213.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- +-from MatlabFuncs import * +-from model import * +-from EnumDefinitions import * +-from numpy import * +-from triangle import * +-from setmask import * +-from parameterize import * +-from setflowequation import * +-from solve import * +- +-md=triangle(model(),'../Exp/Square.exp',200000) +-md=setmask(md,'all','') +-md=parameterize(md,'../Par/SquareShelf.py') +-md.extrude(3,1) +-md=setflowequation(md,'macayeal','all') +- +- +-# control parameters +- +-md.inversion.iscontrol=1 +-md.inversion.control_parameters=['MaterialsRheologyBbar'] +-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1) +-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1) +-md.inversion.nsteps=2 +-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1) +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1) +-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1) +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1) +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1) +-md.inversion.vx_obs=md.initialization.vx +-md.inversion.vy_obs=md.initialization.vy +- +- +-md.cluster=generic('name',oshostname(),'np',3) +-md=solve(md,DiagnosticSolutionEnum()) +- +- +-# Fields and tolerances to track changes +- +-field_names =['Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'] +-field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] +-#field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] +-field_values=[\ +- md.results['DiagnosticSolution'][1]['Gradient1'],\ +- md.results['DiagnosticSolution'][1]['J'],\ +- md.results['DiagnosticSolution'][1]['MaterialsRheologyB'],\ +- md.results['DiagnosticSolution'][1]['Pressure'],\ +- md.results['DiagnosticSolution'][1]['Vel'],\ +- md.results['DiagnosticSolution'][1]['Vx'],\ +- md.results['DiagnosticSolution'][1]['Vy'],\ +-] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test214.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test214.py (revision 13518) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test214.py (revision 13519) +@@ -1,61 +0,0 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test214.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- +-from MatlabFuncs import * +-from model import * +-from EnumDefinitions import * +-from numpy import * +-from triangle import * +-from setmask import * +-from parameterize import * +-from setflowequation import * +-from solve import * +- +-md=triangle(model(),'../Exp/Square.exp',200000) +-md=setmask(md,'all','') +-md=parameterize(md,'../Par/SquareShelf.py') +-md.extrude(3,1) +-md=setflowequation(md,'pattyn','all') +- +- +-# control parameters +- +-md.inversion.iscontrol=1 +-md.inversion.control_parameters=['MaterialsRheologyBbar'] +-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1) +-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1) +-md.inversion.nsteps=2 +-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1) +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1) +-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1) +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1) +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1) +-md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy +- +- +-md.cluster=generic('name',oshostname(),'np',3) +-md=solve(md,DiagnosticSolutionEnum()) +- +- +-# Fields and tolerances to track changes +- +-field_names =['Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'] +-field_tolerances=[1e-07,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08] +-field_values=[\ +- md.results['DiagnosticSolution.Gradient1),\ +- md.results.DiagnosticSolution.J,\ +- md.results['DiagnosticSolution.MaterialsRheologyB),\ +- md.results['DiagnosticSolution'][1]['Pressure'],\ +- md.results['DiagnosticSolution'][1]['Vel'],\ +- md.results['DiagnosticSolution'][1]['Vx'],\ +- md.results['DiagnosticSolution'][1]['Vy'] +-] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test215.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test215.py (revision 13518) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test215.py (revision 13519) +@@ -1,61 +0,0 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test215.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- +-from MatlabFuncs import * +-from model import * +-from EnumDefinitions import * +-from numpy import * +-from triangle import * +-from setmask import * +-from parameterize import * +-from setflowequation import * +-from solve import * +- +-md=triangle(model(),'../Exp/Square.exp',200000) +-md=setmask(md,'all','') +-md=parameterize(md,'../Par/SquareShelf.py') +-md.extrude(3,1) +-md=setflowequation(md,'stokes','all') +- +- +-# control parameters +- +-md.inversion.iscontrol=1 +-md.inversion.control_parameters=['MaterialsRheologyBbar'] +-md.inversion.min_parameters=10^6*ones(md.mesh.numberofvertices,1) +-md.inversion.max_parameters=2*10^9*ones(md.mesh.numberofvertices,1) +-md.inversion.nsteps=2 +-md.inversion.cost_functions=101*ones(md.inversion.nsteps,1) +-md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,1) +-md.inversion.gradient_scaling=10^7*ones(md.inversion.nsteps,1) +-md.inversion.maxiter_per_step=2*ones(md.inversion.nsteps,1) +-md.inversion.step_threshold=0.3*ones(md.inversion.nsteps,1) +-md.inversion.vx_obs=md.initialization.vx md.inversion.vy_obs=md.initialization.vy +- +- +-md.cluster=generic('name',oshostname(),'np',3) +-md=solve(md,DiagnosticSolutionEnum()) +- +- +-# Fields and tolerances to track changes +- +-field_names =['Gradient' 'Misfits' 'MaterialsRheologyBbar' 'Pressure' 'Vel' 'Vx' 'Vy'] +-field_tolerances=[1e-08,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09,1e-09] +-field_values=[\ +- md.results['DiagnosticSolution.Gradient1),\ +- md.results.DiagnosticSolution.J,\ +- md.results['DiagnosticSolution.MaterialsRheologyB),\ +- md.results['DiagnosticSolution'][1]['Pressure'],\ +- md.results['DiagnosticSolution'][1]['Vel'],\ +- md.results['DiagnosticSolution'][1]['Vx'],\ +- md.results['DiagnosticSolution'][1]['Vy'] +-] Index: /issm/oecreview/Archive/13393-13976/ISSM-13519-13520.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13519-13520.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13519-13520.diff (revision 13980) @@ -0,0 +1,109 @@ +Index: ../trunk-jpl/src/m/mesh/triangle.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/triangle.py (revision 13519) ++++ ../trunk-jpl/src/m/mesh/triangle.py (revision 13520) +@@ -1,56 +1,66 @@ +-from numpy import * +-import TriMesh as tm +-import NodeConnectivity as nc +-import ElementConnectivity as ec ++import numpy ++from TriMesh import * ++from NodeConnectivity import * ++from ElementConnectivity import * ++from MatlabFuncs import * + +-def triangle(md, domainname, resolution,riftname=''): +- #TRIANGLE - create model mesh using the triangle package +- # +- # This routine creates a model mesh using TriMesh and a domain outline, to within a certain resolution +- # where md is a @model object, domainname is the name of an Argus domain outline file, +- # and resolution is a characteristic length for the mesh (same unit as the domain outline +- # unit). Riftname is an optional argument (Argus domain outline) describing rifts. +- # +- # Usage: +- # md=triangle(md,domainname,resolution) +- # or md=triangle(md,domainname, resolution, riftname) +- # +- # Examples: +- # md=triangle(md,'DomainOutline.exp',1000); +- # md=triangle(md,'DomainOutline.exp',1000,'Rifts.exp'); ++def triangle(md,domainname,*args): ++ """ ++ TRIANGLE - create model mesh using the triangle package + ++ This routine creates a model mesh using TriMesh and a domain outline, to within a certain resolution ++ where md is a @model object, domainname is the name of an Argus domain outline file, ++ and resolution is a characteristic length for the mesh (same unit as the domain outline ++ unit). Riftname is an optional argument (Argus domain outline) describing rifts. + ++ Usage: ++ md=triangle(md,domainname,resolution) ++ or md=triangle(md,domainname, resolution, riftname) ++ ++ Examples: ++ md=triangle(md,'DomainOutline.exp',1000); ++ md=triangle(md,'DomainOutline.exp',1000,'Rifts.exp'); ++ """ ++ + #Figure out a characteristic area. Resolution is a node oriented concept (ex a 1000m resolution node would + #be made of 1000*1000 area squares). + ++ if len(args)==1: ++ resolution=args[0] ++ riftname='' ++ if len(args)==2: ++ riftname=args[0] ++ resolution=args[1] ++ + #Check that mesh was not already run, and warn user: +- if md.mesh.numberofelements != 0.: +- choice = input('This model already has a mesh. Are you sure you want to go ahead? (y/n)') +- if choice != 'y': ++ if md.mesh.numberofelements: ++ choice = raw_input('This model already has a mesh. Are you sure you want to go ahead? (y/n)') ++ if not strcmp(choice,'y'): + print 'no meshing done ... exiting' +- return [] +- +- area = resolution**2. ++ return None + ++ area = resolution**2 ++ + #Mesh using TriMesh +- [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=tm.TriMesh(domainname,riftname,area) ++ [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,riftname,area) + +- + #Fill in rest of fields: +- md.mesh.numberofelements = len(md.mesh.elements) +- md.mesh.numberofvertices = len(md.mesh.x) +- md.mesh.z = zeros(md.mesh.numberofvertices) +- md.mesh.vertexonboundary = zeros(md.mesh.numberofvertices) ++ md.mesh.numberofelements = numpy.size(md.mesh.elements,axis=0) ++ md.mesh.numberofvertices = numpy.size(md.mesh.x) ++ md.mesh.z = numpy.zeros(md.mesh.numberofvertices) ++ md.mesh.vertexonboundary = numpy.zeros(md.mesh.numberofvertices) + md.mesh.vertexonboundary[md.mesh.segments[:,0:2].astype(int)-1] = 1. +- md.mesh.vertexonbed = ones(md.mesh.numberofvertices) +- md.mesh.vertexonsurface = ones(md.mesh.numberofvertices) +- md.mesh.elementonbed = ones(md.mesh.numberofelements) +- md.mesh.elementonsurface = ones(md.mesh.numberofelements) ++ md.mesh.vertexonbed = numpy.ones(md.mesh.numberofvertices) ++ md.mesh.vertexonsurface = numpy.ones(md.mesh.numberofvertices) ++ md.mesh.elementonbed = numpy.ones(md.mesh.numberofelements) ++ md.mesh.elementonsurface = numpy.ones(md.mesh.numberofelements) + + #Now, build the connectivity tables for this mesh. +- [md.mesh.vertexconnectivity]= nc.NodeConnectivity(md.mesh.elements, md.mesh.numberofvertices) +- [md.mesh.elementconnectivity] = ec.ElementConnectivity(md.mesh.elements, md.mesh.vertexconnectivity) +- ++ [md.mesh.vertexconnectivity]= NodeConnectivity(md.mesh.elements, md.mesh.numberofvertices) ++ [md.mesh.elementconnectivity] = ElementConnectivity(md.mesh.elements, md.mesh.vertexconnectivity) ++ + #type of model + md.mesh.dimension = 2. ++ + return md ++ Index: /issm/oecreview/Archive/13393-13976/ISSM-13520-13521.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13520-13521.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13520-13521.diff (revision 13980) @@ -0,0 +1,289 @@ +Index: ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13520) ++++ ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13521) +@@ -196,6 +196,8 @@ + SurfaceforcingsIssmbgradientsEnum, + SurfaceforcingsMonthlytemperaturesEnum, + SurfaceforcingsHcEnum, ++ SurfaceforcingsHrefEnum, ++ SurfaceforcingsSmbrefEnum, + SurfaceforcingsSmbPosMaxEnum, + SurfaceforcingsSmbPosMinEnum, + SurfaceforcingsAPosEnum, +Index: ../trunk-jpl/src/c/shared/Numerics/UnitConversion.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Numerics/UnitConversion.cpp (revision 13520) ++++ ../trunk-jpl/src/c/shared/Numerics/UnitConversion.cpp (revision 13521) +@@ -71,6 +71,7 @@ + case SurfaceforcingsBPosEnum: scale=yts;break; //m/yr + case SurfaceforcingsANegEnum: scale=yts;break; //m/yr + case SurfaceforcingsBNegEnum: scale=yts;break; //m/yr ++ case SurfaceforcingsSmbrefEnum: scale=yts;break; //m/yr + case MisfitEnum: scale=pow(yts,2);break; //(m/yr)^2 + case MassFluxEnum: scale=pow((IssmDouble)10,-12)*yts;break; // (GigaTon/year) + case TotalSmbEnum: scale=pow((IssmDouble)10,-12)*yts;break; // (GigaTon/year) +Index: ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13520) ++++ ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13521) +@@ -205,6 +205,8 @@ + else if (strcmp(name,"SurfaceforcingsIssmbgradients")==0) return SurfaceforcingsIssmbgradientsEnum; + else if (strcmp(name,"SurfaceforcingsMonthlytemperatures")==0) return SurfaceforcingsMonthlytemperaturesEnum; + else if (strcmp(name,"SurfaceforcingsHc")==0) return SurfaceforcingsHcEnum; ++ else if (strcmp(name,"SurfaceforcingsHref")==0) return SurfaceforcingsHrefEnum; ++ else if (strcmp(name,"SurfaceforcingsSmbref")==0) return SurfaceforcingsSmbrefEnum; + else if (strcmp(name,"SurfaceforcingsSmbPosMax")==0) return SurfaceforcingsSmbPosMaxEnum; + else if (strcmp(name,"SurfaceforcingsSmbPosMin")==0) return SurfaceforcingsSmbPosMinEnum; + else if (strcmp(name,"SurfaceforcingsAPos")==0) return SurfaceforcingsAPosEnum; +@@ -258,12 +260,12 @@ + else if (strcmp(name,"PrognosticAnalysis")==0) return PrognosticAnalysisEnum; + else if (strcmp(name,"PrognosticSolution")==0) return PrognosticSolutionEnum; + else if (strcmp(name,"SteadystateSolution")==0) return SteadystateSolutionEnum; +- else if (strcmp(name,"SurfaceSlopeAnalysis")==0) return SurfaceSlopeAnalysisEnum; +- else if (strcmp(name,"SurfaceSlopeSolution")==0) return SurfaceSlopeSolutionEnum; + else stage=3; + } + if(stage==3){ +- if (strcmp(name,"SurfaceSlopeXAnalysis")==0) return SurfaceSlopeXAnalysisEnum; ++ if (strcmp(name,"SurfaceSlopeAnalysis")==0) return SurfaceSlopeAnalysisEnum; ++ else if (strcmp(name,"SurfaceSlopeSolution")==0) return SurfaceSlopeSolutionEnum; ++ else if (strcmp(name,"SurfaceSlopeXAnalysis")==0) return SurfaceSlopeXAnalysisEnum; + else if (strcmp(name,"SurfaceSlopeYAnalysis")==0) return SurfaceSlopeYAnalysisEnum; + else if (strcmp(name,"ThermalAnalysis")==0) return ThermalAnalysisEnum; + else if (strcmp(name,"ThermalSolution")==0) return ThermalSolutionEnum; +@@ -381,12 +383,12 @@ + else if (strcmp(name,"SurfaceAbsVelMisfit")==0) return SurfaceAbsVelMisfitEnum; + else if (strcmp(name,"SurfaceArea")==0) return SurfaceAreaEnum; + else if (strcmp(name,"SurfaceAverageVelMisfit")==0) return SurfaceAverageVelMisfitEnum; +- else if (strcmp(name,"SurfaceLogVelMisfit")==0) return SurfaceLogVelMisfitEnum; +- else if (strcmp(name,"SurfaceLogVxVyMisfit")==0) return SurfaceLogVxVyMisfitEnum; + else stage=4; + } + if(stage==4){ +- if (strcmp(name,"SurfaceRelVelMisfit")==0) return SurfaceRelVelMisfitEnum; ++ if (strcmp(name,"SurfaceLogVelMisfit")==0) return SurfaceLogVelMisfitEnum; ++ else if (strcmp(name,"SurfaceLogVxVyMisfit")==0) return SurfaceLogVxVyMisfitEnum; ++ else if (strcmp(name,"SurfaceRelVelMisfit")==0) return SurfaceRelVelMisfitEnum; + else if (strcmp(name,"SurfaceSlopeX")==0) return SurfaceSlopeXEnum; + else if (strcmp(name,"SurfaceSlopeY")==0) return SurfaceSlopeYEnum; + else if (strcmp(name,"Temperature")==0) return TemperatureEnum; +@@ -504,12 +506,12 @@ + else if (strcmp(name,"Scaled")==0) return ScaledEnum; + else if (strcmp(name,"Separate")==0) return SeparateEnum; + else if (strcmp(name,"Sset")==0) return SsetEnum; +- else if (strcmp(name,"Verbose")==0) return VerboseEnum; +- else if (strcmp(name,"TriangleInterp")==0) return TriangleInterpEnum; + else stage=5; + } + if(stage==5){ +- if (strcmp(name,"BilinearInterp")==0) return BilinearInterpEnum; ++ if (strcmp(name,"Verbose")==0) return VerboseEnum; ++ else if (strcmp(name,"TriangleInterp")==0) return TriangleInterpEnum; ++ else if (strcmp(name,"BilinearInterp")==0) return BilinearInterpEnum; + else if (strcmp(name,"NearestInterp")==0) return NearestInterpEnum; + else if (strcmp(name,"XY")==0) return XYEnum; + else if (strcmp(name,"XYZP")==0) return XYZPEnum; +Index: ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13520) ++++ ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13521) +@@ -201,6 +201,8 @@ + case SurfaceforcingsIssmbgradientsEnum : return "SurfaceforcingsIssmbgradients"; + case SurfaceforcingsMonthlytemperaturesEnum : return "SurfaceforcingsMonthlytemperatures"; + case SurfaceforcingsHcEnum : return "SurfaceforcingsHc"; ++ case SurfaceforcingsHrefEnum : return "SurfaceforcingsHref"; ++ case SurfaceforcingsSmbrefEnum : return "SurfaceforcingsSmbref"; + case SurfaceforcingsSmbPosMaxEnum : return "SurfaceforcingsSmbPosMax"; + case SurfaceforcingsSmbPosMinEnum : return "SurfaceforcingsSmbPosMin"; + case SurfaceforcingsAPosEnum : return "SurfaceforcingsAPos"; +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp (revision 13520) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Prognostic/UpdateElementsPrognostic.cpp (revision 13521) +@@ -72,6 +72,8 @@ + } + if(issmbgradients){ + iomodel->FetchDataToInput(elements,SurfaceforcingsHcEnum); ++ iomodel->FetchDataToInput(elements,SurfaceforcingsHrefEnum); ++ iomodel->FetchDataToInput(elements,SurfaceforcingsSmbrefEnum); + iomodel->FetchDataToInput(elements,SurfaceforcingsSmbPosMaxEnum); + iomodel->FetchDataToInput(elements,SurfaceforcingsSmbPosMinEnum); + iomodel->FetchDataToInput(elements,SurfaceforcingsAPosEnum); +Index: ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13520) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13521) +@@ -2262,6 +2262,8 @@ + IssmDouble a_neg[NUMVERTICES]; // Hs-SMB relation parameter + IssmDouble b_neg[NUMVERTICES]; // Hs-SMB relation paremeter + IssmDouble Hc[NUMVERTICES]; // elevation of transition between accumulation regime and ablation regime ++ IssmDouble Href[NUMVERTICES]; // reference elevation from which deviations are used to calculate the SMB adjustment ++ IssmDouble Smbref[NUMVERTICES]; // reference SMB to which deviations are added + IssmDouble smb_pos_max[NUMVERTICES]; // maximum SMB value in the accumulation regime + IssmDouble smb_pos_min[NUMVERTICES]; // minimum SMB value in the accumulation regime + IssmDouble rho_water; // density of fresh water +@@ -2272,6 +2274,8 @@ + + /*Recover SmbGradients*/ + GetInputListOnVertices(&Hc[0],SurfaceforcingsHcEnum); ++ GetInputListOnVertices(&Href[0],SurfaceforcingsHrefEnum); ++ GetInputListOnVertices(&Smbref[0],SurfaceforcingsSmbrefEnum); + GetInputListOnVertices(&smb_pos_max[0],SurfaceforcingsSmbPosMaxEnum); + GetInputListOnVertices(&smb_pos_min[0],SurfaceforcingsSmbPosMinEnum); + GetInputListOnVertices(&a_pos[0],SurfaceforcingsAPosEnum); +@@ -2290,15 +2294,24 @@ + // loop over all vertices + for(i=0;iHc[i]){ +- smb[i]=a_pos[i]+b_pos[i]*s[i]; +- if(smb[i]>smb_pos_max[i]){smb[i]=smb_pos_max[i];} +- if(smb[i]Hc[i]){smb[i]=Smbref[i]+b_pos[i]*(s[i]-Href[i]);} ++ if(Href[i]<=Hc[i]){smb[i]=a_pos[i]+b_pos[i]*s[i];} ++ if(smb[i]>smb_pos_max[i]){smb[i]=smb_pos_max[i];} ++ if(smb[i]Hc[i]){smb[i]=a_neg[i]+b_neg[i]*s[i];} ++ if(Href[i]<=Hc[i]){smb[i]=Smbref[i]+b_neg[i]*(s[i]-Href[i]);} + } + smb[i]=smb[i]/rho_ice; // SMB in m/y ice +- } //end of the loop over the vertices ++ /* printf("s %e \n",s[i]); ++ printf("Hsref %e \n",Href[i]); ++ printf("Hc %e \n",Hc[i]); ++ printf("Smbref %e \n",Smbref[i]); ++ printf("b_neg %e \n",b_neg[i]); ++ printf("smb %e \n",smb[i]); ++ _error_("stop-in-code"); */ ++ } //end of the loop over the vertices + /*Update inputs*/ + this->inputs->AddInput(new TriaP1Input(SurfaceforcingsMassBalanceEnum,&smb[0])); + } +Index: ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp (revision 13520) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp (revision 13521) +@@ -2656,6 +2656,8 @@ + IssmDouble a_neg[NUMVERTICES]; // Hs-SMB relation parameter + IssmDouble b_neg[NUMVERTICES]; // Hs-SMB relation paremeter + IssmDouble Hc[NUMVERTICES]; // elevation of transition between accumulation regime and ablation regime ++ IssmDouble Href[NUMVERTICES]; // reference elevation from which deviations are used to calculate the SMB adjustment ++ IssmDouble Smbref[NUMVERTICES]; // reference SMB to which deviations are added + IssmDouble smb_pos_max[NUMVERTICES]; // maximum SMB value in the accumulation regime + IssmDouble smb_pos_min[NUMVERTICES]; // minimum SMB value in the accumulation regime + IssmDouble rho_water; // density of fresh water +@@ -2666,6 +2668,8 @@ + + /*Recover SmbGradients*/ + GetInputListOnVertices(&Hc[0],SurfaceforcingsHcEnum); ++ GetInputListOnVertices(&Href[0],SurfaceforcingsHrefEnum); ++ GetInputListOnVertices(&Smbref[0],SurfaceforcingsSmbrefEnum); + GetInputListOnVertices(&smb_pos_max[0],SurfaceforcingsSmbPosMaxEnum); + GetInputListOnVertices(&smb_pos_min[0],SurfaceforcingsSmbPosMinEnum); + GetInputListOnVertices(&a_pos[0],SurfaceforcingsAPosEnum); +@@ -2682,17 +2686,18 @@ + rho_water=matpar->GetRhoFreshwater(); + + // loop over all vertices +- for(i=0;iHc[i]){ +- smb[i]=a_pos[i]+b_pos[i]*s[i]; +- if(smb[i]>smb_pos_max[i]){smb[i]=smb_pos_max[i];} +- if(smb[i]Hc[i]){smb[i]=Smbref[i]+b_pos[i]*(s[i]-Href[i]);} ++ if(Href[i]<=Hc[i]){smb[i]=a_pos[i]+b_pos[i]*s[i];} ++ if(smb[i]>smb_pos_max[i]){smb[i]=smb_pos_max[i];} ++ if(smb[i]Hc[i]){smb[i]=a_neg[i]+b_neg[i]*s[i];} ++ if(Href[i]<=Hc[i]){smb[i]=Smbref[i]+b_neg[i]*(s[i]-Href[i]);} + } + smb[i]=smb[i]/rho_ice; // SMB in m/y ice +- + } //end of the loop over the vertices + /*Update inputs*/ + this->inputs->AddInput(new PentaP1Input(SurfaceforcingsMassBalanceEnum,&smb[0])); +@@ -3653,11 +3658,11 @@ + GetElementSizes(&hx,&hy,&hz); + vel=sqrt(pow(vx,2.)+pow(vy,2.)+pow(vz,2.))+1.e-14; + h=sqrt( pow(hx*vx/vel,2.) + pow(hy*vy/vel,2.) + pow(hz*vz/vel,2.)); ++ vz=0; ++ K[0][0]=h/(2*vel)*(vx*vx); K[0][1]=h/(2*vel)*(vx*vy); K[0][2]=h/(2*vel)*(vx*vz); ++ K[1][0]=h/(2*vel)*(vy*vx); K[1][1]=h/(2*vel)*(vy*vy); K[1][2]=h/(2*vel)*(vy*vz); ++ K[2][0]=h/(2*vel)*(vz*vx); K[2][1]=h/(2*vel)*(vz*vy); K[2][2]=h/(2*vel)*(vz*vz); + +- K[0][0]=h/(2*vel)*fabs(vx*vx); K[0][1]=h/(2*vel)*fabs(vx*vy); K[0][2]=h/(2*vel)*fabs(vx*vz); +- K[1][0]=h/(2*vel)*fabs(vy*vx); K[1][1]=h/(2*vel)*fabs(vy*vy); K[1][2]=h/(2*vel)*fabs(vy*vz); +- K[2][0]=h/(2*vel)*fabs(vz*vx); K[2][1]=h/(2*vel)*fabs(vz*vy); K[2][2]=h/(2*vel)*fabs(vz*vz); +- + D_scalar_stab=gauss->weight*Jdet; + if(reCast(dt)) D_scalar_stab=D_scalar_stab*dt; + for(i=0;i<3;i++) for(j=0;j<3;j++) K[i][j] = D_scalar_stab*K[i][j]; +@@ -4313,7 +4318,7 @@ + IssmDouble B[numdof]; + IssmDouble B_average,s_average; + int* doflist=NULL; +- //IssmDouble pressure[numdof]; ++ IssmDouble pressure[numdof]; + + /*Get dof list: */ + GetDofList(&doflist,NoneApproximationEnum,GsetEnum); +@@ -4321,9 +4326,9 @@ + /*Use the dof list to index into the solution vector: */ + for(i=0;imatpar->TMeltingPoint(pressure[i])) values[i]=matpar->TMeltingPoint(pressure[i]); +- //if(values[i]TMeltingPoint(pressure[i])-50) values[i]=matpar->TMeltingPoint(pressure[i])-50; ++ GetInputListOnVertices(&pressure[0],PressureEnum); ++ if(values[i]>matpar->TMeltingPoint(pressure[i])) values[i]=matpar->TMeltingPoint(pressure[i]); ++ if(values[i]TMeltingPoint(pressure[i])-50) values[i]=matpar->TMeltingPoint(pressure[i])-50; + + /*Check solution*/ + if(xIsNan(values[i])) _error_("NaN found in solution vector"); +Index: ../trunk-jpl/src/m/classes/surfaceforcings.m +=================================================================== +--- ../trunk-jpl/src/m/classes/surfaceforcings.m (revision 13520) ++++ ../trunk-jpl/src/m/classes/surfaceforcings.m (revision 13521) +@@ -11,6 +11,8 @@ + issmbgradients = 0; + isdelta18o = 0; + hc = NaN; ++ href = NaN; ++ smbref = NaN; + smb_pos_max = NaN; + smb_pos_min = NaN; + a_pos = NaN; +@@ -59,6 +61,8 @@ + end + elseif(obj.issmbgradients) + md = checkfield(md,'surfaceforcings.hc','forcing',1,'NaN',1); ++ md = checkfield(md,'surfaceforcings.href','forcing',1,'NaN',1); ++ md = checkfield(md,'surfaceforcings.smbref','forcing',1,'NaN',1); + md = checkfield(md,'surfaceforcings.smb_pos_max','forcing',1,'NaN',1); + md = checkfield(md,'surfaceforcings.smb_pos_min','forcing',1,'NaN',1); + md = checkfield(md,'surfaceforcings.a_pos','forcing',1,'NaN',1); +@@ -88,6 +92,8 @@ + fielddisplay(obj,'delta18o_surface','surface elevation of the delta18o site, required if pdd is activated and delta18o activated'); + fielddisplay(obj,'issmbgradients','is smb gradients method activated (0 or 1, default is 0)'); + fielddisplay(obj,'hc',' elevation of intersection between accumulation and ablation regime required if smb gradients is activated'); ++ fielddisplay(obj,'href',' reference elevation from which deviation is used to calculate SMB adjustment in smb gradients method'); ++ fielddisplay(obj,'smbref',' reference smb from which deviation is calculated in smb gradients method'); + fielddisplay(obj,'smb_pos_max',' maximum value of positive smb required if smb gradients is activated'); + fielddisplay(obj,'smb_pos_min',' minimum value of positive smb required if smb gradients is activated'); + fielddisplay(obj,'a_pos',' intercept of hs - smb regression line for accumulation regime required if smb gradients is activated'); +@@ -116,6 +122,8 @@ + WriteData(fid,'object',obj,'fieldname','issmbgradients','format','Boolean'); + if obj.issmbgradients, + WriteData(fid,'object',obj,'fieldname','hc','format','DoubleMat','mattype',1); ++ WriteData(fid,'object',obj,'fieldname','href','format','DoubleMat','mattype',1); ++ WriteData(fid,'object',obj,'fieldname','smbref','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','smb_pos_max','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','smb_pos_min','format','DoubleMat','mattype',1); + WriteData(fid,'object',obj,'fieldname','a_pos','format','DoubleMat','mattype',1); Index: /issm/oecreview/Archive/13393-13976/ISSM-13522-13523.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13522-13523.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13522-13523.diff (revision 13980) @@ -0,0 +1,48 @@ +Index: ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13522) ++++ ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13523) +@@ -8,4 +8,4 @@ + % Usage: + % macro=MaximumNumberOfEnums() + +-macro=493; ++macro=495; +Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py +=================================================================== +--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13522) ++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13523) +@@ -1858,6 +1858,26 @@ + + return StringToEnum('SurfaceforcingsHc')[0] + ++def SurfaceforcingsHrefEnum(): ++ """ ++ SURFACEFORCINGSHREFENUM - Enum of SurfaceforcingsHref ++ ++ Usage: ++ macro=SurfaceforcingsHrefEnum() ++ """ ++ ++ return StringToEnum('SurfaceforcingsHref')[0] ++ ++def SurfaceforcingsSmbrefEnum(): ++ """ ++ SURFACEFORCINGSSMBREFENUM - Enum of SurfaceforcingsSmbref ++ ++ Usage: ++ macro=SurfaceforcingsSmbrefEnum() ++ """ ++ ++ return StringToEnum('SurfaceforcingsSmbref')[0] ++ + def SurfaceforcingsSmbPosMaxEnum(): + """ + SURFACEFORCINGSSMBPOSMAXENUM - Enum of SurfaceforcingsSmbPosMax +@@ -4946,5 +4966,5 @@ + macro=MaximumNumberOfEnums() + """ + +- return 493 ++ return 495 + Index: /issm/oecreview/Archive/13393-13976/ISSM-13523-13524.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13523-13524.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13523-13524.diff (revision 13980) @@ -0,0 +1,267 @@ +Index: ../trunk-jpl/src/m/mesh/ElementsFromEdge.m +=================================================================== +--- ../trunk-jpl/src/m/mesh/ElementsFromEdge.m (revision 13523) ++++ ../trunk-jpl/src/m/mesh/ElementsFromEdge.m (revision 13524) +@@ -1,15 +1,15 @@ +-function edgeelements=ElementsFromEdge(elements,A,B) ++function edgeelements=ElementsFromEdge(elements,A,B) + %ELEMENTSFROMEDGE: find elements connected to one edge defined by nodes A and B + % +-% Usage: edgeelements=ElementsFromEdge(elements,A,B) ++% Usage: edgeelements=ElementsFromEdge(elements,A,B) + % +-% Eg: edgeelements=ElementsFromEdge(md.mesh.elements,tip1,tip2) ++% Eg: edgeelements=ElementsFromEdge(md.mesh.elements,tip1,tip2) + % + % + edgeelements=find(... +-(elements(:,1)==A & elements(:,2)==B )| ... +-(elements(:,1)==A & elements(:,3)==B )| ... +-(elements(:,2)==A & elements(:,3)==B )| ... +-(elements(:,2)==A & elements(:,1)==B )| ... +-(elements(:,3)==A & elements(:,1)==B )| ... +-(elements(:,3)==A & elements(:,2)==B )); ++ (elements(:,1)==A & elements(:,2)==B )| ... ++ (elements(:,1)==A & elements(:,3)==B )| ... ++ (elements(:,2)==A & elements(:,3)==B )| ... ++ (elements(:,2)==A & elements(:,1)==B )| ... ++ (elements(:,3)==A & elements(:,1)==B )| ... ++ (elements(:,3)==A & elements(:,2)==B )); +Index: ../trunk-jpl/src/m/mesh/rifts/meshprocessoutsiderifts.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/rifts/meshprocessoutsiderifts.py (revision 0) ++++ ../trunk-jpl/src/m/mesh/rifts/meshprocessoutsiderifts.py (revision 13524) +@@ -0,0 +1,110 @@ ++import numpy ++from ElementsFromEdge import * ++from MatlabFuncs import * ++ ++def meshprocessoutsiderifts(md,domainoutline): ++ """ ++ MESHPROCESSOUTSIDERIFTS - process rifts when they touch the domain outline ++ ++ Usage: ++ md=meshprocessoutsiderifts(md,domain) ++ ++ """ ++ ++ #go through rifts, and figure out which ones touch the domain outline ++ for rift in md.rifts.riftstruct: ++ ++ #first, flag nodes that belong to the domain outline ++ flags=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),domainoutline,'node',0) ++ ++ tips=rift.tips ++ outsidetips=tips[numpy.nonzero(flags[rift.tips-1])[0]] ++ ++ #we have found outsidetips, tips that touch the domain outline. go through them ++ for tip in outsidetips: ++ ++ #find tip in the segments, take first segment (there should be 2) that holds tip, ++ #and node_connected_to_tip is the other node on this segment: ++ tipindex=numpy.nonzero(rift.segments[:,0]==tip)[0] ++ if tipindex: ++ tipindex=tipindex[0] ++ node_connected_to_tip=rift.segments[tipindex,1] ++ else: ++ tipindex=numpy.nonzero(rift.segments[:,1]==tip)[0] ++ tipindex=tipindex[0] ++ node_connected_to_tip=rift.segments[tipindex,1] ++ ++ #ok, we have the tip node, and the first node connected to it, on the rift. Now, ++ #identify all the elements that are connected to the tip, and that are on the same ++ #side of the rift. ++ A=tip ++ B=node_connected_to_tip ++ ++ elements=numpy.empty(0) ++ ++ while flags(B): #as long as B does not belong to the domain outline, keep looking. ++ #detect elements on edge A,B: ++ edgeelements=ElementsFromEdge(md.mesh.elements,A,B) ++ #rule out those we already detected ++ already_detected=ismember(edgeelements,elements) ++ nextelement=edgeelements(numpy.nonzero(numpy.logical_not(already_detected))[0]) ++ #add new detected element to the list of elements we are looking for. ++ elements=numpy.concatenate((elements,nextelement)) ++ #new B: ++ B=md.mesh.elements[nextelement-1,numpy.nonzero(numpy.logical_not(ismember(md.mesh.elements[nextelement-1,:],numpy.array([A,B]))))] ++ ++ #take the list of elements on one side of the rift that connect to the tip, ++ #and duplicate the tip on them, so as to open the rift to the outside. ++ num=numpy.size(md.mesh.x)+1 ++ md.mesh.x=numpy.concatenate((md.mesh.x,md.mesh.x[tip])) ++ md.mesh.y=numpy.concatenate((md.mesh.y,md.mesh.y[tip])) ++ md.mesh.numberofvertices=num ++ ++ #replace tip in elements ++ newelements=md.mesh.elements[elements.astype(int)-1,:] ++ pos=numpy.nonzero(newelements==tip) ++ newelements[pos]=num ++ md.mesh.elements[elements.astype(int)-1,:]=newelements ++ rift.tips=numpy.concatenate((rift.tips,num)) ++ ++ #deal with segments ++ tipsegments=numpy.nonzero(numpy.logical_or(md.mesh.segments[:,0]==tip,md.mesh.segments[:,1]==tip))[0] ++ for segment_index in tipsegments: ++ pos=numpy.nonzero(md.mesh.segments[segment_index,0:2]!=tip)[0] ++ other_node=md.mesh.segments[segment_index,pos] ++ if not isconnected(md.mesh.elements,other_node,tip): ++ pos=numpy.nonzero(md.mesh.segments[segment_index,0:2]==tip)[0] ++ md.mesh.segments[segment_index,pos]=num ++ ++ #Fill in rest of fields: ++ md.mesh.numberofelements=numpy.size(md.mesh.elements,axis=0) ++ md.mesh.numberofvertices=numpy.size(md.mesh.x) ++ md.mesh.z=numpy.zeros(md.mesh.numberofvertices) ++ md.mesh.vertexonboundary=numpy.zeros(numpy.size(md.mesh.x)) ++ md.mesh.vertexonboundary[md.mesh.segments[:,0:2].astype(int)-1]=1 ++ md.rifts.numrifts=length(md.rifts.riftstruct) ++ md.flowequation.element_equation=3.*numpy.ones(md.mesh.numberofelements) ++ md.mesh.vertexonbed=numpy.ones(md.mesh.numberofvertices) ++ md.mesh.vertexonsurface=numpy.ones(md.mesh.numberofvertices) ++ md.mesh.elementonbed=numpy.ones(md.mesh.numberofelements) ++ md.mesh.elementonsurface=numpy.ones(md.mesh.numberofelements) ++ ++ return md ++ ++def isconnected(elements,A,B): # {{{ ++ """ ++ ISCONNECTED: are two nodes connected by a triangulation? ++ ++ Usage: flag=isconnected(elements,A,B) ++ ++ """ ++ ++ elements=ElementsFromEdge(elements,A,B) ++ if not elements: ++ flag=0 ++ else: ++ flag=1 ++ ++ return flag ++ # }}} ++ +Index: ../trunk-jpl/src/m/mesh/rifts/meshprocessrifts.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/rifts/meshprocessrifts.py (revision 0) ++++ ../trunk-jpl/src/m/mesh/rifts/meshprocessrifts.py (revision 13524) +@@ -0,0 +1,64 @@ ++import numpy ++#from TriMeshProcessRifts import * ++from ContourToMesh import * ++from meshprocessoutsiderifts import * ++from GetAreas import * ++ ++def meshprocessrifts(md,domainoutline): ++ """ ++ MESHPROCESSRIFTS - process mesh when rifts are present ++ ++ split rifts inside mesh (rifts are defined by presence of ++ segments inside the domain outline) ++ if domain outline is provided, check for rifts that could touch it, and open them up. ++ ++ Usage: ++ md=meshprocessrifts(md,domainoutline) ++ ++ Ex: ++ md=meshprocessrifts(md,'DomainOutline.exp'); ++ ++ """ ++ ++ #Call MEX file ++ [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers,md.rifts.riftstruct]=TriMeshProcessRifts(md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers) ++ if not isinstance(md.rifts.riftstruct,'list') or not md.rifts.riftstruct: ++ raise RuntimeError("TriMeshProcessRifts did not find any rift") ++ ++ #Fill in rest of fields: ++ numrifts=len(md.rifts.riftstruct) ++ md.mesh.numberofelements=numpy.size(md.mesh.elements,axis=0) ++ md.mesh.numberofvertices=numpy.size(md.mesh.x) ++ md.mesh.z=numpy.zeros(md.mesh.numberofvertices) ++ md.mesh.vertexonboundary=numpy.zeros(numpy.size(md.mesh.x)) ++ md.mesh.vertexonboundary[md.mesh.segments[:,0:2].astype(int)-1]=1 ++ md.mesh.vertexonbed=numpy.ones(md.mesh.numberofvertices) ++ md.mesh.vertexonsurface=numpy.ones(md.mesh.numberofvertices) ++ md.mesh.elementonbed=numpy.ones(md.mesh.numberofelements) ++ md.mesh.elementonsurface=numpy.ones(md.mesh.numberofelements) ++ ++ #get coordinates of rift tips ++ for rift in md.rifts.riftstruct: ++ rift.tip1coordinates=numpy.hstack((md.mesh.x[rift.tips[0].astype(int)-1].reshape(-1,1),md.mesh.y[rift.tips[0].astype(int)-1].reshape(-1,1))) ++ rift.tip2coordinates=numpy.hstack((md.mesh.x[rift.tips[1].astype(int)-1].reshape(-1,1),md.mesh.y[rift.tips[1].astype(int)-1].reshape(-1,1))) ++ ++ #In case we have rifts that open up the domain outline, we need to open them: ++ flags=ContourToMesh(md.mesh.elements,md.mesh.x.reshape(-1,1),md.mesh.y.reshape(-1,1),domainoutline,'node',0) ++ found=0 ++ for rift in md.rifts.riftstruct: ++ if flags[rift.tips[0].astype(int)-1]==0: ++ found=1 ++ break ++ if flags[rift.tips[1].astype(int)-1]==0: ++ found=1 ++ break ++ if found: ++ md=meshprocessoutsiderifts(md,domainoutline) ++ ++ #get elements that are not correctly oriented in the correct direction: ++ aires=GetAreas(md.mesh.elements,md.mesh.x,md.mesh.y) ++ pos=numpy.nonzero(aires<0)[0] ++ md.mesh.elements[pos,:]=numpy.array([[md.mesh.elements[pos,1],md.mesh.elements[pos,0],md.mesh.elements[pos,2]]]) ++ ++ return md ++ +Index: ../trunk-jpl/src/m/mesh/rifts/meshprocessoutsiderifts.m +=================================================================== +--- ../trunk-jpl/src/m/mesh/rifts/meshprocessoutsiderifts.m (revision 13523) ++++ ../trunk-jpl/src/m/mesh/rifts/meshprocessoutsiderifts.m (revision 13524) +@@ -40,7 +40,7 @@ + + elements=[]; + +- while flags(B), %as long as B does not belong to the domain outline, keep looking. ++ while flags(B), %as long as B does not belong to the domain outline, keep looking. + %detect elements on edge A,B: + edgeelements=ElementsFromEdge(md.mesh.elements,A,B); + %rule out those we already detected +@@ -68,7 +68,7 @@ + + %deal with segments + tipsegments=find((md.mesh.segments(:,1)==tip) | (md.mesh.segments(:,2)==tip)); +- for k=1:length(tipsegments), ++ for k=1:length(tipsegments), + segment_index=tipsegments(k); + pos=find(md.mesh.segments(segment_index,1:2)~=tip); + other_node=md.mesh.segments(segment_index,pos); +Index: ../trunk-jpl/src/m/mesh/ElementsFromEdge.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/ElementsFromEdge.py (revision 0) ++++ ../trunk-jpl/src/m/mesh/ElementsFromEdge.py (revision 13524) +@@ -0,0 +1,27 @@ ++import numpy ++ ++def ElementsFromEdge(elements,A,B): ++ """ ++ ELEMENTSFROMEDGE: find elements connected to one edge defined by nodes A and B ++ ++ Usage: edgeelements=ElementsFromEdge(elements,A,B) ++ ++ Eg: edgeelements=ElementsFromEdge(md.mesh.elements,tip1,tip2) ++ ++ """ ++ ++ edgeelements=numpy.nonzero(\ ++ numpy.logical_or( \ ++ numpy.logical_or( \ ++ numpy.logical_or(numpy.logical_and(elements[:,0]==A,elements[:,1]==B), \ ++ numpy.logical_and(elements[:,0]==A,elements[:,2]==B)) \ ++ , \ ++ numpy.logical_or(numpy.logical_and(elements[:,1]==A,elements[:,2]==B), \ ++ numpy.logical_and(elements[:,1]==A,elements[:,0]==B)) \ ++ ), \ ++ numpy.logical_or(numpy.logical_and(elements[:,2]==A,elements[:,0]==B), \ ++ numpy.logical_and(elements[:,2]==A,elements[:,1]==B)) \ ++ ))[0]+1 ++ ++ return edgeelements ++ Index: /issm/oecreview/Archive/13393-13976/ISSM-13524-13525.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13524-13525.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13524-13525.diff (revision 13980) @@ -0,0 +1,225 @@ +Index: ../trunk-jpl/test/NightlyRun/test217.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test217.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test217.py (revision 13525) +@@ -0,0 +1,94 @@ ++""" ++== == == == == == == == == == == == == == == == == == == ++Auto generated python script for ISSM: test217.m ++Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep ++== == == == == == == == == == == == == == == == == == == ++ ++Matlab script conversion into python ++translateToPy.py Author: Michael Pellegrin ++translateToPy.py Date: 09/24/12 ++== == == == == == == == == == == == == == == == == == == ++""" ++ ++from MatlabFuncs import * ++from model import * ++from EnumDefinitions import * ++from numpy import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from paterson import * ++from solve import * ++ ++md=triangle(model(),'../Exp/Square.exp',150000) ++md=setmask(md,'all','') ++md=parameterize(md,'../Par/SquareShelf.py') ++md=setflowequation(md,'macayeal','all') ++md.cluster=generic('name',oshostname(),'np',3) ++ ++# redo the parameter file for this special shelf. ++# constant thickness, constrained (vy=0) flow into an icefront, ++# from 0 m/yr at the grounding line. ++ ++# tighten ++md.diagnostic.restol=10**-4 ++ ++# needed later ++ymin=min(md.mesh.y) ++ymax=max(md.mesh.y) ++xmin=min(md.mesh.x) ++xmax=max(md.mesh.x) ++ ++di=md.materials.rho_ice/md.materials.rho_water ++ ++h=1000. ++md.geometry.thickness=h*ones((md.mesh.numberofvertices,1)) ++md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness ++md.geometry.surface=md.geometry.bed+md.geometry.thickness ++ ++# Initial velocity and pressure ++md.initialization.vx=zeros((md.mesh.numberofvertices,1)) ++md.initialization.vy=zeros((md.mesh.numberofvertices,1)) ++md.initialization.vz=zeros((md.mesh.numberofvertices,1)) ++md.initialization.pressure=zeros((md.mesh.numberofvertices,1)) ++ ++# Materials ++md.initialization.temperature=(273.-20.)*ones((md.mesh.numberofvertices,1)) ++md.materials.rheology_B=paterson(md.initialization.temperature) ++md.materials.rheology_n=3*ones((md.mesh.numberofelements,1)) ++ ++# Boundary conditions: ++md.diagnostic.spcvx=float(nan)*ones((md.mesh.numberofvertices,1)) ++md.diagnostic.spcvy=float(nan)*ones((md.mesh.numberofvertices,1)) ++md.diagnostic.spcvz=float(nan)*ones((md.mesh.numberofvertices,1)) ++ ++# constrain flanks to 0 normal velocity ++pos=numpy.nonzero(numpy.logical_or(md.mesh.x==xmin,md.mesh.x==xmax)) ++md.diagnostic.spcvx[pos]=0 ++md.diagnostic.spcvz[pos]=float(nan) ++ ++# constrain grounding line to 0 velocity ++pos=numpy.nonzero(md.mesh.y==ymin) ++md.diagnostic.spcvx[pos]=0 ++md.diagnostic.spcvy[pos]=0 ++ ++# icefront ++nodeonicefront=zeros(md.mesh.numberofvertices) ++pos=numpy.nonzero(md.mesh.y==ymax) ++nodeonicefront[pos]=1 ++pos=numpy.nonzero(numpy.logical_or(nodeonicefront[md.mesh.segments[:,0].astype(int)-1],nodeonicefront[md.mesh.segments[:,1].astype(int)-1]))[0] ++diagnostic.icefront=md.mesh.segments[pos,:] ++diagnostic.icefront=numpy.hstack((diagnostic.icefront,1.*md.mask.elementonfloatingice[diagnostic.icefront[:,-1].astype(int)-1].reshape(-1,1))) ++md.diagnostic.icefront=diagnostic.icefront ++ ++md=solve(md,DiagnosticSolutionEnum()) ++ ++# create analytical solution: strain rate is constant = ((rho_ice*g*h)/4B)^3 (Paterson, 4th Edition, page 292. ++# ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3; ++# vy_c=ey_c.*md.mesh.y*md.constants.yts; ++ ++# Fields and tolerances to track changes ++field_names =['Vy'] ++field_tolerances=[1e-13] ++field_values=[md.results['DiagnosticSolution'][1]['Vy']] +Index: ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test217.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test217.py (revision 13524) ++++ ../trunk-jpl/test/NightlyRun/InNeedOfDebugging/test217.py (revision 13525) +@@ -1,121 +0,0 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test217.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- +-from MatlabFuncs import * +-from model import * +-from EnumDefinitions import * +-from numpy import * +-from triangle import * +-from setmask import * +-from parameterize import * +-from setflowequation import * +-from solve import * +- +-md=triangle(model(),'../Exp/Square.exp',150000) +-md=setmask(md,'all','') +-md=parameterize(md,'../Par/SquareShelf.py') +-md=setflowequation(md,'macayeal','all') +-md.cluster=generic('name',oshostname(),'np',3) +- +- +-# redo the parameter file for this special shelf. +- +-# constant thickness, constrained (vy=0) flow into an icefront, +- +-# from 0 m/yr at the grounding line. +- +- +- +-# tighten +- +-md.diagnostic.restol=10^-4 +- +- +-# needed later +- +-ymin=min(md.mesh.y) +-ymax=max(md.mesh.y) +-xmin=min(md.mesh.x) +-xmax=max(md.mesh.x) +- +- +-di=md.materials.rho_ice/md.materials.rho_water +- +- +-h=1000 +-md.geometry.thickness=h*ones(md.mesh.numberofvertices,1) +-md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness +-md.geometry.surface=md.geometry.bed+md.geometry.thickness +- +- +-# Initial velocity and pressure +- +-md.initialization.vx=zeros(md.mesh.numberofvertices,1) +-md.initialization.vy=zeros(md.mesh.numberofvertices,1) +-md.initialization.vz=zeros(md.mesh.numberofvertices,1) +-md.initialization.pressure=zeros(md.mesh.numberofvertices,1) +- +- +-# Materials +- +-md.initialization.temperature=(273-20)*ones(md.mesh.numberofvertices,1) +-md.materials.rheology_B=paterson(md.initialization.temperature) +-md.materials.rheology_n=3*ones(md.mesh.numberofelements,1) +- +- +-# Boundary conditions: +- +-md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1) +-md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1) +-md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1) +- +- +-# constrain flanks to 0 normal velocity +- +-pos=numpy.nonzero(md.mesh.x==xmin | md.mesh.x==xmax) +-md.diagnostic.spcvx(pos)=0 +-md.diagnostic.spcvz(pos)=NaN +- +- +-# constrain grounding line to 0 velocity +- +-pos=numpy.nonzero(md.mesh.y==ymin) +-md.diagnostic.spcvx(pos)=0 +-md.diagnostic.spcvy(pos)=0 +- +- +-# icefront +- +-nodeonicefront=zeros(md.mesh.numberofvertices,1) +-pos=numpy.nonzero(md.mesh.y==ymax) +-nodeonicefront(pos)=1 +-pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))) diagnostic.icefront=md.mesh.segments(pos,:) +-diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))] +-md.diagnostic.icefront=diagnostic.icefront +- +- +-md=solve(md,DiagnosticSolutionEnum()) +- +- +-# create analytical solution: strain rate is constant = ((rho_ice*g*h)/4B)^3 (Paterson, 4th Edition, page 292. +- +-# ey_c=(md.materials.rho_ice*md.constants.g*(1-di)*md.geometry.thickness./(4*md.materials.rheology_B)).^3; +- +-# vy_c=ey_c.*md.mesh.y*md.constants.yts; +- +- +- +-# Fields and tolerances to track changes +- +-field_names =['Vy'] +-field_tolerances=[1e-13] +-field_values=[md.results['DiagnosticSolution'][1]['Vy']] Index: /issm/oecreview/Archive/13393-13976/ISSM-13525-13526.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13525-13526.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13525-13526.diff (revision 13980) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/android/helloworld/Google Play Store App Release Tutorial.rtf +=================================================================== +--- ../trunk-jpl/src/android/helloworld/Google Play Store App Release Tutorial.rtf (revision 0) ++++ ../trunk-jpl/src/android/helloworld/Google Play Store App Release Tutorial.rtf (revision 13526) +@@ -0,0 +1,16 @@ ++{\rtf1\ansi\ansicpg1252\cocoartf1138\cocoasubrtf470 ++{\fonttbl\f0\fswiss\fcharset0 Helvetica;} ++{\colortbl;\red255\green255\blue255;} ++\margl1440\margr1440\vieww10800\viewh8400\viewkind0 ++\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural ++ ++\f0\fs24 \cf0 This is a 16-step-by-step guidelines to get an android app on the Google Play Store.\ ++\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural ++\cf0 http://developer.android.com/distribute/googleplay/publish/preparing.html\ ++\ ++\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural ++\cf0 We need to make a developer account first and start from there.\ ++\ ++We don't have to worry about the public accessing our "beta" apps since it's not released/published to the public yet. Once everything is done, we can publish it and it's ready for public use.\ ++\ ++} +\ No newline at end of file Index: /issm/oecreview/Archive/13393-13976/ISSM-13526-13527.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13526-13527.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13526-13527.diff (revision 13980) @@ -0,0 +1,168 @@ +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/CLibHelloWorld.dll +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/CLibHelloWorld.dll +=================================================================== +--- ../trunk-jpl/src/android/helloworld/HelloWorldJNI/CLibHelloWorld.dll (revision 13526) ++++ ../trunk-jpl/src/android/helloworld/HelloWorldJNI/CLibHelloWorld.dll (revision 13527) + +Property changes on: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/CLibHelloWorld.dll +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.class (revision 13526) ++++ ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.class (revision 13527) + +Property changes on: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Results.jpg +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Results.jpg +=================================================================== +--- ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Results.jpg (revision 13526) ++++ ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Results.jpg (revision 13527) + +Property changes on: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Results.jpg +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.h +=================================================================== +--- ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.h (revision 0) ++++ ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.h (revision 13527) +@@ -0,0 +1,21 @@ ++/* DO NOT EDIT THIS FILE - it is machine generated */ ++#include ++/* Header for class HelloWorld */ ++ ++#ifndef _Included_HelloWorld ++#define _Included_HelloWorld ++#ifdef __cplusplus ++extern "C" { ++#endif ++/* ++ * Class: HelloWorld ++ * Method: print ++ * Signature: ()V ++ */ ++JNIEXPORT void JNICALL Java_HelloWorld_print ++ (JNIEnv *, jobject); ++ ++#ifdef __cplusplus ++} ++#endif ++#endif + +Property changes on: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.h +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Main.java +=================================================================== +--- ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Main.java (revision 0) ++++ ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Main.java (revision 13527) +@@ -0,0 +1,8 @@ ++class Main ++{ ++ public static void main (String[] args) ++ { ++ HelloWorld hw = new HelloWorld(); ++ hw.print(); ++ } ++} +\ No newline at end of file + +Property changes on: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Main.java +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Main.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Main.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Main.class (revision 13526) ++++ ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Main.class (revision 13527) + +Property changes on: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/Main.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.java +=================================================================== +--- ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.java (revision 0) ++++ ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.java (revision 13527) +@@ -0,0 +1,16 @@ ++class HelloWorld ++{ ++ public native void print(); //native method ++ static //static initializer code ++ { ++ System.loadLibrary("CLibHelloWorld"); ++ } ++} ++class Main ++{ ++ public static void main (String[] args) ++ { ++ HelloWorld hw = new HelloWorld(); ++ hw.print(); ++ } ++} +\ No newline at end of file + +Property changes on: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.java +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.cpp +=================================================================== +--- ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.cpp (revision 0) ++++ ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.cpp (revision 13527) +@@ -0,0 +1,8 @@ ++#include ++#include ++#include "HelloWorld.h" ++JNIEXPORT void JNICALL Java_HelloWorld_print(JNIEnv *env, jobject obj) ++{ ++ printf("Hello World!\n"); ++ return; ++} +\ No newline at end of file + +Property changes on: ../trunk-jpl/src/android/helloworld/HelloWorldJNI/HelloWorld.cpp +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* Index: /issm/oecreview/Archive/13393-13976/ISSM-13527-13528.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13527-13528.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13527-13528.diff (revision 13980) @@ -0,0 +1,42 @@ +Index: ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp (revision 13527) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp (revision 13528) +@@ -3658,11 +3658,11 @@ + GetElementSizes(&hx,&hy,&hz); + vel=sqrt(pow(vx,2.)+pow(vy,2.)+pow(vz,2.))+1.e-14; + h=sqrt( pow(hx*vx/vel,2.) + pow(hy*vy/vel,2.) + pow(hz*vz/vel,2.)); +- vz=0; +- K[0][0]=h/(2*vel)*(vx*vx); K[0][1]=h/(2*vel)*(vx*vy); K[0][2]=h/(2*vel)*(vx*vz); +- K[1][0]=h/(2*vel)*(vy*vx); K[1][1]=h/(2*vel)*(vy*vy); K[1][2]=h/(2*vel)*(vy*vz); +- K[2][0]=h/(2*vel)*(vz*vx); K[2][1]=h/(2*vel)*(vz*vy); K[2][2]=h/(2*vel)*(vz*vz); + ++ K[0][0]=h/(2*vel)*fabs(vx*vx); K[0][1]=h/(2*vel)*fabs(vx*vy); K[0][2]=h/(2*vel)*fabs(vx*vz); ++ K[1][0]=h/(2*vel)*fabs(vy*vx); K[1][1]=h/(2*vel)*fabs(vy*vy); K[1][2]=h/(2*vel)*fabs(vy*vz); ++ K[2][0]=h/(2*vel)*fabs(vz*vx); K[2][1]=h/(2*vel)*fabs(vz*vy); K[2][2]=h/(2*vel)*fabs(vz*vz); ++ + D_scalar_stab=gauss->weight*Jdet; + if(reCast(dt)) D_scalar_stab=D_scalar_stab*dt; + for(i=0;i<3;i++) for(j=0;j<3;j++) K[i][j] = D_scalar_stab*K[i][j]; +@@ -4318,7 +4318,7 @@ + IssmDouble B[numdof]; + IssmDouble B_average,s_average; + int* doflist=NULL; +- IssmDouble pressure[numdof]; ++ //IssmDouble pressure[numdof]; + + /*Get dof list: */ + GetDofList(&doflist,NoneApproximationEnum,GsetEnum); +@@ -4326,9 +4326,9 @@ + /*Use the dof list to index into the solution vector: */ + for(i=0;imatpar->TMeltingPoint(pressure[i])) values[i]=matpar->TMeltingPoint(pressure[i]); +- if(values[i]TMeltingPoint(pressure[i])-50) values[i]=matpar->TMeltingPoint(pressure[i])-50; ++ //GetInputListOnVertices(&pressure[0],PressureEnum); ++ //if(values[i]>matpar->TMeltingPoint(pressure[i])) values[i]=matpar->TMeltingPoint(pressure[i]); ++ //if(values[i]TMeltingPoint(pressure[i])-50) values[i]=matpar->TMeltingPoint(pressure[i])-50; + + /*Check solution*/ + if(xIsNan(values[i])) _error_("NaN found in solution vector"); Index: /issm/oecreview/Archive/13393-13976/ISSM-13528-13529.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13528-13529.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13528-13529.diff (revision 13980) @@ -0,0 +1,40 @@ +Index: ../trunk-jpl/test/NightlyRun/test328.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test328.m (revision 13528) ++++ ../trunk-jpl/test/NightlyRun/test328.m (revision 13529) +@@ -11,6 +11,15 @@ + md.surfaceforcings.b_neg=250. + 0.000051*md.mesh.x - 0.00011*md.mesh.y; + md.surfaceforcings.hc=(md.surfaceforcings.a_pos-md.surfaceforcings.a_neg)./(md.surfaceforcings.b_neg-md.surfaceforcings.b_pos); + md.transient.requested_outputs=TotalSmbEnum(); ++md.surfaceforcings.href=md.geometry.surface; ++for i=1:size(md.surfaceforcings.hc), ++ if md.geometry.surface(i) *theAdolcEDF_p=new GenericParam(AdolcParamEnum); + theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p=reg_ext_fct(EDF_for_solverx); +@@ -248,9 +233,8 @@ + #endif + #endif + +- + /*end module: */ +- ISSMEND(); ++ IssmEnd(); + + return 0; //unix success return; + } +Index: ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp (revision 0) ++++ ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp (revision 13530) +@@ -0,0 +1,22 @@ ++/*!\file: EnvironmentInit.cpp ++ * \brief: initialize Petsc, MPI, you name it ++ */ ++ ++void EnvironmentInit(int argc,char** argv){ ++ ++ /*Initialize environments: Petsc, MPI, etc...: */ ++ #ifdef _HAVE_PETSC_ ++ ierr=PetscInitialize(&argc,&argv,(char*)0,""); ++ if(ierr) _error_("Could not initialize Petsc"); ++ #else ++ #ifdef _HAVE_MPI_ ++ MPI_Init(&argc,&argv); ++ #endif ++ #endif ++ ++ /*Size and rank: */ ++ #ifdef _HAVE_MPI_ ++ MPI_Comm_rank(MPI_COMM_WORLD,&my_rank); ++ MPI_Comm_size(MPI_COMM_WORLD,&num_procs); ++ #endif ++} +Index: ../trunk-jpl/src/c/solutions/kriging.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/kriging.cpp (revision 13529) ++++ ../trunk-jpl/src/c/solutions/kriging.cpp (revision 13530) +@@ -35,24 +35,10 @@ + IssmDouble *predictions = NULL; + IssmDouble *error = NULL; + +- ISSMBOOT(); ++ IssmBoot(); + +- /*Initialize environments: Petsc, MPI, etc...: */ +-#ifdef _HAVE_PETSC_ +- int ierr=PetscInitialize(&argc,&argv,(char*)0,""); +- if(ierr) _error_("Could not initialize Petsc"); +-#else +-#ifdef _HAVE_MPI_ +- MPI_Init(&argc,&argv); +-#endif +-#endif ++ EnvironmentInit(argc,argv); + +- /*Size and rank: */ +-#ifdef _HAVE_MPI_ +- MPI_Comm_rank(MPI_COMM_WORLD,&my_rank); +- MPI_Comm_size(MPI_COMM_WORLD,&num_procs); +-#endif +- + /*First process inputs*/ + _pprintLine_(""); + _pprintLine_("Ice Sheet System Model (" << PACKAGE_NAME << ") version " << PACKAGE_VERSION); +@@ -111,7 +97,7 @@ + #endif + + /*end module: */ +- ISSMEND(); ++ IssmEnd(); + + return 0; //unix success return; + } +Index: ../trunk-jpl/src/c/include/macros.h +=================================================================== +--- ../trunk-jpl/src/c/include/macros.h (revision 13529) ++++ ../trunk-jpl/src/c/include/macros.h (revision 13530) +@@ -70,16 +70,16 @@ + ((void) 0) + #endif + /*}}}*/ +-/* ISSMBOOT/ISSMEND {{{*/ ++/* IssmBoot/IssmEnd {{{*/ + + /*The following macros hide the error exception handling in a matlab module. Just put +- * ISSMBOOT(); and ISSMEND(); at the beginning and end of a module, and c++ exceptions ++ * IssmBoot(); and IssmEnd(); at the beginning and end of a module, and c++ exceptions + * will be trapped. Really nifty!*/ + +-#define ISSMBOOT(); \ ++#define IssmBoot(); \ + try{ + +-#define ISSMEND(); }\ ++#define IssmEnd(); }\ + catch(ErrorException &exception){\ + exception.Report(); \ + return 1;\ +Index: ../trunk-jpl/src/c/shared/Numerics/adolc_edf.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Numerics/adolc_edf.h (revision 13529) ++++ ../trunk-jpl/src/c/shared/Numerics/adolc_edf.h (revision 13530) +@@ -1,28 +0,0 @@ +-/* +- * adolc_edf.h +- * +- * Created on: Jun 26, 2012 +- * Author: utke +- */ +- +-#ifndef _ADOLC_EDF_H_ +-#define _ADOLC_EDF_H_ +- +-#include "../../include/include.h" +- +-#ifdef _HAVE_ADOLC_ +- +-struct Adolc_edf { +- ext_diff_fct *myEDF_for_solverx_p; +- Adolc_edf() : myEDF_for_solverx_p(0) {} +- inline friend std::ostream& operator << ( ostream&, const Adolc_edf& ); +-}; +- +-std::ostream& operator << ( std::ostream& out, const Adolc_edf& a) { +- out << a.myEDF_for_solverx_p; +- return out; +-} +- +-#endif +- +-#endif +Index: ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13529) ++++ ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13530) +@@ -7,7 +7,6 @@ + #include "../../include/include.h" + #include "../../toolkits/toolkits.h" + #include "../../EnumDefinitions/EnumDefinitions.h" +-#include "../../shared/Numerics/adolc_edf.h" + + + void AutodiffDriversx(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters,Results* results){ +Index: ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13529) ++++ ../trunk-jpl/src/c/modules/Solverx/SolverxSeq.cpp (revision 13530) +@@ -11,6 +11,7 @@ + + #include "./Solverx.h" + #include "../../shared/shared.h" ++#include "../../classes/classes.h" + #include "../../include/include.h" + #include "../../io/io.h" + +@@ -18,10 +19,6 @@ + #include + #endif + +-#ifdef _HAVE_ADOLC_ +-#include "../../shared/Numerics/adolc_edf.h" +-#endif +- + void SolverxSeq(SeqVec** puf,SeqMat* Kff, SeqVec* pf, Parameters* parameters){/*{{{*/ + + #ifdef _HAVE_GSL_ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13529) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13530) +@@ -66,6 +66,7 @@ + ./classes/objects/Segment.h\ + ./classes/objects/Vertex.h\ + ./classes/objects/Vertex.cpp\ ++ ./classes/objects/AdolcEdf.h\ + ./classes/Hook.h\ + ./classes/Hook.cpp\ + ./classes/Patch.h\ +@@ -187,7 +188,6 @@ + ./shared/MemOps/xMemCpy.h\ + ./shared/Matrix/matrix.h\ + ./shared/Matrix/MatrixUtils.cpp\ +- ./shared/Numerics/adolc_edf.h\ + ./shared/Numerics/numerics.h\ + ./shared/Numerics/Verbosity.h\ + ./shared/Numerics/Verbosity.cpp\ +@@ -349,6 +349,7 @@ + ./solutions/ResetBoundaryConditions.cpp\ + ./solutions/AnalysisConfiguration.cpp\ + ./solutions/CorePointerFromSolutionEnum.cpp\ ++ ./solutions/EnvironmentInit.cpp\ + ./solvers/solver_linear.cpp\ + ./solvers/solver_nonlinear.cpp\ + ./solvers/solver_newton.cpp\ +Index: ../trunk-jpl/src/c/classes/objects.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects.h (revision 13529) ++++ ../trunk-jpl/src/c/classes/objects.h (revision 13530) +@@ -1,68 +0,0 @@ +-/* \file objects.h +- * \brief: prototype header for all objects. +- */ +- +-#ifndef ALL_OBJECTS_H_ +-#define ALL_OBJECTS_H_ +- +-/*Abstract classes: */ +-#include "./objects/objects.h" +- +-/*Objects: */ +-#include "./Hook.h" +-#include "./DofIndexing.h" +-#include "./IoModel.h" +-#include "./Patch.h" +-#include "./Update.h" +- +-/*Gauss*/ +-#include "./gauss/GaussTria.h" +-#include "./gauss/GaussPenta.h" +- +-/*Numerics:*/ +-#include "./matrix/ElementMatrix.h" +-#include "./matrix/ElementVector.h" +-#include "./matrix/Vector.h" +-#include "./matrix/Matrix.h" +- +-/*C objects: */ +-#include "./FemModel.h" +-#include "./OptArgs.h" +-#include "./OptPars.h" +- +-/*Bamg: */ +-#include "./bamg/BamgOpts.h" +-#include "./bamg/BamgGeom.h" +-#include "./bamg/BamgMesh.h" +-#include "./bamg/Metric.h" +-#include "./bamg/DoubleAndInt.h" +-#include "./bamg/Direction.h" +-#include "./bamg/BamgVertex.h" +-#include "./bamg/AdjacentTriangle.h" +-#include "./bamg/Edge.h" +-#include "./bamg/GeomVertex.h" +-#include "./bamg/GeomEdge.h" +-#include "./bamg/Curve.h" +-#include "./bamg/Triangle.h" +-#include "./bamg/ListofIntersectionTriangles.h" +-#include "./bamg/GeomSubDomain.h" +-#include "./bamg/SubDomain.h" +-#include "./bamg/VertexOnGeom.h" +-#include "./bamg/VertexOnVertex.h" +-#include "./bamg/VertexOnEdge.h" +-#include "./bamg/CrackedEdge.h" +-#include "./bamg/Mesh.h" +-#include "./bamg/Geometry.h" +-#include "./bamg/BamgQuadtree.h" +-#include "./bamg/SetOfE4.h" +- +-/*Kriging*/ +-#include "./kriging/Variogram.h" +-#include "./kriging/GaussianVariogram.h" +-#include "./kriging/ExponentialVariogram.h" +-#include "./kriging/SphericalVariogram.h" +-#include "./kriging/PowerVariogram.h" +-#include "./kriging/Quadtree.h" +-#include "./kriging/Observation.h" +- +-#endif +Index: ../trunk-jpl/src/c/classes/classes.h +=================================================================== +--- ../trunk-jpl/src/c/classes/classes.h (revision 13529) ++++ ../trunk-jpl/src/c/classes/classes.h (revision 13530) +@@ -29,5 +29,6 @@ + #include "./FemModel.h" + #include "./OptArgs.h" + #include "./OptPars.h" ++#include "./AdolcEdf.h" + + #endif +Index: ../trunk-jpl/src/c/classes/AdolcEdf.h +=================================================================== +--- ../trunk-jpl/src/c/classes/AdolcEdf.h (revision 0) ++++ ../trunk-jpl/src/c/classes/AdolcEdf.h (revision 13530) +@@ -0,0 +1,26 @@ ++/* ++ * adolc_edf.h ++ * ++ * Created on: Jun 26, 2012 ++ * Author: utke ++ */ ++ ++#ifndef _ADOLC_EDF_H_ ++#define _ADOLC_EDF_H_ ++ ++#ifdef _HAVE_ADOLC_ ++ ++struct Adolc_edf { ++ ext_diff_fct *myEDF_for_solverx_p; ++ Adolc_edf() : myEDF_for_solverx_p(0) {} ++ inline friend std::ostream& operator << ( ostream&, const Adolc_edf& ); ++}; ++ ++std::ostream& operator << ( std::ostream& out, const Adolc_edf& a) { ++ out << a.myEDF_for_solverx_p; ++ return out; ++} ++ ++#endif ++ ++#endif +Index: ../trunk-jpl/src/c/classes/kriging/ExponentialVariogram.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/ExponentialVariogram.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/kriging/ExponentialVariogram.cpp (revision 13530) +@@ -10,7 +10,7 @@ + + #include + #include +-#include "../objects.h" ++#include "../objects/objects.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + #include "../../shared/shared.h" + #include "../../include/include.h" +Index: ../trunk-jpl/src/c/classes/kriging/GaussianVariogram.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/GaussianVariogram.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/kriging/GaussianVariogram.cpp (revision 13530) +@@ -10,7 +10,7 @@ + + #include + #include +-#include "../objects.h" ++#include "../objects/objects.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + #include "../../shared/shared.h" + #include "../../include/include.h" +Index: ../trunk-jpl/src/c/classes/kriging/SphericalVariogram.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/SphericalVariogram.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/kriging/SphericalVariogram.cpp (revision 13530) +@@ -10,7 +10,7 @@ + + #include + #include +-#include "../objects.h" ++#include "../objects/objects.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + #include "../../shared/shared.h" + #include "../../include/include.h" +Index: ../trunk-jpl/src/c/classes/kriging/PowerVariogram.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/PowerVariogram.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/kriging/PowerVariogram.cpp (revision 13530) +@@ -10,7 +10,7 @@ + + #include + #include +-#include "../objects.h" ++#include "../objects/objects.h" + #include "../../EnumDefinitions/EnumDefinitions.h" + #include "../../shared/shared.h" + #include "../../include/include.h" +Index: ../trunk-jpl/src/c/classes/kriging/Quadtree.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/Quadtree.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/kriging/Quadtree.cpp (revision 13530) +@@ -1,4 +1,4 @@ +-#include "../objects.h" ++#include "../objects/objects.h" + + /*DOCUMENTATION What is a Quadtree? {{{ + * A Quadtree is a very simple way to group vertices according +Index: ../trunk-jpl/src/c/classes/kriging/Observation.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/kriging/Observation.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/kriging/Observation.cpp (revision 13530) +@@ -3,7 +3,7 @@ + */ + + #include +-#include "../objects.h" ++#include "../objects/objects.h" + + /*Observation constructors and destructor*/ + /*FUNCTION Observation::Observation(){{{*/ +Index: ../trunk-jpl/src/c/classes/bamg/ListofIntersectionTriangles.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/bamg/ListofIntersectionTriangles.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/bamg/ListofIntersectionTriangles.cpp (revision 13530) +@@ -3,7 +3,7 @@ + #include + #include + +-#include "../objects.h" ++#include "../objects/objects.h" + + namespace bamg { + +Index: ../trunk-jpl/src/c/classes/bamg/Triangle.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/bamg/Triangle.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/bamg/Triangle.cpp (revision 13530) +@@ -3,7 +3,7 @@ + #include + #include + +-#include "../objects.h" ++#include "../objects/objects.h" + + namespace bamg { + +Index: ../trunk-jpl/src/c/classes/bamg/BamgOpts.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/bamg/BamgOpts.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/bamg/BamgOpts.cpp (revision 13530) +@@ -1,7 +1,7 @@ + #include + #include "../../shared/shared.h" + #include "../../include/include.h" +-#include "../objects.h" ++#include "../objects/objects.h" + #include "../../io/io.h" + + /*Constructors/Destructors*/ +Index: ../trunk-jpl/src/c/classes/bamg/BamgGeom.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/bamg/BamgGeom.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/bamg/BamgGeom.cpp (revision 13530) +@@ -1,5 +1,5 @@ + #include +-#include "../objects.h" ++#include "../objects/objects.h" + #include "../../io/io.h" + #include "../../shared/shared.h" + +Index: ../trunk-jpl/src/c/classes/bamg/BamgMesh.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/bamg/BamgMesh.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/bamg/BamgMesh.cpp (revision 13530) +@@ -1,5 +1,5 @@ + #include +-#include "../objects.h" ++#include "../objects/objects.h" + #include "../../io/io.h" + #include "../../shared/shared.h" + +Index: ../trunk-jpl/src/c/classes/bamg/Geometry.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/bamg/Geometry.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/bamg/Geometry.cpp (revision 13530) +@@ -3,7 +3,7 @@ + #include + #include + +-#include "../objects.h" ++#include "../objects/objects.h" + #include "../../include/include.h" + #include "../../shared/Exceptions/exceptions.h" + +Index: ../trunk-jpl/src/c/classes/bamg/BamgQuadtree.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/bamg/BamgQuadtree.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/bamg/BamgQuadtree.cpp (revision 13530) +@@ -2,7 +2,7 @@ + #include + #include + +-#include "../objects.h" ++#include "../objects/objects.h" + + namespace bamg { + +Index: ../trunk-jpl/src/c/classes/bamg/BamgVertex.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/bamg/BamgVertex.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/bamg/BamgVertex.cpp (revision 13530) +@@ -3,7 +3,7 @@ + #include + #include + +-#include "../objects.h" ++#include "../objects/objects.h" + + namespace bamg { + +Index: ../trunk-jpl/src/c/classes/bamg/SetOfE4.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/bamg/SetOfE4.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/bamg/SetOfE4.cpp (revision 13530) +@@ -1,4 +1,4 @@ +-#include "../objects.h" ++#include "../objects/objects.h" + + using namespace std; + namespace bamg { +Index: ../trunk-jpl/src/c/classes/bamg/Mesh.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/bamg/Mesh.cpp (revision 13529) ++++ ../trunk-jpl/src/c/classes/bamg/Mesh.cpp (revision 13530) +@@ -3,7 +3,7 @@ + #include + #include + +-#include "../objects.h" ++#include "../objects/objects.h" + + namespace bamg { + Index: /issm/oecreview/Archive/13393-13976/ISSM-13530-13531.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13530-13531.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13530-13531.diff (revision 13980) @@ -0,0 +1,79 @@ +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13530) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13531) +@@ -44,8 +44,10 @@ + IssmPDouble Time_start, Flops_start; + IssmPDouble Solution_time, Memory_use, Current_flops; + +- IssmBoot(); ++ /*Initialize exception trapping: */ ++ ExceptionTrapBegin(); + ++ /*Initialize environment (MPI, PETSC, MUMPS, etc ...)*/ + EnvironmentInit(argc,argv); + + #ifdef _HAVE_MPI_ +@@ -233,8 +235,8 @@ + #endif + #endif + +- /*end module: */ +- IssmEnd(); ++ /*Finalize exception trapping: */ ++ ExceptionTrapEnd(); + + return 0; //unix success return; + } +Index: ../trunk-jpl/src/c/solutions/kriging.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/kriging.cpp (revision 13530) ++++ ../trunk-jpl/src/c/solutions/kriging.cpp (revision 13531) +@@ -35,8 +35,10 @@ + IssmDouble *predictions = NULL; + IssmDouble *error = NULL; + +- IssmBoot(); ++ /*Initialize exception trapping: */ ++ ExceptionTrapBegin(); + ++ /*Initialize environment (MPI, PETSC, MUMPS, etc ...)*/ + EnvironmentInit(argc,argv); + + /*First process inputs*/ +@@ -96,8 +98,8 @@ + #endif + #endif + +- /*end module: */ +- IssmEnd(); ++ /*Finalize exception trapping: */ ++ ExceptionTrapEnd(); + + return 0; //unix success return; + } +Index: ../trunk-jpl/src/c/include/macros.h +=================================================================== +--- ../trunk-jpl/src/c/include/macros.h (revision 13530) ++++ ../trunk-jpl/src/c/include/macros.h (revision 13531) +@@ -70,16 +70,16 @@ + ((void) 0) + #endif + /*}}}*/ +-/* IssmBoot/IssmEnd {{{*/ ++/* ExceptionTrapBegin/ExceptionTrapEnd {{{*/ + + /*The following macros hide the error exception handling in a matlab module. Just put +- * IssmBoot(); and IssmEnd(); at the beginning and end of a module, and c++ exceptions ++ * ExceptionTrapBegin(); and ExceptionTrapEnd(); at the beginning and end of a module, and c++ exceptions + * will be trapped. Really nifty!*/ + +-#define IssmBoot(); \ ++#define ExceptionTrapBegin(); \ + try{ + +-#define IssmEnd(); }\ ++#define ExceptionTrapEnd(); }\ + catch(ErrorException &exception){\ + exception.Report(); \ + return 1;\ Index: /issm/oecreview/Archive/13393-13976/ISSM-13531-13532.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13531-13532.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13531-13532.diff (revision 13980) @@ -0,0 +1,103 @@ +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13531) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13532) +@@ -34,9 +34,8 @@ + char *rootpath = NULL; + + /*time*/ +- IssmPDouble start, finish; ++ IssmPDouble finish; + IssmPDouble start_core, finish_core; +- IssmPDouble start_init, finish_init; + int ierr; + + /*profiling*/ +@@ -50,12 +49,8 @@ + /*Initialize environment (MPI, PETSC, MUMPS, etc ...)*/ + EnvironmentInit(argc,argv); + +- #ifdef _HAVE_MPI_ +- MPI_Barrier(MPI_COMM_WORLD); start=MPI_Wtime(); +- #else +- start=(IssmPDouble)clock(); +- #endif +- ++ /*Some profiling: */ ++ profiler=new Profiler(); profiler->Tag(Start); + + /*First process inputs*/ + _pprintLine_(""); +@@ -68,11 +63,8 @@ + AnalysisConfiguration(&analyses,&numanalyses,solution_type); + + /*Create femmodel, using input file: */ +- #ifdef _HAVE_MPI_ +- MPI_Barrier(MPI_COMM_WORLD); start_init=MPI_Wtime(); +- #else +- start_init=(IssmPDouble)clock(); +- #endif ++ profiler->Tag(StartInit); ++ + femmodel=new FemModel(rootpath,binfilename,outbinfilename,solution_type,analyses,numanalyses); + + /*get type of solution we are going to run: */ +@@ -95,11 +87,8 @@ + femmodel->parameters->FindParam(&profiling,DebugProfilingEnum); + femmodel->parameters->FindParam(&autodiff,AutodiffIsautodiffEnum); + +- #ifdef _HAVE_MPI_ +- MPI_Barrier(MPI_COMM_WORLD); finish_init=MPI_Wtime(); +- #else +- finish_init=(IssmPDouble)clock(); +- #endif ++ /*Profiling: */ ++ profiler->Tag(FinishInit); + + /*If running AD, then initialize a placeholder with which to work: */ + #ifdef _HAVE_ADOLC_ +@@ -118,11 +107,7 @@ + #endif + + _pprintLine_("call computational core:"); +- #ifdef _HAVE_MPI_ +- MPI_Barrier(MPI_COMM_WORLD); start_core=MPI_Wtime( ); +- #else +- start_core=(IssmPDouble)clock(); +- #endif ++ profiler->Tag(StartCore); + + if(profiling)ProfilingStart(&Time_start,&Flops_start); + +@@ -161,12 +146,8 @@ + } + #endif + ++ profiler->Tag(FinishCore); + +- #ifdef _HAVE_MPI_ +- MPI_Barrier(MPI_COMM_WORLD); finish_core=MPI_Wtime( ); +- #else +- finish_core=(IssmPDouble)clock(); +- #endif + + _pprintLine_("write results to disk:"); + OutputResultsx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); +Index: ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp (revision 13531) ++++ ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp (revision 13532) +@@ -1,7 +1,13 @@ + /*!\file: EnvironmentInit.cpp + * \brief: initialize Petsc, MPI, you name it + */ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif + ++ + void EnvironmentInit(int argc,char** argv){ + + /*Initialize environments: Petsc, MPI, etc...: */ Index: /issm/oecreview/Archive/13393-13976/ISSM-13532-13533.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13532-13533.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13532-13533.diff (revision 13980) @@ -0,0 +1,34 @@ +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13532) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13533) +@@ -36,7 +36,6 @@ + /*time*/ + IssmPDouble finish; + IssmPDouble start_core, finish_core; +- int ierr; + + /*profiling*/ + bool profiling = false; +Index: ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp (revision 13532) ++++ ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp (revision 13533) +@@ -6,13 +6,15 @@ + #else + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif ++#include "../include/include.h" ++#include "../toolkits/toolkits.h" ++#include "../include/globals.h" + +- + void EnvironmentInit(int argc,char** argv){ + + /*Initialize environments: Petsc, MPI, etc...: */ + #ifdef _HAVE_PETSC_ +- ierr=PetscInitialize(&argc,&argv,(char*)0,""); ++ int ierr=PetscInitialize(&argc,&argv,(char*)0,""); + if(ierr) _error_("Could not initialize Petsc"); + #else + #ifdef _HAVE_MPI_ Index: /issm/oecreview/Archive/13393-13976/ISSM-13533-13534.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13533-13534.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13533-13534.diff (revision 13980) @@ -0,0 +1,553 @@ +Index: ../trunk-jpl/src/c/solutions/EnvironmentFinalize.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/EnvironmentFinalize.cpp (revision 0) ++++ ../trunk-jpl/src/c/solutions/EnvironmentFinalize.cpp (revision 13534) +@@ -0,0 +1,24 @@ ++/*!\file: EnvironmentFinalize.cpp ++ * \brief: finalize Petsc, MPI, you name it ++ */ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++#include "../include/include.h" ++#include "../toolkits/toolkits.h" ++#include "../shared/shared.h" ++ ++void EnvironmentFinalize(void){ ++ ++ #ifdef _HAVE_PETSC_ ++ _pprintLine_("closing MPI and Petsc"); ++ PetscFinalize(); ++ #else ++ #ifdef _HAVE_MPI_ ++ _pprintLine_("closing MPI and Petsc"); ++ MPI_Finalize(); ++ #endif ++ #endif ++} +Index: ../trunk-jpl/src/c/solutions/solutions.h +=================================================================== +--- ../trunk-jpl/src/c/solutions/solutions.h (revision 13533) ++++ ../trunk-jpl/src/c/solutions/solutions.h (revision 13534) +@@ -45,6 +45,7 @@ + void controlrestart(FemModel* femmodel,IssmDouble* J); + void ResetBoundaryConditions(FemModel* femmodel, int analysis_type); + void EnvironmentInit(int argc,char** argv); ++void EnvironmentFinalize(void); + + //solution configuration + void AnalysisConfiguration(int** panalyses,int* pnumanalyses, int solutiontype); +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13533) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13534) +@@ -5,6 +5,8 @@ + #include "../issm.h" + #include "../include/globals.h" + ++void ProfilerEcho(Profiler* profiler); ++ + int main(int argc,char **argv){ + + /*I/O: */ +@@ -33,11 +35,8 @@ + char *petscfilename = NULL; + char *rootpath = NULL; + +- /*time*/ +- IssmPDouble finish; +- IssmPDouble start_core, finish_core; +- + /*profiling*/ ++ Profiler* profiler=NULL; + bool profiling = false; + IssmPDouble Time_start, Flops_start; + IssmPDouble Solution_time, Memory_use, Current_flops; +@@ -184,39 +183,32 @@ + delete femmodel; + + /*Get finish time and close*/ +- #ifdef _HAVE_MPI_ +- MPI_Barrier(MPI_COMM_WORLD); finish = MPI_Wtime( ); ++ profiler->Tag(Finish); ProfilerEcho(profiler); ++ ++ /*Finalize environment:*/ ++ EnvironmentFinalize(); ++ ++ /*Finalize exception trapping: */ ++ ExceptionTrapEnd(); ++ ++ /*Return unix success: */ ++ return 0; ++} ++ ++ ++ ++void ProfilerEcho(Profiler* profiler){ ++ + _pprintLine_(""); +- _pprintLine_(" "<Delta(StartInit,FinishInit)); ++ _pprintLine_(" "<Delta(StartCore,FinishCore)); + _pprintLine_(""); +- _pprintLine_(" Total elapsed time:"<DeltaModHour(Start,Finish)<<" hrs " ++ <DeltaModMin(Start,Finish)<<" min " ++ <DeltaModSec(Start,Finish)<<" sec" ++ ); + _pprintLine_(""); +- #endif +- +- #ifdef _HAVE_PETSC_ +- _pprintLine_("closing MPI and Petsc"); +- PetscFinalize(); +- #else +- #ifdef _HAVE_MPI_ +- _pprintLine_("closing MPI and Petsc"); +- MPI_Finalize(); +- #endif +- #endif + +- /*Finalize exception trapping: */ +- ExceptionTrapEnd(); ++} + +- return 0; //unix success return; +-} +Index: ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp (revision 13533) ++++ ../trunk-jpl/src/c/solutions/EnvironmentInit.cpp (revision 13534) +@@ -8,9 +8,11 @@ + #endif + #include "../include/include.h" + #include "../toolkits/toolkits.h" +-#include "../include/globals.h" + + void EnvironmentInit(int argc,char** argv){ ++ ++ extern int my_rank; ++ extern int num_procs; + + /*Initialize environments: Petsc, MPI, etc...: */ + #ifdef _HAVE_PETSC_ +Index: ../trunk-jpl/src/c/solutions/kriging.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/kriging.cpp (revision 13533) ++++ ../trunk-jpl/src/c/solutions/kriging.cpp (revision 13534) +@@ -88,15 +88,8 @@ + delete options; + delete results; + +-#ifdef _HAVE_PETSC_ +- _pprintLine_("closing MPI and Petsc"); +- PetscFinalize(); +-#else +-#ifdef _HAVE_MPI_ +- _pprintLine_("closing MPI and Petsc"); +- MPI_Finalize(); +-#endif +-#endif ++ /*Finalize environment:*/ ++ EnvironmentFinalize(); + + /*Finalize exception trapping: */ + ExceptionTrapEnd(); +Index: ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13533) ++++ ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13534) +@@ -322,6 +322,7 @@ + PenpairEnum, + PentaEnum, + PentaP1InputEnum, ++ ProfilerEnum, + MatrixParamEnum, + VectorParamEnum, + RiftfrontEnum, +Index: ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13533) ++++ ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13534) +@@ -326,6 +326,7 @@ + else if (strcmp(name,"Penpair")==0) return PenpairEnum; + else if (strcmp(name,"Penta")==0) return PentaEnum; + else if (strcmp(name,"PentaP1Input")==0) return PentaP1InputEnum; ++ else if (strcmp(name,"Profiler")==0) return ProfilerEnum; + else if (strcmp(name,"MatrixParam")==0) return MatrixParamEnum; + else if (strcmp(name,"VectorParam")==0) return VectorParamEnum; + else if (strcmp(name,"Riftfront")==0) return RiftfrontEnum; +@@ -382,11 +383,11 @@ + else if (strcmp(name,"SegmentOnIceShelf")==0) return SegmentOnIceShelfEnum; + else if (strcmp(name,"SurfaceAbsVelMisfit")==0) return SurfaceAbsVelMisfitEnum; + else if (strcmp(name,"SurfaceArea")==0) return SurfaceAreaEnum; +- else if (strcmp(name,"SurfaceAverageVelMisfit")==0) return SurfaceAverageVelMisfitEnum; + else stage=4; + } + if(stage==4){ +- if (strcmp(name,"SurfaceLogVelMisfit")==0) return SurfaceLogVelMisfitEnum; ++ if (strcmp(name,"SurfaceAverageVelMisfit")==0) return SurfaceAverageVelMisfitEnum; ++ else if (strcmp(name,"SurfaceLogVelMisfit")==0) return SurfaceLogVelMisfitEnum; + else if (strcmp(name,"SurfaceLogVxVyMisfit")==0) return SurfaceLogVxVyMisfitEnum; + else if (strcmp(name,"SurfaceRelVelMisfit")==0) return SurfaceRelVelMisfitEnum; + else if (strcmp(name,"SurfaceSlopeX")==0) return SurfaceSlopeXEnum; +@@ -505,11 +506,11 @@ + else if (strcmp(name,"Regular")==0) return RegularEnum; + else if (strcmp(name,"Scaled")==0) return ScaledEnum; + else if (strcmp(name,"Separate")==0) return SeparateEnum; +- else if (strcmp(name,"Sset")==0) return SsetEnum; + else stage=5; + } + if(stage==5){ +- if (strcmp(name,"Verbose")==0) return VerboseEnum; ++ if (strcmp(name,"Sset")==0) return SsetEnum; ++ else if (strcmp(name,"Verbose")==0) return VerboseEnum; + else if (strcmp(name,"TriangleInterp")==0) return TriangleInterpEnum; + else if (strcmp(name,"BilinearInterp")==0) return BilinearInterpEnum; + else if (strcmp(name,"NearestInterp")==0) return NearestInterpEnum; +Index: ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13533) ++++ ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13534) +@@ -319,6 +319,7 @@ + case PenpairEnum : return "Penpair"; + case PentaEnum : return "Penta"; + case PentaP1InputEnum : return "PentaP1Input"; ++ case ProfilerEnum : return "Profiler"; + case MatrixParamEnum : return "MatrixParam"; + case VectorParamEnum : return "VectorParam"; + case RiftfrontEnum : return "Riftfront"; +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13533) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13534) +@@ -158,6 +158,8 @@ + ./classes/objects/Params/TransientParam.cpp\ + ./classes/objects/Params/DataSetParam.h\ + ./classes/objects/Params/DataSetParam.cpp\ ++ ./classes/objects/Profiler.h\ ++ ./classes/objects/Profiler.cpp\ + ./Container/Container.h\ + ./Container/Constraints.h\ + ./Container/Constraints.cpp\ +@@ -350,6 +352,7 @@ + ./solutions/AnalysisConfiguration.cpp\ + ./solutions/CorePointerFromSolutionEnum.cpp\ + ./solutions/EnvironmentInit.cpp\ ++ ./solutions/EnvironmentFinalize.cpp\ + ./solvers/solver_linear.cpp\ + ./solvers/solver_nonlinear.cpp\ + ./solvers/solver_newton.cpp\ +Index: ../trunk-jpl/src/c/classes/objects/objects.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/objects.h (revision 13533) ++++ ../trunk-jpl/src/c/classes/objects/objects.h (revision 13534) +@@ -12,6 +12,7 @@ + #include "./Contour.h" + #include "./Vertex.h" + #include "./Node.h" ++#include "./Profiler.h" + #include "./DependentObject.h" + #include "./IndependentObject.h" + #include "./Segment.h" +Index: ../trunk-jpl/src/c/classes/objects/Profiler.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Profiler.cpp (revision 0) ++++ ../trunk-jpl/src/c/classes/objects/Profiler.cpp (revision 13534) +@@ -0,0 +1,139 @@ ++/*!\file Profiler.c ++ * \brief: implementation of the Profiler object ++ */ ++ ++/*Include files: {{{*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "./Profiler.h" ++/*}}}*/ ++ ++/*Profiler constructors and destructors:*/ ++/*FUNCTION Profiler::Profiler() default constructor {{{*/ ++Profiler::Profiler(){ ++ this->timetags=new Parameters(); ++} ++/*}}}*/ ++/*FUNCTION Profiler::~Profiler(){{{*/ ++Profiler::~Profiler(){ ++ delete timetags; ++} ++/*}}}*/ ++ ++/*Object virtual functions definitions:*/ ++/*FUNCTION Profiler::Echo{{{*/ ++void Profiler::Echo(void){ ++ ++ _printLine_("Profiler:"); ++ _printLine_(" time tags: "); ++ this->timetags->Echo(); ++ ++} ++/*}}}*/ ++/*FUNCTION Profiler::DeepEcho{{{*/ ++void Profiler::DeepEcho(void){ ++ ++ _printLine_("Profiler:"); ++ _printLine_(" time tags: "); ++ this->timetags->DeepEcho(); ++ ++} ++/*}}}*/ ++/*FUNCTION Profiler::Id{{{*/ ++int Profiler::Id(void){ return -1; } ++/*}}}*/ ++/*FUNCTION Profiler::ObjectEnum{{{*/ ++int Profiler::ObjectEnum(void){ ++ ++ return ProfilerEnum; ++ ++} ++/*}}}*/ ++ ++/*Profiler routines:*/ ++/*FUNCTION Profiler::Tag {{{*/ ++void Profiler::Tag(int tagenum,bool dontmpisync){ ++ ++ double time; ++ ++ /*If mpisync requested, make sure all the cpus are at the same point ++ *in the execution: */ ++ if(!dontmpisync){ ++ #ifdef _HAVE_MPI_ ++ MPI_Barrier(MPI_COMM_WORLD); ++ #endif ++ } ++ ++ /*Now capture time: */ ++ #ifdef _HAVE_MPI_ ++ time=MPI_Wtime(); ++ #else ++ time=(IssmPDouble)clock(); ++ #endif ++ ++ /*Plug into this->timetags: */ ++ this->timetags->AddObject(new DoubleParam(tagenum,time)); ++ ++} ++/*}}}*/ ++/*FUNCTION Profiler::Delta {{{*/ ++double Profiler::Delta(int inittag, int finaltag){ ++ ++ double init, final; ++ this->timetags->FindParam(&init,inittag); ++ this->timetags->FindParam(&final,finaltag); ++ ++ #ifdef _HAVE_MPI_ ++ return final-init; ++ #else ++ return (final-init)/CLOCKS_PER_SEC; ++ #endif ++} ++/*}}}*/ ++/*FUNCTION Profiler::DeltaModHour {{{*/ ++int Profiler::DeltaModHour(int inittag, int finishtag){ ++ ++ double init, finish; ++ this->timetags->FindParam(&init,inittag); ++ this->timetags->FindParam(&finish,finishtag); ++ ++ #ifdef _HAVE_MPI_ ++ return int((finish-init)/3600); ++ #else ++ return int((finish-init)/CLOCKS_PER_SEC/3600); ++ #endif ++ ++} ++/*}}}*/ ++/*FUNCTION Profiler::DeltaModMin {{{*/ ++int Profiler::DeltaModMin(int inittag, int finishtag){ ++ ++ double init, finish; ++ this->timetags->FindParam(&init,inittag); ++ this->timetags->FindParam(&finish,finishtag); ++ ++ #ifdef _HAVE_MPI_ ++ return int(int(finish-init)%3600/60); ++ #else ++ return int(int(finish-init)/CLOCKS_PER_SEC%3600/60); ++ #endif ++} ++/*}}}*/ ++/*FUNCTION Profiler::DeltaModSec {{{*/ ++int Profiler::DeltaModSec(int inittag, int finishtag){ ++ ++ double init, finish; ++ this->timetags->FindParam(&init,inittag); ++ this->timetags->FindParam(&finish,finishtag); ++ ++ #ifdef _HAVE_MPI_ ++ return int(finish-init)%60; ++ #else ++ return int(finish-init)/CLOCKS_PER_SEC%60; ++ #endif ++} ++/*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Profiler.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Profiler.h (revision 0) ++++ ../trunk-jpl/src/c/classes/objects/Profiler.h (revision 13534) +@@ -0,0 +1,52 @@ ++/*!\file Profiler.h ++ * \brief: header file for node object ++ */ ++ ++#ifndef _PROFILER_H_ ++#define _PROFILER_H_ ++ ++/*Headers:*/ ++/*{{{*/ ++#include "./Object.h" ++#include "../../shared/shared.h" ++/*}}}*/ ++ ++class DataSet; ++class Parameters; ++ ++enum ProfilerEnums { ++ Start, ++ StartInit, ++ FinishInit, ++ StartCore, ++ FinishCore, ++ Finish ++}; ++ ++ ++class Profiler: public Object{ ++ ++ public: ++ Parameters* timetags; ++ ++ /*Profiler constructors, destructors {{{*/ ++ Profiler(); ++ ~Profiler(); ++ /*}}}*/ ++ /*Object virtual functions definitions:{{{ */ ++ void Echo(); ++ void DeepEcho(); ++ int Id(); ++ int ObjectEnum(); ++ Object *copy() {_error_("Not implemented yet"); }; ++ /*}}}*/ ++ /*Profiler routines {{{*/ ++ void Tag(int tagenum,bool dontmpisync=false); ++ double Delta(int inittag, int finaltag); ++ int DeltaModHour(int inittag, int finaltag); ++ int DeltaModMin(int inittag, int finaltag); ++ int DeltaModSec(int inittag, int finaltag); ++ /*}}}*/ ++}; ++ ++#endif /* _PROFILER_H_ */ +Index: ../trunk-jpl/src/m/enum/SurfaceforcingsSmbrefEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/SurfaceforcingsSmbrefEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/SurfaceforcingsSmbrefEnum.m (revision 13534) +@@ -0,0 +1,11 @@ ++function macro=SurfaceforcingsSmbrefEnum() ++%SURFACEFORCINGSSMBREFENUM - Enum of SurfaceforcingsSmbref ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=SurfaceforcingsSmbrefEnum() ++ ++macro=StringToEnum('SurfaceforcingsSmbref'); +Index: ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13533) ++++ ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13534) +@@ -8,4 +8,4 @@ + % Usage: + % macro=MaximumNumberOfEnums() + +-macro=495; ++macro=496; +Index: ../trunk-jpl/src/m/enum/SurfaceforcingsHrefEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/SurfaceforcingsHrefEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/SurfaceforcingsHrefEnum.m (revision 13534) +@@ -0,0 +1,11 @@ ++function macro=SurfaceforcingsHrefEnum() ++%SURFACEFORCINGSHREFENUM - Enum of SurfaceforcingsHref ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=SurfaceforcingsHrefEnum() ++ ++macro=StringToEnum('SurfaceforcingsHref'); +Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py +=================================================================== +--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13533) ++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13534) +@@ -3038,6 +3038,16 @@ + + return StringToEnum('PentaP1Input')[0] + ++def ProfilerEnum(): ++ """ ++ PROFILERENUM - Enum of Profiler ++ ++ Usage: ++ macro=ProfilerEnum() ++ """ ++ ++ return StringToEnum('Profiler')[0] ++ + def MatrixParamEnum(): + """ + MATRIXPARAMENUM - Enum of MatrixParam +@@ -4966,5 +4976,5 @@ + macro=MaximumNumberOfEnums() + """ + +- return 495 ++ return 496 + +Index: ../trunk-jpl/src/m/enum/ProfilerEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/ProfilerEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/ProfilerEnum.m (revision 13534) +@@ -0,0 +1,11 @@ ++function macro=ProfilerEnum() ++%PROFILERENUM - Enum of Profiler ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=ProfilerEnum() ++ ++macro=StringToEnum('Profiler'); Index: /issm/oecreview/Archive/13393-13976/ISSM-13534-13535.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13534-13535.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13534-13535.diff (revision 13980) @@ -0,0 +1,24 @@ +Index: ../trunk-jpl/test/NightlyRun/ad_maxalloc.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/ad_maxalloc.m (revision 0) ++++ ../trunk-jpl/test/NightlyRun/ad_maxalloc.m (revision 13535) +@@ -0,0 +1,19 @@ ++md=triangle(model,'../Exp/Square.exp',100000); ++md=setmask(md,'all',''); ++md=parameterize(md,'../Par/SquareShelfConstrained.par'); ++md=setflowequation(md,'macayeal','all'); ++md.cluster=generic('name',oshostname(),'np',3); ++ ++md.autodiff.isautodiff=true; ++md.verbose.autodiff=true; ++md.autodiff.independents={... ++ independent('name','Thickness','type','vertex','nods',md.mesh.numberofvertices,'fov_forward_indices',(1:md.mesh.numberofvertices)') ++ }; ++ ++md.autodiff.dependents={... ++ dependent('name','MaxVel','type','scalar') ++ }; ++ ++md.autodiff.driver='fov_forward'; ++ ++md=solve(md,TransientSolutionEnum); Index: /issm/oecreview/Archive/13393-13976/ISSM-13535-13536.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13535-13536.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13535-13536.diff (revision 13980) @@ -0,0 +1,102 @@ +Index: ../trunk-jpl/src/c/shared/Sys/ProfilingEnd.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Sys/ProfilingEnd.cpp (revision 13535) ++++ ../trunk-jpl/src/c/shared/Sys/ProfilingEnd.cpp (revision 13536) +@@ -1,43 +0,0 @@ +-/*!\file: ProfilingEnd.cpp +- * \brief ProfilingEnd.c: finalize profiling after calling a routine. Needs to mirror a ProfilingStart routine. +- */ +- +-/*Include files: {{{*/ +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +-#include "../../include/macros.h" +-#include "../shared.h" +-#include "../../io/io.h" +-/*}}}*/ +- +-void ProfilingEnd(double* pSolution_time, double* pMemory_use, double* pCurrent_flops, double Time_start, double Flops_start){ +- +- double Solution_time, Memory_use, Current_flops; +- double Time_finish, Flops_finish, memUse; +- +- #ifdef _HAVE_PETSC_ +- PetscGetTime(&Time_finish); +- PetscGetFlops(&Flops_finish); +- PetscMemoryGetCurrentUsage(&memUse); +- +- Solution_time=Time_finish-Time_start; +- Current_flops=Flops_finish-Flops_start; +- _pprintLine_("PETSc elapsed time : " << Solution_time << " Seconds"); +- _pprintLine_("PETSc elapsed flops : " << Current_flops << " Flops"); +- _pprintLine_("PETSc memory used : " << memUse << " Bytes"); +- #else +- _error_("Profiling not supported under this numerical toolkit"); +- #endif +- +- /*Assign pointers: */ +- *pSolution_time=Solution_time; +- *pMemory_use=memUse; +- *pCurrent_flops=Current_flops; +- return; +-} +- +- +- +Index: ../trunk-jpl/src/c/shared/Sys/sys.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Sys/sys.h (revision 13535) ++++ ../trunk-jpl/src/c/shared/Sys/sys.h (revision 13536) +@@ -1,12 +0,0 @@ +-/* \file sys.h +- * \brief: header file for ISSM system routines (profiling, timing, etc ...) +- */ +- +- +-#ifndef _ISSM_SYS_H_ +-#define _ISSM_SYS_H_ +- +-void ProfilingEnd(double* pSolution_time, double* pMemory_use, double* pCurrent_flops, double Time_start, double Flops_start); +-void ProfilingStart(double* pTime_start, double* pFlops_start); +- +-#endif +Index: ../trunk-jpl/src/c/shared/Sys/ProfilingStart.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Sys/ProfilingStart.cpp (revision 13535) ++++ ../trunk-jpl/src/c/shared/Sys/ProfilingStart.cpp (revision 13536) +@@ -1,32 +0,0 @@ +-/*!\file: ProfilingStart.cpp +- * \brief ProfilingStart.c: initialize profiling before calling a routine +- */ +- +- +-/*Include files: {{{*/ +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +-#include "../../include/macros.h" +-#include "../shared.h" +-#include "../../io/io.h" +-/*}}}*/ +- +-void ProfilingStart(double* pTime_start, double* pFlops_start){ +- +- double Time_start, Flops_start; +- +- #ifdef _HAVE_PETSC_ +- PetscGetTime(&Time_start); +- PetscGetFlops(&Flops_start ); +- #else +- _error_("Profiling not supported under this numerical toolkit"); +- #endif +- +- /*Assign pointers: */ +- *pTime_start=Time_start; +- *pFlops_start=Flops_start; +- return; +-} Index: /issm/oecreview/Archive/13393-13976/ISSM-13536-13537.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13536-13537.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13536-13537.diff (revision 13980) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13536) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13537) +@@ -223,9 +223,6 @@ + ./shared/Wrapper/wrappershared.h\ + ./shared/Wrapper/ModuleBoot.cpp\ + ./shared/Wrapper/ModuleEnd.cpp\ +- ./shared/Sys/sys.h\ +- ./shared/Sys/ProfilingStart.cpp\ +- ./shared/Sys/ProfilingEnd.cpp\ + ./toolkits/metis/metisincludes.h\ + ./toolkits/issm/issmtoolkit.h\ + ./toolkits/issm/SeqVec.h\ Index: /issm/oecreview/Archive/13393-13976/ISSM-13537-13538.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13537-13538.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13537-13538.diff (revision 13980) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/c/shared/shared.h +=================================================================== +--- ../trunk-jpl/src/c/shared/shared.h (revision 13537) ++++ ../trunk-jpl/src/c/shared/shared.h (revision 13538) +@@ -15,7 +15,6 @@ + #include "MemOps/xMemCpy.h" + #include "Numerics/numerics.h" + #include "Sorting/sorting.h" +-#include "Sys/sys.h" + #include "Threads/issm_threads.h" + #include "TriMesh/trimesh.h" + #include "Wrapper/wrappershared.h" Index: /issm/oecreview/Archive/13393-13976/ISSM-13538-13539.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13538-13539.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13538-13539.diff (revision 13980) @@ -0,0 +1,1294 @@ +Index: ../trunk-jpl/src/c/solutions/solutions.h +=================================================================== +--- ../trunk-jpl/src/c/solutions/solutions.h (revision 13538) ++++ ../trunk-jpl/src/c/solutions/solutions.h (revision 13539) +@@ -29,6 +29,7 @@ + void slopecompute_core(FemModel* femmodel); + void steadystate_core(FemModel* femmodel); + void transient_core(FemModel* femmodel); ++void dakota_core(FemModel* femmodel); + IssmDouble objectivefunction(IssmDouble search_scalar,OptArgs* optargs); + + //convergence: +@@ -46,10 +47,12 @@ + void ResetBoundaryConditions(FemModel* femmodel, int analysis_type); + void EnvironmentInit(int argc,char** argv); + void EnvironmentFinalize(void); ++int DakotaSpawnCore(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, void* femmodel,int counter); + + //solution configuration + void AnalysisConfiguration(int** panalyses,int* pnumanalyses, int solutiontype); + void CorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype); + void AdjointCorePointerFromSolutionEnum(void (**padjointcore)(FemModel*),int solutiontype); + ++ + #endif +Index: ../trunk-jpl/src/c/solutions/dakota_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/dakota_core.cpp (revision 0) ++++ ../trunk-jpl/src/c/solutions/dakota_core.cpp (revision 13539) +@@ -0,0 +1,129 @@ ++/*!\file: dakota_core.cpp ++ * \brief: wrapper to the Dakota capabilities. qmu fires up Dakota, and registers a Dakota Pluggin ++ * which will be in charge of running the solution sequences repeteadly, to garner statistics. ++ * ++ * This routine deals with running ISSM and Dakota in library mode. In library mode, Dakota does not ++ * run as an execuatble. Its capabilities are linked into the ISSM software. ISSM calls dakota routines ++ * directly from the dakota library. qmu.cpp is the code that is in charge of calling those routines. ++ * ++ * Dakota has its own way of running in parallel (for embarassingly parallel jobs). We do not want that, ++ * as ISSM knows exactly how to run "really parallel" jobs that use all CPUS. To bypass Dakota's parallelism, ++ * we overloaded the constructor for the parallel library (see the Dakota patch in the externalpackages/dakota ++ * directory). This overloaded constructor fires up Dakota serially on CPU 0 only! We take care of broadcasting ++ * to the other CPUS, hence ISSM is running in parallel, and Dakota serially on CPU0. ++ * ++ * Now, how does CPU 0 drive all other CPUS to carry out sensitivity analysese? By synchronizing its call to ++ * our ISSM cores (diagnostic_core, thermal_core, transient_core, etc ...) on CPU 0 with all other CPUS. ++ * This explains the structure of qmu.cpp, where cpu 0 runs Dakota, the Dakota pluggin fires up DakotaSpawnCore.cpp, ++ * while the other CPUS are waiting for a broadcast from CPU0, once they get it, they also fire up ++ * DakotaSpawnCore. In the end, DakotaSpawnCore is fired up on all CPUS, with CPU0 having Dakota inputs, that it will ++ * broacast to other CPUS. ++ * ++ * Now, how does dakota call the DakotaSpawnCore routine? The DakotaSpawnCore is embedded into the DakotaPlugin object ++ * which is derived from the Direct Interface Dakota objct. This is the only way to run Dakota in library ++ * mode (see their developper guide for more info). Dakota registers the DakotaPlugin object into its own ++ * database, and calls on the embedded DakotaSpawnCore from CPU0. ++ * ++ */ ++ ++/*include files: {{{*/ ++#ifdef HAVE_CONFIG_H ++#include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "./solutions.h" ++#include "../shared/shared.h" ++#include "../include/include.h" ++#include "../io/io.h" ++#include "../toolkits/toolkits.h" ++#include "../EnumDefinitions/EnumDefinitions.h" ++#include "../classes/dakota/DakotaPlugin.h" ++ ++#ifdef _HAVE_DAKOTA_ //only works if dakota library has been compiled in. ++#include "ParallelLibrary.H" ++#include "ProblemDescDB.H" ++#include "DakotaStrategy.H" ++#include "DakotaModel.H" ++#include "DakotaInterface.H" ++ ++#endif ++/*}}}*/ ++ ++void dakota_core(FemModel* femmodel){ ++ ++ ++ #ifdef _HAVE_DAKOTA_ //only works if dakota library has been compiled in. ++ ++ extern int my_rank; ++ char* dakota_input_file = NULL; ++ char* dakota_output_file = NULL; ++ char* dakota_error_file = NULL; ++ int status=0; ++ Dakota::ModelLIter ml_iter; ++ Parameters* parameters = NULL; ++ ++ /*Retrieve parameters: */ ++ parameters=femmodel->parameters; ++ ++ /*Recover dakota_input_file, dakota_output_file and dakota_error_file, in the parameters dataset in parallel */ ++ parameters->FindParam(&dakota_input_file,QmuInNameEnum); ++ parameters->FindParam(&dakota_output_file,QmuOutNameEnum); ++ parameters->FindParam(&dakota_error_file,QmuErrNameEnum); ++ ++ if(my_rank==0){ ++ ++ // Instantiate/initialize the parallel library and problem description ++ // database objects. ++ Dakota::ParallelLibrary parallel_lib("serial"); //use our own ISSM Dakota library mode constructor, which only fires up Dakota on CPU 0. ++ Dakota::ProblemDescDB problem_db(parallel_lib); ++ ++ // Manage input file parsing, output redirection, and restart processing ++ // without a CommandLineHandler. This version relies on parsing of an ++ // input file. ++ problem_db.manage_inputs(dakota_input_file); ++ // specify_outputs_restart() is only necessary if specifying non-defaults ++ parallel_lib.specify_outputs_restart(dakota_output_file,dakota_error_file,NULL,NULL); ++ ++ // Instantiate the Strategy object (which instantiates all Model and ++ // Iterator objects) using the parsed information in problem_db. ++ Dakota::Strategy selected_strategy(problem_db); ++ ++ // convenience function for iterating over models and performing any ++ // interface plug-ins ++ Dakota::ModelList& models = problem_db.model_list(); ++ ++ for (ml_iter = models.begin(); ml_iter != models.end(); ml_iter++) { ++ ++ Dakota::Interface& interface = ml_iter->interface(); ++ ++ //set DB nodes to the existing Model specification ++ problem_db.set_db_model_nodes(ml_iter->model_id()); ++ ++ // Serial case: plug in derived Interface object without an analysisComm ++ interface.assign_rep(new SIM::DakotaPlugin(problem_db,(void*)femmodel), false); ++ } ++ ++ // Execute the strategy ++ problem_db.lock(); // prevent run-time DB queries ++ selected_strategy.run_strategy(); ++ ++ //Warn other cpus that we are done running the dakota iterator, by setting the counter to -1: ++ DakotaSpawnCore(NULL,0, NULL,NULL,0,femmodel,-1); ++ ++ } ++ else{ ++ ++ for(;;){ ++ if(!DakotaSpawnCore(NULL,0, NULL,NULL,0,femmodel,0))break; //counter came in at -1 on cpu0, bail out. ++ } ++ } ++ ++ /*Free ressources:*/ ++ xDelete(dakota_input_file); ++ xDelete(dakota_error_file); ++ xDelete(dakota_output_file); ++ ++ #endif //#ifdef _HAVE_DAKOTA_ ++} +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13538) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13539) +@@ -6,6 +6,7 @@ + #include "../include/globals.h" + + void ProfilerEcho(Profiler* profiler); ++void ProfilerEnd(Profiler* profiler, Results* results, Parameters* parameters); + + int main(int argc,char **argv){ + +@@ -37,9 +38,6 @@ + + /*profiling*/ + Profiler* profiler=NULL; +- bool profiling = false; +- IssmPDouble Time_start, Flops_start; +- IssmPDouble Solution_time, Memory_use, Current_flops; + + /*Initialize exception trapping: */ + ExceptionTrapBegin(); +@@ -47,8 +45,9 @@ + /*Initialize environment (MPI, PETSC, MUMPS, etc ...)*/ + EnvironmentInit(argc,argv); + +- /*Some profiling: */ +- profiler=new Profiler(); profiler->Tag(Start); ++ /*Start profiler: */ ++ profiler=new Profiler(); ++ profiler->Tag(Start); + + /*First process inputs*/ + _pprintLine_(""); +@@ -82,7 +81,6 @@ + femmodel->parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum); + femmodel->parameters->FindParam(&control_analysis,InversionIscontrolEnum); + femmodel->parameters->FindParam(&tao_analysis,InversionTaoEnum); +- femmodel->parameters->FindParam(&profiling,DebugProfilingEnum); + femmodel->parameters->FindParam(&autodiff,AutodiffIsautodiffEnum); + + /*Profiling: */ +@@ -105,48 +103,38 @@ + #endif + + _pprintLine_("call computational core:"); ++ ++ + profiler->Tag(StartCore); +- +- if(profiling)ProfilingStart(&Time_start,&Flops_start); +- + if(dakota_analysis){ + #ifdef _HAVE_DAKOTA_ +- Dakotax(femmodel); ++ dakota_core(femmodel); + #else + _error_("ISSM was not compiled with dakota support, cannot carry out dakota analysis!"); + #endif + } + else if(control_analysis){ + #ifdef _HAVE_CONTROL_ +- if(tao_analysis) +- controltao_core(femmodel); +- else +- control_core(femmodel); ++ if(tao_analysis) controltao_core(femmodel); ++ else control_core(femmodel); + #else +- _error_("ISSM was not compiled with control support, cannot carry out dakota analysis!"); ++ _error_("ISSM was not compiled with control support, cannot carry out control analysis!"); + #endif + } + else{ + solutioncore(femmodel); + } + +- if(profiling){ +- ProfilingEnd(&Solution_time,&Memory_use,&Current_flops,Time_start,Flops_start); +- femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1, ProfilingSolutionTimeEnum, Solution_time, 1, 0)); +- femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1, ProfilingCurrentMemEnum, Memory_use, 1, 0)); +- femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1, ProfilingCurrentFlopsEnum, Current_flops, 1, 0)); +- } +- + #ifdef _HAVE_ADOLC_ + if(autodiff){ + trace_off(); + AutodiffDriversx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); + } + #endif +- + profiler->Tag(FinishCore); + +- ++ ProfilerEnd(profiler,femmodel->results,femmodel->parameters); ++ + _pprintLine_("write results to disk:"); + OutputResultsx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); + +@@ -182,8 +170,9 @@ + xDelete(rootpath); + delete femmodel; + +- /*Get finish time and close*/ +- profiler->Tag(Finish); ProfilerEcho(profiler); ++ /*Profiling at the end: */ ++ profiler->Tag(Finish); ++ ProfilerEcho(profiler); + + /*Finalize environment:*/ + EnvironmentFinalize(); +@@ -195,20 +184,44 @@ + return 0; + } + ++void ProfilerEcho(Profiler* profiler){ /*{{{*/ + +- +-void ProfilerEcho(Profiler* profiler){ +- + _pprintLine_(""); +- _pprintLine_(" "<Delta(StartInit,FinishInit)); +- _pprintLine_(" "<Delta(StartCore,FinishCore)); ++ _pprintLine_(" "<DeltaTime(StartInit,FinishInit)); ++ _pprintLine_(" "<DeltaTime(StartCore,FinishCore)); + _pprintLine_(""); + _pprintLine_(" Total elapsed time:" +- <DeltaModHour(Start,Finish)<<" hrs " +- <DeltaModMin(Start,Finish)<<" min " +- <DeltaModSec(Start,Finish)<<" sec" ++ <DeltaTimeModHour(Start,Finish)<<" hrs " ++ <DeltaTimeModMin(Start,Finish)<<" min " ++ <DeltaTimeModSec(Start,Finish)<<" sec" + ); + _pprintLine_(""); + +-} ++} /*}}}*/ ++void ProfilerEnd(Profiler* profiler, Results* results, Parameters* parameters){ /*{{{*/ + ++ bool profiling = false; ++ ++ IssmDouble solution_time; ++ IssmDouble solution_flops; ++ IssmDouble solution_memory; ++ ++ parameters->FindParam(&profiling,DebugProfilingEnum); ++ ++ if(profiling){ ++ ++ solution_time=profiler->DeltaTime(StartCore,FinishCore); ++ solution_flops=profiler->DeltaFlops(StartCore,FinishCore); ++ solution_memory=profiler->Memory(FinishCore); ++ ++ _pprintLine_("Solution elapsed time : " << solution_time << " Seconds"); ++ _pprintLine_("Solution elapsed flops : " << solution_flops << " Flops"); ++ _pprintLine_("Solution memory used : " << solution_memory << " Bytes"); ++ ++ /*Add to results: */ ++ results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingSolutionTimeEnum, solution_time, 1, 0)); ++ results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentMemEnum, solution_memory, 1, 0)); ++ results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentFlopsEnum, solution_flops, 1, 0)); ++ } ++ ++} /*}}}*/ +Index: ../trunk-jpl/src/c/solutions/DakotaSpawnCore.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/DakotaSpawnCore.cpp (revision 0) ++++ ../trunk-jpl/src/c/solutions/DakotaSpawnCore.cpp (revision 13539) +@@ -0,0 +1,198 @@ ++/*!\file: DakotaSpawnCore.cpp ++ ++ * \brief: run core ISSM solution using Dakota inputs coming from CPU 0. ++ * \sa qmu.cpp DakotaPlugin.cpp ++ * ++ * This routine needs to be understood simultaneously with qmu.cpp and DakotaPlugin. ++ * DakotaSpawnCoreParallel is called by all CPUS, with CPU 0 holding Dakota variable values, along ++ * with variable descriptors. ++ * ++ * DakotaSpawnCoreParallel takes care of broadcasting the variables and their descriptors across the MPI ++ * ring. Once this is done, we use the variables to modify the inputs for the solution core. ++ * For ex, if "rho_ice" is provided, for ex 920, we include "rho_ice" in the inputs, then ++ * call the core with the modified inputs. This is the way we get Dakota to explore the parameter ++ * spce of the core. ++ * ++ * Once the core is called, we process the results of the core, and using the processed results, ++ * we compute response functions. The responses are computed on all CPUS, but they are targeted ++ * for CPU 0, which will get these values back to the Dakota engine. ++ * ++ */ ++ ++/*Includes and prototypes: {{{*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#include "../classes/objects/objects.h" ++#include "../io/io.h" ++#include "../EnumDefinitions/EnumDefinitions.h" ++#include "../shared/shared.h" ++#include "../include/include.h" ++#include "../solutions/solutions.h" ++#include "../modules/modules.h" ++ ++void DakotaMPI_Bcast(double** pvariables, char*** pvariables_descriptors,int* pnumvariables, int* pnumresponses); ++void DakotaFree(double** pvariables,char*** pvariables_descriptors,char*** presponses_descriptors,int numvariables,int numresponses); ++ ++/*}}}*/ ++ ++/*Notice the d_, which prefixes anything that is being provided to us by the Dakota pluggin. Careful. some things are ours, some are dakotas!: */ ++int DakotaSpawnCore(double* d_responses, int d_numresponses, double* d_variables, char** d_variables_descriptors,int d_numvariables, void* void_femmodel,int counter){ ++ ++ int i; ++ extern int my_rank; ++ ++ char **responses_descriptors = NULL; //these are our! there are only numresponsedescriptors of them, not d_numresponses!!! ++ int numresponsedescriptors; ++ char *string = NULL; ++ int string_length; ++ int solution_type; ++ bool control_analysis = false; ++ void (*solutioncore)(FemModel*) = NULL; ++ FemModel* femmodel = NULL; ++ ++ ++ /*If counter==-1 on cpu0, it means that the dakota runs are done. In which case, bail out and return 0: */ ++ #ifdef _HAVE_MPI_ ++ MPI_Bcast(&counter,1,MPI_INT,0,MPI_COMM_WORLD); ++ #endif ++ if(counter==-1)return 0; ++ ++ /*cast void_femmodel to FemModel: */ ++ femmodel=(FemModel*)void_femmodel; ++ ++ /*retrieve parameters: */ ++ femmodel->parameters->FindParam(&responses_descriptors,&numresponsedescriptors,QmuResponsedescriptorsEnum); ++ femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); ++ femmodel->parameters->FindParam(&control_analysis,InversionIscontrolEnum); ++ ++ if(VerboseQmu()) _pprintLine_("qmu iteration: " << counter); ++ ++ /* only cpu 0, running dakota is providing us with variables and variables_descriptors and numresponses: broadcast onto other cpus: */ ++ DakotaMPI_Bcast(&d_variables,&d_variables_descriptors,&d_numvariables,&d_numresponses); ++ ++ /*Modify core inputs in objects contained in femmodel, to reflect the dakota variables inputs: */ ++ InputUpdateFromDakotax(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,d_variables,d_variables_descriptors,d_numvariables); ++ ++ /*Determine solution sequence: */ ++ if(VerboseQmu()) _pprintLine_("Starting " << EnumToStringx(solution_type) << " core:"); ++ CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); ++ #ifdef _HAVE_CONTROL_ ++ if(control_analysis)solutioncore=&control_core; ++ #else ++ _error_("ISSM was not compiled with control capabilities, exiting!"); ++ #endif ++ ++ /*Run the core solution sequence: */ ++ solutioncore(femmodel); ++ ++ /*compute responses: */ ++ if(VerboseQmu()) _pprintLine_("compute dakota responses:"); ++ DakotaResponsesx(d_responses,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,responses_descriptors,numresponsedescriptors,d_numresponses); ++ ++ /*Free ressources:*/ ++ DakotaFree(&d_variables,&d_variables_descriptors,&responses_descriptors, d_numvariables, numresponsedescriptors); ++} ++ ++void DakotaMPI_Bcast(double** pvariables, char*** pvariables_descriptors,int* pnumvariables, int* pnumresponses){ /*{{{*/ ++ ++ /* * \brief: broadcast variables_descriptors, variables, numvariables and numresponses ++ * from cpu 0 to all other cpus. ++ */ ++ ++ int i; ++ extern int my_rank; ++ ++ /*inputs and outputs: */ ++ double* variables=NULL; ++ char** variables_descriptors=NULL; ++ int numvariables; ++ int numresponses; ++ ++ /*intermediary: */ ++ char* string=NULL; ++ int string_length; ++ ++ ++ /*recover inputs from pointers: */ ++ variables=*pvariables; ++ variables_descriptors=*pvariables_descriptors; ++ numvariables=*pnumvariables; ++ numresponses=*pnumresponses; ++ ++ /*numvariables: */ ++ MPI_Bcast(&numvariables,1,MPI_INT,0,MPI_COMM_WORLD); ++ ++ /*variables:*/ ++ if(my_rank!=0)variables=xNew(numvariables); ++ MPI_Bcast(variables,numvariables,MPI_DOUBLE,0,MPI_COMM_WORLD); ++ ++ /*variables_descriptors: */ ++ if(my_rank!=0){ ++ variables_descriptors=xNew(numvariables); ++ } ++ for(i=0;i(string_length); ++ MPI_Bcast(string,string_length,MPI_CHAR,0,MPI_COMM_WORLD); ++ if(my_rank!=0)variables_descriptors[i]=string; ++ } ++ ++ /*numresponses: */ ++ MPI_Bcast(&numresponses,1,MPI_INT,0,MPI_COMM_WORLD); ++ ++ /*Assign output pointers:*/ ++ *pnumvariables=numvariables; ++ *pvariables=variables; ++ *pvariables_descriptors=variables_descriptors; ++ *pnumresponses=numresponses; ++} /*}}}*/ ++void DakotaFree(double** pvariables,char*** pvariables_descriptors,char*** presponses_descriptors,int numvariables,int numresponses){ /*{{{*/ ++ ++ /*\brief DakotaFree: free allocations on other cpus, not done by Dakota.*/ ++ ++ int i; ++ extern int my_rank; ++ ++ double *variables = NULL; ++ char **variables_descriptors = NULL; ++ char **responses_descriptors = NULL; ++ char *string = NULL; ++ ++ /*recover pointers: */ ++ variables=*pvariables; ++ variables_descriptors=*pvariables_descriptors; ++ responses_descriptors=*presponses_descriptors; ++ ++ ++ /*Free variables and variables_descriptors only on cpu !=0*/ ++ if(my_rank!=0){ ++ xDelete(variables); ++ for(i=0;i(string); ++ } ++ xDelete(variables_descriptors); ++ } ++ ++ //responses descriptors on every cpu ++ for(i=0;i(string); ++ } ++ //rest of dynamic allocations. ++ xDelete(responses_descriptors); ++ ++ /*Assign output pointers:*/ ++ *pvariables=variables; ++ *pvariables_descriptors=variables_descriptors; ++ *presponses_descriptors=responses_descriptors; ++} /*}}}*/ +Index: ../trunk-jpl/src/c/shared/String/sharedstring.h +=================================================================== +--- ../trunk-jpl/src/c/shared/String/sharedstring.h (revision 13538) ++++ ../trunk-jpl/src/c/shared/String/sharedstring.h (revision 13539) +@@ -7,5 +7,9 @@ + + int DescriptorIndex(char* root, int* pindex,char* descriptor); + ++#ifndef WIN32 ++int stricmp(const char* a,const char* b); ++#endif ++ + #endif //ifndef _SHAREDSTRING_H_ + +Index: ../trunk-jpl/src/c/shared/shared.h +=================================================================== +--- ../trunk-jpl/src/c/shared/shared.h (revision 13538) ++++ ../trunk-jpl/src/c/shared/shared.h (revision 13539) +@@ -15,6 +15,7 @@ + #include "MemOps/xMemCpy.h" + #include "Numerics/numerics.h" + #include "Sorting/sorting.h" ++#include "String/sharedstring.h" + #include "Threads/issm_threads.h" + #include "TriMesh/trimesh.h" + #include "Wrapper/wrappershared.h" +Index: ../trunk-jpl/src/c/modules/Dakotax/SpawnCoreParallel.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Dakotax/SpawnCoreParallel.cpp (revision 13538) ++++ ../trunk-jpl/src/c/modules/Dakotax/SpawnCoreParallel.cpp (revision 13539) +@@ -1,87 +0,0 @@ +-/*!\file: SpawnCoreParallel.cpp +- * \brief: run core ISSM solution using Dakota inputs coming from CPU 0. +- * \sa qmu.cpp DakotaPlugin.cpp +- * +- * This routine needs to be understood simultaneously with qmu.cpp and DakotaPlugin. +- * SpawnCoreParallel is called by all CPUS, with CPU 0 holding Dakota variable values, along +- * with variable descriptors. +- * +- * SpawnCoreParallel takes care of broadcasting the variables and their descriptors across the MPI +- * ring. Once this is done, we use the variables to modify the inputs for the solution core. +- * For ex, if "rho_ice" is provided, for ex 920, we include "rho_ice" in the inputs, then +- * call the core with the modified inputs. This is the way we get Dakota to explore the parameter +- * spce of the core. +- * +- * Once the core is called, we process the results of the core, and using the processed results, +- * we compute response functions. The responses are computed on all CPUS, but they are targeted +- * for CPU 0, which will get these values back to the Dakota engine. +- * +- */ +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +- +-#include "../../classes/objects/objects.h" +-#include "../../io/io.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +-#include "../../io/io.h" +-#include "../../shared/shared.h" +-#include "./Dakotax.h" +-#include "../../include/include.h" +-#include "../../solutions/solutions.h" +-#include "../modules.h" +- +-void SpawnCoreParallel(double* d_responses, int d_numresponses, double* d_variables, char** d_variables_descriptors,int d_numvariables, FemModel* femmodel,int counter){ +- +- /*Notice the d_, which prefixes anything that is being provided to us by the Dakota pluggin. Careful. some things are ours, some are dakotas!: */ +- +- int i; +- extern int my_rank; +- +- char **responses_descriptors = NULL; //these are our! there are only numresponsedescriptors of them, not d_numresponses!!! +- int numresponsedescriptors; +- char *string = NULL; +- int string_length; +- int solution_type; +- bool control_analysis = false; +- void (*solutioncore)(FemModel*) = NULL; +- +- /*synchronize all cpus, as CPU 0 is probably late (it is starting the entire dakota strategy!) : */ +- MPI_Barrier(MPI_COMM_WORLD); +- if(VerboseQmu()) _pprintLine_("qmu iteration: " << counter); +- +- /*retrieve parameters: */ +- femmodel->parameters->FindParam(&responses_descriptors,&numresponsedescriptors,QmuResponsedescriptorsEnum); +- femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); +- femmodel->parameters->FindParam(&control_analysis,InversionIscontrolEnum); +- +- /* only cpu 0, running dakota is providing us with variables and variables_descriptors and numresponses: broadcast onto other cpus: */ +- DakotaMPI_Bcast(&d_variables,&d_variables_descriptors,&d_numvariables,&d_numresponses); +- +- /*Modify core inputs in objects contained in femmodel, to reflect the dakota variables inputs: */ +- InputUpdateFromDakotax(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,d_variables,d_variables_descriptors,d_numvariables); +- +- /*Determine solution sequence: */ +- if(VerboseQmu()) _pprintLine_("Starting " << EnumToStringx(solution_type) << " core:"); +- CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); +- #ifdef _HAVE_CONTROL_ +- if(control_analysis)solutioncore=&control_core; +- #else +- _error_("ISSM was not compiled with control capabilities, exiting!"); +- #endif +- +- /*Run the core solution sequence: */ +- solutioncore(femmodel); +- +- /*compute responses: */ +- if(VerboseQmu()) _pprintLine_("compute dakota responses:"); +- DakotaResponsesx(d_responses,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,responses_descriptors,numresponsedescriptors,d_numresponses); +- +- /*Free ressources:*/ +- DakotaFree(&d_variables,&d_variables_descriptors,&responses_descriptors, d_numvariables, numresponsedescriptors); +-} +- +Index: ../trunk-jpl/src/c/modules/Dakotax/SpawnCore.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Dakotax/SpawnCore.cpp (revision 13538) ++++ ../trunk-jpl/src/c/modules/Dakotax/SpawnCore.cpp (revision 13539) +@@ -1,29 +0,0 @@ +-/*!\file: SpawnCore.cpp +- * \brief: branch into SpawnCoreMatlab and SpawnCoreParallel. +- */ +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +- +-#include "../../classes/objects/objects.h" +-#include "../../io/io.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +-#include "../../shared/shared.h" +-#include "./Dakotax.h" +-#include "../../include/include.h" +- +-int SpawnCore(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, void* femmodel,int counter){ +- +- /*Branch into a serial SpawnCore and a parallel SpawnCore: */ +- +- /*Call SpawnCoreParallel unless counter=-1 on cpu0, in which case, bail out and return 0: */ +- MPI_Bcast(&counter,1,MPI_INT,0,MPI_COMM_WORLD); +- if(counter==-1)return 0; +- +- SpawnCoreParallel(responses, numresponses, variables, variables_descriptors,numvariables, (FemModel*)femmodel,counter); +- return 1; +-} +Index: ../trunk-jpl/src/c/modules/Dakotax/DakotaFree.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Dakotax/DakotaFree.cpp (revision 13538) ++++ ../trunk-jpl/src/c/modules/Dakotax/DakotaFree.cpp (revision 13539) +@@ -1,57 +0,0 @@ +-/*!\file: DakotaFree.cpp +- * \brief DakotaFree: free allocations on other cpus, not done by Dakota. +- +- */ +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-#include "../../Container/Container.h" +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +-#include "../modules.h" +- +- +-void DakotaFree(double** pvariables,char*** pvariables_descriptors,char*** presponses_descriptors,int numvariables,int numresponses){ +- +- int i; +- extern int my_rank; +- +- double *variables = NULL; +- char **variables_descriptors = NULL; +- char **responses_descriptors = NULL; +- char *string = NULL; +- +- /*recover pointers: */ +- variables=*pvariables; +- variables_descriptors=*pvariables_descriptors; +- responses_descriptors=*presponses_descriptors; +- +- +- /*Free variables and variables_descriptors only on cpu !=0*/ +- if(my_rank!=0){ +- xDelete(variables); +- for(i=0;i(string); +- } +- xDelete(variables_descriptors); +- } +- +- //responses descriptors on every cpu +- for(i=0;i(string); +- } +- //rest of dynamic allocations. +- xDelete(responses_descriptors); +- +- /*Assign output pointers:*/ +- *pvariables=variables; +- *pvariables_descriptors=variables_descriptors; +- *presponses_descriptors=responses_descriptors; +-} +Index: ../trunk-jpl/src/c/modules/Dakotax/DakotaMPI_Bcast.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Dakotax/DakotaMPI_Bcast.cpp (revision 13538) ++++ ../trunk-jpl/src/c/modules/Dakotax/DakotaMPI_Bcast.cpp (revision 13539) +@@ -1,66 +0,0 @@ +-/*!\file: DakotaMPI_Bcast +- * \brief: broadcast variables_descriptors, variables, numvariables and numresponses +- * from cpu 0 to all other cpus. +- */ +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-#include "./Dakotax.h" +- +-void DakotaMPI_Bcast(double** pvariables, char*** pvariables_descriptors,int* pnumvariables, int* pnumresponses){ +- +- int i; +- extern int my_rank; +- +- /*inputs and outputs: */ +- double* variables=NULL; +- char** variables_descriptors=NULL; +- int numvariables; +- int numresponses; +- +- /*intermediary: */ +- char* string=NULL; +- int string_length; +- +- +- /*recover inputs from pointers: */ +- variables=*pvariables; +- variables_descriptors=*pvariables_descriptors; +- numvariables=*pnumvariables; +- numresponses=*pnumresponses; +- +- /*numvariables: */ +- MPI_Bcast(&numvariables,1,MPI_INT,0,MPI_COMM_WORLD); +- +- /*variables:*/ +- if(my_rank!=0)variables=xNew(numvariables); +- MPI_Bcast(variables,numvariables,MPI_DOUBLE,0,MPI_COMM_WORLD); +- +- /*variables_descriptors: */ +- if(my_rank!=0){ +- variables_descriptors=xNew(numvariables); +- } +- for(i=0;i(string_length); +- MPI_Bcast(string,string_length,MPI_CHAR,0,MPI_COMM_WORLD); +- if(my_rank!=0)variables_descriptors[i]=string; +- } +- +- /*numresponses: */ +- MPI_Bcast(&numresponses,1,MPI_INT,0,MPI_COMM_WORLD); +- +- /*Assign output pointers:*/ +- *pnumvariables=numvariables; +- *pvariables=variables; +- *pvariables_descriptors=variables_descriptors; +- *pnumresponses=numresponses; +-} +Index: ../trunk-jpl/src/c/modules/Dakotax/DescriptorIndex.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Dakotax/DescriptorIndex.cpp (revision 13538) ++++ ../trunk-jpl/src/c/modules/Dakotax/DescriptorIndex.cpp (revision 13539) +@@ -1,71 +0,0 @@ +-/*!\file: DescriptorIndex: return type of qmu variable: indexed, scaled, nodal or regular +- * + figure out the descriptor root. +- * Ex: scaled_Thickness_1 should return SCALEDENUM, fill root with Thickness, and initialize index +- * to 1. +- */ +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-#include +-#include +-#include +-#include "../../shared/shared.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +- +-int DescriptorIndex(char* root, int* pindex,char* descriptor){ //We assume root has already been allocated, and we just have to copy into it. +- +- char * pch=NULL; +- +- /*retrieve first token, separated by underscore: */ +- pch = strtok (descriptor,"_"); +- if(!pch)_error_("descriptor " << descriptor << " is not correctly formatted!"); +- +- if (strncmp(pch,"scaled",6)==0){ +- /*we have a scaled variable. recover the root: */ +- pch = strtok (NULL, "_"); +- if(!pch)_error_("scaled descriptor " << descriptor << " is not correctly formatted!"); +- memcpy(root,pch,(strlen(pch)+1)*sizeof(char)); +- +- /*now recover the index if it exists: */ +- pch = strtok (NULL, "_"); +- if(!pch){ +- *pindex=-1; +- } +- else{ +- sscanf(pch,"%i",pindex); +- } +- return ScaledEnum; +- } +- else if (strncmp(pch,"indexed",7)==0){ +- /*we have an indexed variable. recover the root: */ +- pch = strtok (NULL, "_"); +- if(!pch)_error_("indexed descriptor " << descriptor << " is not correctly formatted!"); +- memcpy(root,pch,(strlen(pch)+1)*sizeof(char)); +- /*now recover the index: */ +- pch = strtok (NULL, "_"); +- if(!pch)_error_("indexed descriptor " << descriptor << " is not correctly formatted!"); +- sscanf(pch,"%i",pindex); +- return IndexedEnum; +- } +- else if (strncmp(pch,"nodal",5)==0){ +- /*we have an indexed variable. recover the root: */ +- pch = strtok (NULL, "_"); +- if(!pch)_error_("nodal descriptor " << descriptor << " is not correctly formatted!"); +- memcpy(root,pch,(strlen(pch)+1)*sizeof(char)); +- /*now recover the index: */ +- pch = strtok (NULL, "_"); +- if(!pch)_error_("nodal descriptor " << descriptor << " is not correctly formatted!"); +- sscanf(pch,"%i",pindex); +- return NodalEnum; +- } +- else{ +- /*We don't have _ in the name, this is a regular variable: */ +- memcpy(root,pch,(strlen(pch)+1)*sizeof(char)); +- *pindex=-1; +- return RegularEnum; +- } +-} +Index: ../trunk-jpl/src/c/modules/Dakotax/Dakotax.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/Dakotax/Dakotax.cpp (revision 13538) ++++ ../trunk-jpl/src/c/modules/Dakotax/Dakotax.cpp (revision 13539) +@@ -1,128 +0,0 @@ +-/*!\file: Dakotax.cpp +- * \brief: wrapper to the Dakota capabilities. qmu fires up Dakota, and registers a Dakota Pluggin +- * which will be in charge of running the solution sequences repeteadly, to garner statistics. +- * +- * This routine deals with running ISSM and Dakota in library mode. In library mode, Dakota does not +- * run as an execuatble. Its capabilities are linked into the ISSM software. ISSM calls dakota routines +- * directly from the dakota library. qmu.cpp is the code that is in charge of calling those routines. +- * +- * Dakota has its own way of running in parallel (for embarassingly parallel jobs). We do not want that, +- * as ISSM knows exactly how to run "really parallel" jobs that use all CPUS. To bypass Dakota's parallelism, +- * we overloaded the constructor for the parallel library (see the Dakota patch in the externalpackages/dakota +- * directory). This overloaded constructor fires up Dakota serially on CPU 0 only! We take care of broadcasting +- * to the other CPUS, hence ISSM is running in parallel, and Dakota serially on CPU0. +- * +- * Now, how does CPU 0 drive all other CPUS to carry out sensitivity analysese? By synchronizing its call to +- * our ISSM cores (diagnostic_core, thermal_core, transient_core, etc ...) on CPU 0 with all other CPUS. +- * This explains the structure of qmu.cpp, where cpu 0 runs Dakota, the Dakota pluggin fires up SpawnCore.cpp, +- * while the other CPUS are waiting for a broadcast from CPU0, once they get it, they also fire up +- * SpawnCore. In the end, SpawnCore is fired up on all CPUS, with CPU0 having Dakota inputs, that it will +- * broacast to other CPUS. +- * +- * Now, how does dakota call the SpawnCore routine? The SpawnCore is embedded into the DakotaPlugin object +- * which is derived from the Direct Interface Dakota objct. This is the only way to run Dakota in library +- * mode (see their developper guide for more info). Dakota registers the DakotaPlugin object into its own +- * database, and calls on the embedded SpawnCore from CPU0. +- * +- */ +- +-#ifdef HAVE_CONFIG_H +-#include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-#include "./Dakotax.h" +- +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../../io/io.h" +-#include "../../toolkits/toolkits.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +-#include "../../classes/dakota/DakotaPlugin.h" +- +-#ifdef _HAVE_DAKOTA_ //only works if dakota library has been compiled in. +-#include "ParallelLibrary.H" +-#include "ProblemDescDB.H" +-#include "DakotaStrategy.H" +-#include "DakotaModel.H" +-#include "DakotaInterface.H" +- +-#endif +- +-void Dakotax(FemModel* femmodel){ +- +- +- #ifdef _HAVE_DAKOTA_ //only works if dakota library has been compiled in. +- +- extern int my_rank; +- char* dakota_input_file = NULL; +- char* dakota_output_file = NULL; +- char* dakota_error_file = NULL; +- int status=0; +- Dakota::ModelLIter ml_iter; +- Parameters* parameters = NULL; +- +- /*Retrieve parameters: */ +- parameters=femmodel->parameters; +- +- /*Recover dakota_input_file, dakota_output_file and dakota_error_file, in the parameters dataset in parallel */ +- parameters->FindParam(&dakota_input_file,QmuInNameEnum); +- parameters->FindParam(&dakota_output_file,QmuOutNameEnum); +- parameters->FindParam(&dakota_error_file,QmuErrNameEnum); +- +- if(my_rank==0){ +- +- // Instantiate/initialize the parallel library and problem description +- // database objects. +- Dakota::ParallelLibrary parallel_lib("serial"); //use our own ISSM Dakota library mode constructor, which only fires up Dakota on CPU 0. +- Dakota::ProblemDescDB problem_db(parallel_lib); +- +- // Manage input file parsing, output redirection, and restart processing +- // without a CommandLineHandler. This version relies on parsing of an +- // input file. +- problem_db.manage_inputs(dakota_input_file); +- // specify_outputs_restart() is only necessary if specifying non-defaults +- parallel_lib.specify_outputs_restart(dakota_output_file,dakota_error_file,NULL,NULL); +- +- // Instantiate the Strategy object (which instantiates all Model and +- // Iterator objects) using the parsed information in problem_db. +- Dakota::Strategy selected_strategy(problem_db); +- +- // convenience function for iterating over models and performing any +- // interface plug-ins +- Dakota::ModelList& models = problem_db.model_list(); +- +- for (ml_iter = models.begin(); ml_iter != models.end(); ml_iter++) { +- +- Dakota::Interface& interface = ml_iter->interface(); +- +- //set DB nodes to the existing Model specification +- problem_db.set_db_model_nodes(ml_iter->model_id()); +- +- // Serial case: plug in derived Interface object without an analysisComm +- interface.assign_rep(new SIM::DakotaPlugin(problem_db,(void*)femmodel), false); +- } +- +- // Execute the strategy +- problem_db.lock(); // prevent run-time DB queries +- selected_strategy.run_strategy(); +- +- //Warn other cpus that we are done running the dakota iterator, by setting the counter to -1: +- SpawnCore(NULL,0, NULL,NULL,0,femmodel,-1); +- +- } +- else{ +- +- for(;;){ +- if(!SpawnCore(NULL,0, NULL,NULL,0,femmodel,0))break; //counter came in at -1 on cpu0, bail out. +- } +- } +- +- /*Free ressources:*/ +- xDelete(dakota_input_file); +- xDelete(dakota_error_file); +- xDelete(dakota_output_file); +- +- #endif //#ifdef _HAVE_DAKOTA_ +-} +Index: ../trunk-jpl/src/c/modules/Dakotax/Dakotax.h +=================================================================== +--- ../trunk-jpl/src/c/modules/Dakotax/Dakotax.h (revision 13538) ++++ ../trunk-jpl/src/c/modules/Dakotax/Dakotax.h (revision 13539) +@@ -9,13 +9,7 @@ + #include "../../classes/classes.h" + + /* local prototypes: */ +-int SpawnCore(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, void* femmodel,int counter); +-int DescriptorIndex(char* root, int* pindex,char* descriptor); +- + void Dakotax(FemModel* femmodel); +-void SpawnCoreParallel(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, FemModel* femmodel,int counter); +-void DakotaResponses(double* responses,char** responses_descriptors,int numresponses,FemModel* femmodel); +-void DakotaMPI_Bcast(double** pvariables, char*** pvariables_descriptors,int* pnumvariables, int* pnumresponses); +-void DakotaFree(double** pvariables,char*** pvariables_descriptors,char*** presponses_descriptors,int numvariables,int numresponses); ++int DakotaSpawnCore(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, void* femmodel,int counter); + + #endif /* _DAKOTAX_H */ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13538) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13539) +@@ -220,6 +220,7 @@ + ./shared/Elements/PddSurfaceMassBalance.cpp\ + ./shared/Elements/ComputeDelta18oTemperaturePrecipitation.cpp\ + ./shared/String/sharedstring.h\ ++ ./shared/String/DescriptorIndex.cpp\ + ./shared/Wrapper/wrappershared.h\ + ./shared/Wrapper/ModuleBoot.cpp\ + ./shared/Wrapper/ModuleEnd.cpp\ +@@ -372,14 +373,9 @@ + ./modules/InputUpdateFromMatrixDakotax/InputUpdateFromMatrixDakotax.cpp\ + ./modules/AverageOntoPartitionx/AverageOntoPartitionx.cpp\ + ./modules/AverageOntoPartitionx/AverageOntoPartitionx.h\ +- ./modules/Dakotax/Dakotax.h\ +- ./modules/Dakotax/Dakotax.cpp\ +- ./modules/Dakotax/DakotaMPI_Bcast.cpp\ +- ./modules/Dakotax/DakotaFree.cpp\ +- ./modules/Dakotax/SpawnCore.cpp\ +- ./modules/Dakotax/DescriptorIndex.cpp\ + ./modules/ModelProcessorx/Dakota/CreateParametersDakota.cpp\ +- ./modules/Dakotax/SpawnCoreParallel.cpp ++ ./solutions/dakota_core.cpp\ ++ ./solutions/DakotaSpawnCore.cpp + #}}} + #Transient sources {{{ + transient_sources = ./modules/ModelProcessorx/Transient/UpdateElementsTransient.cpp \ +Index: ../trunk-jpl/src/c/classes/objects/Profiler.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Profiler.cpp (revision 13538) ++++ ../trunk-jpl/src/c/classes/objects/Profiler.cpp (revision 13539) +@@ -15,12 +15,12 @@ + /*Profiler constructors and destructors:*/ + /*FUNCTION Profiler::Profiler() default constructor {{{*/ + Profiler::Profiler(){ +- this->timetags=new Parameters(); ++ this->time=new Parameters(); + } + /*}}}*/ + /*FUNCTION Profiler::~Profiler(){{{*/ + Profiler::~Profiler(){ +- delete timetags; ++ delete time; + } + /*}}}*/ + +@@ -30,7 +30,7 @@ + + _printLine_("Profiler:"); + _printLine_(" time tags: "); +- this->timetags->Echo(); ++ this->time->Echo(); + + } + /*}}}*/ +@@ -39,7 +39,7 @@ + + _printLine_("Profiler:"); + _printLine_(" time tags: "); +- this->timetags->DeepEcho(); ++ this->time->DeepEcho(); + + } + /*}}}*/ +@@ -58,7 +58,9 @@ + /*FUNCTION Profiler::Tag {{{*/ + void Profiler::Tag(int tagenum,bool dontmpisync){ + +- double time; ++ IssmDouble t; ++ IssmDouble f; ++ IssmDouble m; + + /*If mpisync requested, make sure all the cpus are at the same point + *in the execution: */ +@@ -68,24 +70,34 @@ + #endif + } + +- /*Now capture time: */ ++ /*Capture time: */ + #ifdef _HAVE_MPI_ +- time=MPI_Wtime(); ++ t=MPI_Wtime(); + #else +- time=(IssmPDouble)clock(); ++ t=(IssmPDouble)clock(); + #endif + +- /*Plug into this->timetags: */ +- this->timetags->AddObject(new DoubleParam(tagenum,time)); ++ /*Capture flops: */ ++ #ifdef _HAVE_PETSC_ ++ PetscGetFlops(&f); ++ PetscMemoryGetCurrentUsage(&m); ++ #else ++ /*do nothing for now:*/ ++ #endif + ++ /*Plug into this->time: */ ++ this->time->AddObject(new DoubleParam(tagenum,t)); ++ this->flops->AddObject(new DoubleParam(tagenum,f)); ++ this->memory->AddObject(new DoubleParam(tagenum,m)); ++ + } + /*}}}*/ +-/*FUNCTION Profiler::Delta {{{*/ +-double Profiler::Delta(int inittag, int finaltag){ ++/*FUNCTION Profiler::DeltaTime {{{*/ ++IssmDouble Profiler::DeltaTime(int inittag, int finaltag){ + +- double init, final; +- this->timetags->FindParam(&init,inittag); +- this->timetags->FindParam(&final,finaltag); ++ IssmDouble init, final; ++ this->time->FindParam(&init,inittag); ++ this->time->FindParam(&final,finaltag); + + #ifdef _HAVE_MPI_ + return final-init; +@@ -94,46 +106,65 @@ + #endif + } + /*}}}*/ +-/*FUNCTION Profiler::DeltaModHour {{{*/ +-int Profiler::DeltaModHour(int inittag, int finishtag){ ++/*FUNCTION Profiler::DeltaFlops {{{*/ ++IssmDouble Profiler::DeltaFlops(int inittag, int finaltag){ + +- double init, finish; +- this->timetags->FindParam(&init,inittag); +- this->timetags->FindParam(&finish,finishtag); ++ IssmDouble init, final; ++ this->flops->FindParam(&init,inittag); ++ this->flops->FindParam(&final,finaltag); + ++ return final-init; ++} ++/*}}}*/ ++/*FUNCTION Profiler::DeltaTimeModHour {{{*/ ++int Profiler::DeltaTimeModHour(int inittag, int finishtag){ ++ ++ IssmDouble init, finish; ++ this->time->FindParam(&init,inittag); ++ this->time->FindParam(&finish,finishtag); ++ + #ifdef _HAVE_MPI_ +- return int((finish-init)/3600); ++ return int((reCast(finish-init))/3600); + #else +- return int((finish-init)/CLOCKS_PER_SEC/3600); ++ return int((reCast(finish-init))/CLOCKS_PER_SEC/3600); + #endif + + } + /*}}}*/ +-/*FUNCTION Profiler::DeltaModMin {{{*/ +-int Profiler::DeltaModMin(int inittag, int finishtag){ ++/*FUNCTION Profiler::DeltaTimeModMin {{{*/ ++int Profiler::DeltaTimeModMin(int inittag, int finishtag){ + +- double init, finish; +- this->timetags->FindParam(&init,inittag); +- this->timetags->FindParam(&finish,finishtag); ++ IssmDouble init, finish; ++ this->time->FindParam(&init,inittag); ++ this->time->FindParam(&finish,finishtag); + + #ifdef _HAVE_MPI_ +- return int(int(finish-init)%3600/60); ++ return int(int(reCast(finish-init))%3600/60); + #else +- return int(int(finish-init)/CLOCKS_PER_SEC%3600/60); ++ return int(int(reCast(finish-init))/CLOCKS_PER_SEC%3600/60); + #endif + } + /*}}}*/ +-/*FUNCTION Profiler::DeltaModSec {{{*/ +-int Profiler::DeltaModSec(int inittag, int finishtag){ ++/*FUNCTION Profiler::DeltaTimeModSec {{{*/ ++int Profiler::DeltaTimeModSec(int inittag, int finishtag){ + +- double init, finish; +- this->timetags->FindParam(&init,inittag); +- this->timetags->FindParam(&finish,finishtag); ++ IssmDouble init, finish; ++ this->time->FindParam(&init,inittag); ++ this->time->FindParam(&finish,finishtag); + + #ifdef _HAVE_MPI_ +- return int(finish-init)%60; ++ return int(reCast(finish-init))%60; + #else +- return int(finish-init)/CLOCKS_PER_SEC%60; ++ return int(reCast(finish-init))/CLOCKS_PER_SEC%60; + #endif + } + /*}}}*/ ++/*FUNCTION Profiler::Memory {{{*/ ++IssmDouble Profiler::Memory(int tag){ ++ ++ IssmDouble m; ++ this->memory->FindParam(&m,tag); ++ ++ return m; ++} ++/*}}}*/ +Index: ../trunk-jpl/src/c/classes/objects/Profiler.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Profiler.h (revision 13538) ++++ ../trunk-jpl/src/c/classes/objects/Profiler.h (revision 13539) +@@ -27,7 +27,9 @@ + class Profiler: public Object{ + + public: +- Parameters* timetags; ++ Parameters* time; ++ Parameters* flops; ++ Parameters* memory; + + /*Profiler constructors, destructors {{{*/ + Profiler(); +@@ -42,10 +44,12 @@ + /*}}}*/ + /*Profiler routines {{{*/ + void Tag(int tagenum,bool dontmpisync=false); +- double Delta(int inittag, int finaltag); +- int DeltaModHour(int inittag, int finaltag); +- int DeltaModMin(int inittag, int finaltag); +- int DeltaModSec(int inittag, int finaltag); ++ IssmDouble Memory(int tag); ++ IssmDouble DeltaTime(int inittag, int finaltag); ++ IssmDouble DeltaFlops(int inittag, int finaltag); ++ int DeltaTimeModHour(int inittag, int finaltag); ++ int DeltaTimeModMin(int inittag, int finaltag); ++ int DeltaTimeModSec(int inittag, int finaltag); + /*}}}*/ + }; + +Index: ../trunk-jpl/src/c/classes/dakota/DakotaPlugin.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/dakota/DakotaPlugin.cpp (revision 13538) ++++ ../trunk-jpl/src/c/classes/dakota/DakotaPlugin.cpp (revision 13539) +@@ -87,7 +87,7 @@ + responses=xNewZeroInit(numFns); + + /*run core solution: */ +- SpawnCore(responses,numFns, variables,variable_descriptors,numACV,femmodel,counter); ++ DakotaSpawnCore(responses,numFns, variables,variable_descriptors,numACV,femmodel,counter); + + /*populate responses: */ + for(i=0;iFindParam(&dakota_analysis,QmuIsdakotaEnum); ++ parameters->FindParam(&control_analysis,InversionIscontrolEnum); ++ parameters->FindParam(&tao_analysis,InversionTaoEnum); ++ ++ if(nodakotacore)dakota_analysis=false; ++ ++ if(dakota_analysis){ ++ #ifdef _HAVE_DAKOTA_ ++ solutioncore=dakota_core; ++ #else ++ _error_("ISSM was not compiled with dakota support, cannot carry out dakota analysis!"); ++ #endif + } +- ++ else if(control_analysis){ ++ #ifdef _HAVE_CONTROL_ ++ if(tao_analysis) solutioncore=controltao_core; ++ else solutioncore=control_core; ++ #else ++ _error_("ISSM was not compiled with control support, cannot carry out control analysis!"); ++ #endif ++ } ++ else PureCorePointerFromSolutionEnum(&solutioncore,parameters,solutiontype); /*This means we retrieve a core solution that is not a wrapper*/ ++ + /*Assign output pointer:*/ + _assert_(psolutioncore); + *psolutioncore=solutioncore; +Index: ../trunk-jpl/src/c/solutions/PureCorePointerFromSolutionEnum.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/PureCorePointerFromSolutionEnum.cpp (revision 0) ++++ ../trunk-jpl/src/c/solutions/PureCorePointerFromSolutionEnum.cpp (revision 13540) +@@ -0,0 +1,106 @@ ++/*!\file: PureCorePointerFromSolutionEnum.cpp ++ * \brief: return type of analyses, number of analyses and core solution function. ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "../toolkits/toolkits.h" ++#include "../classes/objects/objects.h" ++#include "../shared/shared.h" ++#include "../EnumDefinitions/EnumDefinitions.h" ++#include "./solutions.h" ++#include "../modules/modules.h" ++#include "../include/include.h" ++#include "../solvers/solvers.h" ++ ++void PureCorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype){ ++ ++ /*output: */ ++ void (*solutioncore)(FemModel*)=NULL; ++ ++ switch(solutiontype){ ++ ++ case DiagnosticSolutionEnum: ++ #ifdef _HAVE_DIAGNOSTIC_ ++ solutioncore=&diagnostic_core; ++ #else ++ _error_("ISSM was not compiled with diagnostic capabilities. Exiting"); ++ #endif ++ break; ++ case SteadystateSolutionEnum: ++ #ifdef _HAVE_STEADYSTATE_ ++ solutioncore=&steadystate_core; ++ #else ++ _error_("ISSM was not compiled with steady state capabilities. Exiting"); ++ #endif ++ break; ++ case ThermalSolutionEnum: ++ #ifdef _HAVE_THERMAL_ ++ solutioncore=&thermal_core; ++ #else ++ _error_("ISSM was not compiled with thermal capabilities. Exiting"); ++ #endif ++ break; ++ case EnthalpySolutionEnum: ++ #ifdef _HAVE_THERMAL_ ++ solutioncore=&enthalpy_core; ++ #else ++ _error_("ISSM was not compiled with thermal capabilities. Exiting"); ++ #endif ++ break; ++ case BalancethicknessSolutionEnum: ++ #ifdef _HAVE_BALANCED_ ++ solutioncore=&balancethickness_core; ++ #else ++ _error_("ISSM was not compiled with balanced capabilities. Exiting"); ++ #endif ++ break; ++ case HydrologySolutionEnum: ++ #ifdef _HAVE_HYDROLOGY_ ++ solutioncore=&hydrology_core; ++ #else ++ _error_("ISSM was not compiled with hydrology capabilities. Exiting"); ++ #endif ++ break; ++ case SurfaceSlopeSolutionEnum: ++ #ifdef _HAVE_SLOPE_ ++ solutioncore=&surfaceslope_core; ++ #else ++ _error_("ISSM was not compiled with slope capabilities. Exiting"); ++ #endif ++ break; ++ case BedSlopeSolutionEnum: ++ #ifdef _HAVE_SLOPE_ ++ solutioncore=&bedslope_core; ++ #else ++ _error_("ISSM was not compiled with slope capabilities. Exiting"); ++ #endif ++ break; ++ case TransientSolutionEnum: ++ #ifdef _HAVE_TRANSIENT_ ++ solutioncore=&transient_core; ++ #else ++ _error_("ISSM was not compiled with transient capabilities. Exiting"); ++ #endif ++ break; ++ case PrognosticSolutionEnum: ++ #ifdef _HAVE_PROGNOSTIC_ ++ solutioncore=&prognostic_core; ++ #else ++ _error_("ISSM was not compiled with prognostic capabilities. Exiting"); ++ #endif ++ break; ++ default: ++ _error_("solution type: " << EnumToStringx(solutiontype) << " not supported yet!"); ++ break; ++ } ++ ++ /*Assign output pointer:*/ ++ _assert_(psolutioncore); ++ *psolutioncore=solutioncore; ++ ++} +Index: ../trunk-jpl/src/c/solutions/ad_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/ad_core.cpp (revision 0) ++++ ../trunk-jpl/src/c/solutions/ad_core.cpp (revision 13540) +@@ -0,0 +1,301 @@ ++/*!\file ad_core ++ * \brief: compute outputs from the AD mode, using our dependents and independents, and drivers available in Adolc. ++ */ ++ ++/*Includes: {{{*/ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++ ++#include ++#include "../toolkits/toolkits.h" ++#include "../classes/objects/objects.h" ++#include "../shared/shared.h" ++#include "../io/io.h" ++#include "../EnumDefinitions/EnumDefinitions.h" ++#include "./solutions.h" ++#include "../modules/modules.h" ++#include "../include/include.h" ++#include "../solvers/solvers.h" ++/*}}}*/ ++ ++void ad_core(FemModel* femmodel){ ++ ++ /*diverse: */ ++ int i; ++ int dummy; ++ ++ bool isautodiff = false; ++ int num_dependents; ++ int num_independents; ++ char* driver=NULL; ++ ++ /*state variables: */ ++ IssmDouble *axp = NULL; ++ double *xp = NULL; ++ ++ /*AD mode on?: */ ++ femmodel->parameters->FindParam(&isautodiff,AutodiffIsautodiffEnum); ++ ++ if(isautodiff){ ++ ++ #ifdef _HAVE_ADOLC_ ++ ++ if(VerboseAutodiff())_pprintLine_(" start ad core"); ++ ++ /*First, stop tracing: */ ++ trace_off(); ++ ++ /*preliminary checks: */ ++ femmodel->parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); ++ femmodel->parameters->FindParam(&num_independents,AutodiffNumIndependentsEnum); ++ if(!(num_dependents*num_independents)) return; ++ ++ /*retrieve state variable: */ ++ femmodel->parameters->FindParam(&axp,&dummy,AutodiffXpEnum); ++ ++ /* driver argument */ ++ xp=xNew(num_independents); ++ for(i=0;i(axp[i]); ++ } ++ ++ /*get the EDF pointer:*/ ++ ext_diff_fct *anEDF_for_solverx_p=dynamic_cast * >(femmodel->parameters->FindParamObject(AdolcParamEnum))->GetParameterValue().myEDF_for_solverx_p; ++ ++ /*Branch according to AD driver: */ ++ femmodel->parameters->FindParam(&driver,AutodiffDriverEnum); ++ ++ /* these are always needed regardless of the interpreter */ ++ anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); ++ ++ if (strcmp(driver,"fos_forward")==0){ ++ ++ int anIndepIndex; ++ double *tangentDir=NULL; ++ double *jacTimesTangentDir=NULL; ++ double *theOutput=NULL; ++ ++ /*retrieve direction index: */ ++ femmodel->parameters->FindParam(&anIndepIndex,AutodiffFosForwardIndexEnum); ++ ++ if (anIndepIndex<0 || anIndepIndex>=num_independents) _error_("index value for AutodiffFosForwardIndexEnum should be in [0,num_independents-1]"); ++ ++ tangentDir=xNewZeroInit(num_independents); ++ tangentDir[anIndepIndex]=1.0; ++ ++ jacTimesTangentDir=xNew(num_dependents); ++ theOutput=xNew(num_dependents); ++ ++ /*set the forward method function pointer: */ ++ anEDF_for_solverx_p->fos_forward=EDF_fos_forward_for_solverx; ++ ++ /*allocate the space for the parameters to invoke the EDF fos_forward:*/ ++ anEDF_for_solverx_p->dp_X=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dp_Y=xNew(anEDF_for_solverx_p->max_m); ++ ++ /*call driver: */ ++ fos_forward(1,num_dependents,num_independents, 0, xp, tangentDir, theOutput, jacTimesTangentDir ); ++ ++ /*add to results*/ ++ femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,AutodiffJacobianEnum,jacTimesTangentDir,num_dependents,1,1,0.0)); ++ ++ /*free resources :*/ ++ xDelete(theOutput); ++ xDelete(jacTimesTangentDir); ++ xDelete(tangentDir); ++ } ++ else if ((strcmp(driver,"fov_forward")==0) || (strcmp(driver,"fov_forward_all")==0)){ ++ ++ int* indepIndices=NULL; ++ int tangentDirNum; ++ int dummy; ++ double **jacTimesSeed=NULL; ++ double **seed=NULL; ++ double *theOutput=NULL; ++ std::set anIndexSet; ++ ++ ++ /*retrieve directions:*/ ++ if (strcmp(driver,"fov_forward_all")==0){ ++ tangentDirNum=num_independents; ++ indepIndices=xNewZeroInit(tangentDirNum); ++ for(i=0;iparameters->FindParam(&indepIndices,&tangentDirNum,&dummy,AutodiffFovForwardIndicesEnum); ++ } ++ ++ /*Some checks: */ ++ if (tangentDirNum<1 || tangentDirNum>num_independents) _error_("tangentDirNum should be in [1,num_independents]"); ++ ++ /* full Jacobian or Jacobian projection:*/ ++ jacTimesSeed=xNew(num_dependents,tangentDirNum); ++ ++ /*set the forward method function pointers: */ ++ anEDF_for_solverx_p->fov_forward=EDF_fov_forward_for_solverx; ++ // anEDF_for_solverx_p->fov_reverse=EDF_fov_reverse_for_solverx; ++ ++ /*allocate the space for the parameters to invoke EDF fov_forward:*/ ++ anEDF_for_solverx_p->dpp_X=xNew(anEDF_for_solverx_p->max_n, tangentDirNum); ++ anEDF_for_solverx_p->dpp_Y=xNew(anEDF_for_solverx_p->max_m, tangentDirNum); ++ ++ /*seed matrix: */ ++ seed=xNewZeroInit(num_independents,tangentDirNum); ++ ++ /*collect indices in a set to prevent accidental duplicates as long as we don't do compression:*/ ++ for (int i=0; inum_independents) { ++ _error_("indepIndices values must be in [0,num_independents-1]"); ++ } ++ if (anIndexSet.find(indepIndices[i])!=anIndexSet.end()) { ++ _error_("duplicate indepIndices values are not allowed until we implement Jacobian decompression"); ++ } ++ anIndexSet.insert(indepIndices[i]); ++ /* now populate the seed matrix from the set of independent indices; ++ * simple setup with a single 1.0 per column and at most a single 1.0 per row*/ ++ seed[indepIndices[i]][i]=1.0; ++ } ++ ++ /*allocate output: */ ++ theOutput=xNew(num_dependents); ++ ++ /*call driver: */ ++ fov_forward(1,num_dependents,num_independents, tangentDirNum, xp, seed, theOutput, jacTimesSeed ); ++ /*Free resources: */ ++ xDelete(theOutput); ++ xDelete(indepIndices); ++ xDelete(seed); ++ ++ /*add to results: */ ++ femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,AutodiffJacobianEnum,*jacTimesSeed,num_dependents*tangentDirNum,1,1,0.0)); ++ ++ /*Free resources: */ ++ xDelete(jacTimesSeed); ++ xDelete(indepIndices); ++ } ++ else if (strcmp(driver,"fos_reverse")==0) { ++ ++ int aDepIndex=0; ++ double *aWeightVector=NULL; ++ double *weightVectorTimesJac=NULL; ++ ++ /*retrieve direction index: */ ++ femmodel->parameters->FindParam(&aDepIndex,AutodiffFosReverseIndexEnum); ++ ++ if (aDepIndex<0 || aDepIndex>=num_dependents) _error_("index value for AutodiffFosReverseIndexEnum should be in [0,num_dependents-1]"); ++ ++ aWeightVector=xNewZeroInit(num_dependents); ++ aWeightVector[aDepIndex]=1.0; ++ ++ weightVectorTimesJac=xNew(num_independents); ++ ++ /*set the forward method function pointer: */ ++ anEDF_for_solverx_p->fos_reverse=EDF_fos_reverse_for_solverx; ++ ++ /*allocate the space for the parameters to invoke the EDF fos_reverse :*/ ++ anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); ++ ++ /*call driver: */ ++ fos_reverse(1,num_dependents,num_independents, aWeightVector, weightVectorTimesJac ); ++ ++ /*add to results*/ ++ femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,AutodiffJacobianEnum,weightVectorTimesJac,num_independents,1,1,0.0)); ++ ++ /*free resources :*/ ++ xDelete(weightVectorTimesJac); ++ xDelete(aWeightVector); ++ } ++ else if ((strcmp(driver,"fov_reverse")==0) || (strcmp(driver,"fov_reverse_all")==0)){ ++ ++ int* depIndices=NULL; ++ int weightNum; ++ int dummy; ++ double **weightsTimesJac=NULL; ++ double **weights=NULL; ++ std::set anIndexSet; ++ ++ ++ /*retrieve directions:*/ ++ if (strcmp(driver,"fov_reverse_all")==0){ ++ weightNum=num_dependents; ++ depIndices=xNewZeroInit(weightNum); ++ for(i=0;iparameters->FindParam(&depIndices,&weightNum,&dummy,AutodiffFovForwardIndicesEnum); ++ } ++ ++ /*Some checks: */ ++ if (weightNum<1 || weightNum>num_dependents) _error_("tangentDirNum should be in [1,num_dependents]"); ++ ++ /* full Jacobian or Jacobian projection:*/ ++ weightsTimesJac=xNew(weightNum,num_independents); ++ ++ /*set the forward method function pointers: */ ++ anEDF_for_solverx_p->fov_reverse=EDF_fov_reverse_for_solverx; ++ ++ /*allocate the space for the parameters to invoke the EDF fos_reverse :*/ ++ anEDF_for_solverx_p->dpp_U=xNew(weightNum,anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dpp_Z=xNew(weightNum,anEDF_for_solverx_p->max_n); ++ ++ /*seed matrix: */ ++ weights=xNewZeroInit(weightNum,num_dependents); ++ ++ /*collect indices in a set to prevent accidental duplicates as long as we don't do compression:*/ ++ for (int i=0; inum_dependents) { ++ _error_("depIndices values must be in [0,num_dependents-1]"); ++ } ++ if (anIndexSet.find(depIndices[i])!=anIndexSet.end()) { ++ _error_("duplicate depIndices values are not allowed until we implement Jacobian decompression"); ++ } ++ anIndexSet.insert(depIndices[i]); ++ /* now populate the seed matrix from the set of independent indices; ++ * simple setup with a single 1.0 per column and at most a single 1.0 per row*/ ++ weights[depIndices[i]][i]=1.0; ++ } ++ ++ /*call driver: */ ++ fov_reverse(1,num_dependents,num_independents, weightNum, weights, weightsTimesJac ); ++ ++ /*add to results: */ ++ femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,AutodiffJacobianEnum,*weightsTimesJac,weightNum*num_independents,1,1,0.0)); ++ ++ /*Free resources: */ ++ xDelete(weights); ++ xDelete(weightsTimesJac); ++ xDelete(depIndices); ++ } ++ else _error_("driver: " << driver << " not yet supported!"); ++ ++ /* delete the allocated space for the parameters:*/ ++ xDelete(anEDF_for_solverx_p->dp_x); ++ xDelete(anEDF_for_solverx_p->dp_X); ++ xDelete(anEDF_for_solverx_p->dpp_X); ++ xDelete(anEDF_for_solverx_p->dp_y); ++ xDelete(anEDF_for_solverx_p->dp_Y); ++ xDelete(anEDF_for_solverx_p->dpp_Y); ++ xDelete(anEDF_for_solverx_p->dp_U); ++ xDelete(anEDF_for_solverx_p->dpp_U); ++ xDelete(anEDF_for_solverx_p->dp_Z); ++ xDelete(anEDF_for_solverx_p->dpp_Z); ++ ++ /*Free resources: */ ++ xDelete(xp); ++ xDelete(axp); ++ ++ if(VerboseAutodiff())_pprintLine_(" end AD core"); ++ ++ #else ++ _error_("Should not be requesting AD drivers when an AD library is not available!"); ++ #endif ++ } ++} +Index: ../trunk-jpl/src/c/solutions/solutions.h +=================================================================== +--- ../trunk-jpl/src/c/solutions/solutions.h (revision 13539) ++++ ../trunk-jpl/src/c/solutions/solutions.h (revision 13540) +@@ -30,6 +30,7 @@ + void steadystate_core(FemModel* femmodel); + void transient_core(FemModel* femmodel); + void dakota_core(FemModel* femmodel); ++void ad_core(FemModel* femmodel); + IssmDouble objectivefunction(IssmDouble search_scalar,OptArgs* optargs); + + //convergence: +@@ -51,7 +52,8 @@ + + //solution configuration + void AnalysisConfiguration(int** panalyses,int* pnumanalyses, int solutiontype); +-void CorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype); ++void PureCorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype); ++void CorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype,bool nodakotacore=false); + void AdjointCorePointerFromSolutionEnum(void (**padjointcore)(FemModel*),int solutiontype); + + +Index: ../trunk-jpl/src/c/solutions/dakota_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/dakota_core.cpp (revision 13539) ++++ ../trunk-jpl/src/c/solutions/dakota_core.cpp (revision 13540) +@@ -64,13 +64,10 @@ + Dakota::ModelLIter ml_iter; + Parameters* parameters = NULL; + +- /*Retrieve parameters: */ +- parameters=femmodel->parameters; +- + /*Recover dakota_input_file, dakota_output_file and dakota_error_file, in the parameters dataset in parallel */ +- parameters->FindParam(&dakota_input_file,QmuInNameEnum); +- parameters->FindParam(&dakota_output_file,QmuOutNameEnum); +- parameters->FindParam(&dakota_error_file,QmuErrNameEnum); ++ femmodel->parameters->FindParam(&dakota_input_file,QmuInNameEnum); ++ femmodel->parameters->FindParam(&dakota_output_file,QmuOutNameEnum); ++ femmodel->parameters->FindParam(&dakota_error_file,QmuErrNameEnum); + + if(my_rank==0){ + +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13539) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13540) +@@ -14,7 +14,6 @@ + FILE *output_fid = NULL; + FILE *petscoptionsfid = NULL; + bool waitonlock = false; +- bool dakota_analysis,control_analysis,tao_analysis; + + /*AD: */ + bool autodiff=false; +@@ -78,9 +77,6 @@ + + /*get parameters: */ + femmodel->parameters->FindParam(&waitonlock,SettingsWaitonlockEnum); +- femmodel->parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum); +- femmodel->parameters->FindParam(&control_analysis,InversionIscontrolEnum); +- femmodel->parameters->FindParam(&tao_analysis,InversionTaoEnum); + femmodel->parameters->FindParam(&autodiff,AutodiffIsautodiffEnum); + + /*Profiling: */ +@@ -103,36 +99,9 @@ + #endif + + _pprintLine_("call computational core:"); +- +- +- profiler->Tag(StartCore); +- if(dakota_analysis){ +- #ifdef _HAVE_DAKOTA_ +- dakota_core(femmodel); +- #else +- _error_("ISSM was not compiled with dakota support, cannot carry out dakota analysis!"); +- #endif +- } +- else if(control_analysis){ +- #ifdef _HAVE_CONTROL_ +- if(tao_analysis) controltao_core(femmodel); +- else control_core(femmodel); +- #else +- _error_("ISSM was not compiled with control support, cannot carry out control analysis!"); +- #endif +- } +- else{ +- solutioncore(femmodel); +- } +- +- #ifdef _HAVE_ADOLC_ +- if(autodiff){ +- trace_off(); +- AutodiffDriversx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); +- } +- #endif +- profiler->Tag(FinishCore); +- ++ profiler->Tag(StartCore); solutioncore(femmodel); profiler->Tag(FinishCore); ++ profiler->Tag(StartAdCore); ad_core(femmodel); profiler->Tag(FinishAdCore); ++ + ProfilerEnd(profiler,femmodel->results,femmodel->parameters); + + _pprintLine_("write results to disk:"); +@@ -219,9 +188,9 @@ + _pprintLine_("Solution memory used : " << solution_memory << " Bytes"); + + /*Add to results: */ +- results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingSolutionTimeEnum, solution_time, 1, 0)); +- results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentMemEnum, solution_memory, 1, 0)); +- results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentFlopsEnum, solution_flops, 1, 0)); ++ results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingSolutionTimeEnum, solution_time, 1, 0)); ++ results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentMemEnum, solution_memory, 1, 0)); ++ results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentFlopsEnum, solution_flops, 1, 0)); + } + + } /*}}}*/ +Index: ../trunk-jpl/src/c/solutions/DakotaSpawnCore.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/DakotaSpawnCore.cpp (revision 13539) ++++ ../trunk-jpl/src/c/solutions/DakotaSpawnCore.cpp (revision 13540) +@@ -54,6 +54,7 @@ + bool control_analysis = false; + void (*solutioncore)(FemModel*) = NULL; + FemModel* femmodel = NULL; ++ bool nodakotacore = true; + + + /*If counter==-1 on cpu0, it means that the dakota runs are done. In which case, bail out and return 0: */ +@@ -80,12 +81,7 @@ + + /*Determine solution sequence: */ + if(VerboseQmu()) _pprintLine_("Starting " << EnumToStringx(solution_type) << " core:"); +- CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); +- #ifdef _HAVE_CONTROL_ +- if(control_analysis)solutioncore=&control_core; +- #else +- _error_("ISSM was not compiled with control capabilities, exiting!"); +- #endif ++ CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type,nodakotacore); + + /*Run the core solution sequence: */ + solutioncore(femmodel); +@@ -96,6 +92,8 @@ + + /*Free ressources:*/ + DakotaFree(&d_variables,&d_variables_descriptors,&responses_descriptors, d_numvariables, numresponsedescriptors); ++ ++ return 1; //this is critical! do not return 0, otherwise, dakota_core will stop running! + } + + void DakotaMPI_Bcast(double** pvariables, char*** pvariables_descriptors,int* pnumvariables, int* pnumresponses){ /*{{{*/ +Index: ../trunk-jpl/src/c/solutions/control_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/control_core.cpp (revision 13539) ++++ ../trunk-jpl/src/c/solutions/control_core.cpp (revision 13540) +@@ -61,7 +61,7 @@ + femmodel->parameters->SetParam(false,SaveResultsEnum); + + /*out of solution_type, figure out solution core and adjoint function pointer*/ +- CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); ++ PureCorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); + AdjointCorePointerFromSolutionEnum(&adjointcore,solution_type); + + /*Launch once a complete solution to set up all inputs*/ +Index: ../trunk-jpl/src/c/solutions/controltao_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/controltao_core.cpp (revision 13539) ++++ ../trunk-jpl/src/c/solutions/controltao_core.cpp (revision 13540) +@@ -93,7 +93,7 @@ + if(VerboseControl()) _pprintLine_(" preparing final solution"); + femmodel->parameters->SetParam(true,SaveResultsEnum); + void (*solutioncore)(FemModel*)=NULL; +- CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); ++ PureCorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); + solutioncore(femmodel); + + /*Clean up and return*/ +Index: ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13539) ++++ ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.cpp (revision 13540) +@@ -1,286 +0,0 @@ +-/*!\file AutodiffDriversx +- * \brief: compute outputs from the AD mode, using our dependents and independents, and drivers available in Adolc. +- */ +-#include +-#include "../../modules/modules.h" +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../../toolkits/toolkits.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +- +- +-void AutodiffDriversx(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters,Results* results){ +- +- +- /*diverse: */ +- int i; +- int dummy; +- +- bool isautodiff = false; +- int num_dependents; +- int num_independents; +- char* driver=NULL; +- +- /*state variables: */ +- IssmDouble *axp = NULL; +- double *xp = NULL; +- +- /*AD mode on?: */ +- parameters->FindParam(&isautodiff,AutodiffIsautodiffEnum); +- +- if(isautodiff){ +- +- #ifdef _HAVE_ADOLC_ +- +- if(VerboseAutodiff())_pprintLine_(" start AD driver"); +- +- /*preliminary checks: */ +- parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); +- parameters->FindParam(&num_independents,AutodiffNumIndependentsEnum); +- if(!(num_dependents*num_independents)) return; +- +- /*retrieve state variable: */ +- parameters->FindParam(&axp,&dummy,AutodiffXpEnum); +- +- /* driver argument */ +- xp=xNew(num_independents); +- for(i=0;i(axp[i]); +- } +- +- /*get the EDF pointer:*/ +- ext_diff_fct *anEDF_for_solverx_p=dynamic_cast * >(parameters->FindParamObject(AdolcParamEnum))->GetParameterValue().myEDF_for_solverx_p; +- +- /*Branch according to AD driver: */ +- parameters->FindParam(&driver,AutodiffDriverEnum); +- +- /* these are always needed regardless of the interpreter */ +- anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); +- anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); +- +- if (strcmp(driver,"fos_forward")==0){ +- +- int anIndepIndex; +- double *tangentDir=NULL; +- double *jacTimesTangentDir=NULL; +- double *theOutput=NULL; +- +- /*retrieve direction index: */ +- parameters->FindParam(&anIndepIndex,AutodiffFosForwardIndexEnum); +- +- if (anIndepIndex<0 || anIndepIndex>=num_independents) _error_("index value for AutodiffFosForwardIndexEnum should be in [0,num_independents-1]"); +- +- tangentDir=xNewZeroInit(num_independents); +- tangentDir[anIndepIndex]=1.0; +- +- jacTimesTangentDir=xNew(num_dependents); +- theOutput=xNew(num_dependents); +- +- /*set the forward method function pointer: */ +- anEDF_for_solverx_p->fos_forward=EDF_fos_forward_for_solverx; +- +- /*allocate the space for the parameters to invoke the EDF fos_forward:*/ +- anEDF_for_solverx_p->dp_X=xNew(anEDF_for_solverx_p->max_n); +- anEDF_for_solverx_p->dp_Y=xNew(anEDF_for_solverx_p->max_m); +- +- /*call driver: */ +- fos_forward(1,num_dependents,num_independents, 0, xp, tangentDir, theOutput, jacTimesTangentDir ); +- +- /*add to results*/ +- results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,jacTimesTangentDir,num_dependents,1,1,0.0)); +- +- /*free resources :*/ +- xDelete(theOutput); +- xDelete(jacTimesTangentDir); +- xDelete(tangentDir); +- } +- else if ((strcmp(driver,"fov_forward")==0) || (strcmp(driver,"fov_forward_all")==0)){ +- +- int* indepIndices=NULL; +- int tangentDirNum; +- int dummy; +- double **jacTimesSeed=NULL; +- double **seed=NULL; +- double *theOutput=NULL; +- std::set anIndexSet; +- +- +- /*retrieve directions:*/ +- if (strcmp(driver,"fov_forward_all")==0){ +- tangentDirNum=num_independents; +- indepIndices=xNewZeroInit(tangentDirNum); +- for(i=0;iFindParam(&indepIndices,&tangentDirNum,&dummy,AutodiffFovForwardIndicesEnum); +- } +- +- /*Some checks: */ +- if (tangentDirNum<1 || tangentDirNum>num_independents) _error_("tangentDirNum should be in [1,num_independents]"); +- +- /* full Jacobian or Jacobian projection:*/ +- jacTimesSeed=xNew(num_dependents,tangentDirNum); +- +- /*set the forward method function pointers: */ +- anEDF_for_solverx_p->fov_forward=EDF_fov_forward_for_solverx; +- // anEDF_for_solverx_p->fov_reverse=EDF_fov_reverse_for_solverx; +- +- /*allocate the space for the parameters to invoke EDF fov_forward:*/ +- anEDF_for_solverx_p->dpp_X=xNew(anEDF_for_solverx_p->max_n, tangentDirNum); +- anEDF_for_solverx_p->dpp_Y=xNew(anEDF_for_solverx_p->max_m, tangentDirNum); +- +- /*seed matrix: */ +- seed=xNewZeroInit(num_independents,tangentDirNum); +- +- /*collect indices in a set to prevent accidental duplicates as long as we don't do compression:*/ +- for (int i=0; inum_independents) { +- _error_("indepIndices values must be in [0,num_independents-1]"); +- } +- if (anIndexSet.find(indepIndices[i])!=anIndexSet.end()) { +- _error_("duplicate indepIndices values are not allowed until we implement Jacobian decompression"); +- } +- anIndexSet.insert(indepIndices[i]); +- /* now populate the seed matrix from the set of independent indices; +- * simple setup with a single 1.0 per column and at most a single 1.0 per row*/ +- seed[indepIndices[i]][i]=1.0; +- } +- +- /*allocate output: */ +- theOutput=xNew(num_dependents); +- +- /*call driver: */ +- fov_forward(1,num_dependents,num_independents, tangentDirNum, xp, seed, theOutput, jacTimesSeed ); +- /*Free resources: */ +- xDelete(theOutput); +- xDelete(indepIndices); +- xDelete(seed); +- +- /*add to results: */ +- results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,*jacTimesSeed,num_dependents*tangentDirNum,1,1,0.0)); +- +- /*Free resources: */ +- xDelete(jacTimesSeed); +- xDelete(indepIndices); +- } +- else if (strcmp(driver,"fos_reverse")==0) { +- +- int aDepIndex=0; +- double *aWeightVector=NULL; +- double *weightVectorTimesJac=NULL; +- +- /*retrieve direction index: */ +- parameters->FindParam(&aDepIndex,AutodiffFosReverseIndexEnum); +- +- if (aDepIndex<0 || aDepIndex>=num_dependents) _error_("index value for AutodiffFosReverseIndexEnum should be in [0,num_dependents-1]"); +- +- aWeightVector=xNewZeroInit(num_dependents); +- aWeightVector[aDepIndex]=1.0; +- +- weightVectorTimesJac=xNew(num_independents); +- +- /*set the forward method function pointer: */ +- anEDF_for_solverx_p->fos_reverse=EDF_fos_reverse_for_solverx; +- +- /*allocate the space for the parameters to invoke the EDF fos_reverse :*/ +- anEDF_for_solverx_p->dp_U=xNew(anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dp_Z=xNew(anEDF_for_solverx_p->max_n); +- +- /*call driver: */ +- fos_reverse(1,num_dependents,num_independents, aWeightVector, weightVectorTimesJac ); +- +- /*add to results*/ +- results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,weightVectorTimesJac,num_independents,1,1,0.0)); +- +- /*free resources :*/ +- xDelete(weightVectorTimesJac); +- xDelete(aWeightVector); +- } +- else if ((strcmp(driver,"fov_reverse")==0) || (strcmp(driver,"fov_reverse_all")==0)){ +- +- int* depIndices=NULL; +- int weightNum; +- int dummy; +- double **weightsTimesJac=NULL; +- double **weights=NULL; +- std::set anIndexSet; +- +- +- /*retrieve directions:*/ +- if (strcmp(driver,"fov_reverse_all")==0){ +- weightNum=num_dependents; +- depIndices=xNewZeroInit(weightNum); +- for(i=0;iFindParam(&depIndices,&weightNum,&dummy,AutodiffFovForwardIndicesEnum); +- } +- +- /*Some checks: */ +- if (weightNum<1 || weightNum>num_dependents) _error_("tangentDirNum should be in [1,num_dependents]"); +- +- /* full Jacobian or Jacobian projection:*/ +- weightsTimesJac=xNew(weightNum,num_independents); +- +- /*set the forward method function pointers: */ +- anEDF_for_solverx_p->fov_reverse=EDF_fov_reverse_for_solverx; +- +- /*allocate the space for the parameters to invoke the EDF fos_reverse :*/ +- anEDF_for_solverx_p->dpp_U=xNew(weightNum,anEDF_for_solverx_p->max_m); +- anEDF_for_solverx_p->dpp_Z=xNew(weightNum,anEDF_for_solverx_p->max_n); +- +- /*seed matrix: */ +- weights=xNewZeroInit(weightNum,num_dependents); +- +- /*collect indices in a set to prevent accidental duplicates as long as we don't do compression:*/ +- for (int i=0; inum_dependents) { +- _error_("depIndices values must be in [0,num_dependents-1]"); +- } +- if (anIndexSet.find(depIndices[i])!=anIndexSet.end()) { +- _error_("duplicate depIndices values are not allowed until we implement Jacobian decompression"); +- } +- anIndexSet.insert(depIndices[i]); +- /* now populate the seed matrix from the set of independent indices; +- * simple setup with a single 1.0 per column and at most a single 1.0 per row*/ +- weights[depIndices[i]][i]=1.0; +- } +- +- /*call driver: */ +- fov_reverse(1,num_dependents,num_independents, weightNum, weights, weightsTimesJac ); +- +- /*add to results: */ +- results->AddObject(new GenericExternalResult(results->Size()+1,AutodiffJacobianEnum,*weightsTimesJac,weightNum*num_independents,1,1,0.0)); +- +- /*Free resources: */ +- xDelete(weights); +- xDelete(weightsTimesJac); +- xDelete(depIndices); +- } +- else _error_("driver: " << driver << " not yet supported!"); +- +- /* delete the allocated space for the parameters:*/ +- xDelete(anEDF_for_solverx_p->dp_x); +- xDelete(anEDF_for_solverx_p->dp_X); +- xDelete(anEDF_for_solverx_p->dpp_X); +- xDelete(anEDF_for_solverx_p->dp_y); +- xDelete(anEDF_for_solverx_p->dp_Y); +- xDelete(anEDF_for_solverx_p->dpp_Y); +- xDelete(anEDF_for_solverx_p->dp_U); +- xDelete(anEDF_for_solverx_p->dpp_U); +- xDelete(anEDF_for_solverx_p->dp_Z); +- xDelete(anEDF_for_solverx_p->dpp_Z); +- +- /*Free resources: */ +- xDelete(xp); +- xDelete(axp); +- +- if(VerboseAutodiff())_pprintLine_(" end AD driver"); +- +- #else +- _error_("Should not be requesting AD drivers when an AD library is not available!"); +- #endif +- } +-} +Index: ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.h +=================================================================== +--- ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.h (revision 13539) ++++ ../trunk-jpl/src/c/modules/AutodiffDriversx/AutodiffDriversx.h (revision 13540) +@@ -1,13 +0,0 @@ +-/*!\file: AutodiffDriversx.h +- * \brief header file for requesting AD results (gradient, jacobian, etc ...) +- */ +- +-#ifndef _AUTODIFF_DRIVERSX_H_ +-#define _AUTODIFF_DRIVERSX_H_ +- +-#include "../../Container/Container.h" +- +-/* local prototypes: */ +-void AutodiffDriversx(Elements* elements,Nodes* nodes,Vertices* vertices,Loads* loads,Materials* materials,Parameters* parameters,Results* results); +- +-#endif /* _AUTODIFF_DRIVERSX_H_*/ +Index: ../trunk-jpl/src/c/modules/modules.h +=================================================================== +--- ../trunk-jpl/src/c/modules/modules.h (revision 13539) ++++ ../trunk-jpl/src/c/modules/modules.h (revision 13540) +@@ -7,7 +7,6 @@ + + /*Modules: */ + #include "./AddExternalResultx/AddExternalResultx.h" +-#include "./AutodiffDriversx/AutodiffDriversx.h" + #include "./AverageFilterx/AverageFilterx.h" + #include "./AverageOntoPartitionx/AverageOntoPartitionx.h" + #include "./Bamgx/Bamgx.h" +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13539) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13540) +@@ -326,8 +326,6 @@ + ./modules/RequestedOutputsx/RequestedOutputsx.cpp\ + ./modules/RequestedDependentsx/RequestedDependentsx.h\ + ./modules/RequestedDependentsx/RequestedDependentsx.cpp\ +- ./modules/AutodiffDriversx/AutodiffDriversx.h\ +- ./modules/AutodiffDriversx/AutodiffDriversx.cpp\ + ./modules/ResetConstraintsx/ResetConstraintsx.h\ + ./modules/ResetConstraintsx/ResetConstraintsx.cpp\ + ./modules/ResetCoordinateSystemx/ResetCoordinateSystemx.h\ +@@ -349,8 +347,10 @@ + ./solutions/ResetBoundaryConditions.cpp\ + ./solutions/AnalysisConfiguration.cpp\ + ./solutions/CorePointerFromSolutionEnum.cpp\ ++ ./solutions/PureCorePointerFromSolutionEnum.cpp\ + ./solutions/EnvironmentInit.cpp\ + ./solutions/EnvironmentFinalize.cpp\ ++ ./solutions/ad_core.cpp\ + ./solvers/solver_linear.cpp\ + ./solvers/solver_nonlinear.cpp\ + ./solvers/solver_newton.cpp\ +Index: ../trunk-jpl/src/c/classes/objects/Profiler.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Profiler.cpp (revision 13539) ++++ ../trunk-jpl/src/c/classes/objects/Profiler.cpp (revision 13540) +@@ -16,6 +16,8 @@ + /*FUNCTION Profiler::Profiler() default constructor {{{*/ + Profiler::Profiler(){ + this->time=new Parameters(); ++ this->flops=new Parameters(); ++ this->memory=new Parameters(); + } + /*}}}*/ + /*FUNCTION Profiler::~Profiler(){{{*/ +Index: ../trunk-jpl/src/c/classes/objects/Profiler.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Profiler.h (revision 13539) ++++ ../trunk-jpl/src/c/classes/objects/Profiler.h (revision 13540) +@@ -20,6 +20,8 @@ + FinishInit, + StartCore, + FinishCore, ++ StartAdCore, ++ FinishAdCore, + Finish + }; + Index: /issm/oecreview/Archive/13393-13976/ISSM-13541-13542.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13541-13542.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13541-13542.diff (revision 13980) @@ -0,0 +1,70 @@ +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13541) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13542) +@@ -60,7 +60,6 @@ + + /*Create femmodel, using input file: */ + profiler->Tag(StartInit); +- + femmodel=new FemModel(rootpath,binfilename,outbinfilename,solution_type,analyses,numanalyses); + + /*get type of solution we are going to run: */ +@@ -82,22 +81,6 @@ + /*Profiling: */ + profiler->Tag(FinishInit); + +- /*If running AD, then initialize a placeholder with which to work: */ +- #ifdef _HAVE_ADOLC_ +- GenericParam *theAdolcEDF_p=new GenericParam(AdolcParamEnum); +- theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p=reg_ext_fct(EDF_for_solverx); +- // to save some space: +- // we know we won't use adolc inside of the solver: +- theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->nestedAdolc=false; +- // the solution vector is just allocated and doesn't have a meaningfull prior value +- theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->dp_y_priorRequired=false; +- // the solver wrapper makes sure the matrix and the right hand side don't change +- theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->dp_x_changes=false; +- femmodel->parameters->AddObject(theAdolcEDF_p); +- #else +- if(autodiff) _error_("ISSM was not compiled with ADOLC support, cannot carry out autodiff analysis!"); +- #endif +- + _pprintLine_("call computational core:"); + profiler->Tag(StartCore); solutioncore(femmodel); profiler->Tag(FinishCore); + profiler->Tag(StartAdCore); ad_core(femmodel); profiler->Tag(FinishAdCore); +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13541) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13542) +@@ -6,9 +6,10 @@ + #include "../../../toolkits/toolkits.h" + #include "../../../io/io.h" + #include "../../../EnumDefinitions/EnumDefinitions.h" +-#include "../../../classes/objects/objects.h" ++#include "../../../classes/classes.h" + #include "../../../shared/shared.h" + #include "../../../include/include.h" ++#include "../../Solverx/Solverx.h" + #include "../ModelProcessorx.h" + + void CreateParametersAutodiff(Parameters** pparameters,IoModel* iomodel,int solution_type,int analysis_type){ +@@ -107,6 +108,18 @@ + /*Don't forget to copy iomodel->independent_objects to parameters: */ + parameters->AddObject(new DataSetParam(AutodiffIndependentObjectsEnum,iomodel->independent_objects)); + /*}}}*/ ++ /*initialize a placeholder to store solver pointers: {{{*/ ++ GenericParam *theAdolcEDF_p=new GenericParam(AdolcParamEnum); ++ theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p=reg_ext_fct(EDF_for_solverx); ++ // to save some space: ++ // we know we won't use adolc inside of the solver: ++ theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->nestedAdolc=false; ++ // the solution vector is just allocated and doesn't have a meaningfull prior value ++ theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->dp_y_priorRequired=false; ++ // the solver wrapper makes sure the matrix and the right hand side don't change ++ theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->dp_x_changes=false; ++ parameters->AddObject(theAdolcEDF_p); ++ /*}}}*/ + + /*Assign output pointer: */ + *pparameters=parameters; Index: /issm/oecreview/Archive/13393-13976/ISSM-13542-13543.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13542-13543.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13542-13543.diff (revision 13980) @@ -0,0 +1,96 @@ +Index: ../trunk-jpl/src/c/solutions/ad_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/ad_core.cpp (revision 13542) ++++ ../trunk-jpl/src/c/solutions/ad_core.cpp (revision 13543) +@@ -32,6 +32,7 @@ + int num_dependents; + int num_independents; + char* driver=NULL; ++ size_t tape_stats[11]; + + /*state variables: */ + IssmDouble *axp = NULL; +@@ -287,13 +288,23 @@ + xDelete(anEDF_for_solverx_p->dpp_U); + xDelete(anEDF_for_solverx_p->dp_Z); + xDelete(anEDF_for_solverx_p->dpp_Z); +- ++ ++ /*Print statistics: {{{*/ ++ tapestats(1,tape_stats); //reading of tape statistics ++ if(VerboseAutodiff()){ ++ _pprintLine_(" ADOLC statistics: "); ++ _pprintLine_(" "<parameters,petscoptionsfid); + pfclose(petscoptionsfid,petscfilename); + +- /*get parameters: */ +- femmodel->parameters->FindParam(&waitonlock,SettingsWaitonlockEnum); +- femmodel->parameters->FindParam(&autodiff,AutodiffIsautodiffEnum); +- +- /*Profiling: */ + profiler->Tag(FinishInit); + ++ /*call cores: */ + _pprintLine_("call computational core:"); + profiler->Tag(StartCore); solutioncore(femmodel); profiler->Tag(FinishCore); + profiler->Tag(StartAdCore); ad_core(femmodel); profiler->Tag(FinishAdCore); +@@ -90,24 +82,9 @@ + _pprintLine_("write results to disk:"); + OutputResultsx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); + +- /*If running AD, close our tape, print statistics: {{{*/ +- #ifdef _HAVE_ADOLC_ +- if(autodiff){ +- tapestats(1,tape_stats); //reading of tape statistics +- if(VerboseAutodiff()){ +- _pprintLine_(" ADOLC statistics: "); +- _pprintLine_(" "<parameters->FindParam(&waitonlock,SettingsWaitonlockEnum); + if (waitonlock>0){ + _pprintLine_("write lock file:"); + WriteLockFile(lockfilename); Index: /issm/oecreview/Archive/13393-13976/ISSM-13543-13544.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13543-13544.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13543-13544.diff (revision 13980) @@ -0,0 +1,23 @@ +Index: ../trunk-jpl/externalpackages/python/install-2.7.3-macosx-lion.sh +=================================================================== +--- ../trunk-jpl/externalpackages/python/install-2.7.3-macosx-lion.sh (revision 13543) ++++ ../trunk-jpl/externalpackages/python/install-2.7.3-macosx-lion.sh (revision 13544) +@@ -7,7 +7,7 @@ + mkdir install src + + #Download from ISSM server +-#$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz ++$ISSM_DIR/scripts/DownloadExternalPackage.py http://issm.jpl.nasa.gov/files/externalpackages/Python-2.7.3.tgz Python-2.7.3.tgz + + #Untar and move python into install directory + tar -zxvf Python-2.7.3.tgz +@@ -16,7 +16,8 @@ + + #Configure and compile + cd src +-./configure --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" ++./configure \ ++ --enable-framework="$ISSM_DIR/externalpackages/python/install/Library/Frameworks" + if [ $# -eq 0 ]; then + make + else Index: /issm/oecreview/Archive/13393-13976/ISSM-13544-13545.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13544-13545.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13544-13545.diff (revision 13980) @@ -0,0 +1,108 @@ +Index: ../trunk-jpl/src/c/solutions/ad_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/ad_core.cpp (revision 13544) ++++ ../trunk-jpl/src/c/solutions/ad_core.cpp (revision 13545) +@@ -25,18 +25,17 @@ + void ad_core(FemModel* femmodel){ + + /*diverse: */ +- int i; +- int dummy; ++ int i; ++ int dummy; ++ int num_dependents; ++ int num_independents; ++ bool isautodiff = false; ++ char *driver = NULL; ++ size_t tape_stats[11]; + +- bool isautodiff = false; +- int num_dependents; +- int num_independents; +- char* driver=NULL; +- size_t tape_stats[11]; +- + /*state variables: */ +- IssmDouble *axp = NULL; +- double *xp = NULL; ++ IssmDouble *axp = NULL; ++ double *xp = NULL; + + /*AD mode on?: */ + femmodel->parameters->FindParam(&isautodiff,AutodiffIsautodiffEnum); +@@ -71,15 +70,15 @@ + femmodel->parameters->FindParam(&driver,AutodiffDriverEnum); + + /* these are always needed regardless of the interpreter */ +- anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); +- anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); ++ anEDF_for_solverx_p->dp_x=xNew(anEDF_for_solverx_p->max_n); ++ anEDF_for_solverx_p->dp_y=xNew(anEDF_for_solverx_p->max_m); + + if (strcmp(driver,"fos_forward")==0){ + + int anIndepIndex; +- double *tangentDir=NULL; +- double *jacTimesTangentDir=NULL; +- double *theOutput=NULL; ++ double *tangentDir = NULL; ++ double *jacTimesTangentDir = NULL; ++ double *theOutput = NULL; + + /*retrieve direction index: */ + femmodel->parameters->FindParam(&anIndepIndex,AutodiffFosForwardIndexEnum); +@@ -112,14 +111,13 @@ + } + else if ((strcmp(driver,"fov_forward")==0) || (strcmp(driver,"fov_forward_all")==0)){ + +- int* indepIndices=NULL; +- int tangentDirNum; +- int dummy; +- double **jacTimesSeed=NULL; +- double **seed=NULL; +- double *theOutput=NULL; ++ int tangentDirNum; ++ int dummy; ++ int *indepIndices = NULL; ++ double **jacTimesSeed = NULL; ++ double **seed = NULL; ++ double *theOutput = NULL; + std::set anIndexSet; +- + + /*retrieve directions:*/ + if (strcmp(driver,"fov_forward_all")==0){ +@@ -301,6 +299,7 @@ + _pprintLine_(" "<Tag(StartCore); solutioncore(femmodel); profiler->Tag(FinishCore); +- profiler->Tag(StartAdCore); ad_core(femmodel); profiler->Tag(FinishAdCore); +- ++ profiler->Tag(StartCore); solutioncore(femmodel); profiler->Tag(FinishCore); ++ profiler->Tag(StartAdCore); ad_core(femmodel); profiler->Tag(FinishAdCore); + ProfilerEnd(profiler,femmodel->results,femmodel->parameters); + + _pprintLine_("write results to disk:"); Index: /issm/oecreview/Archive/13393-13976/ISSM-13545-13546.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13545-13546.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13545-13546.diff (revision 13980) @@ -0,0 +1,76 @@ +Index: ../trunk-jpl/src/c/solutions/ad_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/ad_core.cpp (revision 13545) ++++ ../trunk-jpl/src/c/solutions/ad_core.cpp (revision 13546) +@@ -44,7 +44,6 @@ + + #ifdef _HAVE_ADOLC_ + +- if(VerboseAutodiff())_pprintLine_(" start ad core"); + + /*First, stop tracing: */ + trace_off(); +@@ -54,6 +53,8 @@ + femmodel->parameters->FindParam(&num_independents,AutodiffNumIndependentsEnum); + if(!(num_dependents*num_independents)) return; + ++ if(VerboseAutodiff())_pprintLine_(" start ad core"); ++ + /*retrieve state variable: */ + femmodel->parameters->FindParam(&axp,&dummy,AutodiffXpEnum); + +@@ -119,6 +120,7 @@ + double *theOutput = NULL; + std::set anIndexSet; + ++ + /*retrieve directions:*/ + if (strcmp(driver,"fov_forward_all")==0){ + tangentDirNum=num_independents; +@@ -275,6 +277,7 @@ + } + else _error_("driver: " << driver << " not yet supported!"); + ++ + /* delete the allocated space for the parameters:*/ + xDelete(anEDF_for_solverx_p->dp_x); + xDelete(anEDF_for_solverx_p->dp_X); +@@ -287,7 +290,7 @@ + xDelete(anEDF_for_solverx_p->dp_Z); + xDelete(anEDF_for_solverx_p->dpp_Z); + +- /*Print statistics: {{{*/ ++ /*Print statistics:*/ + tapestats(1,tape_stats); //reading of tape statistics + if(VerboseAutodiff()){ + _pprintLine_(" ADOLC statistics: "); +@@ -299,7 +302,6 @@ + _pprintLine_(" "<Constant(&autodiff_analysis,AutodiffIsautodiffEnum); + + if(autodiff_analysis){ ++ ++ #ifdef _HAVE_ADOLC_ + + /*Copy some parameters from IoModel to parameters dataset: */ + parameters->AddObject(iomodel->CopyConstantObject(AutodiffKeepEnum)); +@@ -121,6 +123,8 @@ + parameters->AddObject(theAdolcEDF_p); + /*}}}*/ + ++ #endif ++ + /*Assign output pointer: */ + *pparameters=parameters; + Index: /issm/oecreview/Archive/13393-13976/ISSM-13546-13547.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13546-13547.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13546-13547.diff (revision 13980) @@ -0,0 +1,46 @@ +Index: ../trunk-jpl/src/c/modules/Dakotax/Dakotax.h +=================================================================== +--- ../trunk-jpl/src/c/modules/Dakotax/Dakotax.h (revision 13546) ++++ ../trunk-jpl/src/c/modules/Dakotax/Dakotax.h (revision 13547) +@@ -1,15 +0,0 @@ +-/*!\file: Dakotax.h +- * \brief header file for Qmu engine using Dakota +- */ +- +-#ifndef _DAKOTAX_H +-#define _DAKOTAX_H +- +-#include "../../Container/Container.h" +-#include "../../classes/classes.h" +- +-/* local prototypes: */ +-void Dakotax(FemModel* femmodel); +-int DakotaSpawnCore(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, void* femmodel,int counter); +- +-#endif /* _DAKOTAX_H */ +Index: ../trunk-jpl/src/c/modules/modules.h +=================================================================== +--- ../trunk-jpl/src/c/modules/modules.h (revision 13546) ++++ ../trunk-jpl/src/c/modules/modules.h (revision 13547) +@@ -97,7 +97,6 @@ + #include "./PointCloudFindNeighborsx/PointCloudFindNeighborsx.h" + #include "./PositiveDegreeDayx/PositiveDegreeDayx.h" + #include "./PropagateFlagsFromConnectivityx/PropagateFlagsFromConnectivityx.h" +-#include "./Dakotax/Dakotax.h" + #include "./Reduceloadx/Reduceloadx.h" + #include "./Reducevectorgtosx/Reducevectorgtosx.h" + #include "./Reducevectorgtofx/Reducevectorgtofx.h" +Index: ../trunk-jpl/src/c/classes/dakota/DakotaPlugin.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/dakota/DakotaPlugin.cpp (revision 13546) ++++ ../trunk-jpl/src/c/classes/dakota/DakotaPlugin.cpp (revision 13547) +@@ -24,8 +24,8 @@ + /*Standard ISSM includes: */ + #include "../../shared/shared.h" + #include "../../include/include.h" ++#include "../../solutions/solutions.h" + #include "../classes.h" +-#include "../../modules/Dakotax/Dakotax.h" + + /*Standard includes: */ + #include Index: /issm/oecreview/Archive/13393-13976/ISSM-13547-13548.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13547-13548.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13547-13548.diff (revision 13980) @@ -0,0 +1,54 @@ +Index: ../trunk-jpl/src/c/classes/dakota/DakotaPlugin.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/dakota/DakotaPlugin.cpp (revision 13547) ++++ ../trunk-jpl/src/c/classes/dakota/DakotaPlugin.cpp (revision 13548) +@@ -42,19 +42,16 @@ + + namespace SIM { + +-//constructor +-DakotaPlugin::DakotaPlugin(const Dakota::ProblemDescDB& problem_db,void* in_femmodel):Dakota::DirectApplicInterface(problem_db){ ++DakotaPlugin::DakotaPlugin(const Dakota::ProblemDescDB& problem_db,void* in_femmodel):Dakota::DirectApplicInterface(problem_db){/*{{{*/ + +- + femmodel=in_femmodel; + counter=0; +-} ++}/*}}}*/ ++DakotaPlugin::~DakotaPlugin(){/*{{{*/ ++ /* Virtual destructor handles referenceCount at Interface level. */ ++}/*}}}*/ ++int DakotaPlugin::derived_map_ac(const Dakota::String& driver){/*{{{*/ + +-//destructor +-DakotaPlugin::~DakotaPlugin(){ /* Virtual destructor handles referenceCount at Interface level. */ } +- +-int DakotaPlugin::derived_map_ac(const Dakota::String& driver) { +- + int i; + IssmDouble* variables=NULL; + char** variable_descriptors=NULL; +@@ -94,7 +91,6 @@ + fnVals[i]=responses[i]; + } + +- + /*Free ressources:*/ + xDelete(variables); + for(i=0;i(responses); + + return 0; +-} +- +- +-int DakotaPlugin::GetCounter(){ ++}/*}}}*/ ++int DakotaPlugin::GetCounter(){/*{{{*/ + return counter; +-} ++}/*}}}*/ + + } // namespace SIM + Index: /issm/oecreview/Archive/13393-13976/ISSM-13548-13549.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13548-13549.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13548-13549.diff (revision 13980) @@ -0,0 +1,394 @@ +Index: ../trunk-jpl/src/c/solutions/WriteLockFile.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/WriteLockFile.cpp (revision 13548) ++++ ../trunk-jpl/src/c/solutions/WriteLockFile.cpp (revision 13549) +@@ -1,25 +0,0 @@ +-/*!\file: WriteLockFile.cpp +- * \brief +- */ +-#include +-#include "../shared/shared.h" +-#include "../include/include.h" +- +-void WriteLockFile(char* filename){ +- +- int i; +- extern int my_rank; +- +- /* output: */ +- FILE* fid=NULL; +- +- /* Open lock file and write 1 into it: */ +- if(my_rank==0){ +- fid=fopen(filename,"w"); +- if(fid==NULL) _error_("error message: could not open lock file " << filename); +- +- /*Close file: */ +- if(fclose(fid)!=0) _error_("could not close lock file " << filename); +- } +- +-} +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13548) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13549) +@@ -10,11 +10,6 @@ + + int main(int argc,char **argv){ + +- /*I/O: */ +- FILE *output_fid = NULL; +- FILE *petscoptionsfid = NULL; +- bool waitonlock = false; +- + /*FemModel: */ + FemModel *femmodel = NULL; + +@@ -49,31 +44,20 @@ + _pprintLine_("Ice Sheet System Model (" << PACKAGE_NAME << ") version " << PACKAGE_VERSION); + _pprintLine_("(website: " << PACKAGE_URL << " contact: " << PACKAGE_BUGREPORT << ")"); + _pprintLine_(""); ++ + ProcessArguments(&solution_type,&binfilename,&outbinfilename,&petscfilename,&lockfilename,&rootpath,argc,argv); + + /*out of solution_type, figure out types of analyses needed in the femmodel: */ + AnalysisConfiguration(&analyses,&numanalyses,solution_type); + +- /*Create femmodel, using input file: */ ++ /*Create femmodel from input files: */ + profiler->Tag(StartInit); +- femmodel=new FemModel(rootpath,binfilename,outbinfilename,solution_type,analyses,numanalyses); +- +- /*get type of solution we are going to run: */ +- CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); +- +- /*Open output file once for all*/ +- output_fid=pfopen(outbinfilename,"wb"); +- femmodel->parameters->SetParam(output_fid,OutputFilePointerEnum); +- +- /*add petsc options to parameters: */ +- petscoptionsfid=pfopen(petscfilename,"r"); +- ParsePetscOptionsx(femmodel->parameters,petscoptionsfid); +- pfclose(petscoptionsfid,petscfilename); +- ++ femmodel=new FemModel(rootpath,binfilename,outbinfilename,petscfilename,lockfilename,solution_type,analyses,numanalyses); + profiler->Tag(FinishInit); + + /*call cores: */ + _pprintLine_("call computational core:"); ++ CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); + profiler->Tag(StartCore); solutioncore(femmodel); profiler->Tag(FinishCore); + profiler->Tag(StartAdCore); ad_core(femmodel); profiler->Tag(FinishAdCore); + ProfilerEnd(profiler,femmodel->results,femmodel->parameters); +@@ -81,14 +65,10 @@ + _pprintLine_("write results to disk:"); + OutputResultsx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); + +- /*Close output and petsc options file and write lock file if requested*/ +- pfclose(output_fid,lockfilename); +- femmodel->parameters->FindParam(&waitonlock,SettingsWaitonlockEnum); +- if (waitonlock>0){ +- _pprintLine_("write lock file:"); +- WriteLockFile(lockfilename); +- } +- ++ /*Profiling at the end: */ ++ profiler->Tag(Finish); ++ ProfilerEcho(profiler); ++ + /*Free resources */ + xDelete(analyses); + xDelete(lockfilename); +@@ -98,10 +78,6 @@ + xDelete(rootpath); + delete femmodel; + +- /*Profiling at the end: */ +- profiler->Tag(Finish); +- ProfilerEcho(profiler); +- + /*Finalize environment:*/ + EnvironmentFinalize(); + +Index: ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13548) ++++ ../trunk-jpl/src/c/EnumDefinitions/EnumDefinitions.h (revision 13549) +@@ -511,6 +511,8 @@ + NodalEnum, + OldGradientEnum, + OutputFilePointerEnum, ++ OutputFileNameEnum, ++ LockFileNameEnum, + PetscOptionsAnalysesEnum, + PetscOptionsStringsEnum, + QmuErrNameEnum, +Index: ../trunk-jpl/src/c/io/Disk/WriteLockFile.cpp +=================================================================== +--- ../trunk-jpl/src/c/io/Disk/WriteLockFile.cpp (revision 0) ++++ ../trunk-jpl/src/c/io/Disk/WriteLockFile.cpp (revision 13549) +@@ -0,0 +1,25 @@ ++/*!\file: WriteLockFile.cpp ++ * \brief ++ */ ++#include ++#include "../../shared/shared.h" ++#include "../../include/include.h" ++ ++void WriteLockFile(char* filename){ ++ ++ int i; ++ extern int my_rank; ++ ++ /* output: */ ++ FILE* fid=NULL; ++ ++ /* Open lock file and write 1 into it: */ ++ if(my_rank==0){ ++ fid=fopen(filename,"w"); ++ if(fid==NULL) _error_("error message: could not open lock file " << filename); ++ ++ /*Close file: */ ++ if(fclose(fid)!=0) _error_("could not close lock file " << filename); ++ } ++ ++} +Index: ../trunk-jpl/src/c/io/Disk/diskio.h +=================================================================== +--- ../trunk-jpl/src/c/io/Disk/diskio.h (revision 13548) ++++ ../trunk-jpl/src/c/io/Disk/diskio.h (revision 13549) +@@ -9,5 +9,6 @@ + + FILE* pfopen(char* filename,const char* format); + void pfclose(FILE* fid,char* filename); ++void WriteLockFile(char* filename); + + #endif /* _IO_H_ */ +Index: ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13548) ++++ ../trunk-jpl/src/c/modules/StringToEnumx/StringToEnumx.cpp (revision 13549) +@@ -498,18 +498,20 @@ + else if (strcmp(name,"Nodal")==0) return NodalEnum; + else if (strcmp(name,"OldGradient")==0) return OldGradientEnum; + else if (strcmp(name,"OutputFilePointer")==0) return OutputFilePointerEnum; ++ else if (strcmp(name,"OutputFileName")==0) return OutputFileNameEnum; ++ else if (strcmp(name,"LockFileName")==0) return LockFileNameEnum; + else if (strcmp(name,"PetscOptionsAnalyses")==0) return PetscOptionsAnalysesEnum; + else if (strcmp(name,"PetscOptionsStrings")==0) return PetscOptionsStringsEnum; + else if (strcmp(name,"QmuErrName")==0) return QmuErrNameEnum; + else if (strcmp(name,"QmuInName")==0) return QmuInNameEnum; + else if (strcmp(name,"QmuOutName")==0) return QmuOutNameEnum; + else if (strcmp(name,"Regular")==0) return RegularEnum; +- else if (strcmp(name,"Scaled")==0) return ScaledEnum; +- else if (strcmp(name,"Separate")==0) return SeparateEnum; + else stage=5; + } + if(stage==5){ +- if (strcmp(name,"Sset")==0) return SsetEnum; ++ if (strcmp(name,"Scaled")==0) return ScaledEnum; ++ else if (strcmp(name,"Separate")==0) return SeparateEnum; ++ else if (strcmp(name,"Sset")==0) return SsetEnum; + else if (strcmp(name,"Verbose")==0) return VerboseEnum; + else if (strcmp(name,"TriangleInterp")==0) return TriangleInterpEnum; + else if (strcmp(name,"BilinearInterp")==0) return BilinearInterpEnum; +Index: ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13548) ++++ ../trunk-jpl/src/c/modules/EnumToStringx/EnumToStringx.cpp (revision 13549) +@@ -488,6 +488,8 @@ + case NodalEnum : return "Nodal"; + case OldGradientEnum : return "OldGradient"; + case OutputFilePointerEnum : return "OutputFilePointer"; ++ case OutputFileNameEnum : return "OutputFileName"; ++ case LockFileNameEnum : return "LockFileName"; + case PetscOptionsAnalysesEnum : return "PetscOptionsAnalyses"; + case PetscOptionsStringsEnum : return "PetscOptionsStrings"; + case QmuErrNameEnum : return "QmuErrName"; +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13548) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13549) +@@ -235,6 +235,7 @@ + ./io/Disk/diskio.h\ + ./io/Disk/pfopen.cpp\ + ./io/Disk/pfclose.cpp\ ++ ./io/Disk/WriteLockFile.cpp\ + ./io/PrintfFunction.cpp\ + ./EnumDefinitions/EnumDefinitions.h\ + ./modules/ModelProcessorx/ModelProcessorx.h\ +@@ -343,7 +344,6 @@ + ./modules/InputConvergencex/InputConvergencex.h\ + ./solutions/convergence.cpp\ + ./solutions/ProcessArguments.cpp\ +- ./solutions/WriteLockFile.cpp\ + ./solutions/ResetBoundaryConditions.cpp\ + ./solutions/AnalysisConfiguration.cpp\ + ./solutions/CorePointerFromSolutionEnum.cpp\ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13548) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13549) +@@ -19,12 +19,14 @@ + + /*Object constructors and destructor*/ + /*FUNCTION FemModel::constructor {{{*/ +-FemModel::FemModel(char* rootpath, char* inputfilename, char* outputfilename, const int in_solution_type,const int* analyses,const int nummodels){ ++FemModel::FemModel(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){ + + /*intermediary*/ + int i; + int analysis_type; + FILE *IOMODEL = NULL; ++ FILE *petscoptionsfid = NULL; ++ FILE *output_fid = NULL; + extern int my_rank; + + /*Open input file on cpu 0: */ +@@ -70,8 +72,18 @@ + /*Close input file descriptors: */ + if(my_rank==0) pfclose(IOMODEL,inputfilename); + +- /*Add output file name to parameters: */ +- this->parameters->AddObject(new StringParam(OutputfilenameEnum,outputfilename)); ++ /*Open output file once for all and add output file name and file descriptor to parameters*/ ++ output_fid=pfopen(outputfilename,"wb"); ++ this->parameters->AddObject(new StringParam(OutputFileNameEnum,outputfilename)); ++ this->parameters->SetParam(output_fid,OutputFilePointerEnum); ++ ++ /*Save lock file name for later: */ ++ this->parameters->AddObject(new StringParam(LockFileNameEnum,lockfilename)); ++ ++ /*Now, deal with petsc options, which need to be put into the parameters dataset: */ ++ petscoptionsfid=pfopen(petscfilename,"r"); ++ ParsePetscOptionsx(this->parameters,petscoptionsfid); ++ pfclose(petscoptionsfid,petscfilename); + } + /*}}}*/ + /*FUNCTION FemModel::destructor {{{*/ +@@ -79,9 +91,28 @@ + + /*Intermediary*/ + int i; ++ FILE* output_fid; ++ char* outbinfilename=NULL; ++ char* lockfilename=NULL; ++ bool waitonlock=false; + ++ /*Close output file: */ ++ this->parameters->FindParam(&output_fid,OutputFilePointerEnum); ++ this->parameters->FindParam(&outbinfilename,OutputFileNameEnum); ++ pfclose(output_fid,outbinfilename); ++ ++ /*Write lock file if requested: */ ++ this->parameters->FindParam(&waitonlock,SettingsWaitonlockEnum); ++ this->parameters->FindParam(&lockfilename,LockFileNameEnum); ++ if (waitonlock>0){ ++ _pprintLine_("write lock file:"); ++ WriteLockFile(lockfilename); ++ } ++ + /*Delete all the datasets: */ + xDelete(analysis_type_list); ++ xDelete(outbinfilename); ++ xDelete(lockfilename); + delete elements; + delete nodes; + delete vertices; +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 13548) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 13549) +@@ -42,7 +42,7 @@ + Results *results; //results that cannot be fit into the elements + + /*constructors, destructors: */ +- FemModel(char* rootpath, char* inputfilename, char* outputfilename, const int solution_type,const int* analyses,const int nummodels); ++ FemModel(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int solution_type,const int* analyses,const int nummodels); + ~FemModel(); + + /*Methods: */ +Index: ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m +=================================================================== +--- ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13548) ++++ ../trunk-jpl/src/m/enum/MaximumNumberOfEnums.m (revision 13549) +@@ -8,4 +8,4 @@ + % Usage: + % macro=MaximumNumberOfEnums() + +-macro=496; ++macro=498; +Index: ../trunk-jpl/src/m/enum/OutputfilenameEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/OutputfilenameEnum.m (revision 13548) ++++ ../trunk-jpl/src/m/enum/OutputfilenameEnum.m (revision 13549) +@@ -1,11 +1,11 @@ +-function macro=OutputfilenameEnum() +-%OUTPUTFILENAMEENUM - Enum of Outputfilename ++function macro=OutputFileNameEnum() ++%OUTPUTFILENAMEENUM - Enum of OutputFileName + % + % WARNING: DO NOT MODIFY THIS FILE + % this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh + % Please read src/c/EnumDefinitions/README for more information + % + % Usage: +-% macro=OutputfilenameEnum() ++% macro=OutputFileNameEnum() + +-macro=StringToEnum('Outputfilename'); ++macro=StringToEnum('OutputFileName'); +Index: ../trunk-jpl/src/m/enum/EnumDefinitions.py +=================================================================== +--- ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13548) ++++ ../trunk-jpl/src/m/enum/EnumDefinitions.py (revision 13549) +@@ -4728,6 +4728,26 @@ + + return StringToEnum('OutputFilePointer')[0] + ++def OutputFileNameEnum(): ++ """ ++ OUTPUTFILENAMEENUM - Enum of OutputFileName ++ ++ Usage: ++ macro=OutputFileNameEnum() ++ """ ++ ++ return StringToEnum('OutputFileName')[0] ++ ++def LockFileNameEnum(): ++ """ ++ LOCKFILENAMEENUM - Enum of LockFileName ++ ++ Usage: ++ macro=LockFileNameEnum() ++ """ ++ ++ return StringToEnum('LockFileName')[0] ++ + def PetscOptionsAnalysesEnum(): + """ + PETSCOPTIONSANALYSESENUM - Enum of PetscOptionsAnalyses +@@ -4976,5 +4996,5 @@ + macro=MaximumNumberOfEnums() + """ + +- return 496 ++ return 498 + +Index: ../trunk-jpl/src/m/enum/LockFileNameEnum.m +=================================================================== +--- ../trunk-jpl/src/m/enum/LockFileNameEnum.m (revision 0) ++++ ../trunk-jpl/src/m/enum/LockFileNameEnum.m (revision 13549) +@@ -0,0 +1,11 @@ ++function macro=LockFileNameEnum() ++%LOCKFILENAMEENUM - Enum of LockFileName ++% ++% WARNING: DO NOT MODIFY THIS FILE ++% this file has been automatically generated by src/c/EnumDefinitions/Synchronize.sh ++% Please read src/c/EnumDefinitions/README for more information ++% ++% Usage: ++% macro=LockFileNameEnum() ++ ++macro=StringToEnum('LockFileName'); Index: /issm/oecreview/Archive/13393-13976/ISSM-13549-13550.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13549-13550.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13549-13550.diff (revision 13980) @@ -0,0 +1,47 @@ +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13549) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 13550) +@@ -110,23 +110,26 @@ + /*Don't forget to copy iomodel->independent_objects to parameters: */ + parameters->AddObject(new DataSetParam(AutodiffIndependentObjectsEnum,iomodel->independent_objects)); + /*}}}*/ +- /*initialize a placeholder to store solver pointers: {{{*/ +- GenericParam *theAdolcEDF_p=new GenericParam(AdolcParamEnum); +- theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p=reg_ext_fct(EDF_for_solverx); +- // to save some space: +- // we know we won't use adolc inside of the solver: +- theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->nestedAdolc=false; +- // the solution vector is just allocated and doesn't have a meaningfull prior value +- theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->dp_y_priorRequired=false; +- // the solver wrapper makes sure the matrix and the right hand side don't change +- theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->dp_x_changes=false; +- parameters->AddObject(theAdolcEDF_p); +- /*}}}*/ + + #endif ++ } ++ ++ #ifdef _HAVE_ADOLC_ ++ /*initialize a placeholder to store solver pointers: {{{*/ ++ GenericParam *theAdolcEDF_p=new GenericParam(AdolcParamEnum); ++ theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p=reg_ext_fct(EDF_for_solverx); ++ // to save some space: ++ // we know we won't use adolc inside of the solver: ++ theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->nestedAdolc=false; ++ // the solution vector is just allocated and doesn't have a meaningfull prior value ++ theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->dp_y_priorRequired=false; ++ // the solver wrapper makes sure the matrix and the right hand side don't change ++ theAdolcEDF_p->GetParameterValue().myEDF_for_solverx_p->dp_x_changes=false; ++ parameters->AddObject(theAdolcEDF_p); ++ /*}}}*/ ++ #endif ++ ++ /*Assign output pointer: */ ++ *pparameters=parameters; + +- /*Assign output pointer: */ +- *pparameters=parameters; +- +- } + } Index: /issm/oecreview/Archive/13393-13976/ISSM-13550-13551.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13550-13551.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13550-13551.diff (revision 13980) @@ -0,0 +1,21 @@ +Index: ../trunk-jpl/externalpackages/adolc/install-update-dev.sh +=================================================================== +--- ../trunk-jpl/externalpackages/adolc/install-update-dev.sh (revision 13550) ++++ ../trunk-jpl/externalpackages/adolc/install-update-dev.sh (revision 13551) +@@ -6,13 +6,13 @@ + #repo. + + #Some cleanup +-rm -rf install adolc_v220_issm ++rm -rf install adolc_issm + + #symlink: +-ln -s /u/astrid-r1b/larour/issm-uci/trunk-jpl/externalpackages/adolc/adolc_v220_issm ./adolc_v220_issm ++ln -s /u/astrid-r1b/larour/issm-uci/trunk-jpl/externalpackages/adolc/adolc_issm ./adolc_issm + + #update and compile +-cd adolc_v220_issm ++cd adolc_issm + git pull + + autoreconf -f -i Index: /issm/oecreview/Archive/13393-13976/ISSM-13551-13552.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13551-13552.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13551-13552.diff (revision 13980) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/test/NightlyRun/test3015.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3015.m (revision 13551) ++++ ../trunk-jpl/test/NightlyRun/test3015.m (revision 13552) +@@ -73,5 +73,5 @@ + + %Fields and tolerances to track changes + field_names ={'dV/dh-dV/dh0'}; +-field_tolerances={1e-1}; ++field_tolerances={1e-13}; + field_values={dVdh_ad-dVdh_an}; +Index: ../trunk-jpl/test/Archives/Archive3020.nc +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/13393-13976/ISSM-13552-13553.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13552-13553.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13552-13553.diff (revision 13980) @@ -0,0 +1,237 @@ +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13552) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13553) +@@ -13,69 +13,36 @@ + /*FemModel: */ + FemModel *femmodel = NULL; + +- /*configuration: */ +- void (*solutioncore)(FemModel*)=NULL; //core solution function pointer +- int* analyses=NULL; +- int numanalyses; +- int solution_type; ++ /*Print starting banner: {{{*/ ++ _pprintLine_(""); ++ _pprintLine_("Ice Sheet System Model (" << PACKAGE_NAME << ") version " << PACKAGE_VERSION); ++ _pprintLine_("(website: " << PACKAGE_URL << " contact: " << PACKAGE_BUGREPORT << ")"); ++ _pprintLine_(""); ++ /*}}}*/ + +- /*File names*/ +- char *lockfilename = NULL; +- char *binfilename = NULL; +- char *outbinfilename = NULL; +- char *petscfilename = NULL; +- char *rootpath = NULL; +- +- /*profiling*/ +- Profiler* profiler=NULL; +- + /*Initialize exception trapping: */ + ExceptionTrapBegin(); + + /*Initialize environment (MPI, PETSC, MUMPS, etc ...)*/ + EnvironmentInit(argc,argv); +- +- /*Start profiler: */ +- profiler=new Profiler(); +- profiler->Tag(Start); +- +- /*First process inputs*/ +- _pprintLine_(""); +- _pprintLine_("Ice Sheet System Model (" << PACKAGE_NAME << ") version " << PACKAGE_VERSION); +- _pprintLine_("(website: " << PACKAGE_URL << " contact: " << PACKAGE_BUGREPORT << ")"); +- _pprintLine_(""); ++ ++ /*Initialize femmodel from arguments provided command line: */ ++ femmodel=new FemModel(argc,argv); + +- ProcessArguments(&solution_type,&binfilename,&outbinfilename,&petscfilename,&lockfilename,&rootpath,argc,argv); ++ /*Solve: */ ++ femmodel->Solve(); + +- /*out of solution_type, figure out types of analyses needed in the femmodel: */ +- AnalysisConfiguration(&analyses,&numanalyses,solution_type); ++ /*Some profiling: */ ++ ProfilerEnd(femmodel->profiler,femmodel->results,femmodel->parameters); + +- /*Create femmodel from input files: */ +- profiler->Tag(StartInit); +- femmodel=new FemModel(rootpath,binfilename,outbinfilename,petscfilename,lockfilename,solution_type,analyses,numanalyses); +- profiler->Tag(FinishInit); +- +- /*call cores: */ +- _pprintLine_("call computational core:"); +- CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); +- profiler->Tag(StartCore); solutioncore(femmodel); profiler->Tag(FinishCore); +- profiler->Tag(StartAdCore); ad_core(femmodel); profiler->Tag(FinishAdCore); +- ProfilerEnd(profiler,femmodel->results,femmodel->parameters); +- + _pprintLine_("write results to disk:"); + OutputResultsx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); + + /*Profiling at the end: */ +- profiler->Tag(Finish); +- ProfilerEcho(profiler); ++ femmodel->profiler->Tag(Finish); ++ ProfilerEcho(femmodel->profiler); + +- /*Free resources */ +- xDelete(analyses); +- xDelete(lockfilename); +- xDelete(binfilename); +- xDelete(outbinfilename); +- xDelete(petscfilename); +- xDelete(rootpath); ++ /*Wrap up: */ + delete femmodel; + + /*Finalize environment:*/ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13552) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13553) +@@ -11,6 +11,7 @@ + #include + #include "../Container/Container.h" + #include "../modules/ModelProcessorx/ModelProcessorx.h" ++#include "../solutions/solutions.h" + #include "../io/io.h" + #include "./classes.h" + #include "../include/include.h" +@@ -18,9 +19,57 @@ + #include "../modules/modules.h" + + /*Object constructors and destructor*/ +-/*FUNCTION FemModel::constructor {{{*/ ++/*FUNCTION FemModel::FemModel(int argc,char** argv){{{*/ ++FemModel::FemModel(int argc,char** argv){ ++ ++ /*configuration: */ ++ int* analyses=NULL; ++ int numanalyses; ++ int solution_type; ++ ++ /*File names*/ ++ char *lockfilename = NULL; ++ char *binfilename = NULL; ++ char *outbinfilename = NULL; ++ char *petscfilename = NULL; ++ char *rootpath = NULL; ++ ++ /*Start profiler: */ ++ this->profiler=new Profiler(); ++ profiler->Tag(Start); ++ ++ /*From command line arguments, retrieve different filenames needed to create the FemModel: */ ++ ProcessArguments(&solution_type,&binfilename,&outbinfilename,&petscfilename,&lockfilename,&rootpath,argc,argv); ++ ++ /*out of solution_type, figure out types of analyses needed in the femmodel: */ ++ AnalysisConfiguration(&analyses,&numanalyses,solution_type); ++ ++ /*Create femmodel from input files: */ ++ profiler->Tag(StartInit); ++ this->InitFromFiles(rootpath,binfilename,outbinfilename,petscfilename,lockfilename,solution_type,analyses,numanalyses); ++ profiler->Tag(FinishInit); ++ ++ /*Free resources */ ++ xDelete(analyses); ++ xDelete(lockfilename); ++ xDelete(binfilename); ++ xDelete(outbinfilename); ++ xDelete(petscfilename); ++ xDelete(rootpath); ++ ++} ++/*}}}*/ ++/*FUNCTION FemModel::FemModel(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){{{*/ + FemModel::FemModel(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){ + ++ /*Call InitFromFiles. This constructor is just a wrapper: */ ++ this->InitFromFiles(rootpath, inputfilename, outputfilename, petscfilename, lockfilename, in_solution_type,analyses,nummodels); ++ ++} ++/*}}}*/ ++/*FUNCTION FemModel::InitFromFiles(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){{{*/ ++void FemModel::InitFromFiles(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int in_solution_type,const int* analyses,const int nummodels){ ++ + /*intermediary*/ + int i; + int analysis_type; +@@ -121,11 +170,39 @@ + delete materials; + delete parameters; + delete results; ++ delete profiler; + + } + /*}}}*/ + + /*Object management*/ ++/*FUNCTION FemModel::Solve {{{*/ ++void FemModel::Solve(void){ ++ ++ int solution_type; ++ void (*solutioncore)(FemModel*)=NULL; //core solution function pointer ++ ++ _pprintLine_("call computational core:"); ++ ++ /*Retrieve solution_type from parameters: */ ++ this->parameters->FindParam(&solution_type,SolutionTypeEnum); ++ ++ /*Figure out which solution core we are going to run with the current solution type: */ ++ CorePointerFromSolutionEnum(&solutioncore,this->parameters,solution_type); ++ ++ /*run solutoin core: */ ++ profiler->Tag(StartCore); ++ solutioncore(this); ++ profiler->Tag(FinishCore); ++ ++ /*run AD core if needed: */ ++ profiler->Tag(StartAdCore); ++ ad_core(this); ++ profiler->Tag(FinishAdCore); ++ ++ ++} ++/*}}}*/ + /*FUNCTION FemModel::Echo {{{*/ + void FemModel::Echo(void){ + +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 13552) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 13553) +@@ -18,6 +18,7 @@ + class Constraints; + class Loads; + class Materials; ++class Profiler; + /*}}}*/ + + +@@ -32,6 +33,8 @@ + int *analysis_type_list; //list of analyses this femmodel is going to carry out + int analysis_counter; //counter into analysis_type_list + ++ Profiler* profiler; //keep time, cpu and mem statistics while we are running. ++ + Elements *elements; //elements (one set for all analyses) + Nodes *nodes; //one set of nodes + Vertices *vertices; //one set of vertices +@@ -42,11 +45,14 @@ + Results *results; //results that cannot be fit into the elements + + /*constructors, destructors: */ ++ FemModel(int argc,char** argv); + FemModel(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int solution_type,const int* analyses,const int nummodels); + ~FemModel(); ++ void InitFromFiles(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int solution_type,const int* analyses,const int nummodels); + + /*Methods: */ + void Echo(); ++ void Solve(void); + + /*Fem: */ + void SetCurrentConfiguration(int configuration_type); Index: /issm/oecreview/Archive/13393-13976/ISSM-13553-13554.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13553-13554.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13553-13554.diff (revision 13980) @@ -0,0 +1,269 @@ +Index: ../trunk-jpl/src/c/solutions/solutions.h +=================================================================== +--- ../trunk-jpl/src/c/solutions/solutions.h (revision 13553) ++++ ../trunk-jpl/src/c/solutions/solutions.h (revision 13554) +@@ -49,6 +49,7 @@ + void EnvironmentInit(int argc,char** argv); + void EnvironmentFinalize(void); + int DakotaSpawnCore(double* responses, int numresponses, double* variables, char** variables_descriptors,int numvariables, void* femmodel,int counter); ++void PrintBanner(void); + + //solution configuration + void AnalysisConfiguration(int** panalyses,int* pnumanalyses, int solutiontype); +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13553) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13554) +@@ -1,25 +1,14 @@ + /*!\file: issm.cpp +- * \brief: ISSM main parallel program ++ * \brief: ISSM main program + */ + + #include "../issm.h" +-#include "../include/globals.h" + +-void ProfilerEcho(Profiler* profiler); +-void ProfilerEnd(Profiler* profiler, Results* results, Parameters* parameters); +- + int main(int argc,char **argv){ + +- /*FemModel: */ +- FemModel *femmodel = NULL; ++ /*Print starting banner:*/ ++ PrintBanner(); + +- /*Print starting banner: {{{*/ +- _pprintLine_(""); +- _pprintLine_("Ice Sheet System Model (" << PACKAGE_NAME << ") version " << PACKAGE_VERSION); +- _pprintLine_("(website: " << PACKAGE_URL << " contact: " << PACKAGE_BUGREPORT << ")"); +- _pprintLine_(""); +- /*}}}*/ +- + /*Initialize exception trapping: */ + ExceptionTrapBegin(); + +@@ -27,21 +16,14 @@ + EnvironmentInit(argc,argv); + + /*Initialize femmodel from arguments provided command line: */ +- femmodel=new FemModel(argc,argv); ++ FemModel *femmodel = new FemModel(argc,argv); + + /*Solve: */ + femmodel->Solve(); + +- /*Some profiling: */ +- ProfilerEnd(femmodel->profiler,femmodel->results,femmodel->parameters); +- +- _pprintLine_("write results to disk:"); +- OutputResultsx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); ++ /*Output results: */ ++ femmodel->OutputResults(); + +- /*Profiling at the end: */ +- femmodel->profiler->Tag(Finish); +- ProfilerEcho(femmodel->profiler); +- + /*Wrap up: */ + delete femmodel; + +@@ -54,45 +36,3 @@ + /*Return unix success: */ + return 0; + } +- +-void ProfilerEcho(Profiler* profiler){ /*{{{*/ +- +- _pprintLine_(""); +- _pprintLine_(" "<DeltaTime(StartInit,FinishInit)); +- _pprintLine_(" "<DeltaTime(StartCore,FinishCore)); +- _pprintLine_(""); +- _pprintLine_(" Total elapsed time:" +- <DeltaTimeModHour(Start,Finish)<<" hrs " +- <DeltaTimeModMin(Start,Finish)<<" min " +- <DeltaTimeModSec(Start,Finish)<<" sec" +- ); +- _pprintLine_(""); +- +-} /*}}}*/ +-void ProfilerEnd(Profiler* profiler, Results* results, Parameters* parameters){ /*{{{*/ +- +- bool profiling = false; +- +- IssmDouble solution_time; +- IssmDouble solution_flops; +- IssmDouble solution_memory; +- +- parameters->FindParam(&profiling,DebugProfilingEnum); +- +- if(profiling){ +- +- solution_time=profiler->DeltaTime(StartCore,FinishCore); +- solution_flops=profiler->DeltaFlops(StartCore,FinishCore); +- solution_memory=profiler->Memory(FinishCore); +- +- _pprintLine_("Solution elapsed time : " << solution_time << " Seconds"); +- _pprintLine_("Solution elapsed flops : " << solution_flops << " Flops"); +- _pprintLine_("Solution memory used : " << solution_memory << " Bytes"); +- +- /*Add to results: */ +- results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingSolutionTimeEnum, solution_time, 1, 0)); +- results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentMemEnum, solution_memory, 1, 0)); +- results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentFlopsEnum, solution_flops, 1, 0)); +- } +- +-} /*}}}*/ +Index: ../trunk-jpl/src/c/solutions/PrintBanner.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/PrintBanner.cpp (revision 0) ++++ ../trunk-jpl/src/c/solutions/PrintBanner.cpp (revision 13554) +@@ -0,0 +1,15 @@ ++/*!\file: PrintBanner.cpp ++ * \brief: print banner information on ISSM ++ */ ++ ++#include "../include/include.h" ++#include "../shared/shared.h" ++ ++void PrintBanner(void){ ++ ++ _pprintLine_(""); ++ _pprintLine_("Ice Sheet System Model (" << PACKAGE_NAME << ") version " << PACKAGE_VERSION); ++ _pprintLine_("(website: " << PACKAGE_URL << " contact: " << PACKAGE_BUGREPORT << ")"); ++ _pprintLine_(""); ++} ++ +Index: ../trunk-jpl/src/c/solutions/kriging.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/kriging.cpp (revision 13553) ++++ ../trunk-jpl/src/c/solutions/kriging.cpp (revision 13554) +@@ -3,7 +3,6 @@ + */ + + #include "../issm.h" +-#include "../include/globals.h" + + /*Local prototypes*/ + void ProcessArguments2(char** pbinfilename,char** poutbinfilename,char** plockfilename,char** prootpath,int argc,char **argv); +Index: ../trunk-jpl/src/c/issm.h +=================================================================== +--- ../trunk-jpl/src/c/issm.h (revision 13553) ++++ ../trunk-jpl/src/c/issm.h (revision 13554) +@@ -11,6 +11,7 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + ++#include "./include/globals.h" //only include this header file once! + #include "./include/include.h" + #include "./shared/shared.h" + #include "./classes/classes.h" +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13553) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13554) +@@ -342,6 +342,7 @@ + ./modules/InputToResultx/InputToResultx.h\ + ./modules/InputConvergencex/InputConvergencex.cpp\ + ./modules/InputConvergencex/InputConvergencex.h\ ++ ./solutions/PrintBanner.cpp\ + ./solutions/convergence.cpp\ + ./solutions/ProcessArguments.cpp\ + ./solutions/ResetBoundaryConditions.cpp\ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13553) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13554) +@@ -170,22 +170,54 @@ + delete materials; + delete parameters; + delete results; ++ ++ /*Before we delete the profiler, report statistics for this run: */ ++ profiler->Tag(Finish); //final tagging ++ _pprintLine_(""); ++ _pprintLine_(" "<DeltaTime(StartInit,FinishInit)); ++ _pprintLine_(" "<DeltaTime(StartCore,FinishCore)); ++ _pprintLine_(""); ++ _pprintLine_(" Total elapsed time:" ++ <DeltaTimeModHour(Start,Finish)<<" hrs " ++ <DeltaTimeModMin(Start,Finish)<<" min " ++ <DeltaTimeModSec(Start,Finish)<<" sec" ++ ); ++ _pprintLine_(""); ++ ++ /*Now delete: */ + delete profiler; + + } + /*}}}*/ + + /*Object management*/ ++/*FUNCTION FemModel::OutputResults {{{*/ ++void FemModel::OutputResults(void){ ++ ++ _pprintLine_("write results to disk:"); ++ ++ /*Just call the OutputResultsx module: */ ++ OutputResultsx(this->elements, this->nodes, this->vertices, this->loads, this->materials, this->parameters,this->results); ++ ++} ++/*}}}*/ + /*FUNCTION FemModel::Solve {{{*/ + void FemModel::Solve(void){ + ++ /*profiling: */ ++ bool profiling = false; ++ IssmDouble solution_time; ++ IssmDouble solution_flops; ++ IssmDouble solution_memory; ++ ++ /*solution: */ + int solution_type; + void (*solutioncore)(FemModel*)=NULL; //core solution function pointer + + _pprintLine_("call computational core:"); + + /*Retrieve solution_type from parameters: */ +- this->parameters->FindParam(&solution_type,SolutionTypeEnum); ++ parameters->FindParam(&solution_type,SolutionTypeEnum); + + /*Figure out which solution core we are going to run with the current solution type: */ + CorePointerFromSolutionEnum(&solutioncore,this->parameters,solution_type); +@@ -200,7 +232,24 @@ + ad_core(this); + profiler->Tag(FinishAdCore); + ++ /*some profiling results for the core: */ ++ parameters->FindParam(&profiling,DebugProfilingEnum); ++ if(profiling){ + ++ solution_time=profiler->DeltaTime(StartCore,FinishCore); ++ solution_flops=profiler->DeltaFlops(StartCore,FinishCore); ++ solution_memory=profiler->Memory(FinishCore); ++ ++ _pprintLine_("Solution elapsed time : " << solution_time << " Seconds"); ++ _pprintLine_("Solution elapsed flops : " << solution_flops << " Flops"); ++ _pprintLine_("Solution memory used : " << solution_memory << " Bytes"); ++ ++ /*Add to results: */ ++ results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingSolutionTimeEnum, solution_time, 1, 0)); ++ results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentMemEnum, solution_memory, 1, 0)); ++ results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentFlopsEnum, solution_flops, 1, 0)); ++ } ++ + } + /*}}}*/ + /*FUNCTION FemModel::Echo {{{*/ +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 13553) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 13554) +@@ -53,6 +53,7 @@ + /*Methods: */ + void Echo(); + void Solve(void); ++ void OutputResults(void); + + /*Fem: */ + void SetCurrentConfiguration(int configuration_type); Index: /issm/oecreview/Archive/13393-13976/ISSM-13554-13555.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13554-13555.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13554-13555.diff (revision 13980) @@ -0,0 +1,183 @@ +Index: ../trunk-jpl/src/c/toolkits/mpi/patches/MPI_Boundariesfromrange.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/patches/MPI_Boundariesfromrange.cpp (revision 13554) ++++ ../trunk-jpl/src/c/toolkits/mpi/patches/MPI_Boundariesfromrange.cpp (revision 13555) +@@ -1,38 +0,0 @@ +-/*!\file MPI_Boundariesfromrange.cpp +- * \brief: routine to figure out from a range distribution, the lower and upper +- * bounds for the current cpu. +- */ +- +-#include "./mpipatches.h" +-#include "../../../shared/shared.h" +- +-int MPI_Boundariesfromrange(int* plower_row, int* pupper_row,int range){ +- +- extern int num_procs; +- extern int my_rank; +- +- /*output: */ +- int lower_row,upper_row; +- +- /*intermediary: */ +- int i; +- int* allranges=NULL; +- +- /*Gather all range values into allranges, for all nodes*/ +- allranges=xNew(num_procs); +- MPI_Allgather(&range,1,MPI_INT,allranges,1,MPI_INT,MPI_COMM_WORLD); +- +- /*From all ranges, get lower row and upper row*/ +- lower_row=0; +- upper_row=lower_row+allranges[0]; +- for (i=1;i<=my_rank;i++){ +- lower_row=lower_row+allranges[i-1]; +- upper_row=upper_row+allranges[i]; +- } +- +- /*Assign output pointers: */ +- xDelete(allranges); +- *plower_row=lower_row; +- *pupper_row=upper_row; +- return 1; +-} +Index: ../trunk-jpl/src/c/toolkits/mpi/patches/MPI_Lowerrow.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/patches/MPI_Lowerrow.cpp (revision 13554) ++++ ../trunk-jpl/src/c/toolkits/mpi/patches/MPI_Lowerrow.cpp (revision 13555) +@@ -1,27 +0,0 @@ +-/*!\file MPI_Lowerrow.cpp +- * \brief: routine to distribute jobs in parallel. +- * This handy routine will provide, along with the MPI_Upperrow, a distributed range +- * for an index (like i,j, in a for loop). +- * Ex: for(i=MPI_Lowerrow(num_procs)0;i + #include "../../../shared/shared.h" + +-int DetermineLocalSize(int global_size){ ++int DetermineLocalSize(int global_size,MPI_Comm comm){ + ++ /*size of comm: */ ++ int my_rank,num_procs; ++ + /*output: */ + int local_size; + +@@ -16,10 +19,15 @@ + int row_rest; + int* num_local_rows=NULL; + +- /*from MPI: */ +- extern int num_procs; +- extern int my_rank; +- ++ /*retrieve my_rank: */ ++ #ifdef _HAVE_MPI_ ++ MPI_Comm_rank(comm,&my_rank); ++ MPI_Comm_size(comm,&num_procs); ++ #else ++ my_rank=0; ++ num_procs=1; ++ #endif ++ + /*We are not bound by any library, just use what seems most logical*/ + num_local_rows=xNew(num_procs); + +Index: ../trunk-jpl/src/c/toolkits/mpi/patches/mpipatches.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/patches/mpipatches.h (revision 13554) ++++ ../trunk-jpl/src/c/toolkits/mpi/patches/mpipatches.h (revision 13555) +@@ -5,14 +5,5 @@ + + #ifndef MPI_PATCHES_H_ + #define MPI_PATCHES_H_ +- +- +-int MPI_Boundariesfromrange(int* plower_row, int* pupper_row,int range); +-int MPI_Lowerrow(int n); +-int MPI_Upperrow(int n); +-int DetermineLocalSize(int global_size); +- +- +- +- ++int DetermineLocalSize(int global_size,MPI_Comm comm); + #endif +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13554) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13555) +@@ -792,10 +792,7 @@ + #Mpi sources {{{ + mpi_sources= ./toolkits/mpi/mpiincludes.h\ + ./toolkits/mpi/patches/mpipatches.h\ +- ./toolkits/mpi/patches/DetermineLocalSize.cpp\ +- ./toolkits/mpi/patches/MPI_Upperrow.cpp\ +- ./toolkits/mpi/patches/MPI_Lowerrow.cpp\ +- ./toolkits/mpi/patches/MPI_Boundariesfromrange.cpp ++ ./toolkits/mpi/patches/DetermineLocalSize.cpp + #}}} + #Metis sources {{{ + metis_sources= ./toolkits/metis/patches/metispatches.h\ Index: /issm/oecreview/Archive/13393-13976/ISSM-13555-13556.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13555-13556.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13555-13556.diff (revision 13980) @@ -0,0 +1,155 @@ +Index: ../trunk-jpl/src/c/toolkits/petsc/patches/MatPartition.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/patches/MatPartition.cpp (revision 13555) ++++ ../trunk-jpl/src/c/toolkits/petsc/patches/MatPartition.cpp (revision 13556) +@@ -1,138 +0,0 @@ +-/*!\file: MatPartition.cpp +- * \brief partition matrix according to node sets +- */ +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-/*Petsc includes: */ +-#include "petscmat.h" +-#include "petscvec.h" +-#include "petscksp.h" +- +-#include "../../../shared/shared.h" +-#include "../../mpi/patches/mpipatches.h" +- +-int MatPartition(Mat* poutmatrix,Mat matrixA,double* row_partition_vector,int row_partition_vector_size , +- double* col_partition_vector,int col_partition_vector_size){ +- +- int i; +- +- /*Petsc matrix*/ +- int d_nz; +- int o_nz; +- int* node_rows=NULL; +- int* node_cols=NULL; +- int count; +- IS col_index=NULL; +- IS row_index=NULL; +- int lower_row,upper_row,range; +- int MA,NA; //matrixA dimensions +- const char* type=NULL; +- int csize; +- +- /*output*/ +- Mat outmatrix=NULL; +- +- /*get input matrix size: */ +- MatGetSize(matrixA,&MA,&NA); +- +- /*If one of the partitioning row or col vectors has a 0 dimension, we return a NILL matrix. Return it with the same type as matrixA.*/ +- +- if ((row_partition_vector_size==0) || (col_partition_vector==0)){ +- MatGetType(matrixA,&type); +- if (strcmp(type,"mpiaij")==0){ +- d_nz=0; +- o_nz=0; +- #if _PETSC_MAJOR_ == 3 && _PETSC_MINOR_ > 2 +- MatCreateAIJ(MPI_COMM_WORLD,PETSC_DETERMINE,PETSC_DETERMINE, 0,0,d_nz,PETSC_NULL,o_nz,PETSC_NULL,&outmatrix); +- #else +- MatCreateMPIAIJ(MPI_COMM_WORLD,PETSC_DETERMINE,PETSC_DETERMINE, 0,0,d_nz,PETSC_NULL,o_nz,PETSC_NULL,&outmatrix); +- #endif +- } +- else if (strcmp(type,"mpidense")==0){ +- #if _PETSC_MAJOR_ == 3 && _PETSC_MINOR_ > 2 +- MatCreateDense(MPI_COMM_WORLD,PETSC_DETERMINE,PETSC_DETERMINE, 0,0,PETSC_NULL,&outmatrix); +- #else +- MatCreateMPIDense(MPI_COMM_WORLD,PETSC_DETERMINE,PETSC_DETERMINE, 0,0,PETSC_NULL,&outmatrix); +- #endif +- } +- else{ +- _error_("MatType " << type << " not supported yet"); +- } +- /*Assemble*/ +- MatAssemblyBegin(outmatrix,MAT_FINAL_ASSEMBLY); +- MatAssemblyEnd(outmatrix,MAT_FINAL_ASSEMBLY); +- } +- else{ +- /*Both vectors are non nill, use MatGetSubMatrix to condense out*/ +- /*Figure out which rows each node is going to get from matrix A.*/ +- MatGetOwnershipRange(matrixA,&lower_row,&upper_row); +- upper_row--; +- range=upper_row-lower_row+1; +- +- count=0; +- if (range){ +- node_rows=xNew(range); //this is the maximum number of rows one node can extract. +- +- for (i=0;i=(lower_row+1)) && ((int)(*(row_partition_vector+i))<=(upper_row+1)) ){ +- *(node_rows+count)=(int)*(row_partition_vector+i)-1; +- count++; +- } +- } +- } +- else{ +- count=0; +- } +- +- /*Now each node has a node_rows vectors holding which rows they should extract from matrixA. Create an Index Set from node_rows.*/ +- #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) +- ISCreateGeneral(MPI_COMM_WORLD,count,node_rows,&row_index); +- #else +- ISCreateGeneral(MPI_COMM_WORLD,count,node_rows,PETSC_COPY_VALUES,&row_index); +- #endif +- +- /*Same deal for columns*/ +- node_cols=xNew(col_partition_vector_size); +- for (i=0;i= 3 +- MatGetSubMatrix(matrixA,row_index,col_index,MAT_INITIAL_MATRIX,&outmatrix); +- #else +- MatGetSubMatrix(matrixA,row_index,col_index,count,MAT_INITIAL_MATRIX,&outmatrix); +- #endif +- } +- else{ +- #if _PETSC_MAJOR_ >= 3 +- MatGetSubMatrix(matrixA,row_index,col_index,MAT_INITIAL_MATRIX,&outmatrix); +- #else +- MatGetSubMatrix(matrixA,row_index,col_index,csize,MAT_INITIAL_MATRIX,&outmatrix); +- #endif +- } +- +- } +- +- /*Free ressources:*/ +- xDelete(node_rows); +- xDelete(node_cols); +- ISFree(&col_index); +- ISFree(&row_index); +- +- /*Assign output pointers:*/ +- *poutmatrix=outmatrix; +- return 1; +-} +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13555) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13556) +@@ -772,7 +772,6 @@ + ./toolkits/petsc/patches/MatFree.cpp\ + ./toolkits/petsc/patches/GetOwnershipBoundariesFromRange.cpp\ + ./toolkits/petsc/patches/VecPartition.cpp\ +- ./toolkits/petsc/patches/MatPartition.cpp\ + ./toolkits/petsc/patches/MatInvert.cpp\ + ./toolkits/petsc/patches/MatMultPatch.cpp\ + ./toolkits/petsc/patches/ISSMToPetscMatrixType.cpp\ Index: /issm/oecreview/Archive/13393-13976/ISSM-13556-13557.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13556-13557.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13556-13557.diff (revision 13980) @@ -0,0 +1,45 @@ +Index: ../trunk-jpl/src/c/toolkits/petsc/patches/ISFree.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/patches/ISFree.cpp (revision 13556) ++++ ../trunk-jpl/src/c/toolkits/petsc/patches/ISFree.cpp (revision 13557) +@@ -1,28 +0,0 @@ +-/*!\file: ISFree.cpp +- * \brief wrapper to ISDestroy +- */ +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +- +-/*Petsc includes: */ +-#include "petscmat.h" +-#include "petscmat.h" +-#include "petscksp.h" +- +-void ISFree(IS* pis){ +- +- #if _PETSC_MAJOR_ < 3 || (_PETSC_MAJOR_ == 3 && _PETSC_MINOR_ < 2) +- if(*pis)ISDestroy(*pis); +- *pis=NULL; +- #else +- if(*pis)ISDestroy(pis); +- *pis=NULL; +- #endif +- +-} +- +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13556) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13557) +@@ -768,7 +768,6 @@ + ./toolkits/petsc/patches/PetscVectorToDoubleVector.cpp\ + ./toolkits/petsc/patches/VecDuplicatePatch.cpp\ + ./toolkits/petsc/patches/KSPFree.cpp\ +- ./toolkits/petsc/patches/ISFree.cpp\ + ./toolkits/petsc/patches/MatFree.cpp\ + ./toolkits/petsc/patches/GetOwnershipBoundariesFromRange.cpp\ + ./toolkits/petsc/patches/VecPartition.cpp\ Index: /issm/oecreview/Archive/13393-13976/ISSM-13557-13558.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13557-13558.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13557-13558.diff (revision 13980) @@ -0,0 +1,37 @@ +Index: ../trunk-jpl/src/c/toolkits/mpi/patches/DetermineLocalSize.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/patches/DetermineLocalSize.cpp (revision 13557) ++++ ../trunk-jpl/src/c/toolkits/mpi/patches/DetermineLocalSize.cpp (revision 13558) +@@ -6,11 +6,8 @@ + #include + #include "../../../shared/shared.h" + +-int DetermineLocalSize(int global_size,MPI_Comm comm){ ++int DetermineLocalSize(int global_size){ + +- /*size of comm: */ +- int my_rank,num_procs; +- + /*output: */ + int local_size; + +@@ -19,15 +16,10 @@ + int row_rest; + int* num_local_rows=NULL; + +- /*retrieve my_rank: */ +- #ifdef _HAVE_MPI_ +- MPI_Comm_rank(comm,&my_rank); +- MPI_Comm_size(comm,&num_procs); +- #else +- my_rank=0; +- num_procs=1; +- #endif +- ++ /*from MPI: */ ++ extern int num_procs; ++ extern int my_rank; ++ + /*We are not bound by any library, just use what seems most logical*/ + num_local_rows=xNew(num_procs); + Index: /issm/oecreview/Archive/13393-13976/ISSM-13558-13559.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13558-13559.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13558-13559.diff (revision 13980) @@ -0,0 +1,11 @@ +Index: ../trunk-jpl/src/c/toolkits/mpi/patches/mpipatches.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/patches/mpipatches.h (revision 13558) ++++ ../trunk-jpl/src/c/toolkits/mpi/patches/mpipatches.h (revision 13559) +@@ -5,5 +5,5 @@ + + #ifndef MPI_PATCHES_H_ + #define MPI_PATCHES_H_ +-int DetermineLocalSize(int global_size,MPI_Comm comm); ++int DetermineLocalSize(int global_size); + #endif Index: /issm/oecreview/Archive/13393-13976/ISSM-13559-13560.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13559-13560.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13559-13560.diff (revision 13980) @@ -0,0 +1,721 @@ +Index: ../trunk-jpl/src/android/helloworld/My First App/.classpath +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/.classpath (revision 0) ++++ ../trunk-jpl/src/android/helloworld/My First App/.classpath (revision 13560) +@@ -0,0 +1,8 @@ ++ ++ ++ ++ ++ ++ ++ ++ +Index: ../trunk-jpl/src/android/helloworld/My First App/project.properties +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/project.properties (revision 0) ++++ ../trunk-jpl/src/android/helloworld/My First App/project.properties (revision 13560) +@@ -0,0 +1,14 @@ ++# This file is automatically generated by Android Tools. ++# Do not modify this file -- YOUR CHANGES WILL BE ERASED! ++# ++# This file must be checked in Version Control Systems. ++# ++# To customize properties used by the Ant build system edit ++# "ant.properties", and override values to adapt the script to your ++# project structure. ++# ++# To enable ProGuard to shrink and obfuscate your code, uncomment this (available properties: sdk.dir, user.home): ++#proguard.config=${sdk.dir}/tools/proguard/proguard-android.txt:proguard-project.txt ++ ++# Project target. ++target=android-16 +Index: ../trunk-jpl/src/android/helloworld/My First App/.project +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/.project (revision 0) ++++ ../trunk-jpl/src/android/helloworld/My First App/.project (revision 13560) +@@ -0,0 +1,33 @@ ++ ++ ++ My First App ++ ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.ResourceManagerBuilder ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.PreCompilerBuilder ++ ++ ++ ++ ++ org.eclipse.jdt.core.javabuilder ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.ApkBuilder ++ ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.AndroidNature ++ org.eclipse.jdt.core.javanature ++ ++ +Index: ../trunk-jpl/src/android/helloworld/My First App/proguard-project.txt +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/proguard-project.txt (revision 0) ++++ ../trunk-jpl/src/android/helloworld/My First App/proguard-project.txt (revision 13560) +@@ -0,0 +1,20 @@ ++# To enable ProGuard in your project, edit project.properties ++# to define the proguard.config property as described in that file. ++# ++# Add project specific ProGuard rules here. ++# By default, the flags in this file are appended to flags specified ++# in ${sdk.dir}/tools/proguard/proguard-android.txt ++# You can edit the include path and order by changing the ProGuard ++# include property in project.properties. ++# ++# For more details, see ++# http://developer.android.com/guide/developing/tools/proguard.html ++ ++# Add any project specific keep options here: ++ ++# If your project uses WebView with JS, uncomment the following ++# and specify the fully qualified class name to the JavaScript interface ++# class: ++#-keepclassmembers class fqcn.of.javascript.interface.for.webview { ++# public *; ++#} +Index: ../trunk-jpl/src/android/helloworld/My First App/AndroidManifest.xml +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/AndroidManifest.xml (revision 0) ++++ ../trunk-jpl/src/android/helloworld/My First App/AndroidManifest.xml (revision 13560) +@@ -0,0 +1,25 @@ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ +\ No newline at end of file +Index: ../trunk-jpl/src/android/helloworld/My First App/src/com/example/my/first/app/MainActivity.java +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/src/com/example/my/first/app/MainActivity.java (revision 0) ++++ ../trunk-jpl/src/android/helloworld/My First App/src/com/example/my/first/app/MainActivity.java (revision 13560) +@@ -0,0 +1,103 @@ ++package com.example.my.first.app; ++ ++import android.app.Activity; ++import android.content.Context; ++import android.os.Bundle; ++import android.util.AttributeSet; ++import android.view.Menu; ++import android.view.View; ++import android.widget.SeekBar; ++import android.widget.SeekBar.OnSeekBarChangeListener; ++import android.widget.TextView; ++import android.widget.Toast; ++import android.graphics.*; ++import android.graphics.drawable.ShapeDrawable; ++import android.graphics.drawable.shapes.RectShape; ++ ++public class MainActivity extends Activity implements OnSeekBarChangeListener{ ++ private SeekBar bar; ++ private TextView textProgress,textAction; ++ //CustomDrawableView mCustomDrawableView; ++ ++ /*public class CustomDrawableView extends View { ++ private ShapeDrawable mDrawable; ++ ++ public CustomDrawableView(Context context, AttributeSet attrs) { ++ super(context, attrs); ++ ++ ++ ++ int x = 10; ++ int y = 10; ++ int width = 300; ++ int height = 50; ++ ++ mDrawable = new ShapeDrawable(new RectShape()); ++ mDrawable.getPaint().setColor(0xff74AC23); ++ mDrawable.setBounds(x, y, x + width, y + height); ++ } ++ ++ protected void onDraw(Canvas canvas) { ++ mDrawable.draw(canvas); ++ } ++ }*/ ++ ++ @Override ++ public void onCreate(Bundle savedInstanceState) { ++ super.onCreate(savedInstanceState); ++ setContentView(R.layout.activity_main); ++ ++ Toast.makeText(MainActivity.this,"You clicked me!", Toast.LENGTH_LONG).show(); ++ bar = (SeekBar)findViewById(R.id.seekBar1); // make seekbar object ++ bar.setOnSeekBarChangeListener(this); // set seekbar listener. ++ // since we are using this class as the listener the class is "this" ++ ++ // make text label for progress value ++ textProgress = (TextView)findViewById(R.id.textViewProgress); ++ // make text label for action ++ textAction = (TextView)findViewById(R.id.textViewAction); ++ ++ //Bitmap b = Bitmap.createBitmap(100, 100, Bitmap.Config.ARGB_8888); ++ //Canvas c = new Canvas(b); ++ //mCustomDrawableView = (CustomDrawableView) findViewById(R.id.custom_drawable_view); ++ ++ } ++ ++ ++ @Override ++ public void onProgressChanged(SeekBar seekBar, int progress, ++ boolean fromUser) ++ { ++ // change progress text label with current seekbar value ++ textProgress.setText("The value is: "+progress); ++ // change action text label to changing ++ textAction.setText("changing"); ++ //drawPoints() ++ } ++ @Override ++ public void onStartTrackingTouch(SeekBar seekBar) { ++ // TODO Auto-generated method stub ++ textAction.setText("starting to track touch"); ++ ++ } ++ @Override ++ public void onStopTrackingTouch(SeekBar seekBar) { ++ // TODO Auto-generated method stub ++ seekBar.setSecondaryProgress(seekBar.getProgress()); // set the shade of the previous value. ++ textAction.setText("ended tracking touch"); ++ } ++ @Override ++ public boolean onCreateOptionsMenu(Menu menu) { ++ getMenuInflater().inflate(R.menu.activity_main, menu); ++ return true; ++ } ++ ++ ++ ++ ++ ++} ++ ++ ++ ++ +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/AndroidManifest.xml +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/AndroidManifest.xml (revision 0) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/AndroidManifest.xml (revision 13560) +@@ -0,0 +1,25 @@ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ +\ No newline at end of file +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/jarlist.cache +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/jarlist.cache (revision 0) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/jarlist.cache (revision 13560) +@@ -0,0 +1,3 @@ ++# cache for current jar dependecy. DO NOT EDIT. ++# format is ++# Encoding is UTF-8 +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$string.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$string.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$string.class (revision 13559) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$string.class (revision 13560) + +Property changes on: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$string.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$attr.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$attr.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$attr.class (revision 13559) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$attr.class (revision 13560) + +Property changes on: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$attr.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/MainActivity.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/MainActivity.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/MainActivity.class (revision 13559) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/MainActivity.class (revision 13560) + +Property changes on: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/MainActivity.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R.class (revision 13559) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R.class (revision 13560) + +Property changes on: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$id.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$id.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$id.class (revision 13559) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$id.class (revision 13560) + +Property changes on: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$id.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$layout.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$layout.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$layout.class (revision 13559) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$layout.class (revision 13560) + +Property changes on: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$layout.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/BuildConfig.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/BuildConfig.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/BuildConfig.class (revision 13559) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/BuildConfig.class (revision 13560) + +Property changes on: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/BuildConfig.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$style.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$style.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$style.class (revision 13559) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$style.class (revision 13560) + +Property changes on: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$style.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$drawable.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$drawable.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$drawable.class (revision 13559) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$drawable.class (revision 13560) + +Property changes on: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$drawable.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$menu.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$menu.class +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$menu.class (revision 13559) ++++ ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$menu.class (revision 13560) + +Property changes on: ../trunk-jpl/src/android/helloworld/My First App/bin/classes/com/example/my/first/app/R$menu.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/gen/com/example/my/first/app/R.java +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/gen/com/example/my/first/app/R.java (revision 0) ++++ ../trunk-jpl/src/android/helloworld/My First App/gen/com/example/my/first/app/R.java (revision 13560) +@@ -0,0 +1,41 @@ ++/* AUTO-GENERATED FILE. DO NOT MODIFY. ++ * ++ * This class was automatically generated by the ++ * aapt tool from the resource data it found. It ++ * should not be modified by hand. ++ */ ++ ++package com.example.my.first.app; ++ ++public final class R { ++ public static final class attr { ++ } ++ public static final class drawable { ++ public static final int ic_action_search=0x7f020000; ++ public static final int ic_launcher=0x7f020001; ++ } ++ public static final class id { ++ public static final int button1=0x7f070001; ++ public static final int edit_message=0x7f070000; ++ public static final int menu_settings=0x7f070005; ++ public static final int seekBar1=0x7f070002; ++ public static final int textViewAction=0x7f070004; ++ public static final int textViewProgress=0x7f070003; ++ } ++ public static final class layout { ++ public static final int activity_main=0x7f030000; ++ } ++ public static final class menu { ++ public static final int activity_main=0x7f060000; ++ } ++ public static final class string { ++ public static final int app_name=0x7f040000; ++ public static final int button_send=0x7f040002; ++ public static final int edit_message=0x7f040001; ++ public static final int menu_settings=0x7f040003; ++ public static final int title_activity_main=0x7f040004; ++ } ++ public static final class style { ++ public static final int AppTheme=0x7f050000; ++ } ++} +Index: ../trunk-jpl/src/android/helloworld/My First App/gen/com/example/my/first/app/BuildConfig.java +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/gen/com/example/my/first/app/BuildConfig.java (revision 0) ++++ ../trunk-jpl/src/android/helloworld/My First App/gen/com/example/my/first/app/BuildConfig.java (revision 13560) +@@ -0,0 +1,6 @@ ++/** Automatically generated file. DO NOT MODIFY */ ++package com.example.my.first.app; ++ ++public final class BuildConfig { ++ public final static boolean DEBUG = true; ++} +\ No newline at end of file +Index: ../trunk-jpl/src/android/helloworld/My First App/libs/android-support-v4.jar +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/libs/android-support-v4.jar +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/libs/android-support-v4.jar (revision 13559) ++++ ../trunk-jpl/src/android/helloworld/My First App/libs/android-support-v4.jar (revision 13560) + +Property changes on: ../trunk-jpl/src/android/helloworld/My First App/libs/android-support-v4.jar +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/helloworld/My First App/res/values/styles.xml +=================================================================== +--- ../trunk-jpl/src/android/helloworld/My First App/res/values/styles.xml (revision 0) ++++ ../trunk-jpl/src/android/helloworld/My First App/res/values/styles.xml (revision 13560) +@@ -0,0 +1,5 @@ ++ ++ ++ ++ ++ ++
++

Linux Sysadmin Blog

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HowTo: Get Started With Amazon EC2 Api Tools

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++ ++ ++ ++ ++Posted by Marius Ducea ++ ++ - ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ | Comments ++ ++

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++ ++ ++

This article is meant to be a quick quide that will introduce the things needed to get you started with Amazon EC2. ++ All this information can be found in the EC2 api docs, and this is not ++meant to be a replacement of the documentation, just trying to show the ++things needed in a clear and short form.

++ ++

Getting Started

++ ++

First of all you will need one Amazon AWS account and enable the EC2 service; in case you don’t have this already now is the time to create your account. Once you do that you can safely return to this doc ;-)

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Once you have your account working, while still on the aws site, go and create a new X.509 certificate ++ (under the AWS Access Identifiers page, in the X.509 certificate ++section near the bottom, click Create New). Once this is done, you will ++want to download locally the private key file and X.509 certificate.

++ ++

EC2 API tools

++ ++

Next you will have to download ++ and install the Amazon EC2 api tools on one system (controlling ++machine) that will be used to start your EC2 army of servers, and ++control their usage. You will want to use the latest version (2009-05-15 ++ at this time) as it will support all the features Amazon is offering ++for the EC2 service.

++ ++

The only real dependency of the EC2 API tools is java (at ++ least version 1.5) so we will want to install that first. If you are ++running debian you can easily do this just by running (for lenny): ++aptitude install sun-java6-jre ++while for etch you will have to use: aptitude install sun-java5-jre ++For other distributions you can either use their internal packaging ++mechanism (in case they provide sun-java packages) or just download the ++binary from sun and install it manually.

++ ++

Extract the EC2 APi tools (it is a zip archive called ec2-api-tools.zip) and move it under a folder of your preferece. I like to use ~/.ec2 for this, but you can use any folder you prefer. Also copy the private key and X.509 certificate in the same directory. Those files will look like cert-xxx.pem and pk-xxx.pem.

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Next we will have to export some shell variables. A good place to put this is in ~/.bashrc:

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export EC2_HOME=~/.ec2
++export PATH=$PATH:$EC2_HOME/bin
++export EC2_PRIVATE_KEY=$EC2_HOME/pk-xxx.pem
++export EC2_CERT=$EC2_HOME/cert-xxx.pem
++#Java home for debian default install path:
++export JAVA_HOME=/usr
++#add ec2 tools to default path
++export PATH=~/.ec2/bin:$PATH
++ ++ ++

Finally source the file to have the changes active in your current shell session: ++source ~/.bashrc ++or just open a new shell before starting to use the API tools.

++ ++

EC2 Keypair

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We will need to create one keypair that will be used to connect using ssh to the EC2 instances we will be using. We will use the ec2-add-keypair utility to create the key and register it with amazon: ++ec2-add-keypair my-keypair ++This will print out the private key that we will have to save in a file: ++`cat > ~/.ec2/id_rsa-my-keypair

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paste the private key content

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sudo chmod 600 `~/.ec2/id_rsa-my-keypair

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Running your first EC2 instance

++ ++

Amazon EC2 uses the concept of AMIs = Amazon Machine ++ Images. Any EC2 instance is started from one AMI. You can either use ++standard, public AMIs or create and customize your own private images. ++Creating or modifying existing AMIs is beyond the scope of this article, ++ but just as a general information this is done using special AMI tools. ++ Also before building your AMI you will want to ensure if you want to ++use a ‘small’ type of image (i386 os) or a ‘large’ type of instance ++(64bit os). These are described under http://aws.amazon.com/ec2/instance-types/

++ ++

For the scope of our article we will find a standard public image and ++ start one instance of it to see that all is working properly with the ++EC2 api tools. You can see all the public images using: ++ec2-describe-images -a ++(over 2,300 images ;) ). You should probably grep the result to get any ++useful information. There are many good public images to use, like for ++example the alestic ones (for debian and ubuntu) ++Having the AMI id of the image we want to use we are ready to start our fist EC2 instance: ++ec2-run-instances ami-e348af8a -k my-keypair ++that will start a small instance with a 32bit debian lenny server instance from alestic.com.

++ ++

ec2-describe-instances ++- this will describe the status of all the running instances, with their hostname, instance id, etc.

++ ++

ec2-authorize default -p 22 ++- in order to connect to your instance you will need to customize the ++‘default’ firewall rules for your account. The above rule will allow ssh ++ on port 22 from anywhere. If you want to open http traffic you will ++have to add a rule like this: ++ec2-authorize default -p 80

++ ++

Finally we can ssh to the ec2 instance using: ++ssh -i ~/.ec2/id_rsa-my-keypair root@ec2-XXX-XXX-XXX-XXX.z-2.compute-1.amazonaws.com ++where ec2-XXX-XXX-XXX-XXX.z-2.compute-1.amazonaws.com is the actual ++hostname of the instance as obtained from ec2-describe-instances.

++ ++

Note: don’t forget to stop your instance ++when you no longer need it. EC2 is a service paid as you use, hence if ++you forget your instance running you will be billed for it ;-). You can ++do this by running shutdown inside the instance or by using: ++ec2-terminate-instances i-yourinstance ++and verify with ec2-describe-instances that the instance is indeed stopped.

++ ++

Next step is to create/customize your own EC2 AMI images based on ++your needs. This will be covered in a future article. Hopefully you ++found this article useful, and it will get you on track quickly with ++Amazon EC2 api tools.

++
++ ++ ++ ++
++ ++
++

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++ Copyright © 2012 - Promet OPS Team - ++ Powered by Octopress ++

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++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ +\ No newline at end of file +Index: ../trunk-jpl/externalpackages/ec2api/doc/ec2-ug.pdf +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/externalpackages/ec2api/doc/ec2-ug.pdf +=================================================================== +--- ../trunk-jpl/externalpackages/ec2api/doc/ec2-ug.pdf (revision 13841) ++++ ../trunk-jpl/externalpackages/ec2api/doc/ec2-ug.pdf (revision 13842) + +Property changes on: ../trunk-jpl/externalpackages/ec2api/doc/ec2-ug.pdf +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/externalpackages/ec2api/doc/mpi-cluster-with-python-and-amazon-ec2-part-2-of-3.html +=================================================================== +--- ../trunk-jpl/externalpackages/ec2api/doc/mpi-cluster-with-python-and-amazon-ec2-part-2-of-3.html (revision 0) ++++ ../trunk-jpl/externalpackages/ec2api/doc/mpi-cluster-with-python-and-amazon-ec2-part-2-of-3.html (revision 13842) +@@ -0,0 +1,1111 @@ ++ ++ ++ ++ MPI Cluster with Python and Amazon EC2 (part 2 of 3) » Data Wrangling Blog ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++
++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++
++
++
++
++

++ MPI Cluster with Python and Amazon EC2 (part 2 of 3) ++

++
++

Posted by Peter Skomoroch on Apr 09, 2007 to cluster computing, python, mpi, amazon ec2, and cloud computing

++

Today I posted a public AMI which can be used to run a small beowulf cluster on Amazon EC2 and do some parallel computations with C, Fortran, or Python. ++ If you prefer another language (Java, Ruby, etc) just install the ++appropriate MPI library and rebundle the EC2 image. The following set ++of Python scripts automate the launch and configuration of an MPI cluster on EC2 (currently limited to 20 nodes while EC2 is in beta):

++ ++

Update (3-19-08): Code for running a cluster with large ++or xlarge 64 bit EC2 instances is now hosted on google code. The new ++images include NFS, ganglia, IPython1, and other useful python packages.

++ ++

http://code.google.com/p/elasticwulf/

++ ++

Update (7-24-07): I've made some important bug fixes to ++the scripts to address issues mentioned in the comments. See the README ++ file for details

++ ++ ++ ++ ++

The file contains some quick scripts I threw together using the AWS ++Python example code. This is the approach I'm using to bootstrap an MPI ++ cluster until one of the major linux cluster distros is ported to run on EC2. Details on what is included in the public AMI were covered in Part 1 ++ of the tutorial, Part 3 will cover cluster operation on EC2 in more ++detail and show how to use Python to carry out some neat parallel ++computations.

++ ++

The cluster launch process is pretty simple once you have an Amazon ++EC2 account and keys, just download the Python scripts and you can be ++running a compute cluster in a few minutes. In a later post I will look ++ at cluster bandwidth and performance in detail. If you have only an ++occasional need for running large jobs, $2/hour for a 20 node MPI ++cluster on EC2 is not a bad deal considering the ~ $20K price for ++building your own comparable system.

++ ++ ++ ++ ++

Prerequisites:

++ ++
    ++
  1. Get a valid Amazon EC2 account
    2. ++
  2. Complete the most recent "getting started guide" tutorial on Amazon EC2 and create all needed web service accounts, authorizations, and keypairs
    3. ++
  3. Download and install the Amazon EC2 Python library
    4. ++
  4. Download the Amazon EC2 MPI cluster management scripts
    5. ++
++ ++ ++

Launching the EC2 nodes

++ ++ ++

First , unzip the cluster management scripts and modify the ++configuration parameters in '''EC2config.py''', substituting your own ++EC2 keys and changing the cluster size if desired:

++ ++
#replace these with your AWS keys
++AWS_ACCESS_KEY_ID = 'YOUR_KEY_ID_HERE'
++AWS_SECRET_ACCESS_KEY = 'YOUR_KEY_HERE'
++#change this to your keypair location (see the EC2 getting started guide tutorial on using ec2-add-keypair)
++KEYNAME = "gsg-keypair"
++KEY_LOCATION = "/Users/pskomoroch/id_rsa-gsg-keypair"
++# remove these next two lines when you've updated your credentials.
++print "update %s with your AWS credentials" % sys.argv[0]
++sys.exit()
++
++MASTER_IMAGE_ID = "ami-3e836657"
++IMAGE_ID = "ami-3e836657"
++
++DEFAULT_CLUSTER_SIZE = 5
++
++
++ ++ ++

Launch the EC2 cluster by running the '''ec2-start_cluster.py''' script from your local machine:

++ ++
 
++peter-skomorochs-computer:~/AmazonEC2_MPI_scripts pskomoroch$ ./ec2-start-cluster.py 
++
++image ami-3e836657
++master image ami-3e836657
++----- starting master -----
++RESERVATION r-275eb84e  027811143419    default
++INSTANCE    i-0ed33167  ami-3e836657            pending
++----- starting workers -----
++RESERVATION r-265eb84f  027811143419    default
++INSTANCE    i-01d33168  ami-3e836657            pending
++INSTANCE    i-00d33169  ami-3e836657            pending
++INSTANCE    i-03d3316a  ami-3e836657            pending
++INSTANCE    i-02d3316b  ami-3e836657            pending
++
++ ++ ++

Verify the EC2 nodes are running with '''./ec2-check-instances.py''':

++ ++

++peter-skomorochs-computer:~/AmazonEC2_MPI_scripts pskomoroch$ ./ec2-check-instances.py 
++----- listing instances -----
++
++RESERVATION     r-aec420c7      027811143419    default
++INSTANCE        i-ab41a6c2      ami-3e836657    domU-12-31-33-00-02-5A.usma1.compute.amazonaws.com      running
++INSTANCE        i-aa41a6c3      ami-3e836657    domU-12-31-33-00-01-E3.usma1.compute.amazonaws.com      running
++INSTANCE        i-ad41a6c4      ami-3e836657    domU-12-31-33-00-03-AA.usma1.compute.amazonaws.com      running
++INSTANCE        i-ac41a6c5      ami-3e836657    domU-12-31-33-00-04-19.usma1.compute.amazonaws.com      running
++INSTANCE        i-af41a6c6      ami-3e836657    domU-12-31-33-00-03-E3.usma1.compute.amazonaws.com      running
++
++ ++ ++ ++ ++

Cluster Configuration and Booting MPI

++ ++ ++

Run '''ec2-mpi-config.py''' to configure MPI on the nodes, this will take a minute or two depending on the number of nodes.

++ ++

++peter-skomorochs-computer:~/AmazonEC2_MPI_scripts pskomoroch$ ./ec2-mpi-config.py 
++
++---- MPI Cluster Details ----
++Numer of nodes = 5
++Instance= i-ab41a6c2 hostname= domU-12-31-33-00-02-5A.usma1.compute.amazonaws.com state= running
++Instance= i-aa41a6c3 hostname= domU-12-31-33-00-01-E3.usma1.compute.amazonaws.com state= running
++Instance= i-ad41a6c4 hostname= domU-12-31-33-00-03-AA.usma1.compute.amazonaws.com state= running
++Instance= i-ac41a6c5 hostname= domU-12-31-33-00-04-19.usma1.compute.amazonaws.com state= running
++Instance= i-af41a6c6 hostname= domU-12-31-33-00-03-E3.usma1.compute.amazonaws.com state= running
++
++The master node is ec2-72-44-46-78.z-2.compute-1.amazonaws.com 
++
++
++... ...
++
++Configuration complete, ssh into the master node as lamuser and boot the cluster:
++$ ssh lamuser@ec2-72-44-46-78.z-2.compute-1.amazonaws.com 
++> mpdboot -n 5 -f mpd.hosts 
++> mpdtrace
++
++ ++ ++

Login to the master node, boot the MPI cluster, and test the connectivity:

++ ++

++
++peter-skomorochs-computer:~/AmazonEC2_MPI_scripts pskomoroch$ ssh lamuser@ec2-72-44-46-78.z-2.compute-1.amazonaws.com 
++
++
++
++Sample Fedora Core 6 + MPICH2 + Numpy/PyMPI compute node image 
++
++http://www.datawrangling.com/on-demand-mpi-cluster-with-python-and-ec2-part-1-of-3
++
++---- Modified From Marcin's Cool Images: Cool Fedora Core 6 Base + Updates Image v1.0 ---
++
++see http://developer.amazonwebservices.com/connect/entry.jspa?externalID=554&categoryID=101
++
++
++Like Marcin's image, standard disclaimer applies, use as you please...
++
++Amazon EC2 MPI Compute Node Image
++Copyright (c) 2006 DataWrangling. All rights reserved.
++
++Redistribution and use in source and binary forms, with or without
++modification, are permitted provided that the following conditions are
++met:
++
++    * Redistributions of source code must retain the above copyright
++       notice, this list of conditions and the following disclaimer.
++
++    * Redistributions in binary form must reproduce the above
++       copyright notice, this list of conditions and the following
++       disclaimer in the documentation and/or other materials provided
++       with the distribution.
++
++    * Neither the name of the DataWrangling nor the names of any
++       contributors may be used to endorse or promote products derived
++       from this software without specific prior written permission.
++
++THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
++"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
++LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
++A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
++OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
++SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
++LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
++DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
++THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
++(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
++OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
++[lamuser@domU-12-31-33-00-02-5A ~]$ 
++[lamuser@domU-12-31-33-00-02-5A ~]$ mpdboot -n 5 -f mpd.hosts 
++[lamuser@domU-12-31-33-00-02-5A ~]$ mpdtrace
++domU-12-31-33-00-02-5A
++domU-12-31-33-00-01-E3
++domU-12-31-33-00-03-E3
++domU-12-31-33-00-03-AA
++domU-12-31-33-00-04-19
++
++
++ ++ ++

The results of the mpdtrace command show we have an MPI cluster ++running on 5 nodes. In the next section, we will verify that we can run ++some basic MPI tasks. For more detailed information on these mpi ++commands (and MPI in general), see the MPICH2 documentation.

++ ++

Testing the MPI Cluster

++ ++ ++

Next we execute a sample C program bundled with MPICH2 which estimates pi using the cluster:

++ ++

++[lamuser@domU-12-31-33-00-02-5A ~]$  mpiexec -n 5 /usr/local/src/mpich2-1.0.5/examples/cpi
++Process 0 of 5 is on domU-12-31-33-00-02-5A
++Process 1 of 5 is on domU-12-31-33-00-01-E3
++Process 2 of 5 is on domU-12-31-33-00-03-E3
++Process 3 of 5 is on domU-12-31-33-00-03-AA
++Process 4 of 5 is on domU-12-31-33-00-04-19
++pi is approximately 3.1415926544231230, Error is 0.0000000008333298
++wall clock time = 0.007539
++
++
++ ++ ++

Test the message travel time for the ring of nodes you just created:

++ ++

++[lamuser@domU-12-31-33-00-02-5A ~]$ mpdringtest 100
++time for 100 loops = 0.14577794075 seconds
++
++
++ ++ ++

Verify that the cluster can run a multiprocess job:

++ ++

++[lamuser@domU-12-31-33-00-02-5A ~]$ mpiexec -l -n 5 hostname
++3: domU-12-31-33-00-03-AA
++0: domU-12-31-33-00-02-5A
++1: domU-12-31-33-00-01-E3
++4: domU-12-31-33-00-04-19
++2: domU-12-31-33-00-03-E3
++
++
++ ++ ++ ++ ++

Testing PyMPI

++ ++ ++

Lets verify that the PyMPI install is working with our running cluster of 5 nodes. Execute the following on the master node:

++ ++

++[lamuser@domU-12-31-33-00-02-5A ~]$ mpirun -np 5 pyMPI /usr/local/src/pyMPI-2.4b2/examples/fractal.py
++Starting computation (groan)
++
++process 1 done with computation!!
++process 3 done with computation!!
++process 4 done with computation!!
++process 2 done with computation!!
++process 0 done with computation!!
++Header length is  54
++BMP size is  (400, 400)
++Data length is  480000
++[lamuser@domU-12-31-33-00-02-5A ~]$ ls
++hosts  id_rsa.pub  mpd.hosts  output.bmp
++
++
++ ++ ++

This produced the following fractal image (output.bmp):

++ ++

output.bmp

++ ++

We will show some more examples using PyMPI in the next post.

++ ++

Changing the Cluster Size

++ ++ ++

If we want to modify the number of nodes in the cluster we first need to kill the mpi cluster from the master node as follows:

++ ++

++[lamuser@domU-12-31-33-00-02-5A ~]$ mpdallexit
++[lamuser@domU-12-31-33-00-02-5A ~]$ mpdcleanup
++
++ ++ ++

Once this is done, you can start additional instances of the public ++AMI from your local machine, then re-run the ec2-mpi-config.py script ++and reboot the cluster.

++ ++

Cluster Shutdown

++ ++ ++

Run '''ec2-stop-cluster.py''' to stop all EC2 MPI nodes. If you just want to stop the slave nodes, run ec2-stop-slaves.py

++ ++

++
++peter-skomorochs-computer:~/AmazonEC2_MPI_scripts pskomoroch$ ./ec2-stop-cluster.py
++This will stop all your EC2 MPI images, are you sure (yes/no)? yes
++----- listing instances -----
++RESERVATION     r-aec420c7      027811143419    default
++INSTANCE        i-ab41a6c2      ami-3e836657    domU-12-31-33-00-02-5A.usma1.compute.amazonaws.com      running
++INSTANCE        i-aa41a6c3      ami-3e836657    domU-12-31-33-00-01-E3.usma1.compute.amazonaws.com      running
++INSTANCE        i-ad41a6c4      ami-3e836657    domU-12-31-33-00-03-AA.usma1.compute.amazonaws.com      running
++INSTANCE        i-ac41a6c5      ami-3e836657    domU-12-31-33-00-04-19.usma1.compute.amazonaws.com      running
++INSTANCE        i-af41a6c6      ami-3e836657    domU-12-31-33-00-03-E3.usma1.compute.amazonaws.com      running
++
++---- Stopping instance Id's ----
++Stoping Instance Id = i-ab41a6c2 
++Stoping Instance Id = i-aa41a6c3 
++Stoping Instance Id = i-ad41a6c4 
++Stoping Instance Id = i-ac41a6c5 
++Stoping Instance Id = i-af41a6c6 
++
++Waiting for shutdown ....
++----- listing new state of instances -----
++RESERVATION     r-aec420c7      027811143419    default
++INSTANCE        i-ab41a6c2      ami-3e836657    domU-12-31-33-00-02-5A.usma1.compute.amazonaws.com      shutting-down
++INSTANCE        i-aa41a6c3      ami-3e836657    domU-12-31-33-00-01-E3.usma1.compute.amazonaws.com      shutting-down
++INSTANCE        i-ad41a6c4      ami-3e836657    domU-12-31-33-00-03-AA.usma1.compute.amazonaws.com      shutting-down
++INSTANCE        i-ac41a6c5      ami-3e836657    domU-12-31-33-00-04-19.usma1.compute.amazonaws.com      shutting-down
++INSTANCE        i-af41a6c6      ami-3e836657    domU-12-31-33-00-03-E3.usma1.compute.amazonaws.com      shutting-down
++
++
++ ++ ++
++ ++ ++ ++ ++

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  • Aarthi 8288 3 comments collapsed Collapse Expand

    Hi,

    ++ ++

    I was trying to launch a cluster using the given scripts. I got the following error :

    ++ ++

    # ./ec2-start-cluster.py
    Traceback (most recent call last):
    File "./ec2-start-cluster.py", line 23, in <module>
    import EC2
    ImportError: No module named EC2

    ++ ++

    Can anyone help me out ?
    </module>

  • Adeel Jan 1 comment collapsed Collapse Expand

    I think you need to get python library :)

    ++ ++

    Adeel Jan.

  • Lukearron 1 comment collapsed Collapse Expand

    Did ++ anyone solve this problem?  I had the same problem, and I ++downloaded and unpacked the libraries, but perhaps the python library ++needs to be _placed_ somewhere?

  • Easwar 1 comment collapsed Collapse Expand

    Dear Sir,

    ++ ++

      I am trying to use MPI for
    running Data parallel ++applications. I read this post and on following up, I have few queries. ++Would be great, if I can get answers to them.

    ++ ++

    a) As of now, I am choosing AMI using the browser interface of ++Amazon. You have uploaded two AMI's one for master (ami-e813f681) and ++another for slave (ami-eb13f682).
    When I launch an instance, I can only choose one. Which one should I
    choose ? (Or how should I choose both, in case I need to)  ? Do these
    AMI's has OPEMPI implementation ?

    ++ ++

    b) Secondly, if I launch multiple instances of a Large CPU (say 3
    instances), ++ I would be get many nodes (say m nodes per one instance, hence i would ++have m*3 nodes). Can I communicate between nodes
    of different instances just as we normally do in MPI ?

    ++ ++

    c) Are you aware any MPI image with ubuntu ?

    ++ ++

    d) I am using browser, since I have to connect through proxy. How/Where
    do set proxy connections, if I need to start cluster using your python
    scripts ?

    ++ ++

    Easwar

  • Johnliu 1 comment collapsed Collapse Expand

    Hi,

    ++ ++

    Does anyone have this running under cygwin in windows?

    ++ ++

    If so, can you please post your code for ec2-mpi-config.py? I tried using the current file but get lots of errors.

    ++ ++

    Thanks,
    John

  • Supriyamunshaw 2 comments collapsed Collapse Expand

    I have sucessfully connected to 5 nodes but am having trouble with the ec2-mpi-config.py script. When I run it, I repeatedly get the following:

    ++ ++

    ---- MPI Cluster Details ----
    Numer of nodes = 5
    Instance= i-8d2949e7 external_name = ec2-184-72-183-113.compute-1.a... hostname= ip-10-212-239-33.ec2.internal state=
    Instance= i-832949e9 external_name = ec2-174-129-138-43.compute-1.a... hostname= domU-12-31-39-10-6C-13.compute-1.internal state=
    Instance= i-812949eb external_name = ec2-184-72-141-241.compute-1.a... hostname= domU-12-31-39-0B-00-F8.compute-1.internal state=
    Instance= i-872949ed external_name = ec2-174-129-131-171.compute-1.... hostname= domU-12-31-39-09-C4-24.compute-1.internal state=
    Instance= i-852949ef external_name = ec2-174-129-61-151.compute-1.a... hostname= domU-12-31-39-0C-D8-57.compute-1.internal state=
    5

    ++ ++

    The master node is ec2-184-72-183-113.compute-1.a...

    ++ ++

    Writing out mpd.hosts file

    ++ ++

    scp -i id_rsa-gsg-keypair -o "StrictHostKeyChecking no" id_rsa-gsg-keypair root@ec2-184-72-183-113.compute-1.amaz...:~/.ssh/id_rsa-gsg-keypair

    ++ ++

    ssh: connect to host ec2-184-72-183-113.compute-1.a... port 22: Connection timed out
    lost connection

    ++ ++

    ssh -o "StrictHostKeyChecking no" root@ec2-184-72-183-113.compute-1.amaz... "touch .ssh/authorized_keys"

    ++ ++

    ssh: connect to host ec2-184-72-183-113.compute-1.a... port 22: Connection timed out

    ++ ++

    ssh -o "StrictHostKeyChecking no" root@ec2-184-72-183-113.compute-1.amaz... "cp -r .ssh /home/lamuser/"

    ++ ++

    It seems I'm having a connection problem. Does anyone what I can do about this?

  • Supriyamunshaw 1 comment collapsed Collapse Expand

    ok, i figured it out. the connection was being made through my default security group where port 22 was not open.

  • Henrywang41 1 comment collapsed Collapse Expand

    Can someone please help? mc2-mpi-config.py is giving the following error:

    ++ ++

    ---- MPI Cluster Details ----
    Numer of nodes = 2
    Instance= i-bf90f5d5 external_name = ec2-184-73-36-216.compute-1.am... hostname= ip-10-242-1
    18-239.ec2.internal state= running
    Instance= i-bd90f5d7 external_name = ec2-174-129-77-216.compute-1.a... hostname= ip-10-242-
    117-139.ec2.internal state= running

    ++ ++

    The master node is ec2-184-73-36-216.compute-1.am...

    ++ ++

    Writing out mpd.hosts file
    Traceback (most recent call last):
    File "ec2-mpi-config.py", line 210, in <module>
    sys.exit(main())
    File "ec2-mpi-config.py", line 65, in main
    configure()
    File "ec2-mpi-config.py", line 151, in configure
    rsakeys = open(homedir + "/.ssh/id_rsa", 'r').read()
    IOError: [Errno 2] No such file or directory: 'C:\\Documents and Settings\\Yunzhi Ma/.ssh/id_rsa'

    ++ ++

    Could this possibly be due to anything about chunk and parsed_response? I printed out parsedresponse:

    ++ ++

    [['RESERVATION', 'r-30733b5b', '219669225938', 'default'], ['INSTANCE', 'i-bf90f5d5', 'ami-e813f681'
    , 'ec2-184-73-36-216.compute-1.am...', 'ip-10-242-118-239.ec2.internal', 'running'], ['RESER
    VATION', 'r-36733b5d', '219669225938', 'default'], ['INSTANCE', 'i-bd90f5d7', 'ami-eb13f682', 'ec2-1
    74-129-77-216.compute-1.amazon...', 'ip-10-242-117-139.ec2.internal', 'running']]

    ++ ++

    Thanks so much,
    Henry</module>

  • Henrywang41 1 comment collapsed Collapse Expand

    Hi,

    ++ ++

    Amazon just recently (last month) released a cloud computing instance (http://developer.amazonwebserv...

    ++ ++

    Does the code and what you describe here work for this new released ++instance for HPC? (It's CentOS HVM AMI, ami-7ea24a17 under U.S. East)

    ++ ++

    Thanks,

    ++ ++

    Henry

  • Henrywang41 1 comment collapsed Collapse Expand

    Hi,

    ++ ++

    Is Elasticwulf and MPI essentially the same thing? I'm trying to run ++some high performance computing using an Amazon EC2 cluster.

    ++ ++

    Also, is boto necessary to set up a cluster on amazon EC2? What's the difference between boto and Elasticwulf?

    ++ ++

    Thanks,

    ++ ++

    Henry

  • Henrywang41 1 comment collapsed Collapse Expand

    Hi,

    ++ ++

    What exactly is the difference between Elasticwulf and MPI? Are they ++the same thing? I'm trying to launch a cluster for HPC, which one is ++more suitable?

    ++ ++

    Also, is boto necessary too for launching a cluster?

    ++ ++

    Thanks,
    Henry

  • bearrito 1 comment collapsed Collapse Expand

    Little late on the thread here but would still like some feedback.

    ++ ++

    My issues:

    ++ ++

    1. I was also being prompted for my password. I ended up using the solution that Raghave suggested.

    ++ ++

    2. I am not seeing /usr/local/src/pyMPI-2.4b2/. That directory ++doesn't appear to be present. I tried to get around this by copying in fractal.py from my local machine. I end up with the following:

    ++ ++

    mpirun -np 2 pyMPI /home/lamuser/fractal.py
    pyMPI: can't open file '/home/lamuser/fractal.py': [Errno 2] No such file or directory

    ++ ++

    fractal.py is in that directory.

    ++ ++

    Advice?

  • miccloud 1 comment collapsed Collapse Expand

    I have a python script that calls a program installed on the master node and slave nodes.
    Can I run it from the master node and get the results with mpirun?

    ++ ++

    Thanks a lot.

  • miccloud 1 comment collapsed Collapse Expand

    Can I execute bash script in a node with a job?

    ++ ++

    Thanks.

  • Harry 1 comment collapsed Collapse Expand

    Hello everybody,

    ++ ++

    I had error with Fortran 77 library in AMI ami-e813f681 (Fedora core 6 ++ x86- 64 bit) because of two libraries: libf2c or libg2c in the AMI.
    (....
    checking for f_exit in -lf2c... no
    checking for f_exit in -lg2c... no
    checking for dummy main to link with Fortran 77 libraries... unknown
    configure: error: linking to Fortran libraries from C fails
    )

    ++ ++

    Could anybody help me solve the problem? Thanks so much!

    ++ ++

    best regards,

    ++ ++

    Harry

  • Pete 9 comments collapsed Collapse Expand

    Jeff,


    I'm ++ actually working on a new version of Elasticwulf right now. Shoot me ++an email at pete@datawrangling.com and I'll try to include what you need ++ for Rmpi. If you have some sample Rmpi code you want to test and that ++you don't mind releasing, we can build that into the AMI to ensure ++everything you need is installed.


    Here are the MPI installs that were included on that Fedora 64 bit image:


    # mpich2 
    
++
++
    cd /usr/local/src/
    wget http://www.mcs.anl.gov/researc...
    tar -xzvf mpich2-1.0.6p1.tar.gz
    cd mpich2-1.0.6p1
    ./configure --enable-sharedlibs=gcc --prefix=/usr/local/mpich2
    make
    make install
    
++
++
    # openmpi
    
++
++
    cd /usr/local/src/
    wget http://www.open-mpi.org/softwa...
    #wget http://www.open-mpi.de/softwar...
    tar -zxf openmpi-1.2.5.tar.gz
    cd openmpi-1.2.5
    ./configure --prefix=/usr/local/openmpi
    make all
    make install
    
++
++
    #lam
    cd /usr/local/src/
    wget http://www.lam-mpi.org/downloa...
    tar -xzvf lam-7.1.2.tar.gz
    cd lam-7.1.2
    ./configure --enable-shared --prefix=/usr/local/lam
    make 
    make install
    
++
++
    # mpich1
    cd /usr/local/src/
    wget http://www-unix.mcs.anl.gov/mp...
    tar -zxf mpich.tar.gz
    cd mpich-1.2.7p1/
    ./configure --enable-sharedlib --prefix=/usr/local/mpich
    make
    make install

  • Andrew Lonie 8 comments collapsed Collapse Expand

    Hi ++ - I'd be very interested in a Elasticwulf cluster that supports R, too. ++ Did anything come of this? I'd be happy to be involved.

    ++ ++

    Andrew

  • pskomoroch 7 comments collapsed Collapse Expand

    Yes, ++ I have a Rails REST web service on github now for spawning MPI clusters ++ that support R. Haven't had time yet to finish the docs or write a ++blog post about it. Works fine in operation...

    ++ ++

    http://github.com/datawranglin...

  • Soren Macbeth, Chief Data Scientist @yieldbot. Co-founder of @StockTwits 3 comments collapsed Collapse Expand

    Hey Peter,

    ++ ++

    Thanks for the awesome ec2cluster project! I forked it on github so ++that I could add the ability to install R packages from CRAN across all ++the nodes in the cluster. Basically I added the following to ubuntu_installs.sh:
    --snip--
    # Custom R packages
    cat <<eof>> /home/ec2cluster/install_custom_packages.R
    install.packages("DEoptim",repos="http://cran.stat.ucla.edu")
    EOF

    R CMD BATCH /home/ec2cluster/install_custom_packages.R
    --snip--

    ++ ++

    A bit crude I know, but something people wanting to do things with R will probably find useful.

    ++ ++

    To actually run the R code, I was successful with the follow approach:

    ++ ++

    1) put your R code in a file and save it as foo.R
    2) add the following line to a shellscript: mpirun -n 1 -hostfile /mnt/ec2cluster/openmpi_hostfile R CMD BATCH foo.R
    3) call the shellscript and grab the produced .Rout file to your S3 bucket!
    </eof>

  • pskomoroch 2 comments collapsed Collapse Expand

    Soren,

    ++ ++

    Glad ec2cluster helped, are you guys big R users at StockTwits?

    ++ ++

    -Pete

  • Soren Macbeth, Chief Data Scientist @yieldbot. Co-founder of @StockTwits 1 comment collapsed Collapse Expand

    The ++ very first StockTwits prototype used R to generate some statistics as ++well as generate charts of the stocks being talked about in tweets :)

  • Andrew Lonie 3 comments collapsed Collapse Expand

    Thanks ++ - this is impressive, and a web interface for building clusters would ++be very nice, but maybe I'm after something slightly closer to your ++original solution. You might already know that R has an in-language ++cluster support API built on Rmpi, called SNOW (Simple network of ++workstations). It allows for various script commands like ++clusterExport(data) and clusterApply(vector, function) which let you ++interactively cluster jobs according to the parameter values in a list.
    Would ++ this be compatible with your cluster app? I notice that it's more ++schedule-focused and the nodes need to talk to the app; is the app ++acting as the master rather than one of the ec2 nodes? Ideally my ++architecture would be something like master Rmpi node running on ec2 ++talking to arbitrary slave #nodes, accessed through maybe something like ++ the Biocep remote R client (http://biocep-distrib.r-forge.... clustering done in-session.

  • pskomoroch 2 comments collapsed Collapse Expand

    Yes, ++ this is compatible with the cluster app. One of the bundled examples ++runs some calculations with R and SNOW, another uses Rmpi (see the code ++on Github http://bit.ly/ocKCn ).

    ++ ++

    The web interface can be run anywhere, but needs to be https ++accessible to the EC2 nodes. I usually just run it as a small ec2 ++instance as shown in the docs. You can start a job from the API or the ++web console with shutdown_after_complete = false, and the cluster will ++remain live for interactive work, just ssh into the master node like you ++ would with Elasticwulf. The app is not acting as the MPI master node, ++but the cluster nodes do talk to the app to handle configuration etc.

  • Andrew Lonie 1 comment collapsed Collapse Expand

    OK thanks I understand. I'll try this out properly; it sounds like exactly what I'm after.

  • Jeff Howbert 1 comment collapsed Collapse Expand

    Hello Pete -


    Thanks ++ for putting together your ElsticWulf scripts and AMIs. They have saved ++ me a huge amount of time and effort compared with building my own from ++scratch.


    I am interested in parallelizing some machine ++learning algorithms written in R. My interest in ElasticWulf comes ++partly from the fact that R is already bundled with its AMIs. I ++discovered, however, that Rmpi is not one of the installed packages. ++What were your intentions/plans with R in the ElasticWulf environment? ++Did you plan for parallel communication using a mechanism other than ++MPI?


    It wasn't hard to install Rmpi on top of the ElasticWulf ++AMI, but despite a couple of days' struggle, I haven't found a ++combination of Rmpi version and paths to the AMI's existing MPI ++libraries that fully works. The best I've been able to do is spawn an R ++ cluster where all the nodes are running on the master node.


    Could ++ you tell me what version of R and the various MPI implementations ++(OpenMPI, MPICH, LAM) went into your 64-bit AMI? That might help me ++sort things out. A couple of observations, for what they're worth:


    1) ++ Once I have an ElasticWulf cluster up and have run mpdboot, I find that ++ mpiexec works, but orterun (the equivalent in OpenMPI) does not.


    2) There has been at least one report of problems between the latest version of Rmpi and OpenMPI:


    https://stat.ethz.ch/pipermail...


    Much thanks.


    Jeff Howbert

  • Ben Racine 1 comment collapsed Collapse Expand

    Hello,


    I ++ get the same problem that Michael Creel was having. I am able to start ++ the instances and get them "running" successfully, by pointing them to ++my keypair with the KEYNAME variable, but I believe my KEY_LOCATION ++variable in my EC2config.py file must be causing the prompt for a password.


    This is all per the default block of code in EC2config.py:

    ++ ++

    change this to your keypair location (see the EC2 getting started guide tutorial on using ec2-add-keypair)

    ++ ++

    KEYNAME = "my_keypair"
    KEY_LOCATION = "/Users/pskomoroch/id_rsa-gsg-keypair"


    I ++ believe this requires me to go back through the "getting started ++guide", but I just wanted to update my progress in case others are ++seeing the same thing.


    Many thanks for sharing your progress Peter!


    Ben Racine

  • ej 1 comment collapsed Collapse Expand

    @Pete - Feb08



    Can’t get the ec-mpi-config to work. Says list >index out of range for mpi-externalnames[0] on >line 108



    You are right - the output from ec2-describe-instances has changed. Do the following..


    Change


    machine_state.append(chunk[-1])


    to


    machine_state.append(chunk[5])


    in "ec2-mpi-config.py"


    Or, ++ if the output changes again - just do an "ec2-describe-instances" and ++match up the required fields to the index on the chunk[] array

  • Pete 1 comment collapsed Collapse Expand

    Joanne,


    Try ++ logging in and running your commands as "lamuser" instead of root. The ++ default configuration assumes lamuser is running all commands.


    $ ssh lamuser@ec2-72-44-46-78.z-2.compute-1.ama...


    See part 1 of the post for details on changing the configuration to run MPI as root.


    -Pete

  • jjiyunlee 1 comment collapsed Collapse Expand

    Hi,


    Thanks ++ for your writeup! It's very helpful. I'm running into an error with ++mpdtrace and was hoping for some of your insight into it. I am running ++mpd as root, with one node for simplicity.


    I can successfully start up mpd on the instance and "mpd &":
    root@...:/etc# mpdboot -n 1 -f mpd.hosts
    root@...:/etc# mpd &
    [1] 2280


    but "mpdtrace -l" gives me an error:
    root@ip-10-251-143-0:/etc# mpdtrace -l
    mpdtrace: unexpected msg from mpd=:{'error_msg': 'invalid secretword to root mpd'}:


    I ++ have tried all pairwise combinations of having MPD_SECRETWORD= or ++secretword= in ~/.mpd.conf and /etc/mpd.conf, all of which were set to ++read/write for root only.


    I also can't do "mpdallexit":
    I can't mpdallexit:
    root@...:~# mpdallexit
    mpdallexit: mpd_uncaught_except_tb handling:
    : 'cmd'
    /usr/local/bin/mpich2-install/bin/mpdallexit 53 mpdallexit
    elif msg['cmd'] != 'mpdallexit_ack':
    /usr/local/bin/mpich2-install/bin/mpdallexit 59
    mpdallexit()


    I can also run mpdcheck as a server and have it listen for mpdcheck as a client from the same instance (in a different window).


    Suggestions/help? I'd greatly appreciate any advice you have on this problem. Thanks --


    <ul>
    <li>Joanne</li>
    </ul>

  • Tim Salimans 1 comment collapsed Collapse Expand

    Got it working using OpenSSH, guess PuTTy was the problem after all.

  • Tim Salimans 1 comment collapsed Collapse Expand

    Great ++ project and thanks very much for sharing! I do have some trouble ++getting it all to work though. Everything works fine until it tries to ++run the create_hosts.py:


    /////// OUTPUT ///////////////


    Creating hosts file on master node and copying hosts file to compute nodes...


    pscp -scp -i D:\grid\keys\keypair.ppk -q create_hosts.py root@ec2-67-202-19-253.
    compute-1.amazonaws.com:/etc/


    plink -ssh -i D:\grid\keys\keypair.ppk root@ec2-67-202-19-253.compute-1.amazonaw
    s.com "python /etc/create_hosts.py"


    exporting 10.252.31.48:/home/beowulf
    exporting 10.252.31.48:/mnt/data
    @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
    @ WARNING: UNPROTECTED PRIVATE KEY FILE! @
    @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
    Permissions 0644 for '/root/.ssh/id_rsa' are too open.
    It is recommended that your private key files are NOT accessible by others.
    This private key will be ignored.
    bad permissions: ignore key: /root/.ssh/id_rsa
    Permission denied, please try again.
    Permission denied, please try again.
    Permission denied (publickey,gssapi-with-mic,password).
    lost connection
    @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
    @ WARNING: UNPROTECTED PRIVATE KEY FILE! @
    @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
    Permissions 0644 for '/root/.ssh/id_rsa' are too open.
    It is recommended that your private key files are NOT accessible by others.
    This private key will be ignored.
    bad permissions: ignore key: /root/.ssh/id_rsa
    Permission denied, please try again.
    Permission denied, please try again.
    Permission denied (publickey,gssapi-with-mic,password).
    lost connection


    etcetera


    //////////////////////////////////


    As ++ you can see I made some small modifications in order to use PuTTy as my ++ SSH client, but that does not seem to be the problem... Does anyone ++else have this problem, and does anyone know how to fix it?

  • Pete 4 comments collapsed Collapse Expand

    Magg,


    I ++ wouldn't recommend it, the latency would be huge and I'm not sure how ++MPI would handle that. You would also need to open the mpi ports to the ++ outside world using the EC2 security group authorize commands.


    An ++ alternative is to open an X11 session and connect to the head node or ++maybe VNC in to the instance. The 64 bit elasticwulf images are set up ++for X11 sessions and adding a desktop package would allow you to VNC in ++if you prefer that route.


    -Pete

  • Abhimanyu 3 comments collapsed Collapse Expand

    I am facing the same problem. I am able to set up the ring manually but mpdboot complains:

    ++ ++

    mpdboot_domU-blah(handle_mpd_output 414): from mpd on domU-blah-,
    invalid port info:
    no_port

    ++ ++

    any word on this?

  • Abhimanyu 1 comment collapsed Collapse Expand

    I ++ found the problem. Apparently I had forgotten to include the "chown -R ++user:user /home/user" command. It didnt have access to the id_rsa file. ++As root mpdboot would work. Rather silly error message though.

  • pskomoroch 1 comment collapsed Collapse Expand

    I ++ think there are some SGE grid solutions now that allow you to add EC2 ++nodes to your existing cluster, but again the performance of MPI from a ++local network to EC2 would be horrible...

    ++ ++

    If you are interested in running MPI on EC2, I have a new project on Github I'll be announcing soon:

    ++ ++

    http://github.com/datawranglin...

  • magg 1 comment collapsed Collapse Expand

    Hi Peter,


    Have ++ you tried to connect EC2 instances with your local desktops? I am ++trying to do that with mpich2 1.0.7 but I am not successful at all. ++mpdboot complains about invalid port info (no_port) - actually no port ++when I try to do mpdboot -n 2. Even when I tried to mpd& on EC2 ++machine and then mpdtrace -l and then unblock the port and then mpd -h ++ec2-blabla -p ec2-mpdtrace-l-port still I have no luck. Have you faced ++similar problems?


    Thanks
    - magg

  • Pete 1 comment collapsed Collapse Expand

    @Theo,


    I'm attending MMDS this week at Stanford (http://www.stanford.edu/group/mmds/), ++ and had a chance to ask James Demmel a few questions. He gave a talk ++titled "Avoiding communication in linear algebra algorithms", which was ++very relevant. His advice for matrix multiplication in a high latency ++environment like EC2 was to try dialing up the block size as much as ++possible in the standard MPI solvers and see how performance was ++affected.


    -Pete

  • Pete 1 comment collapsed Collapse Expand

    I found the secret to avoiding a lot of MPI errors on EC2, but haven't found time to do an additional post...


    The ++ secret seems to be that just because Amazon says that an instance is ++"running", doesn't mean that the ssh daemons are available. This caused ++ all kinds of intermittent problems setting up the hosts and my old ++scripts would fail silently.


    In my current codebase, I do some checks like the following:


        print "Instance is %s" % BOOTING_INSTANCE
        
        # wait for instance description to return "running" and grab HOSTNAME variable
        print "Polling server status (ec2-describe-instances %s)" % BOOTING_INSTANCE
        while 1:
          print "waiting for instance to boot..."
          HOSTNAME = commands.getoutput("ec2-describe-instances %s | grep running | awk '{print $4}'" % BOOTING_INSTANCE)
          if len(HOSTNAME) > 1:
            print "-------Instance booted, The server is available at %s" % HOSTNAME
            DOM_NAME = commands.getoutput("ec2-describe-instances %s | grep running | awk '{print $5}'" % BOOTING_INSTANCE).split('.')[0]
            break
          time.sleep(1)    
        
        # sometimes it takes a while for the ssh service to start, even when the ec2 api describes an instance as running.
        # A machine in the "running" state may not have finished booting. Try executing a no-op command until a valid response is found
        print "verifying ssh daemon has started..."
        counter=0
        while 1:
          print "Waiting for ssh daemon to start..."
          counter += 1        
          REPLY = commands.getoutput('''ssh %s "root@%s" 'echo "hello"' ''' % (SSH_OPTS, HOSTNAME) )
          if REPLY == 'hello':
            print "-------ssh has started, proceeding with AMI build"
            break
          if counter > 24:
            print "Instance not respoding to SSH hails, aborting..."
            ## sshd should not take more than 2 minutes to launch
            terminate_status = commands.getoutput('ec2-terminate-instances %s' % BOOTING_INSTANCE)
            ec2_launch_failed = True
            print "Base Instance terminated"
            break
          time.sleep(5)
        
        if ec2_launch_failed:
            print "Aborting build"
            return
        
    
++
++

  • Patrick 1 comment collapsed Collapse Expand

    Thanks, Peter. The original EC2.py was the problem. I now have the large AMIs up and running. Thanks again for the article and help!


    Patrick

  • Theo 1 comment collapsed Collapse Expand

    Peter:


    I ++ am diving into Hadoop with Map/Reduce as we speak. As you know Google ++implemented its environment in C++, so I was a bit disappointed that ++Hadoop had chosen Java VM to do its bidding. Java makes interfacing with ++ hardcore numerical operations much harder. The particular problems I am ++ looking at are large scale Lanczos solvers to find eigen values/vectors ++ of large systems of equations. These systems are of interest in ++advertising, quantitative finance, and sensor networks. Problem is that ++they all are environments in which latency is of the essence. So you ++have a capacity component in terms of the size of the system and a ++latency issue in terms of the data rate coming in and the opportunity ++cost for somebody to get to the answer faster.


    I would be ++interested in working on this particular benchmark problem: pick a big ++eigen value/vector problem and solve it on a cluster, EC2, and via ++Hadoop/Map-reduce. Clearly this is going to be a lot of work so this ++should be publishing worthy. I am sure many folks would be interested in ++ this experiment, so let me know if this is something that could invest ++time in.


    Theo

  • Pete 1 comment collapsed Collapse Expand

    Patrick,


    Did you start with a clean install of the 64 bit scripts? I made some changes to EC2.py in the new scripts to handle the new instance types...

  • Patrick 1 comment collapsed Collapse Expand

    Peter,


    Very ++ useful tool! I've gotten a cluster up and running using the small ++instance type but am having difficulty launching the _64 AMIs.


    $ ./ec2-start-cluster.py
    m1.large
    image ami-eb13f682
    master image ami-e813f681
    ----- starting master -----
    Traceback (most recent call last):
    File "./ec2-start-cluster.py", line 39, in ?
    ++ master_response = conn.run_instances(imageId=MASTER_IMAGE_ID, ++minCount=1, maxCount=1, keyName= KEYNAME, instanceType=INSTANCE_TYPE )
    TypeError: run_instances() got an unexpected keyword argument 'instanceType'


    If I try to start the cluster without passing an INSTANCE_TYPE arg I get the following:
    $ ./ec2-start-cluster.py
    m1.large
    image ami-eb13f682
    master image ami-e813f681
    ----- starting master -----
    InvalidParameterValue: ++ The requested instance type's architecture (i386) does not match the ++architecture in the manifest for ami-e813f681 (x86_64)
    ----- starting workers -----
    InvalidParameterValue: ++ The requested instance type's architecture (i386) does not match the ++architecture in the manifest for ami-eb13f682 (x86_64)


    Any ideas? Thanks!

  • Pete 1 comment collapsed Collapse Expand

    Raghav,


    You can ssh in as root instead of lamuser, or compile the output file into your home directory.


    Check out the new AMI and managment code:


    http://www.datawrangling.com/pycon-2008-elasticwulf-slides.html


    The ++ new AMI includes a preconfigured NFS mounted directory /home/beowulf. ++If you compiled the file there, hellompi would be available on all ++nodes.


    Note that the new images default to the 'large' instance type which charges .40 cents/hour for each node.


    -Pete

  • raghav 1 comment collapsed Collapse Expand

    i am trying to compile a simple c mpi file "hellompi.c" using the command:



    mpicc -o /usr/hellompi /usr/local/src/hellompi.c



    why does it give me the following error?


    /usr/bin/ld: cannot open output file /usr/hellompi: Permission denied
    collect2: ld returned 1 exit status


    how do I get root priveledges?

  • Kurt Grandis 1 comment collapsed Collapse Expand

    Thanks ++ Pete. I wish I had made the PyCon session, but these posts have been ++very helpful. The cluster went up pretty quickly and I have already used ++ it to crunch a few minor data runs.
    In setting everything up I also ++ran into a similar problem as Raghav and ended up solving it in a ++similar manner by forcing the -i credentials switch. I imagine it has ++something to do with the way I configured and placed my certs.

  • raghav 1 comment collapsed Collapse Expand

    Thanks pete. For your prompt reply!!

  • raghav 1 comment collapsed Collapse Expand

    Hey guys,
    Actually I made a change in the ec2-mpi-cluster.py file. I have no clue about python and I dono why it worked but it worked.


    I modified:


    template = ssh -o "StrictHostKeyChecking no" %(user)s@%(host)s "%(cmd)s"
    to
    template = 'ssh -i "/home/id_rsa-gsg-keypair" %(user)s@%(host)s "%(cmd)s"


    and


    template = '%(cmd)s %(switches)s -o "StrictHostKeyChecking no" %(src)s %(user)s@%(host)s:%(dest)s'
    to
    template = '%(cmd)s %(switches)s -i "/home/id_rsa-gsg-keypair" %(src)s %(user)s@%(host)s:%(dest)s'


    And it started working perfectly fine. I was able to log in to the master node and the pi problem executed perfectly fine.


    Thanks a lot guys


    Cheers,
    Raghav

  • Pete 1 comment collapsed Collapse Expand

    raghav,


    Another suggestion is to make sure the instances are running with ./ec2-check-instances.py and then retry the script, sometimes it takes a while for sshd to start up on EC2.


    -Pete

  • Pete 1 comment collapsed Collapse Expand

    raghav,


    I assume you were able to start the instances with ec2-start-cluster.py? ++ The text on the terminal is normal, but it shouldn't ask you for a ++password (I should probably add a verbose option instead of streaming ++out text by default). There was a path issue on windows with an earlier ++version of the scripts, so that may be the problem.


    If you send me the script version number from the README and/or terminal output, I can try to track down what is going on...


    peter.skomoroch@gmail.com


    -Pete

  • raghav 1 comment collapsed Collapse Expand

    Why does it ask me for a password when i try to run the ec2-mpi-config.py file.?
    it says root@xxx password:
    And I get a lot of text on the terminal when I try running the file.

  • Pete 1 comment collapsed Collapse Expand

    No ++ problem, thanks for finding the typos. These were meant to be some ++quick hacks, but took on a life of their own after a while.


    I found this worked for configuring LAM, I'll send you more details in an email...


    The contents of bash_profile should be as follows:


     
    -bash-3.1# more .bash_profile 
    # .bash_profile
    
++
++
    # Get the aliases and functions
    if [ -f ~/.bashrc ]; then
            . ~/.bashrc
    fi
    
++
++
    # User specific environment and startup programs
    
++
++
    LAMRSH="ssh -x"
    export LAMRSH
    
++
++
    LD_LIBRARY_PATH="/usr/local/lam-7.1.2/lib/"
    export LD_LIBRARY_PATH
    
++
++
    MPICH_PORT_RANGE="2000:8000"
    export MPICH_PORT_RANGE
    
++
++
    PATH=$PATH:$HOME/bin
    
++
++
    PATH=/usr/local/lam-7.1.2/bin:$PATH
    
++
++
    MANPATH=/usr/local/lam-7.1.2/man:$MANPATH
    
++
++
    export PATH
    export MANPATH

    Launch the cluster on EC2 and try booting LAM manually:


    [lamuser@domU-12-31-33-00-04-4B ~]$ lamboot /etc/mpd.hosts
    
++
++
    [lamuser@domU-12-31-33-00-04-4B ~]$ lamnodes
    n0      domU-12-31-33-00-04-4B.usma1.c...:1:origin,this_node
    n1      domU-12-31-33-00-03-35.usma1.c...:1:
    n2      domU-12-31-33-00-03-3C.usma1.c...:1:
    n3      domU-12-31-34-00-00-55.usma2.c...:1:
    
++
++
    [lamuser@domU-12-31-33-00-04-4B ~]$ tping N -c3
      1 byte from 3 remote nodes and 1 local node: 0.039 secs
      1 byte from 3 remote nodes and 1 local node: 0.004 secs
      1 byte from 3 remote nodes and 1 local node: 0.002 secs

  • pete 1 comment collapsed Collapse Expand

    Found ++ another typo too, ok I'm nit picking. In the stop-cluster script the ++message says Stoping as opposed to stopping. A year ago when you first ++posted this stuff you mentioned that the reason why the non-root user ++was called lamuser was that the scripts were used for LAM in some ++previous incarnation. Since I'm actually trying to use LAM, if you have ++any LAM stuff around that might help me to iron out one or two problems I ++ still have.


    Anyway, thanks again,
    Pete

  • Pete 1 comment collapsed Collapse Expand

    pete ++ found the error... the image Ids he entered into the config module ++inadvertently contained a capital letter. This doesn’t cause any ++problems for starting images since string case is ignored by Amazon. The ++ corresponding image id response string from AWS is always lowercase, so ++ the python script comparison on image ID string fails.


    In the ++ next version of the scripts, I will handle upper/lowercase differences ++in the ami strings. For now, just make sure to use all lower case or ++call the python .lower() method,


     
    >>> test = 'ami-fE9a7f97'
    >>> test.lower()
    'ami-fe9a7f97'
    >>> 
    
++
++

  • pete 1 comment collapsed Collapse Expand

    Can't get the ec-mpi-config to work. Says list index out of range for mpi-externalnames[0] on line 108
    start cluster and check instances are OK so I think that python, EC, elementree
    are OK
    Any ++ ideas why? Has AWS changed the format of the response you're parsing ++(yes I have had a look at the python code but since I haven't used ++python before I can't see anything obvious to me)
    BTW you have a typo in mpi config Numer of nodes as opposed to Number of nodes , it even shows in your example above.
    Otherwise I like what you've done, I'd just like it to work for me.
    Thanks,
    Pete

  • Pete 1 comment collapsed Collapse Expand

    Theo,


    Sorry ++ for the delay in posting this and responding. I've been working on a ++startup for the past 7 months and was in serious crunch mode. Don't ++read too much into the large gap in posts, it is just me working on this ++ as a side-project. I finished moving the blog to another host and ++finally have some time to get back to the EC2 work. This experience has ++ taught me to never name a series of blog posts "part 1 of N" :)


    You ++ make some excellent points. One thing that has changed since I wrote ++the first post is that EC2 now offers larger 64bit machine images with ++better I/O (you can provision an entire physical server and not be ++limited by sharing network resources in the virtual instance). I'd like ++ to see if this improves the network performance. I'm giving a talk on ++this in March, so I'm on the hook to have some benchmarks by then.


    I ++ also agree on the mapreduce side. For embarrassingly parallel ++problems, hadoop on ec2 is potentially much more attractive...more ++robust, easier for most people to program. Ideally, I would like to do ++some comparisons between the two approaches and run the numbers.


    The ++ performance of an EC2 MPI cluster is definitely going to be worse than ++your own custom hardware, but it still might fit certain niche ++situations. In my case, I needed to run some MPI code for a large ++problem and didn't have access to a large enough cluster. The ++performance on EC2 was nowhere near what you get on a high-end cluster, ++but it got the job done for a reasonable price.


    This discussion on the beowulf list goes into more detail on the pros/cons:


    http://www.beowulf.org/pipermail/beowulf/2008-January/020490.html


    -Pete

  • Theo 1 comment collapsed Collapse Expand

    Does the 5 month hiatus in this project mean that it was a bad idea and you guys have learnt enough to waste no more time on it?


    Given ++ the virtualization uncertainty, finding the right ++communication/computation balance for typical MPI programs appears to be ++ very unrewarding. Secondly, MPI development and debug and then QA and ++scale out are not addressed, which doesn't bode well. It appears most ++productive to have a local small cluster for development and debug, and ++then do QA and scale out on EC2, but some benchmarking numbers would ++really help.


    If EC2 is only robust for embarrassingly parallel ++ problems, then MapReduce style programs are more attractive. There the ++size of the data set and how well it integrates in a distributed file ++system appear to be the problems to focus on. Or BOINC like approaches ++if there is no integrated DFS. Anyone have operational data on these ++approaches?

  • Patrick Ball 1 comment collapsed Collapse Expand


    the first two parts really set the stage ... Part 3?


    :)

  • Soo.. 1 comment collapsed Collapse Expand

    What about that Part 3? :)

  • Pete 1 comment collapsed Collapse Expand

    Update (7-24-07): I’ve made some important bug fixes to the scripts to address issues mentioned in the comments.


    Specific changes made:


    <ul>
    <li>fixed lamuser home directory permissions bug</li>
    <li>fixed section of ec2-mpi-config.py which clobbered existing rsa keys on the client machine</li>
    <li>Updated calls of AWS python EC2 library to use API version 2007-01-19
    http://developer.amazonwebserv...</li>
    <li>fixed mpdboot issue by using amazon internal DNS names in hosts files</li>
    <li>scripts should now work on windows/cygwin client environments</li>
    </ul>

    After ++ I run some benchmarks, I'm hoping to find some time to add LAM and ++OpenMPI to the EC2 image along with NFS configuration, C3 cluster tools, ++ Ganglia, and a benchmarking package.

  • Pete 1 comment collapsed Collapse Expand

    Ralph,


    More ++ good points. I've been tied up with some other projects, but it sounds ++like enough feedback is in to make a revised version of the image and ++scripts. I expect the latency to vary a bit depending on the random EC2 ++network topology when a cluster is launched...(instances on the same box ++ vs. over ethernet) that might explain the ringtest. The mutual ssh ++access was set up since we do a lot of file/data shuffling between nodes ++ outside of MPI.


    Thanks again, looking forward to hearing how the regression test system works out.


    -Pete

  • Ralph Giles 1 comment collapsed Collapse Expand

    Yeah, that would work better. Some more detailed comments:


    <ul>
    <li>

    Your image has /home/lamuser/.mpd.conf owned by root. I had to chown it to lamuser before I could start mpd.

    </li>
    <li>

    You ++ script passes the public dns names for the nodes into mpd.hosts. For ++that to work, a hole has to be opened in the firewall for the ports the ++mpi daemon is using. A simpler solution is to just pass the internal dns ++ names. Then all the traffic happens behind the firewall, which probably ++ also improves latency. (Although my ringtest was noticably slower than ++yours, averaging 2.2e-3 seconds/loop so who knows?)

    </li>
    <li>

    I ++ was surprised that when I originally ran ec2-add-keypair in the EC2 ++tutorial that it uploaded the public key (ok) and printed out the ++private key (ok I guess) but didn't print out the public key locally ++(weird). Your scripts seem to assume the public key is available as ++id_rsa.pub on the client machine. Shouldn't this first be copied either ++from /root/.ssh/authorized_keys on the master node (as installed by ++amazon) or retrieved through the query interface?

    </li>
    </ul>

    Is ++ the mutual ssh access required for more than just launching the MPI ++daemon? If all subsequent traffic goes through the mpi daemons, starting ++ mpd from the client machine, or automatically from the init scripts ++after pulling mpd.hosts from S3 would save the whole trouble, including ++uploading the private key at all.

  • Pete 1 comment collapsed Collapse Expand

    Ralph,


    Good catch. Thanks for pointing that out. I just lifted those passwordless ssh lines straight from an MPI tutorial.


    This might solve the clobbering as well (from http://www.maclife.com/forums/topic/61520):


    cat id_rsa.pub >> .ssh/authorized_keys


    "The ++ above command will create the "authorized_keys" file in the ".ssh" ++directory if that file doesn't already exist, and it will append the new ++ id_rsa.pub file to it if it does already exist."


    I'll add ++that change to the scripts. Good luck with the regression cluster, I ++heard Oracle developers do something like that using Condor on otherwise ++ idle desktops (see http://www.cs.wisc.edu/condor/doc/nmi-lisa2006-slides.pdf).


    -Pete

  • Ralph Giles 1 comment collapsed Collapse Expand

    ===== DO NOT USE THESE SCRIPTS! =====


    This section of ec2-mpi-config.py is a bit problematic:


    os.system('cp %s ~/id_rsa.pub' % KEY_LOCATION )
    os.system('cp ~/id_rsa.pub ~/.ssh/id_rsa')


    This ++ will clobber any existing rsa key on the initiating machine's account, ++and with break normal auth on the next login if you have a different ++default rsa key!


    The script should instead copy the private key directly from KEY_LOCATION to the nodes.


    ===== DO NOT USE THESE SCRIPTS! =====


    Otherwise, ++ way cool. Thanks for putting this tutorial together. We're trying EC2 ++clusters out as a way to get quicker feedback from regression tests ++after changes to our software. Unfortunately, with the one hour ++granularity I don't think it will be price competitive. We want 20-100 ++nodes for about 5 minutes at a time.

  • Pete 1 comment collapsed Collapse Expand

    Mike ++ Cariaso modified my scripts to fix some path issues and got it working ++on a windows laptop, he might have also fixed some other errors I didn't ++ notice. I haven't had a chance to try them yet, but you can download ++the modified scripts here:


    http://mpiblast.pbwiki.com/AmazonEC2

  • Michael Creel 1 comment collapsed Collapse Expand

    Yep, ++ I run the mpi-config script right after creating the instances, doing ++just what you suggest. The fact that the instances start up at all seems ++ to me to mean that the keypair information is ok. Do you know if anyone ++ but you has been able to launch a cluster? Very cool stuff. I'm going ++to be looking into making a Debian AMI that works the same way.

  • Pete 1 comment collapsed Collapse Expand

    Michael,


    I ++ haven't had the scripts prompt me for a password before, are you ++running them from your local machine? The mpi-config script expects the ++keyname and keypair location to match what was used to start the ++instance. Take a look at your EC2config.py ++ file and make sure the instances were all started with your own keypair ++ (i used the gsg keypair I created on my laptop in the Amazon "getting ++started guide" tutorial):





    AWS_ACCESS_KEY_ID = ‘YOUR_KEY_ID_HERE’
    AWS_SECRET_ACCESS_KEY = ‘YOUR_KEY_HERE’
    MASTER_IMAGE_ID = "ami-3e836657"
    IMAGE_ID = "ami-3e836657"
    KEYNAME = "gsg-keypair"
    KEY_LOCATION = "~/id_rsa-gsg-keypair"
    DEFAULT_CLUSTER_SIZE = 5





    I'm ++ working on an updated version of the scripts and EC2 image which should ++ make things a bit cleaner. Sorry the code is ugly right now in terms ++of error handling...I just wanted to toss something together to get ++people started :)

  • Michael Creel 1 comment collapsed Collapse Expand

    A little report on my trial.
    1) ./ec2-start_cluster.py ++ is not always successful in getting the requested number of nodes to ++come up. The instances sometimes have status "terminated" before ++anything is done with them.


    2) When the 5 nodes all come up, I still get a problem with ./ec2-mpi-config.py requesting a root password:


    michael@yosemite:~/ec2/AmazonEC2_MPI_scripts$ ./ec2-mpi-config.py


    ---- MPI Cluster Details ----
    Numer of nodes = 5
    Instance= i-e39c7a8a hostname= ec2-72-44-45-138.z-2.compute-1... state= running
    Instance= i-e29c7a8b hostname= ec2-72-44-45-185.z-2.compute-1... state= running
    Instance= i-e59c7a8c hostname= ec2-72-44-45-186.z-2.compute-1... state= running
    Instance= i-e49c7a8d hostname= ec2-72-44-45-122.z-2.compute-1... state= running
    Instance= i-e79c7a8e hostname= ec2-72-44-45-60.z-2.compute-1.... state= running


    The master node is ec2-72-44-45-138.z-2.compute-1...


    Writing out mpd.hosts file
    nslookup ec2-72-44-45-138.z-2.compute-1...
    (0, 'Server:\t\t158.109.0.1\nAddress:\t158.109.0.1#53\n\nNon-authoritative answer:\nName:\tec2-72-44-45-138.z-2.compute-...\nAddress: 72.44.45.138\n')
    nslookup ec2-72-44-45-185.z-2.compute-1...
    (0, 'Server:\t\t158.109.0.1\nAddress:\t158.109.0.1#53\n\nNon-authoritative answer:\nName:\tec2-72-44-45-185.z-2.compute-...\nAddress: 72.44.45.185\n')
    nslookup ec2-72-44-45-186.z-2.compute-1...
    (0, 'Server:\t\t158.109.0.1\nAddress:\t158.109.0.1#53\n\nNon-authoritative answer:\nName:\tec2-72-44-45-186.z-2.compute-...\nAddress: 72.44.45.186\n')
    nslookup ec2-72-44-45-122.z-2.compute-1...
    (0, 'Server:\t\t158.109.0.1\nAddress:\t158.109.0.1#53\n\nNon-authoritative answer:\nName:\tec2-72-44-45-122.z-2.compute-...\nAddress: 72.44.45.122\n')
    nslookup ec2-72-44-45-60.z-2.compute-1....
    (0, 'Server:\t\t158.109.0.1\nAddress:\t158.109.0.1#53\n\nNon-authoritative answer:\nName:\tec2-72-44-45-60.z-2.compute-1...\nAddress: 72.44.45.60\n')
    Warning: Permanently added 'ec2-72-44-45-138.z-2.compute-1...,72.44.45.138' (RSA) to the list of known hosts.
    id_rsa.pub 100% 1675 1.6KB/s 00:00
    root@ec2-72-44-45-138.z-2.compute-1.am...'s password:


    This is as far as I can get at the moment. Looks like a minor problem. Cheers, M.

  • Michael Creel 1 comment collapsed Collapse Expand

    One question, do you know if something like an NFS shared home directory is possible. Using S3, possibly?

  • Michael Creel 1 comment collapsed Collapse Expand

    Excellent ++ stuff! I've gotten started with EC2 and I'll be trying your images out ++soon. I doubt that I'll be trying to make ParallelKnoppix work on EC2, ++because your approach is the right one, I think. PK is designed to use ++when the hardware is not known ahead of time. With EC2, the hardware is ++known, so a tailor-made image is the way to go. Your scripts allow an ++on-demand cluster to be created in minutes, and that's all that PK ++offers, anyway. PK usually needs some remastering so that users can add ++their own packages. Re-bundling an EC2 image is completely analogous. ++I'm planning on doing just that, probably starting with your images, and ++ doing some testing of latency on tasks that require different degrees ++of internode communication. Thanks for all this, it'll make the rest an ++easy job.

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++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ +\ No newline at end of file +Index: ../trunk-jpl/externalpackages/ec2api +=================================================================== +--- ../trunk-jpl/externalpackages/ec2api (revision 13841) ++++ ../trunk-jpl/externalpackages/ec2api (revision 13842) + +Property changes on: ../trunk-jpl/externalpackages/ec2api +___________________________________________________________________ +Added: svn:ignore +## -0,0 +1,3 ## ++ec2-api-tools.zip ++ec2-api-tools-* ++ Index: /issm/oecreview/Archive/13393-13976/ISSM-13842-13843.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13842-13843.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13842-13843.diff (revision 13980) @@ -0,0 +1,49 @@ +Index: ../trunk-jpl/externalpackages/ec2ami/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/ec2ami/install.sh (revision 0) ++++ ../trunk-jpl/externalpackages/ec2ami/install.sh (revision 13843) +@@ -0,0 +1,12 @@ ++#!/bin/bash ++set -eu ++ ++#Some cleanup ++rm -rf ec2-api-tools.zip ++rm -rf ec2-api-tools-1.4.0.7 ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ec2-api-tools.zip' 'ec2-api-tools.zip' ++ ++#Untar ++unzip ec2-api-tools.zip + +Property changes on: ../trunk-jpl/externalpackages/ec2ami/install.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/externalpackages/ec2ami/ec2-ami-tools.zip +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/externalpackages/ec2ami/ec2-ami-tools.zip +=================================================================== +--- ../trunk-jpl/externalpackages/ec2ami/ec2-ami-tools.zip (revision 13842) ++++ ../trunk-jpl/externalpackages/ec2ami/ec2-ami-tools.zip (revision 13843) + +Property changes on: ../trunk-jpl/externalpackages/ec2ami/ec2-ami-tools.zip +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/externalpackages/ec2ami +=================================================================== +--- ../trunk-jpl/externalpackages/ec2ami (revision 13842) ++++ ../trunk-jpl/externalpackages/ec2ami (revision 13843) + +Property changes on: ../trunk-jpl/externalpackages/ec2ami +___________________________________________________________________ +Added: svn:ignore +## -0,0 +1,3 ## ++ec2-ami-tools-* ++*.zip ++ Index: /issm/oecreview/Archive/13393-13976/ISSM-13843-13844.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13843-13844.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13843-13844.diff (revision 13980) @@ -0,0 +1,4 @@ +Index: ../trunk-jpl/externalpackages/ec2ami/ec2-ami-tools.zip +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/13393-13976/ISSM-13844-13845.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13844-13845.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13844-13845.diff (revision 13980) @@ -0,0 +1,48 @@ +Index: ../trunk-jpl/externalpackages/android/android-sdk +=================================================================== +--- ../trunk-jpl/externalpackages/android/android-sdk (revision 13844) ++++ ../trunk-jpl/externalpackages/android/android-sdk (revision 13845) + +Property changes on: ../trunk-jpl/externalpackages/android/android-sdk +___________________________________________________________________ +Modified: svn:ignore +## -1,2 +1,3 ## ++*.zip + install-sdk + install-ant +Index: ../trunk-jpl/externalpackages/android/android-ndk +=================================================================== +--- ../trunk-jpl/externalpackages/android/android-ndk (revision 13844) ++++ ../trunk-jpl/externalpackages/android/android-ndk (revision 13845) + +Property changes on: ../trunk-jpl/externalpackages/android/android-ndk +___________________________________________________________________ +Modified: svn:ignore +## -1 +1,3 ## ++android-ndk-r* ++*.bz2 + install +Index: ../trunk-jpl/externalpackages/gmake +=================================================================== +--- ../trunk-jpl/externalpackages/gmake (revision 13844) ++++ ../trunk-jpl/externalpackages/gmake (revision 13845) + +Property changes on: ../trunk-jpl/externalpackages/gmake +___________________________________________________________________ +Modified: svn:ignore +## -1,2 +1,3 ## ++*.gz + install + src +Index: ../trunk-jpl/externalpackages/esmf +=================================================================== +--- ../trunk-jpl/externalpackages/esmf (revision 13844) ++++ ../trunk-jpl/externalpackages/esmf (revision 13845) + +Property changes on: ../trunk-jpl/externalpackages/esmf +___________________________________________________________________ +Modified: svn:ignore +## -1,2 +1,3 ## ++esmf-gfortran* + esmf + *.gz Index: /issm/oecreview/Archive/13393-13976/ISSM-13845-13846.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13845-13846.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13845-13846.diff (revision 13980) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/configs/config-macosx64-larour.sh +=================================================================== +--- ../trunk-jpl/configs/config-macosx64-larour.sh (revision 13845) ++++ ../trunk-jpl/configs/config-macosx64-larour.sh (revision 13846) +@@ -9,7 +9,6 @@ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ +- --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ Index: /issm/oecreview/Archive/13393-13976/ISSM-13846-13847.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13846-13847.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13846-13847.diff (revision 13980) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/etc/environment.sh +=================================================================== +--- ../trunk-jpl/etc/environment.sh (revision 13846) ++++ ../trunk-jpl/etc/environment.sh (revision 13847) +@@ -2,7 +2,7 @@ + + pathprepend(){ #{{{ + if [ -d "$1" ] && [[ ":$PATH:" != *":$1:"* ]]; then +- PATH="$1:$PATH" ++ export PATH="$1:$PATH" + fi + } #}}} + pathappend(){ #{{{ +@@ -101,7 +101,7 @@ + pathappend "$CPPCHECK_DIR/bin" + + GDAL_DIR="$ISSM_DIR/externalpackages/gdal/install" +-pathprepend "$GDAL_DIR/bin:$PATH" ++pathprepend "$GDAL_DIR/bin" + libpathappend "$GDAL_DIR/lib" + + MERCURIAL_DIR="$ISSM_DIR/externalpackages/mercurial/install" Index: /issm/oecreview/Archive/13393-13976/ISSM-13847-13848.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13847-13848.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13847-13848.diff (revision 13980) @@ -0,0 +1,52 @@ +Index: ../trunk-jpl/externalpackages/gdal/install_macosx.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gdal/install_macosx.sh (revision 0) ++++ ../trunk-jpl/externalpackages/gdal/install_macosx.sh (revision 13848) +@@ -0,0 +1,41 @@ ++#!/bin/bash ++set -eu ++ ++#Some cleanup ++rm -rf src ++rm -rf install ++rm -rf gdal-1.6.0 ++mkdir src install ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' ++ ++#Untar ++tar -zxvf gdal-1.6.0.tar.gz ++ ++#Move gdal into src directory ++mv gdal-1.6.0/* src ++rm -rf gdal-1.6.0 ++ ++#Configure gdal ++cd src ++./configure \ ++ --prefix="$ISSM_DIR/externalpackages/gdal/install" \ ++ --without-python \ ++ --without-png \ ++ --with-netcdf=no \ ++ --with-jasper=no \ ++ --without-ld-shared \ ++ --with-unix-stdio-64=no \ ++ --with-expat-lib=/usr/lib64/libexpat.so ++ ++#Patch GDALmake.opt ++#patch GDALmake.opt ../GDALmake.opt.patch ++ ++#Compile and install gdal ++if [ $# -eq 0 ]; then ++ make ++else ++ make -j $1 ++fi ++make install + +Property changes on: ../trunk-jpl/externalpackages/gdal/install_macosx.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* Index: /issm/oecreview/Archive/13393-13976/ISSM-13848-13849.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13848-13849.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13848-13849.diff (revision 13980) @@ -0,0 +1,65 @@ +Index: ../trunk-jpl/externalpackages/gdal/install_astrid.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gdal/install_astrid.sh (revision 0) ++++ ../trunk-jpl/externalpackages/gdal/install_astrid.sh (revision 13849) +@@ -0,0 +1,41 @@ ++#!/bin/bash ++set -eu ++ ++#Some cleanup ++rm -rf src ++rm -rf install ++rm -rf gdal-1.6.0 ++mkdir src install ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' ++ ++#Untar ++tar -zxvf gdal-1.6.0.tar.gz ++ ++#Move gdal into src directory ++mv gdal-1.6.0/* src ++rm -rf gdal-1.6.0 ++ ++#Configure gdal ++cd src ++./configure \ ++ --prefix="$ISSM_DIR/externalpackages/gdal/install" \ ++ --without-python \ ++ --without-png \ ++ --with-netcdf=no \ ++ --with-jasper=no \ ++ --without-ld-shared \ ++ --with-unix-stdio-64=no \ ++ --with-expat-lib=/usr/lib64/libexpat.so ++ ++#Patch GDALmake.opt ++patch GDALmake.opt ../GDALmake.opt.patch.2 ++ ++#Compile and install gdal ++if [ $# -eq 0 ]; then ++ make ++else ++ make -j $1 ++fi ++make install + +Property changes on: ../trunk-jpl/externalpackages/gdal/install_astrid.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/externalpackages/gdal/GDALmake.opt.patch.astrid +=================================================================== +--- ../trunk-jpl/externalpackages/gdal/GDALmake.opt.patch.astrid (revision 0) ++++ ../trunk-jpl/externalpackages/gdal/GDALmake.opt.patch.astrid (revision 13849) +@@ -0,0 +1,8 @@ ++31c31 ++< LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib -lexpat -ljpeg -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ ++--- ++> LIBS = $(SDE_LIB) -I/usr/include -lsqlite3 -L/usr/lib64 -lexpat -ljpeg -lz -lm -lrt -ldl $(KAK_LIBS) $(DWG_LIBS) $(CURL_LIB) \ ++225c225 ++< CURL_LIB = -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz ++--- ++> CURL_LIB = -L/usr/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz Index: /issm/oecreview/Archive/13393-13976/ISSM-13849-13850.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13849-13850.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13849-13850.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/externalpackages/gdal/install_astrid.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gdal/install_astrid.sh (revision 13849) ++++ ../trunk-jpl/externalpackages/gdal/install_astrid.sh (revision 13850) +@@ -30,7 +30,7 @@ + --with-expat-lib=/usr/lib64/libexpat.so + + #Patch GDALmake.opt +-patch GDALmake.opt ../GDALmake.opt.patch.2 ++patch GDALmake.opt ../GDALmake.opt.patch.astrid + + #Compile and install gdal + if [ $# -eq 0 ]; then Index: /issm/oecreview/Archive/13393-13976/ISSM-13850-13851.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13850-13851.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13850-13851.diff (revision 13980) @@ -0,0 +1,333 @@ +Index: ../trunk-jpl/externalpackages/gdal/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gdal/install.sh (revision 13850) ++++ ../trunk-jpl/externalpackages/gdal/install.sh (revision 13851) +@@ -1,41 +0,0 @@ +-#!/bin/bash +-set -eu +- +-#Some cleanup +-rm -rf src +-rm -rf install +-rm -rf gdal-1.6.0 +-mkdir src install +- +-#Download from ISSM server +-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' +- +-#Untar +-tar -zxvf gdal-1.6.0.tar.gz +- +-#Move gdal into src directory +-mv gdal-1.6.0/* src +-rm -rf gdal-1.6.0 +- +-#Configure gdal +-cd src +-./configure \ +- --prefix="$ISSM_DIR/externalpackages/gdal/install" \ +- --without-python \ +- --without-png \ +- --with-netcdf=no \ +- --with-jasper=no \ +- --without-ld-shared \ +- --with-unix-stdio-64=no \ +- --with-expat-lib=/usr/lib64/libexpat.so +- +-#Patch GDALmake.opt +-patch GDALmake.opt ../GDALmake.opt.patch +- +-#Compile and install gdal +-if [ $# -eq 0 ]; then +- make +-else +- make -j $1 +-fi +-make install +Index: ../trunk-jpl/externalpackages/gdal/install-murdo.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gdal/install-murdo.sh (revision 13850) ++++ ../trunk-jpl/externalpackages/gdal/install-murdo.sh (revision 13851) +@@ -1,39 +0,0 @@ +-#!/bin/bash +-set -eu +- +-#Some cleanup +-rm -rf src +-rm -rf install +-rm -rf gdal-1.6.0 +-mkdir src install +- +-#Download from ISSM server +-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' +- +-#Untar +-tar -zxvf gdal-1.6.0.tar.gz +- +-#Move gdal into src directory +-mv gdal-1.6.0/* src +-rm -rf gdal-1.6.0 +- +-#Configure gdal +-cd src +-./configure --prefix="$ISSM_DIR/externalpackages/gdal/install" \ +- --without-python \ +- --without-png \ +- --with-netcdf=no \ +- --with-jasper=no \ +- --without-ld-shared \ +- --with-unix-stdio-64=no +- +-#Patch GDALmake.opt +-patch GDALmake.opt ../GDALmake.opt.patch +- +-#Compile and install gdal +-if [ $# -eq 0 ]; then +- make +-else +- make -j $1 +-fi +-make install +Index: ../trunk-jpl/externalpackages/gdal/install_astrid.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gdal/install_astrid.sh (revision 13850) ++++ ../trunk-jpl/externalpackages/gdal/install_astrid.sh (revision 13851) +@@ -1,41 +0,0 @@ +-#!/bin/bash +-set -eu +- +-#Some cleanup +-rm -rf src +-rm -rf install +-rm -rf gdal-1.6.0 +-mkdir src install +- +-#Download from ISSM server +-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' +- +-#Untar +-tar -zxvf gdal-1.6.0.tar.gz +- +-#Move gdal into src directory +-mv gdal-1.6.0/* src +-rm -rf gdal-1.6.0 +- +-#Configure gdal +-cd src +-./configure \ +- --prefix="$ISSM_DIR/externalpackages/gdal/install" \ +- --without-python \ +- --without-png \ +- --with-netcdf=no \ +- --with-jasper=no \ +- --without-ld-shared \ +- --with-unix-stdio-64=no \ +- --with-expat-lib=/usr/lib64/libexpat.so +- +-#Patch GDALmake.opt +-patch GDALmake.opt ../GDALmake.opt.patch.astrid +- +-#Compile and install gdal +-if [ $# -eq 0 ]; then +- make +-else +- make -j $1 +-fi +-make install +Index: ../trunk-jpl/externalpackages/gdal/install_macosx.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gdal/install_macosx.sh (revision 13850) ++++ ../trunk-jpl/externalpackages/gdal/install_macosx.sh (revision 13851) +@@ -1,41 +0,0 @@ +-#!/bin/bash +-set -eu +- +-#Some cleanup +-rm -rf src +-rm -rf install +-rm -rf gdal-1.6.0 +-mkdir src install +- +-#Download from ISSM server +-$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' +- +-#Untar +-tar -zxvf gdal-1.6.0.tar.gz +- +-#Move gdal into src directory +-mv gdal-1.6.0/* src +-rm -rf gdal-1.6.0 +- +-#Configure gdal +-cd src +-./configure \ +- --prefix="$ISSM_DIR/externalpackages/gdal/install" \ +- --without-python \ +- --without-png \ +- --with-netcdf=no \ +- --with-jasper=no \ +- --without-ld-shared \ +- --with-unix-stdio-64=no \ +- --with-expat-lib=/usr/lib64/libexpat.so +- +-#Patch GDALmake.opt +-#patch GDALmake.opt ../GDALmake.opt.patch +- +-#Compile and install gdal +-if [ $# -eq 0 ]; then +- make +-else +- make -j $1 +-fi +-make install +Index: ../trunk-jpl/externalpackages/gdal/install-macosx64.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gdal/install-macosx64.sh (revision 0) ++++ ../trunk-jpl/externalpackages/gdal/install-macosx64.sh (revision 13851) +@@ -0,0 +1,38 @@ ++#!/bin/bash ++set -eu ++ ++#Some cleanup ++rm -rf src ++rm -rf install ++rm -rf gdal-1.6.0 ++mkdir src install ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' ++ ++#Untar ++tar -zxvf gdal-1.6.0.tar.gz ++ ++#Move gdal into src directory ++mv gdal-1.6.0/* src ++rm -rf gdal-1.6.0 ++ ++#Configure gdal ++cd src ++./configure \ ++ --prefix="$ISSM_DIR/externalpackages/gdal/install" \ ++ --without-python \ ++ --without-png \ ++ --with-netcdf=no \ ++ --with-jasper=no \ ++ --without-ld-shared \ ++ --with-unix-stdio-64=no \ ++ --with-expat-lib=/usr/lib64/libexpat.so ++ ++#Compile and install gdal ++if [ $# -eq 0 ]; then ++ make ++else ++ make -j $1 ++fi ++make install + +Property changes on: ../trunk-jpl/externalpackages/gdal/install-macosx64.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/externalpackages/gdal/install-linux64-astrid.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gdal/install-linux64-astrid.sh (revision 0) ++++ ../trunk-jpl/externalpackages/gdal/install-linux64-astrid.sh (revision 13851) +@@ -0,0 +1,41 @@ ++#!/bin/bash ++set -eu ++ ++#Some cleanup ++rm -rf src ++rm -rf install ++rm -rf gdal-1.6.0 ++mkdir src install ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' ++ ++#Untar ++tar -zxvf gdal-1.6.0.tar.gz ++ ++#Move gdal into src directory ++mv gdal-1.6.0/* src ++rm -rf gdal-1.6.0 ++ ++#Configure gdal ++cd src ++./configure \ ++ --prefix="$ISSM_DIR/externalpackages/gdal/install" \ ++ --without-python \ ++ --without-png \ ++ --with-netcdf=no \ ++ --with-jasper=no \ ++ --without-ld-shared \ ++ --with-unix-stdio-64=no \ ++ --with-expat-lib=/usr/lib64/libexpat.so ++ ++#Patch GDALmake.opt ++patch GDALmake.opt ../GDALmake.opt.patch.astrid ++ ++#Compile and install gdal ++if [ $# -eq 0 ]; then ++ make ++else ++ make -j $1 ++fi ++make install + +Property changes on: ../trunk-jpl/externalpackages/gdal/install-linux64-astrid.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/externalpackages/gdal/install-linux64-murdo.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gdal/install-linux64-murdo.sh (revision 0) ++++ ../trunk-jpl/externalpackages/gdal/install-linux64-murdo.sh (revision 13851) +@@ -0,0 +1,39 @@ ++#!/bin/bash ++set -eu ++ ++#Some cleanup ++rm -rf src ++rm -rf install ++rm -rf gdal-1.6.0 ++mkdir src install ++ ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/gdal-1.6.0.tar.gz' 'gdal-1.6.0.tar.gz' ++ ++#Untar ++tar -zxvf gdal-1.6.0.tar.gz ++ ++#Move gdal into src directory ++mv gdal-1.6.0/* src ++rm -rf gdal-1.6.0 ++ ++#Configure gdal ++cd src ++./configure --prefix="$ISSM_DIR/externalpackages/gdal/install" \ ++ --without-python \ ++ --without-png \ ++ --with-netcdf=no \ ++ --with-jasper=no \ ++ --without-ld-shared \ ++ --with-unix-stdio-64=no ++ ++#Patch GDALmake.opt ++patch GDALmake.opt ../GDALmake.opt.patch ++ ++#Compile and install gdal ++if [ $# -eq 0 ]; then ++ make ++else ++ make -j $1 ++fi ++make install + +Property changes on: ../trunk-jpl/externalpackages/gdal/install-linux64-murdo.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* Index: /issm/oecreview/Archive/13393-13976/ISSM-13851-13852.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13851-13852.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13851-13852.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/solutions/controltao_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/controltao_core.cpp (revision 13851) ++++ ../trunk-jpl/src/c/solutions/controltao_core.cpp (revision 13852) +@@ -134,7 +134,7 @@ + /*Compute solution and adjoint*/ + void (*solutioncore)(FemModel*)=NULL; + void (*adjointcore)(FemModel*)=NULL; +- CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); ++ PureCorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); + AdjointCorePointerFromSolutionEnum(&adjointcore,solution_type); + solutioncore(femmodel); + adjointcore(femmodel); Index: /issm/oecreview/Archive/13393-13976/ISSM-13852-13853.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13852-13853.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13852-13853.diff (revision 13980) @@ -0,0 +1,192 @@ +Index: ../trunk-jpl/configs/config-linux64-astrid-python.sh +=================================================================== +--- ../trunk-jpl/configs/config-linux64-astrid-python.sh (revision 13852) ++++ ../trunk-jpl/configs/config-linux64-astrid-python.sh (revision 13853) +@@ -1,25 +0,0 @@ +-#!/bin/sh +- +-#External packages versions: +-#petsc 3.1 or 3.2 +-#mpich 1.4 +- +-./configure \ +- --prefix=$ISSM_DIR \ +- --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ +- --with-python-dir=$ISSM_DIR/externalpackages/python/install\ +- --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ +- --with-python-version=2.7\ +- --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ +- --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ +- --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ +- --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich " \ +- --with-petsc-arch=$ISSM_ARCH \ +- --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ +- --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +- --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ +- --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" \ +- --with-graphics-lib=/usr/lib64/libX11.so \ +- --with-cxxoptflags="-march=opteron -O2 -lutil" \ +- --with-numthreads=32 \ +- --enable-debugging +Index: ../trunk-jpl/configs/config-macosx-snowleopard-python.sh +=================================================================== +--- ../trunk-jpl/configs/config-macosx-snowleopard-python.sh (revision 13852) ++++ ../trunk-jpl/configs/config-macosx-snowleopard-python.sh (revision 13853) +@@ -3,14 +3,11 @@ + #petsc 3.2 + #mpich 1.4 + +-pythonversion=2.7 +- + ./configure \ + --prefix=$ISSM_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ +- --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy\ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ +Index: ../trunk-jpl/configs/config-macosx64-larour-nopetsc.sh +=================================================================== +--- ../trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 13852) ++++ ../trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 13853) +@@ -1,13 +1,10 @@ + #!/bin/sh + +-pythonversion=3.2 +- + ./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ +- --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/3.2/lib/python3.2/site-packages/numpy/core/include/numpy\ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-math-lib="/usr/lib/libm.dylib" \ + --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ +Index: ../trunk-jpl/configs/config-macosx64-chris-bothapis.sh +=================================================================== +--- ../trunk-jpl/configs/config-macosx64-chris-bothapis.sh (revision 13852) ++++ ../trunk-jpl/configs/config-macosx64-chris-bothapis.sh (revision 13853) +@@ -3,13 +3,11 @@ + #petsc 3.2 + #mpich 1.4 + +-pythonversion=2.7 +- + ./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install \ +- --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy\ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy\ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ +@@ -27,4 +25,3 @@ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ + #--with-fortran-lib="/usr/local/gfortran/lib/gcc/x86_64-apple-darwin10/4.6.2/libgfortran.a" \ +- #--with-python-version=$pythonversion \ +Index: ../trunk-jpl/configs/config-macosx64-larour-python.sh +=================================================================== +--- ../trunk-jpl/configs/config-macosx64-larour-python.sh (revision 13852) ++++ ../trunk-jpl/configs/config-macosx64-larour-python.sh (revision 13853) +@@ -3,14 +3,11 @@ + #petsc 3.2 + #mpich 1.4 + +-pythonversion=2.7 +- + ./configure \ + --prefix=$ISSM_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ +- --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ +Index: ../trunk-jpl/configs/config-macosx-snowleopard-bothapis.sh +=================================================================== +--- ../trunk-jpl/configs/config-macosx-snowleopard-bothapis.sh (revision 13852) ++++ ../trunk-jpl/configs/config-macosx-snowleopard-bothapis.sh (revision 13853) +@@ -3,20 +3,12 @@ + #petsc 3.2 + #mpich 1.4 + +-#export FCFLAGS=" -m32" +-#export FFLAGS=" -m32" +-#export CFLAGS=" -arch i386" +-#export CXXFLAGS=" -arch i386" +- +-pythonversion=2.7 +- + ./configure \ + --prefix=$ISSM_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ +- --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include/numpy\ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ +Index: ../trunk-jpl/configs/config-macosx64-chris-python.sh +=================================================================== +--- ../trunk-jpl/configs/config-macosx64-chris-python.sh (revision 13852) ++++ ../trunk-jpl/configs/config-macosx64-chris-python.sh (revision 13853) +@@ -3,14 +3,11 @@ + #petsc 3.2 + #mpich 1.4 + +-pythonversion=2.7 +- + ./configure \ + --prefix=$ISSM_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ +- --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ +Index: ../trunk-jpl/configs/config-linux64-astrid.sh +=================================================================== +--- ../trunk-jpl/configs/config-linux64-astrid.sh (revision 13852) ++++ ../trunk-jpl/configs/config-linux64-astrid.sh (revision 13853) +@@ -12,7 +12,6 @@ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ + --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ +- --with-python-version=2.7\ + --with-tao-dir=$ISSM_DIR/externalpackages/tao/install \ + --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ +Index: ../trunk-jpl/configs/config-macosx64-lion-helene.sh +=================================================================== +--- ../trunk-jpl/configs/config-macosx64-lion-helene.sh (revision 13852) ++++ ../trunk-jpl/configs/config-macosx64-lion-helene.sh (revision 13853) +@@ -3,15 +3,12 @@ + #petsc 3.2 + #mpich 1.4 + +-pythonversion=2.7 +- + ./configure \ + --prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_DIR \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-python-dir=$ISSM_DIR/externalpackages/python/install\ +- --with-python-version=$pythonversion \ +- --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ ++ --with-python-numpy-dir=$ISSM_DIR/externalpackages/python/install/lib/python2.7/site-packages/numpy/core/include/numpy\ + --with-metis-dir=$ISSM_DIR/externalpackages/metis/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include \ + --with-mpi-lib=" $ISSM_DIR/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpich.a $ISSM_DIR/externalpackages/mpich2/install/lib/libmpl.a " \ Index: /issm/oecreview/Archive/13393-13976/ISSM-13853-13854.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13853-13854.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13853-13854.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/etc/environment.csh +=================================================================== +--- ../trunk-jpl/etc/environment.csh (revision 13853) ++++ ../trunk-jpl/etc/environment.csh (revision 13854) +@@ -87,7 +87,7 @@ + #CMAKE + set CMAKE_DIR="$ISSM_DIR/externalpackages/cmake/install" + if (-d $CMAKE_DIR) then +- setenv PATH {$PATH}:{$CMAKE_DIR}/bin ++ setenv PATH {$CMAKE_DIR}/bin:{$PATH} + endif + + #YAMS Index: /issm/oecreview/Archive/13393-13976/ISSM-13854-13855.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13854-13855.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13854-13855.diff (revision 13980) @@ -0,0 +1,402 @@ +Index: ../trunk-jpl/src/c/solutions/PureCorePointerFromSolutionEnum.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/PureCorePointerFromSolutionEnum.cpp (revision 13854) ++++ ../trunk-jpl/src/c/solutions/PureCorePointerFromSolutionEnum.cpp (revision 13855) +@@ -1,106 +0,0 @@ +-/*!\file: PureCorePointerFromSolutionEnum.cpp +- * \brief: return type of analyses, number of analyses and core solution function. +- */ +- +-#ifdef HAVE_CONFIG_H +- #include +-#else +-#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" +-#endif +- +-#include "../toolkits/toolkits.h" +-#include "../classes/objects/objects.h" +-#include "../shared/shared.h" +-#include "../EnumDefinitions/EnumDefinitions.h" +-#include "./solutions.h" +-#include "../modules/modules.h" +-#include "../include/include.h" +-#include "../solvers/solvers.h" +- +-void PureCorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype){ +- +- /*output: */ +- void (*solutioncore)(FemModel*)=NULL; +- +- switch(solutiontype){ +- +- case DiagnosticSolutionEnum: +- #ifdef _HAVE_DIAGNOSTIC_ +- solutioncore=&diagnostic_core; +- #else +- _error_("ISSM was not compiled with diagnostic capabilities. Exiting"); +- #endif +- break; +- case SteadystateSolutionEnum: +- #ifdef _HAVE_STEADYSTATE_ +- solutioncore=&steadystate_core; +- #else +- _error_("ISSM was not compiled with steady state capabilities. Exiting"); +- #endif +- break; +- case ThermalSolutionEnum: +- #ifdef _HAVE_THERMAL_ +- solutioncore=&thermal_core; +- #else +- _error_("ISSM was not compiled with thermal capabilities. Exiting"); +- #endif +- break; +- case EnthalpySolutionEnum: +- #ifdef _HAVE_THERMAL_ +- solutioncore=&enthalpy_core; +- #else +- _error_("ISSM was not compiled with thermal capabilities. Exiting"); +- #endif +- break; +- case BalancethicknessSolutionEnum: +- #ifdef _HAVE_BALANCED_ +- solutioncore=&balancethickness_core; +- #else +- _error_("ISSM was not compiled with balanced capabilities. Exiting"); +- #endif +- break; +- case HydrologySolutionEnum: +- #ifdef _HAVE_HYDROLOGY_ +- solutioncore=&hydrology_core; +- #else +- _error_("ISSM was not compiled with hydrology capabilities. Exiting"); +- #endif +- break; +- case SurfaceSlopeSolutionEnum: +- #ifdef _HAVE_SLOPE_ +- solutioncore=&surfaceslope_core; +- #else +- _error_("ISSM was not compiled with slope capabilities. Exiting"); +- #endif +- break; +- case BedSlopeSolutionEnum: +- #ifdef _HAVE_SLOPE_ +- solutioncore=&bedslope_core; +- #else +- _error_("ISSM was not compiled with slope capabilities. Exiting"); +- #endif +- break; +- case TransientSolutionEnum: +- #ifdef _HAVE_TRANSIENT_ +- solutioncore=&transient_core; +- #else +- _error_("ISSM was not compiled with transient capabilities. Exiting"); +- #endif +- break; +- case PrognosticSolutionEnum: +- #ifdef _HAVE_PROGNOSTIC_ +- solutioncore=&prognostic_core; +- #else +- _error_("ISSM was not compiled with prognostic capabilities. Exiting"); +- #endif +- break; +- default: +- _error_("solution type: " << EnumToStringx(solutiontype) << " not supported yet!"); +- break; +- } +- +- /*Assign output pointer:*/ +- _assert_(psolutioncore); +- *psolutioncore=solutioncore; +- +-} +Index: ../trunk-jpl/src/c/solutions/CorePointerFromSolutionEnum.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/CorePointerFromSolutionEnum.cpp (revision 13854) ++++ ../trunk-jpl/src/c/solutions/CorePointerFromSolutionEnum.cpp (revision 13855) +@@ -17,41 +17,87 @@ + #include "../include/include.h" + #include "../solvers/solvers.h" + +-void CorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype,bool nodakotacore){ ++void CorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype){ + + /*output: */ + void (*solutioncore)(FemModel*)=NULL; + +- /*parameters: */ +- bool control_analysis=false; +- bool tao_analysis=false; +- bool dakota_analysis=false; ++ switch(solutiontype){ + +- /* retrieve some parameters that tell us whether wrappers are allowed, or whether we return +- * a pure core. Wrappers can be dakota_core (which samples many solution_cores) or control_core (which +- * carries out adjoint based inversion on a certain core: */ +- parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum); +- parameters->FindParam(&control_analysis,InversionIscontrolEnum); +- parameters->FindParam(&tao_analysis,InversionTaoEnum); +- +- if(nodakotacore)dakota_analysis=false; +- +- if(dakota_analysis){ +- #ifdef _HAVE_DAKOTA_ +- solutioncore=dakota_core; +- #else +- _error_("ISSM was not compiled with dakota support, cannot carry out dakota analysis!"); +- #endif ++ case DiagnosticSolutionEnum: ++ #ifdef _HAVE_DIAGNOSTIC_ ++ solutioncore=&diagnostic_core; ++ #else ++ _error_("ISSM was not compiled with diagnostic capabilities. Exiting"); ++ #endif ++ break; ++ case SteadystateSolutionEnum: ++ #ifdef _HAVE_STEADYSTATE_ ++ solutioncore=&steadystate_core; ++ #else ++ _error_("ISSM was not compiled with steady state capabilities. Exiting"); ++ #endif ++ break; ++ case ThermalSolutionEnum: ++ #ifdef _HAVE_THERMAL_ ++ solutioncore=&thermal_core; ++ #else ++ _error_("ISSM was not compiled with thermal capabilities. Exiting"); ++ #endif ++ break; ++ case EnthalpySolutionEnum: ++ #ifdef _HAVE_THERMAL_ ++ solutioncore=&enthalpy_core; ++ #else ++ _error_("ISSM was not compiled with thermal capabilities. Exiting"); ++ #endif ++ break; ++ case BalancethicknessSolutionEnum: ++ #ifdef _HAVE_BALANCED_ ++ solutioncore=&balancethickness_core; ++ #else ++ _error_("ISSM was not compiled with balanced capabilities. Exiting"); ++ #endif ++ break; ++ case HydrologySolutionEnum: ++ #ifdef _HAVE_HYDROLOGY_ ++ solutioncore=&hydrology_core; ++ #else ++ _error_("ISSM was not compiled with hydrology capabilities. Exiting"); ++ #endif ++ break; ++ case SurfaceSlopeSolutionEnum: ++ #ifdef _HAVE_SLOPE_ ++ solutioncore=&surfaceslope_core; ++ #else ++ _error_("ISSM was not compiled with slope capabilities. Exiting"); ++ #endif ++ break; ++ case BedSlopeSolutionEnum: ++ #ifdef _HAVE_SLOPE_ ++ solutioncore=&bedslope_core; ++ #else ++ _error_("ISSM was not compiled with slope capabilities. Exiting"); ++ #endif ++ break; ++ case TransientSolutionEnum: ++ #ifdef _HAVE_TRANSIENT_ ++ solutioncore=&transient_core; ++ #else ++ _error_("ISSM was not compiled with transient capabilities. Exiting"); ++ #endif ++ break; ++ case PrognosticSolutionEnum: ++ #ifdef _HAVE_PROGNOSTIC_ ++ solutioncore=&prognostic_core; ++ #else ++ _error_("ISSM was not compiled with prognostic capabilities. Exiting"); ++ #endif ++ break; ++ default: ++ _error_("solution type: " << EnumToStringx(solutiontype) << " not supported yet!"); ++ break; + } +- else if(control_analysis){ +- #ifdef _HAVE_CONTROL_ +- if(tao_analysis) solutioncore=controltao_core; +- else solutioncore=control_core; +- #else +- _error_("ISSM was not compiled with control support, cannot carry out control analysis!"); +- #endif +- } +- else PureCorePointerFromSolutionEnum(&solutioncore,parameters,solutiontype); /*This means we retrieve a core solution that is not a wrapper*/ + + /*Assign output pointer:*/ + _assert_(psolutioncore); +Index: ../trunk-jpl/src/c/solutions/AdjointCorePointerFromSolutionEnum.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/AdjointCorePointerFromSolutionEnum.cpp (revision 13854) ++++ ../trunk-jpl/src/c/solutions/AdjointCorePointerFromSolutionEnum.cpp (revision 13855) +@@ -1,4 +1,4 @@ +-/*!\file: CorePointerFromSolutionEnum.cpp ++/*!\file: AdjointCorePointerFromSolutionEnum.cpp + * \brief: return type of analyses, number of analyses and core solution function. + */ + +Index: ../trunk-jpl/src/c/solutions/WrapperCorePointerFromSolutionEnum.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/WrapperCorePointerFromSolutionEnum.cpp (revision 0) ++++ ../trunk-jpl/src/c/solutions/WrapperCorePointerFromSolutionEnum.cpp (revision 13855) +@@ -0,0 +1,60 @@ ++/*!\file: WrapperCorePointerFromSolutionEnum.cpp ++ * \brief: return type of analyses, number of analyses and core solution function. ++ */ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#include "../toolkits/toolkits.h" ++#include "../classes/objects/objects.h" ++#include "../shared/shared.h" ++#include "../EnumDefinitions/EnumDefinitions.h" ++#include "./solutions.h" ++#include "../modules/modules.h" ++#include "../include/include.h" ++#include "../solvers/solvers.h" ++ ++void WrapperCorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype,bool nodakotacore){ ++ ++ /*output: */ ++ void (*solutioncore)(FemModel*)=NULL; ++ ++ /*parameters: */ ++ bool control_analysis=false; ++ bool tao_analysis=false; ++ bool dakota_analysis=false; ++ ++ /* retrieve some parameters that tell us whether wrappers are allowed, or whether we return ++ * a pure core. Wrappers can be dakota_core (which samples many solution_cores) or control_core (which ++ * carries out adjoint based inversion on a certain core: */ ++ parameters->FindParam(&dakota_analysis,QmuIsdakotaEnum); ++ parameters->FindParam(&control_analysis,InversionIscontrolEnum); ++ parameters->FindParam(&tao_analysis,InversionTaoEnum); ++ ++ if(nodakotacore)dakota_analysis=false; ++ ++ if(dakota_analysis){ ++ #ifdef _HAVE_DAKOTA_ ++ solutioncore=dakota_core; ++ #else ++ _error_("ISSM was not compiled with dakota support, cannot carry out dakota analysis!"); ++ #endif ++ } ++ else if(control_analysis){ ++ #ifdef _HAVE_CONTROL_ ++ if(tao_analysis) solutioncore=controltao_core; ++ else solutioncore=control_core; ++ #else ++ _error_("ISSM was not compiled with control support, cannot carry out control analysis!"); ++ #endif ++ } ++ else CorePointerFromSolutionEnum(&solutioncore,parameters,solutiontype); /*This means we retrieve a core solution that is not a wrapper*/ ++ ++ /*Assign output pointer:*/ ++ _assert_(psolutioncore); ++ *psolutioncore=solutioncore; ++ ++} +Index: ../trunk-jpl/src/c/solutions/solutions.h +=================================================================== +--- ../trunk-jpl/src/c/solutions/solutions.h (revision 13854) ++++ ../trunk-jpl/src/c/solutions/solutions.h (revision 13855) +@@ -54,8 +54,8 @@ + + //solution configuration + void AnalysisConfiguration(int** panalyses,int* pnumanalyses, int solutiontype); +-void PureCorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype); +-void CorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype,bool nodakotacore=false); ++void CorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype); ++void WrapperCorePointerFromSolutionEnum(void (**psolutioncore)(FemModel*),Parameters* parameters,int solutiontype,bool nodakotacore=false); + void AdjointCorePointerFromSolutionEnum(void (**padjointcore)(FemModel*),int solutiontype); + + #endif +Index: ../trunk-jpl/src/c/solutions/DakotaSpawnCore.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/DakotaSpawnCore.cpp (revision 13854) ++++ ../trunk-jpl/src/c/solutions/DakotaSpawnCore.cpp (revision 13855) +@@ -75,7 +75,7 @@ + + /*Determine solution sequence: */ + if(VerboseQmu()) _pprintLine_("Starting " << EnumToStringx(solution_type) << " core:"); +- CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type,nodakotacore); ++ WrapperCorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type,nodakotacore); + + /*Run the core solution sequence: */ + solutioncore(femmodel); +Index: ../trunk-jpl/src/c/solutions/control_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/control_core.cpp (revision 13854) ++++ ../trunk-jpl/src/c/solutions/control_core.cpp (revision 13855) +@@ -61,7 +61,7 @@ + femmodel->parameters->SetParam(false,SaveResultsEnum); + + /*out of solution_type, figure out solution core and adjoint function pointer*/ +- PureCorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); ++ CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); + AdjointCorePointerFromSolutionEnum(&adjointcore,solution_type); + + /*Launch once a complete solution to set up all inputs*/ +Index: ../trunk-jpl/src/c/solutions/controltao_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/controltao_core.cpp (revision 13854) ++++ ../trunk-jpl/src/c/solutions/controltao_core.cpp (revision 13855) +@@ -93,11 +93,12 @@ + if(VerboseControl()) _pprintLine_(" preparing final solution"); + femmodel->parameters->SetParam(true,SaveResultsEnum); + void (*solutioncore)(FemModel*)=NULL; +- PureCorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); ++ CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); + solutioncore(femmodel); + + /*Clean up and return*/ + xDelete(control_list); ++ xDelete(user.J); + xdelete(&X); + TaoDestroy(&tao); + TaoFinalize(); +@@ -134,7 +135,7 @@ + /*Compute solution and adjoint*/ + void (*solutioncore)(FemModel*)=NULL; + void (*adjointcore)(FemModel*)=NULL; +- PureCorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); ++ CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); + AdjointCorePointerFromSolutionEnum(&adjointcore,solution_type); + solutioncore(femmodel); + adjointcore(femmodel); +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13854) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13855) +@@ -324,8 +324,8 @@ + ./solutions/ProcessArguments.cpp\ + ./solutions/ResetBoundaryConditions.cpp\ + ./solutions/AnalysisConfiguration.cpp\ ++ ./solutions/WrapperCorePointerFromSolutionEnum.cpp\ + ./solutions/CorePointerFromSolutionEnum.cpp\ +- ./solutions/PureCorePointerFromSolutionEnum.cpp\ + ./solutions/EnvironmentInit.cpp\ + ./solutions/EnvironmentFinalize.cpp\ + ./solutions/ad_core.cpp\ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13854) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13855) +@@ -303,7 +303,7 @@ + parameters->FindParam(&solution_type,SolutionTypeEnum); + + /*Figure out which solution core we are going to run with the current solution type: */ +- CorePointerFromSolutionEnum(&solutioncore,this->parameters,solution_type); ++ WrapperCorePointerFromSolutionEnum(&solutioncore,this->parameters,solution_type); + + /*run solutoin core: */ + profiler->Tag(StartCore); Index: /issm/oecreview/Archive/13393-13976/ISSM-13855-13856.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13855-13856.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13855-13856.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/m/classes/inversion.py +=================================================================== +--- ../trunk-jpl/src/m/classes/inversion.py (revision 13855) ++++ ../trunk-jpl/src/m/classes/inversion.py (revision 13856) +@@ -172,7 +172,7 @@ + + #process control parameters + num_control_parameters=len(self.control_parameters) +- data=numpy.array([StringToEnum(control_parameter)[0] for control_parameter in self.control_parameters]) ++ data=numpy.array([StringToEnum(control_parameter)[0] for control_parameter in self.control_parameters]).reshape(1,-1) + WriteData(fid,'data',data,'enum',InversionControlParametersEnum(),'format','DoubleMat','mattype',3) + WriteData(fid,'data',num_control_parameters,'enum',InversionNumControlParametersEnum(),'format','Integer') + Index: /issm/oecreview/Archive/13393-13976/ISSM-13856-13857.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13856-13857.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13856-13857.diff (revision 13980) @@ -0,0 +1,937 @@ +Index: ../trunk-jpl/src/m/mesh/bamg.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/bamg.py (revision 13856) ++++ ../trunk-jpl/src/m/mesh/bamg.py (revision 13857) +@@ -122,7 +122,7 @@ + + elif numpy.any(numpy.logical_not(flags)): + #We LOTS of work to do +- print("Rift tip outside of or on the domain has been detected and is being processed...") ++ print "Rift tip outside of or on the domain has been detected and is being processed..." + + #check that only one point is outside (for now) + if numpy.sum(numpy.logical_not(flags).astype(int))!=1: +@@ -165,7 +165,7 @@ + tipdis=numpy.array([sqrt((x-x3)**2+(y-y3)**2),sqrt((x-x4)**2+(y-y4)**2)]) + + if numpy.min(tipdis)/segdis < options.getfieldvalue('toltip',0): +- print("moving tip-domain intersection point") ++ print "moving tip-domain intersection point" + + #Get position of the closer point + if tipdis[0]>tipdis[1]: +@@ -349,7 +349,7 @@ + + raise RuntimeError("bamg.py/processgeometry is not complete.") + #Deal with edges +- print("Checking Edge crossing...") ++ print "Checking Edge crossing..." + i=0 + while (i1, %do not use ~isnan because there are some NaNs... +- %renumber first two columns +- pos=find(md2.mesh.edges(:,4)~=-1); +- md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1)); +- md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2)); +- md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3)); +- md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4)); +- %remove edges when the 2 vertices are not in the domain. +- md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:); +- %Replace all zeros by -1 in the last two columns; +- pos=find(md2.mesh.edges(:,3)==0); +- md2.mesh.edges(pos,3)=-1; +- pos=find(md2.mesh.edges(:,4)==0); +- md2.mesh.edges(pos,4)=-1; +- %Invert -1 on the third column with last column (Also invert first two columns!!) +- pos=find(md2.mesh.edges(:,3)==-1); +- md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4); +- md2.mesh.edges(pos,4)=-1; +- values=md2.mesh.edges(pos,2); +- md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1); +- md2.mesh.edges(pos,1)=values; +- %Finally remove edges that do not belong to any element +- pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1); +- md2.mesh.edges(pos,:)=[]; +- end ++ md2.mesh.numberofelements2d=numpy.size(pos_elem_2d) ++ md2.mesh.numberofvertices2d=numpy.size(pos_node_2d) ++ md2.mesh.elements2d=md1.mesh.elements2d[pos_elem_2d,:] ++ md2.mesh.elements2d[:,0]=Pnode[md2.mesh.elements2d[:,0].astype(int)-1] ++ md2.mesh.elements2d[:,1]=Pnode[md2.mesh.elements2d[:,1].astype(int)-1] ++ md2.mesh.elements2d[:,2]=Pnode[md2.mesh.elements2d[:,2].astype(int)-1] + +- %Penalties +- if ~isnan(md2.diagnostic.vertex_pairing), +- for i=1:size(md1.diagnostic.vertex_pairing,1); +- md2.diagnostic.vertex_pairing(i,:)=Pnode(md1.diagnostic.vertex_pairing(i,:)); +- end +- md2.diagnostic.vertex_pairing=md2.diagnostic.vertex_pairing(find(md2.diagnostic.vertex_pairing(:,1)),:); +- end +- if ~isnan(md2.prognostic.vertex_pairing), +- for i=1:size(md1.prognostic.vertex_pairing,1); +- md2.prognostic.vertex_pairing(i,:)=Pnode(md1.prognostic.vertex_pairing(i,:)); +- end +- md2.prognostic.vertex_pairing=md2.prognostic.vertex_pairing(find(md2.prognostic.vertex_pairing(:,1)),:); +- end ++ md2.mesh.x2d=md1.mesh.x[pos_node_2d] ++ md2.mesh.y2d=md1.mesh.y[pos_node_2d] + +- %recreate segments +- if md1.mesh.dimension==2 +- md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices); +- md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity); +- md2.mesh.segments=contourenvelope(md2); +- md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1; +- else +- %First do the connectivity for the contourenvelope in 2d +- md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d); +- md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity); +- md2.mesh.segments=contourenvelope(md2); +- md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1; +- md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1); +- %Then do it for 3d as usual +- md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices); +- md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity); +- end ++ #Edges ++ if len(numpy.shape(md2.mesh.edges))>1 and numpy.size(md2.mesh.edges,axis=1)>1: #do not use ~isnan because there are some NaNs... ++ #renumber first two columns ++ pos=numpy.nonzero(md2.mesh.edges[:,3]!=-1)[0] ++ md2.mesh.edges[: ,0]=Pnode[md2.mesh.edges[:,0].astype(int)-1] ++ md2.mesh.edges[: ,1]=Pnode[md2.mesh.edges[:,1].astype(int)-1] ++ md2.mesh.edges[: ,2]=Pelem[md2.mesh.edges[:,2].astype(int)-1] ++ md2.mesh.edges[pos,3]=Pelem[md2.mesh.edges[pos,3].astype(int)-1] ++ #remove edges when the 2 vertices are not in the domain. ++ md2.mesh.edges=md2.mesh.edges[numpy.nonzero(numpy.logical_and(md2.mesh.edges[:,0],md2.mesh.edges[:,1]))[0],:] ++ #Replace all zeros by -1 in the last two columns ++ pos=numpy.nonzero(md2.mesh.edges[:,2]==0)[0] ++ md2.mesh.edges[pos,2]=-1 ++ pos=numpy.nonzero(md2.mesh.edges[:,3]==0)[0] ++ md2.mesh.edges[pos,3]=-1 ++ #Invert -1 on the third column with last column (Also invert first two columns!!) ++ pos=numpy.nonzero(md2.mesh.edges[:,2]==-1)[0] ++ md2.mesh.edges[pos,2]=md2.mesh.edges[pos,3] ++ md2.mesh.edges[pos,3]=-1 ++ values=md2.mesh.edges[pos,1] ++ md2.mesh.edges[pos,1]=md2.mesh.edges[pos,0] ++ md2.mesh.edges[pos,0]=values ++ #Finally remove edges that do not belong to any element ++ pos=numpy.nonzero(numpy.logical_and(md2.mesh.edges[:,1]==-1,md2.mesh.edges[:,2]==-1))[0] ++ md2.mesh.edges=numpy.delete(md2.mesh.edges,pos,axis=0) + +- %Boundary conditions: Dirichlets on new boundary +- %Catch the elements that have not been extracted +- orphans_elem=find(~flag_elem); +- orphans_node=unique(md1.mesh.elements(orphans_elem,:))'; +- %Figure out which node are on the boundary between md2 and md1 +- nodestoflag1=intersect(orphans_node,pos_node); +- nodestoflag2=Pnode(nodestoflag1); +- if numel(md1.diagnostic.spcvx)>1 & numel(md1.diagnostic.spcvy)>2 & numel(md1.diagnostic.spcvz)>2, +- if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1 +- md2.diagnostic.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2); +- md2.diagnostic.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2); +- else +- md2.diagnostic.spcvx(nodestoflag2)=NaN; +- md2.diagnostic.spcvy(nodestoflag2)=NaN; +- disp(' ') +- disp('!! extract warning: spc values should be checked !!') +- disp(' ') +- end +- %put 0 for vz +- md2.diagnostic.spcvz(nodestoflag2)=0; +- end +- if ~isnan(md1.thermal.spctemperature), +- md2.thermal.spctemperature(nodestoflag2,1)=1; +- end ++ #Penalties ++ if numpy.any(numpy.logical_not(numpy.isnan(md2.diagnostic.vertex_pairing))): ++ for i in xrange(numpy.size(md1.diagnostic.vertex_pairing,axis=0)): ++ md2.diagnostic.vertex_pairing[i,:]=Pnode[md1.diagnostic.vertex_pairing[i,:]] ++ md2.diagnostic.vertex_pairing=md2.diagnostic.vertex_pairing[numpy.nonzero(md2.diagnostic.vertex_pairing[:,0])[0],:] ++ if numpy.any(numpy.logical_not(numpy.isnan(md2.prognostic.vertex_pairing))): ++ for i in xrange(numpy.size(md1.prognostic.vertex_pairing,axis=0)): ++ md2.prognostic.vertex_pairing[i,:]=Pnode[md1.prognostic.vertex_pairing[i,:]] ++ md2.prognostic.vertex_pairing=md2.prognostic.vertex_pairing[numpy.nonzero(md2.prognostic.vertex_pairing[:,0])[0],:] + +- %Diagnostic +- if ~isnan(md2.diagnostic.icefront) +- md2.diagnostic.icefront(:,1)=Pnode(md1.diagnostic.icefront(:,1)); +- md2.diagnostic.icefront(:,2)=Pnode(md1.diagnostic.icefront(:,2)); +- md2.diagnostic.icefront(:,end-1)=Pelem(md1.diagnostic.icefront(:,end-1)); +- if md1.mesh.dimension==3 +- md2.diagnostic.icefront(:,3)=Pnode(md1.diagnostic.icefront(:,3)); +- md2.diagnostic.icefront(:,4)=Pnode(md1.diagnostic.icefront(:,4)); +- end +- md2.diagnostic.icefront=md2.diagnostic.icefront(find(md2.diagnostic.icefront(:,1) & md2.diagnostic.icefront(:,2) & md2.diagnostic.icefront(:,end)),:); +- end ++ #recreate segments ++ if md1.mesh.dimension==2: ++ [md2.mesh.vertexconnectivity]=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices) ++ [md2.mesh.elementconnectivity]=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity) ++ md2.mesh.segments=contourenvelope(md2) ++ md2.mesh.vertexonboundary=numpy.zeros(numberofvertices2) ++ md2.mesh.vertexonboundary[md2.mesh.segments[:,0:2].astype(int)-1]=1 ++ else: ++ #First do the connectivity for the contourenvelope in 2d ++ [md2.mesh.vertexconnectivity]=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d) ++ [md2.mesh.elementconnectivity]=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity) ++ md2.mesh.segments=contourenvelope(md2) ++ md2.mesh.vertexonboundary=numpy.zeros(numberofvertices2/md2.mesh.numberoflayers) ++ md2.mesh.vertexonboundary[md2.mesh.segments[:,0:2].astype(int)-1]=1 ++ md2.mesh.vertexonboundary=numpy.tile(md2.mesh.vertexonboundary,md2.mesh.numberoflayers) ++ #Then do it for 3d as usual ++ [md2.mesh.vertexconnectivity]=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices) ++ [md2.mesh.elementconnectivity]=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity) + +- %Results fields +- if isstruct(md1.results), +- md2.results=struct(); +- solutionfields=fields(md1.results); +- for i=1:length(solutionfields), +- %get subfields +- solutionsubfields=fields(md1.results.(solutionfields{i})); +- for j=1:length(solutionsubfields), +- field=md1.results.(solutionfields{i}).(solutionsubfields{j}); +- if length(field)==numberofvertices1, +- md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node); +- elseif length(field)==numberofelements1, +- md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem); +- else +- md2.results.(solutionfields{i}).(solutionsubfields{j})=field; +- end +- end +- end +- end ++ #Boundary conditions: Dirichlets on new boundary ++ #Catch the elements that have not been extracted ++ orphans_elem=numpy.nonzero(numpy.logical_not(flag_elem))[0] ++ orphans_node=numpy.unique(md1.mesh.elements[orphans_elem,:]).astype(int)-1 ++ #Figure out which node are on the boundary between md2 and md1 ++ nodestoflag1=numpy.intersect1d(orphans_node,pos_node) ++ nodestoflag2=Pnode[nodestoflag1].astype(int)-1 ++ if numpy.size(md1.diagnostic.spcvx)>1 and numpy.size(md1.diagnostic.spcvy)>2 and numpy.size(md1.diagnostic.spcvz)>2: ++ if numpy.size(md1.inversion.vx_obs)>1 and numpy.size(md1.inversion.vy_obs)>1: ++ md2.diagnostic.spcvx[nodestoflag2]=md2.inversion.vx_obs[nodestoflag2] ++ md2.diagnostic.spcvy[nodestoflag2]=md2.inversion.vy_obs[nodestoflag2] ++ else: ++ md2.diagnostic.spcvx[nodestoflag2]=float('NaN') ++ md2.diagnostic.spcvy[nodestoflag2]=float('NaN') ++ print "\n!! extract warning: spc values should be checked !!\n\n" ++ #put 0 for vz ++ md2.diagnostic.spcvz[nodestoflag2]=0 ++ if numpy.any(numpy.logical_not(numpy.isnan(md1.thermal.spctemperature))): ++ md2.thermal.spctemperature[nodestoflag2,0]=1 + +- %Keep track of pos_node and pos_elem +- md2.mesh.extractedvertices=pos_node; +- md2.mesh.extractedelements=pos_elem; +- end % }}} +- """ ++ #Diagnostic ++ if numpy.any(numpy.logical_not(numpy.isnan(md2.diagnostic.icefront))): ++ md2.diagnostic.icefront[:,0]=Pnode[md1.diagnostic.icefront[:,0].astype(int)-1] ++ md2.diagnostic.icefront[:,1]=Pnode[md1.diagnostic.icefront[:,1].astype(int)-1] ++ md2.diagnostic.icefront[:,-2]=Pelem[md1.diagnostic.icefront[:,-2].astype(int)-1] ++ if md1.mesh.dimension==3: ++ md2.diagnostic.icefront[:,2]=Pnode[md1.diagnostic.icefront[:,2].astype(int)-1] ++ md2.diagnostic.icefront[:,3]=Pnode[md1.diagnostic.icefront[:,3].astype(int)-1] ++ md2.diagnostic.icefront=md2.diagnostic.icefront[numpy.nonzero(numpy.logical_and(numpy.logical_and(md2.diagnostic.icefront[:,0],md2.diagnostic.icefront[:,1]),md2.diagnostic.icefront[:,-1]))[0],:] + ++ #Results fields ++ if md1.results: ++ md2.results=OrderedDict() ++ for solutionfield in md1.results.iterkeys(): ++ #get time step ++ for i in m1.results[solutionfield].iterkeys(): ++ #get subfields ++ for solutionsubfield,field in m1.results[solutionfield][i].iteritems(): ++ if numpy.size(field)==numberofvertices1: ++ md2.results[solutionfield][i][solutionsubfield]=field[pos_node] ++ elif numpy.size(field)==numberofelements1: ++ md2.results[solutionfield][i][solutionsubfield]=field[pos_elem] ++ else: ++ md2.results[solutionfield][i][solutionsubfield]=field ++ ++ #Keep track of pos_node and pos_elem ++ md2.mesh.extractedvertices=pos_node.astype(float)+1 ++ md2.mesh.extractedelements=pos_elem.astype(float)+1 ++ ++ return md2 ++ # }}} ++ + def extrude(md,*args): # {{{ + """ + EXTRUDE - vertically extrude a 2d mesh +Index: ../trunk-jpl/src/m/classes/model/model.m +=================================================================== +--- ../trunk-jpl/src/m/classes/model/model.m (revision 13856) ++++ ../trunk-jpl/src/m/classes/model/model.m (revision 13857) +@@ -251,7 +251,6 @@ + % extract2d, add '~' to the name of the domain file (ex: '~Pattyn.exp'); + % an empty string '' will be considered as an empty domain + % a string 'all' will be considered as the entire domain +- % add an argument 0 if you do not want the elements to be checked (faster) + % + % Usage: + % md2=extract(md,area); +@@ -271,13 +270,6 @@ + error('extract error message: bad usage'); + end + +- %get check option +- if (nargin==3 & varargin{1}==0), +- checkoutline=0; +- else +- checkoutline=1; +- end +- + %get elements that are inside area + flag_elem=FlagElements(md1,area); + if ~any(flag_elem), +@@ -310,7 +302,7 @@ + Pnode=zeros(numberofvertices1,1); + Pnode(pos_node)=[1:numberofvertices2]'; + +- %renumber the elements (some node won't exist anymore) ++ %renumber the elements (some nodes won't exist anymore) + elements_1=md1.mesh.elements; + elements_2=elements_1(pos_elem,:); + elements_2(:,1)=Pnode(elements_2(:,1)); +@@ -322,9 +314,9 @@ + elements_2(:,6)=Pnode(elements_2(:,6)); + end + +- %OK, now create the new model ! ++ %OK, now create the new model! + +- %take every fields from model ++ %take every field from model + md2=md1; + + %automatically modify fields +@@ -346,7 +338,7 @@ + md2.(model_fields{i}).(object_fields{j})=field(pos_node,:); + elseif (fieldsize(1)==numberofvertices1+1) + md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)]; +- %size = number of elements * n ++ %size = number of elements * n + elseif fieldsize(1)==numberofelements1 + md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:); + end +@@ -357,7 +349,7 @@ + md2.(model_fields{i})=field(pos_node,:); + elseif (fieldsize(1)==numberofvertices1+1) + md2.(model_fields{i})=[field(pos_node,:); field(end,:)]; +- %size = number of elements * n ++ %size = number of elements * n + elseif fieldsize(1)==numberofelements1 + md2.(model_fields{i})=field(pos_elem,:); + end +@@ -412,13 +404,13 @@ + if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs... + %renumber first two columns + pos=find(md2.mesh.edges(:,4)~=-1); +- md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1)); +- md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2)); ++ md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1)); ++ md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2)); + md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3)); + md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4)); + %remove edges when the 2 vertices are not in the domain. + md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:); +- %Replace all zeros by -1 in the last two columns; ++ %Replace all zeros by -1 in the last two columns + pos=find(md2.mesh.edges(:,3)==0); + md2.mesh.edges(pos,3)=-1; + pos=find(md2.mesh.edges(:,4)==0); +Index: ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.py +=================================================================== +--- ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.py (revision 13856) ++++ ../trunk-jpl/src/m/boundaryconditions/SetMarineIceSheetBC.py (revision 13857) +@@ -37,7 +37,7 @@ + # pos=find(md.mesh.vertexonboundary & ~vertexonicefront); + pos=numpy.nonzero(numpy.logical_and(md.mesh.vertexonboundary,numpy.logical_not(vertexonicefront)))[0] + if not numpy.size(pos): +- print("SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet found. Dirichlet must be added manually.") ++ print "SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet found. Dirichlet must be added manually." + + md.diagnostic.spcvx=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) + md.diagnostic.spcvy=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) +@@ -49,11 +49,11 @@ + + #Dirichlet Values + if isinstance(md.inversion.vx_obs,numpy.ndarray) and numpy.size(md.inversion.vx_obs,axis=0)==md.mesh.numberofvertices and isinstance(md.inversion.vy_obs,numpy.ndarray) and numpy.size(md.inversion.vy_obs,axis=0)==md.mesh.numberofvertices: +- print(" boundary conditions for diagnostic model: spc set as observed velocities") ++ print " boundary conditions for diagnostic model: spc set as observed velocities" + md.diagnostic.spcvx[pos]=md.inversion.vx_obs[pos] + md.diagnostic.spcvy[pos]=md.inversion.vy_obs[pos] + else: +- print(" boundary conditions for diagnostic model: spc set as zero") ++ print " boundary conditions for diagnostic model: spc set as zero" + + md.hydrology.spcwatercolumn=numpy.zeros((md.mesh.numberofvertices,2)) + pos=numpy.nonzero(md.mesh.vertexonboundary)[0] +@@ -82,16 +82,16 @@ + #Create zeros basalforcings and surfaceforcings + if numpy.all(numpy.isnan(md.surfaceforcings.precipitation)) and (md.surfaceforcings.ispdd==1): + md.surfaceforcings.precipitation=numpy.zeros((md.mesh.numberofvertices,1)) +- print(" no surfaceforcings.precipitation specified: values set as zero") ++ print " no surfaceforcings.precipitation specified: values set as zero" + if numpy.all(numpy.isnan(md.surfaceforcings.mass_balance)) and (md.surfaceforcings.ispdd==0): + md.surfaceforcings.mass_balance=numpy.zeros((md.mesh.numberofvertices,1)) +- print(" no surfaceforcings.mass_balance specified: values set as zero") ++ print " no surfaceforcings.mass_balance specified: values set as zero" + if numpy.all(numpy.isnan(md.basalforcings.melting_rate)): + md.basalforcings.melting_rate=numpy.zeros((md.mesh.numberofvertices,1)) +- print(" no basalforcings.melting_rate specified: values set as zero") ++ print " no basalforcings.melting_rate specified: values set as zero" + if numpy.all(numpy.isnan(md.balancethickness.thickening_rate)): + md.balancethickness.thickening_rate=numpy.zeros((md.mesh.numberofvertices,1)) +- print(" no balancethickness.thickening_rate specified: values set as zero") ++ print " no balancethickness.thickening_rate specified: values set as zero" + + md.prognostic.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) + md.balancethickness.spcthickness=float('nan')*numpy.ones((md.mesh.numberofvertices,1)) +@@ -103,9 +103,9 @@ + md.thermal.spctemperature[pos]=md.initialization.temperature[pos] #impose observed temperature on surface + if not isinstance(md.basalforcings.geothermalflux,numpy.ndarray) or not numpy.size(md.basalforcings.geothermalflux,axis=0)==md.mesh.numberofvertices: + md.basalforcings.geothermalflux=numpy.zeros((md.mesh.numberofvertices,1)) +- md.basalforcings.geothermalflux[numpy.nonzero(md.mask.vertexongroundedice)]=50.*10.**-3; #50mW/m2 ++ md.basalforcings.geothermalflux[numpy.nonzero(md.mask.vertexongroundedice)]=50.*10.**-3 #50mW/m2 + else: +- print(" no thermal boundary conditions created: no observed temperature found"); ++ print " no thermal boundary conditions created: no observed temperature found" + + return md + +Index: ../trunk-jpl/src/m/parameterization/contourenvelope.m +=================================================================== +--- ../trunk-jpl/src/m/parameterization/contourenvelope.m (revision 13856) ++++ ../trunk-jpl/src/m/parameterization/contourenvelope.m (revision 13857) +@@ -19,7 +19,6 @@ + + if ischar(flags), + file=flags; +- file=varargin{1}; + if ~exist(file), + error(['contourenvelope error message: file ' file ' not found']); + end +@@ -28,7 +27,7 @@ + %do nothing for now + isfile=0; + else +- error('contourenvelope error message: second argument should a file or an elements flag'); ++ error('contourenvelope error message: second argument should be a file or an elements flag'); + end + end + +@@ -69,10 +68,10 @@ + mesh.elementconnectivity(find(ismember(mesh.elementconnectivity,elemout)))=0; + else + %get flag list of elements and nodes inside the contour +- nodein=zeros(mesh.numberofvertices,1); +- elemin=zeros(mesh.numberofelements,1); ++ nodein=zeros(mesh.numberofvertices,1); ++ elemin=zeros(mesh.numberofelements,1); + +- pos=find(flags); ++ pos=find(flags); + elemin(pos)=1; + nodein(mesh.elements(pos,:))=1; + +@@ -94,7 +93,7 @@ + %Find segments on boundary + pos=find(elementonboundary); + num_segments=length(pos); +-segments=zeros(num_segments,3); ++segments=zeros(num_segments*3,3); + count=1; + + for i=1:num_segments, +@@ -137,3 +136,5 @@ + end + end + end ++segments=segments(1:count-1,:); ++ +Index: ../trunk-jpl/src/m/parameterization/contourenvelope.py +=================================================================== +--- ../trunk-jpl/src/m/parameterization/contourenvelope.py (revision 0) ++++ ../trunk-jpl/src/m/parameterization/contourenvelope.py (revision 13857) +@@ -0,0 +1,134 @@ ++import os.path ++import numpy ++import copy ++from NodeConnectivity import * ++from ElementConnectivity import * ++from mesh import * ++ ++def contourenvelope(md,*args): ++ """ ++ CONTOURENVELOPE - build a set of segments enveloping a contour .exp ++ ++ Usage: ++ segments=contourenvelope(md,varargin) ++ ++ Example: ++ segments=contourenvelope(md,'Stream.exp'); ++ segments=contourenvelope(md,md.mask.elementonfloatingice) ++ segments=contourenvelope(md); ++ """ ++ ++ #some checks ++ if len(args)>1: ++ raise RuntimeError("contourenvelope error message: bad usage") ++ ++ if len(args)==1: ++ flags=args[0] ++ ++ if isinstance(flags,(str,unicode)): ++ file=flags ++ if not os.path.exists(file): ++ raise IOError("contourenvelope error message: file '%s' not found" % file) ++ isfile=1 ++ elif isinstance(flags,(bool,int,long,float)): ++ #do nothing for now ++ isfile=0 ++ else: ++ raise TypeError("contourenvelope error message: second argument should be a file or an elements flag") ++ ++ #Now, build the connectivity tables for this mesh. ++ #Computing connectivity ++ if numpy.size(md.mesh.vertexconnectivity,axis=0)!=md.mesh.numberofvertices and numpy.size(md.mesh.vertexconnectivity,axis=0)!=md.mesh.numberofvertices2d: ++ [md.mesh.vertexconnectivity]=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices) ++ if numpy.size(md.mesh.elementconnectivity,axis=0)!=md.mesh.numberofelements and numpy.size(md.mesh.elementconnectivity,axis=0)!=md.mesh.numberofelements2d: ++ [md.mesh.elementconnectivity]=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity) ++ ++ #get nodes inside profile ++ mesh.elementconnectivity=copy.deepcopy(md.mesh.elementconnectivity) ++ if md.mesh.dimension==2: ++ mesh.elements=copy.deepcopy(md.mesh.elements) ++ mesh.x=copy.deepcopy(md.mesh.x) ++ mesh.y=copy.deepcopy(md.mesh.y) ++ mesh.numberofvertices=copy.deepcopy(md.mesh.numberofvertices) ++ mesh.numberofelements=copy.deepcopy(md.mesh.numberofelements) ++ else: ++ mesh.elements=copy.deepcopy(md.mesh.elements2d) ++ mesh.x=copy.deepcopy(md.mesh.x2d) ++ mesh.y=copy.deepcopy(md.mesh.y2d) ++ mesh.numberofvertices=copy.deepcopy(md.mesh.numberofvertices2d) ++ mesh.numberofelements=copy.deepcopy(md.mesh.numberofelements2d) ++ ++ if len(args)==1: ++ ++ if isfile: ++ #get flag list of elements and nodes inside the contour ++ nodein=ContourToMesh(mesh.elements,mesh.x,mesh.y,file,'node',1) ++ elemin=(numpy.sum(nodein(mesh.elements),axis=1)==numpy.size(mesh.elements,axis=1)) ++ #modify element connectivity ++ elemout=numpy.nonzero(numpy.logical_not(elemin))[0] ++ mesh.elementconnectivity[elemout,:]=0 ++ mesh.elementconnectivity[numpy.nonzero(ismember(mesh.elementconnectivity,elemout+1))]=0 ++ else: ++ #get flag list of elements and nodes inside the contour ++ nodein=numpy.zeros(mesh.numberofvertices) ++ elemin=numpy.zeros(mesh.numberofelements) ++ ++ pos=numpy.nonzero(flags) ++ elemin[pos]=1 ++ nodein[mesh.elements[pos,:].astype(int)-1]=1 ++ ++ #modify element connectivity ++ elemout=numpy.nonzero(numpy.logical_not(elemin))[0] ++ mesh.elementconnectivity[elemout,:]=0 ++ mesh.elementconnectivity[numpy.nonzero(ismember(mesh.elementconnectivity,elemout+1))]=0 ++ ++ #Find element on boundary ++ #First: find elements on the boundary of the domain ++ flag=copy.deepcopy(mesh.elementconnectivity) ++ if len(args)==1: ++ flag[numpy.nonzero(flag)]=elemin[flag[numpy.nonzero(flag)]] ++ elementonboundary=numpy.logical_and(numpy.prod(flag,axis=1)==0,numpy.sum(flag,axis=1)>0).astype(float) ++ ++ #Find segments on boundary ++ pos=numpy.nonzero(elementonboundary)[0] ++ num_segments=numpy.size(pos) ++ segments=numpy.zeros((num_segments*3,3)) ++ count=0 ++ ++ for el1 in pos: ++ els2=mesh.elementconnectivity[el1,numpy.nonzero(mesh.elementconnectivity[el1,:])[0]].astype(int)-1 ++ if numpy.size(els2)>1: ++ flag=numpy.intersect1d(mesh.elements[els2[0],:],mesh.elements[els2[1],:]) ++ nods1=mesh.elements[el1,:] ++ nods1=numpy.delete(nods1,numpy.nonzero(nods1==flag)) ++ segments[count,:]=[nods1[0],nods1[1],el1+1] ++ ++ ord1=numpy.nonzero(nods1[0]==mesh.elements[el1,:])[0][0] ++ ord2=numpy.nonzero(nods1[1]==mesh.elements[el1,:])[0][0] ++ ++ #swap segment nodes if necessary ++ if ( (ord1==0 and ord2==1) or (ord1==1 and ord2==2) or (ord1==2 and ord2==0) ): ++ temp=segments[count,0] ++ segments[count,0]=segments[count,1] ++ segments[count,1]=temp ++ segments[count,0:2]=numpy.flipud(segments[count,0:2]) ++ count+=1 ++ else: ++ nods1=mesh.elements[el1,:] ++ flag=numpy.setdiff1d(nods1,mesh.elements[els2,:]) ++ for j in xrange(0,3): ++ nods=numpy.delete(nods1,j) ++ if numpy.any(ismember(flag,nods)): ++ segments[count,:]=[nods[0],nods[1],el1+1] ++ ord1=numpy.nonzero(nods[0]==mesh.elements[el1,:])[0][0] ++ ord2=numpy.nonzero(nods[1]==mesh.elements[el1,:])[0][0] ++ if ( (ord1==0 and ord2==1) or (ord1==1 and ord2==2) or (ord1==2 and ord2==0) ): ++ temp=segments[count,0] ++ segments[count,0]=segments[count,1] ++ segments[count,1]=temp ++ segments[count,0:2]=numpy.flipud(segments[count,0:2]) ++ count+=1 ++ segments=segments[0:count,:] ++ ++ return segments ++ Index: /issm/oecreview/Archive/13393-13976/ISSM-13857-13858.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13857-13858.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13857-13858.diff (revision 13980) @@ -0,0 +1,167 @@ +Index: ../trunk-jpl/test/NightlyRun/test511.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test511.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test511.py (revision 13858) +@@ -0,0 +1,50 @@ ++import numpy ++from model import * ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from EnumDefinitions import * ++from solve import * ++from MatlabFuncs import * ++ ++md=triangle(model(),'../Exp/Pig.exp',10000.) ++md=setmask(md,'../Exp/PigShelves.exp','../Exp/PigIslands.exp') ++md=parameterize(md,'../Par/Pig.py') ++ ++#impose hydrostatic equilibrium (required by Stokes) ++md.geometry.bed=-md.materials.rho_ice/md.materials.rho_water*md.geometry.thickness ++md.geometry.surface=md.geometry.bed+md.geometry.thickness ++md.extrude(3,1.) ++md=setflowequation(md,'stokes','all') ++md=md.extract(md.mask.elementonfloatingice) ++ ++#control parameters ++md.inversion.iscontrol=1 ++md.inversion.control_parameters=['MaterialsRheologyBbar'] ++md.inversion.min_parameters=10.**6*numpy.ones((md.mesh.numberofvertices,1)) ++md.inversion.max_parameters=2.*10**9*numpy.ones((md.mesh.numberofvertices,1)) ++md.inversion.nsteps=2 ++md.inversion.cost_functions=101*numpy.ones((md.inversion.nsteps,1)) ++md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,1)) ++md.inversion.gradient_scaling=10.**8*numpy.ones((md.inversion.nsteps,1)) ++md.inversion.maxiter_per_step=2.*numpy.ones((md.inversion.nsteps,1)) ++md.inversion.step_threshold=0.99*numpy.ones((md.inversion.nsteps,1)) ++md.inversion.vx_obs=md.initialization.vx ++md.inversion.vy_obs=md.initialization.vy ++ ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,DiagnosticSolutionEnum()) ++ ++#Fields and tolerances to track changes ++field_names =['Gradient','Misfits','MaterialsRheologyB','Pressure','Vel','Vx','Vy'] ++field_tolerances=[1e-11,1e-12,1e-12,1e-09,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12] ++field_values=[\ ++ md.results['DiagnosticSolution'][1]['Gradient1'],\ ++ md.results['DiagnosticSolution'][1]['J'],\ ++ md.results['DiagnosticSolution'][1]['MaterialsRheologyB'],\ ++ md.results['DiagnosticSolution'][1]['Pressure'],\ ++ md.results['DiagnosticSolution'][1]['Vel'],\ ++ md.results['DiagnosticSolution'][1]['Vx'],\ ++ md.results['DiagnosticSolution'][1]['Vy'],\ ++] +Index: ../trunk-jpl/test/NightlyRun/python_test_guidelines.txt +=================================================================== +--- ../trunk-jpl/test/NightlyRun/python_test_guidelines.txt (revision 13857) ++++ ../trunk-jpl/test/NightlyRun/python_test_guidelines.txt (revision 13858) +@@ -7,4 +7,6 @@ + - Be careful with vectors vs. column arrays (unfortunately Matlab does not distinguish). Documentation (like in the class def) showing whether more than one column is possible is very helpful. + - Be careful with variable names that might be reserved words in other languages (e.g. "list"). + - Weird shortcuts for a particular language are not very general. ++- Since some languages are base 0 and some are base 1, it would be nice to name variables to clearly delineate which are indices and which are ID's (e.g., indices into node/element arrays vs. node/element ID's). ++- Checks like isnan(array) may be ambiguous, depending on the language, so use "any" or "all" to clarify. (Matlab seems to default to "all", though it may depend on context.) + +Index: ../trunk-jpl/test/NightlyRun/test511.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test511.m (revision 13857) ++++ ../trunk-jpl/test/NightlyRun/test511.m (revision 13858) +@@ -30,7 +30,7 @@ + field_tolerances={1e-11,1e-12,1e-12,1e-09,1e-12,1e-12,1e-12,1e-12,1e-12,1e-12}; + field_values={... + (md.results.DiagnosticSolution.Gradient1),... +- md.results.DiagnosticSolution.J,... ++ (md.results.DiagnosticSolution.J),... + (md.results.DiagnosticSolution.MaterialsRheologyB),... + (md.results.DiagnosticSolution.Pressure),... + (md.results.DiagnosticSolution.Vel),... +Index: ../trunk-jpl/test/NightlyRun/python_skipped_tests.txt +=================================================================== +--- ../trunk-jpl/test/NightlyRun/python_skipped_tests.txt (revision 13857) ++++ ../trunk-jpl/test/NightlyRun/python_skipped_tests.txt (revision 13858) +@@ -10,5 +10,3 @@ + test417 needs Dakota + test418 needs Dakota + test420 needs Dakota +-test511 needs extract +-test613 needs extract +Index: ../trunk-jpl/test/NightlyRun/test613.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test613.py (revision 0) ++++ ../trunk-jpl/test/NightlyRun/test613.py (revision 13858) +@@ -0,0 +1,52 @@ ++import numpy ++import copy ++from model import * ++from triangle import * ++from meshconvert import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from EnumDefinitions import * ++from solve import * ++from MatlabFuncs import * ++ ++md=triangle(model(),'../Exp/79North.exp',10000.) ++md=meshconvert(md) ++md=setmask(md,'../Exp/79NorthShelf.exp','') ++md=parameterize(md,'../Par/79North.py') ++md=setflowequation(md,'macayeal','all') ++ ++#Ice sheet only ++md=md.extract(md.mask.elementongroundedice) ++pos=numpy.nonzero(md.mesh.vertexonboundary) ++md.balancethickness.spcthickness[pos]=md.geometry.thickness[pos] ++ ++#control parameters ++md.inversion.thickness_obs=copy.deepcopy(md.geometry.thickness) ++md.inversion.iscontrol=1 ++md.inversion.nsteps=2 ++md.inversion.control_parameters=['Vx','Vy'] ++md.balancethickness.stabilization=1 ++md.inversion.gradient_scaling=numpy.hstack((10./md.constants.yts*numpy.ones((md.inversion.nsteps,1)),10./md.constants.yts*numpy.ones((md.inversion.nsteps,1)))) ++md.inversion.min_parameters=numpy.hstack((-2000.*numpy.ones((md.mesh.numberofvertices,1)),-2000.*numpy.ones((md.mesh.numberofvertices,1)))) ++md.inversion.max_parameters=numpy.hstack((+2000.*numpy.ones((md.mesh.numberofvertices,1)),+2000.*numpy.ones((md.mesh.numberofvertices,1)))) ++md.inversion.cost_functions=201*numpy.ones((md.inversion.nsteps,1)) ++md.inversion.cost_functions_coefficients=numpy.ones((md.mesh.numberofvertices,1)) ++md.inversion.maxiter_per_step=4*numpy.ones((md.inversion.nsteps,1)) ++md.inversion.step_threshold=0.99*numpy.ones((md.inversion.nsteps,1)) ++ ++md.verbose.control=1 ++md.cluster=generic('name',oshostname(),'np',3) ++md=solve(md,BalancethicknessSolutionEnum()) ++ ++#Fields and tolerances to track changes ++field_names =['Gradient1','Gradient2','Misfits','Vx','Vy','Thickness'] ++field_tolerances=[1e-12,1e-12,1e-12,1e-12,1e-12,1e-12] ++field_values=[\ ++ md.results['BalancethicknessSolution'][1]['Gradient1'],\ ++ md.results['BalancethicknessSolution'][1]['Gradient2'],\ ++ md.results['BalancethicknessSolution'][1]['J'],\ ++ md.results['BalancethicknessSolution'][1]['Vx'],\ ++ md.results['BalancethicknessSolution'][1]['Vy'],\ ++ md.results['BalancethicknessSolution'][1]['Thickness'],\ ++] +Index: ../trunk-jpl/test/NightlyRun/test613.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test613.m (revision 13857) ++++ ../trunk-jpl/test/NightlyRun/test613.m (revision 13858) +@@ -12,7 +12,6 @@ + %control parameters + md.inversion.thickness_obs=md.geometry.thickness; + md.inversion.iscontrol=1; +-md.inversion.thickness_obs=md.geometry.thickness; + md.inversion.nsteps=2; + md.inversion.control_parameters={'Vx','Vy'}; + md.balancethickness.stabilization=1; +@@ -34,7 +33,7 @@ + field_values={... + (md.results.BalancethicknessSolution.Gradient1),... + (md.results.BalancethicknessSolution.Gradient2),... +- md.results.BalancethicknessSolution.J,... ++ (md.results.BalancethicknessSolution.J),... + (md.results.BalancethicknessSolution.Vx),... + (md.results.BalancethicknessSolution.Vy),... + (md.results.BalancethicknessSolution.Thickness) Index: /issm/oecreview/Archive/13393-13976/ISSM-13858-13859.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13858-13859.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13858-13859.diff (revision 13980) @@ -0,0 +1,352 @@ +Index: ../trunk-jpl/src/m/miscellaneous/BinRead.py +=================================================================== +--- ../trunk-jpl/src/m/miscellaneous/BinRead.py (revision 13858) ++++ ../trunk-jpl/src/m/miscellaneous/BinRead.py (revision 13859) +@@ -1,168 +0,0 @@ +-#! /usr/bin/env python +- +-import os +-import sys +-import numpy +-import math +-import struct +- +-def BinRead(filin,filout=''): +- +- from MatlabFuncs import * +- from EnumDefinitions import * +- from EnumToString import EnumToString +- +- print "reading binary file." +- f=open(filin,'rb') +- +- if filout: +- sys.stdout=open(filout,'w') +- +- while True: +- try: +- #Step 1: read the enum to identify this record uniquely +- enum=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- except struct.error as e: +- print "probable EOF: %s" % e +- break +- print "\nenum = %d (%s)" % (enum,EnumToString(enum)[0]) +- +- #Step 2: read the data itself. +- #first read length of record +- reclen=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- print "reclen = %d" % reclen +- +- #read data code: +- code=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- print "code = %d" % code +- +- if code == FormatToCode('Boolean'): +-# bval=struct.unpack('b',f.read(reclen-struct.calcsize('i')))[0] +- bval=struct.unpack('i',f.read(reclen-struct.calcsize('i')))[0] +- print "bval = %d" % bval +- +- elif code == FormatToCode('Integer'): +- ival=struct.unpack('i',f.read(reclen-struct.calcsize('i')))[0] +- print "ival = %d" % ival +- +- elif code == FormatToCode('Double'): +- dval=struct.unpack('d',f.read(reclen-struct.calcsize('i')))[0] +- print "dval = %f" % dval +- +- elif code == FormatToCode('String'): +- strlen=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- print "strlen = %d" % strlen +- sval=struct.unpack('%ds' % strlen,f.read(strlen))[0] +- print "sval = '%s'" % sval +- +- elif code == FormatToCode('BooleanMat'): +- #read matrix type: +- mattype=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- print "mattype = %d" % mattype +- +- #now read matrix +- s=[0,0] +- s[0]=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- s[1]=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- print "s = [%dx%d]" % (s[0],s[1]) +- data=numpy.zeros((s[0],s[1])) +- for i in xrange(s[0]): +- for j in xrange(s[1]): +- data[i][j]=struct.unpack('d',f.read(struct.calcsize('d')))[0] #get to the "c" convention, hence the transpose +- print "data[%d,%d] = %f" % (i,j,data[i][j]) +- +- elif code == FormatToCode('IntMat'): +- #read matrix type: +- mattype=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- print "mattype = %d" % mattype +- +- #now read matrix +- s=[0,0] +- s[0]=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- s[1]=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- print "s = [%dx%d]" % (s[0],s[1]) +- data=numpy.zeros((s[0],s[1])) +- for i in xrange(s[0]): +- for j in xrange(s[1]): +- data[i][j]=struct.unpack('d',f.read(struct.calcsize('d')))[0] #get to the "c" convention, hence the transpose +- print "data[%d,%d] = %f" % (i,j,data[i][j]) +- +- elif code == FormatToCode('DoubleMat'): +- #read matrix type: +- mattype=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- print "mattype = %d" % mattype +- +- #now read matrix +- s=[0,0] +- s[0]=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- s[1]=struct.unpack('i',f.read(struct.calcsize('i')))[0] +- print "s = [%dx%d]" % (s[0],s[1]) +- data=numpy.zeros((s[0],s[1])) +- for i in xrange(s[0]): +- for j in xrange(s[1]): +- data[i][j]=struct.unpack('d',f.read(struct.calcsize('d')))[0] #get to the "c" convention, hence the transpose +- print "data[%d,%d] = %f" % (i,j,data[i][j]) +- +- elif code == FormatToCode('MatArray'): +- fid.seek(reclen-4,1) +- print "skipping %d bytes for code %d." % (code, reclen-4) +- +- elif code == FormatToCode('StringArray'): +- fid.seek(reclen-4,1) +- print "skipping %d bytes for code %d." % (code, reclen-4) +- +- else: +- raise TypeError('BinRead error message: data type: %d not supported yet! (%s)' % (code,EnumToString(enum)[0])) +- +- f.close() +- +-def FormatToCode(format): # {{{ +- """ +- This routine takes the format string, and hardcodes it into an integer, which +- is passed along the record, in order to identify the nature of the dataset being +- sent. +- """ +- +- if strcmpi(format,'Boolean'): +- code=1 +- elif strcmpi(format,'Integer'): +- code=2 +- elif strcmpi(format,'Double'): +- code=3 +- elif strcmpi(format,'String'): +- code=4 +- elif strcmpi(format,'BooleanMat'): +- code=5 +- elif strcmpi(format,'IntMat'): +- code=6 +- elif strcmpi(format,'DoubleMat'): +- code=7 +- elif strcmpi(format,'MatArray'): +- code=8 +- elif strcmpi(format,'StringArray'): +- code=9 +- else: +- raise InputError('FormatToCode error message: data type not supported yet!') +- +- return code +-# }}} +- +-if __name__ == '__main__': +- if 'PYTHONSTARTUP' in os.environ: +- PYTHONSTARTUP=os.environ['PYTHONSTARTUP'] +- print 'PYTHONSTARTUP =',PYTHONSTARTUP +- if os.path.exists(PYTHONSTARTUP): +- try: +- execfile(PYTHONSTARTUP) +- except Exception as e: +- print "PYTHONSTARTUP error: ",e +- else: +- print "PYTHONSTARTUP file '%s' does not exist." % PYTHONSTARTUP +- +- import argparse +- parser = argparse.ArgumentParser(description='BinRead - function to read binary input file.') +- parser.add_argument('-f','--filin', help='name of binary input file', default='') +- args = parser.parse_args() +- +- BinRead(args.filin) +- +Index: ../trunk-jpl/scripts/BinRead.py +=================================================================== +--- ../trunk-jpl/scripts/BinRead.py (revision 0) ++++ ../trunk-jpl/scripts/BinRead.py (revision 13859) +@@ -0,0 +1,168 @@ ++#! /usr/bin/env python ++ ++import os ++import sys ++import numpy ++import math ++import struct ++ ++def BinRead(filin,filout=''): ++ ++ from MatlabFuncs import * ++ from EnumDefinitions import * ++ from EnumToString import EnumToString ++ ++ print "reading binary file." ++ f=open(filin,'rb') ++ ++ if filout: ++ sys.stdout=open(filout,'w') ++ ++ while True: ++ try: ++ #Step 1: read the enum to identify this record uniquely ++ enum=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ except struct.error as e: ++ print "probable EOF: %s" % e ++ break ++ print "\nenum = %d (%s)" % (enum,EnumToString(enum)[0]) ++ ++ #Step 2: read the data itself. ++ #first read length of record ++ reclen=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ print "reclen = %d" % reclen ++ ++ #read data code: ++ code=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ print "code = %d" % code ++ ++ if code == FormatToCode('Boolean'): ++# bval=struct.unpack('b',f.read(reclen-struct.calcsize('i')))[0] ++ bval=struct.unpack('i',f.read(reclen-struct.calcsize('i')))[0] ++ print "bval = %d" % bval ++ ++ elif code == FormatToCode('Integer'): ++ ival=struct.unpack('i',f.read(reclen-struct.calcsize('i')))[0] ++ print "ival = %d" % ival ++ ++ elif code == FormatToCode('Double'): ++ dval=struct.unpack('d',f.read(reclen-struct.calcsize('i')))[0] ++ print "dval = %f" % dval ++ ++ elif code == FormatToCode('String'): ++ strlen=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ print "strlen = %d" % strlen ++ sval=struct.unpack('%ds' % strlen,f.read(strlen))[0] ++ print "sval = '%s'" % sval ++ ++ elif code == FormatToCode('BooleanMat'): ++ #read matrix type: ++ mattype=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ print "mattype = %d" % mattype ++ ++ #now read matrix ++ s=[0,0] ++ s[0]=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ s[1]=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ print "s = [%dx%d]" % (s[0],s[1]) ++ data=numpy.zeros((s[0],s[1])) ++ for i in xrange(s[0]): ++ for j in xrange(s[1]): ++ data[i][j]=struct.unpack('d',f.read(struct.calcsize('d')))[0] #get to the "c" convention, hence the transpose ++ print "data[%d,%d] = %f" % (i,j,data[i][j]) ++ ++ elif code == FormatToCode('IntMat'): ++ #read matrix type: ++ mattype=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ print "mattype = %d" % mattype ++ ++ #now read matrix ++ s=[0,0] ++ s[0]=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ s[1]=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ print "s = [%dx%d]" % (s[0],s[1]) ++ data=numpy.zeros((s[0],s[1])) ++ for i in xrange(s[0]): ++ for j in xrange(s[1]): ++ data[i][j]=struct.unpack('d',f.read(struct.calcsize('d')))[0] #get to the "c" convention, hence the transpose ++ print "data[%d,%d] = %f" % (i,j,data[i][j]) ++ ++ elif code == FormatToCode('DoubleMat'): ++ #read matrix type: ++ mattype=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ print "mattype = %d" % mattype ++ ++ #now read matrix ++ s=[0,0] ++ s[0]=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ s[1]=struct.unpack('i',f.read(struct.calcsize('i')))[0] ++ print "s = [%dx%d]" % (s[0],s[1]) ++ data=numpy.zeros((s[0],s[1])) ++ for i in xrange(s[0]): ++ for j in xrange(s[1]): ++ data[i][j]=struct.unpack('d',f.read(struct.calcsize('d')))[0] #get to the "c" convention, hence the transpose ++ print "data[%d,%d] = %f" % (i,j,data[i][j]) ++ ++ elif code == FormatToCode('MatArray'): ++ fid.seek(reclen-4,1) ++ print "skipping %d bytes for code %d." % (code, reclen-4) ++ ++ elif code == FormatToCode('StringArray'): ++ fid.seek(reclen-4,1) ++ print "skipping %d bytes for code %d." % (code, reclen-4) ++ ++ else: ++ raise TypeError('BinRead error message: data type: %d not supported yet! (%s)' % (code,EnumToString(enum)[0])) ++ ++ f.close() ++ ++def FormatToCode(format): # {{{ ++ """ ++ This routine takes the format string, and hardcodes it into an integer, which ++ is passed along the record, in order to identify the nature of the dataset being ++ sent. ++ """ ++ ++ if strcmpi(format,'Boolean'): ++ code=1 ++ elif strcmpi(format,'Integer'): ++ code=2 ++ elif strcmpi(format,'Double'): ++ code=3 ++ elif strcmpi(format,'String'): ++ code=4 ++ elif strcmpi(format,'BooleanMat'): ++ code=5 ++ elif strcmpi(format,'IntMat'): ++ code=6 ++ elif strcmpi(format,'DoubleMat'): ++ code=7 ++ elif strcmpi(format,'MatArray'): ++ code=8 ++ elif strcmpi(format,'StringArray'): ++ code=9 ++ else: ++ raise InputError('FormatToCode error message: data type not supported yet!') ++ ++ return code ++# }}} ++ ++if __name__ == '__main__': ++ if 'PYTHONSTARTUP' in os.environ: ++ PYTHONSTARTUP=os.environ['PYTHONSTARTUP'] ++ print 'PYTHONSTARTUP =',PYTHONSTARTUP ++ if os.path.exists(PYTHONSTARTUP): ++ try: ++ execfile(PYTHONSTARTUP) ++ except Exception as e: ++ print "PYTHONSTARTUP error: ",e ++ else: ++ print "PYTHONSTARTUP file '%s' does not exist." % PYTHONSTARTUP ++ ++ import argparse ++ parser = argparse.ArgumentParser(description='BinRead - function to read binary input file.') ++ parser.add_argument('-f','--filin', help='name of binary input file', default='') ++ args = parser.parse_args() ++ ++ BinRead(args.filin) ++ + +Property changes on: ../trunk-jpl/scripts/BinRead.py +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* Index: /issm/oecreview/Archive/13393-13976/ISSM-13859-13860.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13859-13860.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13859-13860.diff (revision 13980) @@ -0,0 +1,110 @@ +Index: ../trunk-jpl/src/c/classes/objects/Elements/Element.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Element.h (revision 13859) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Element.h (revision 13860) +@@ -28,6 +28,7 @@ + + virtual void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters)=0; + virtual void SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters)=0; ++ virtual void SetwiseNodeConnectivity(int* d_nz,int* o_nz,Node* node,bool* flags,int set1_enum,int set2_enum)=0; + virtual void CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df)=0; + virtual void CreatePVector(Vector* pf)=0; + virtual void CreateJacobianMatrix(Matrix* Jff)=0; +Index: ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13859) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13860) +@@ -161,6 +161,69 @@ + } + } + /*}}}*/ ++/*FUNCTION Tria::GetDofList {{{*/ ++void Tria::SetwiseNodeConnectivity(int* pd_nz,int* po_nz,Node* node,bool* flags,int set1_enum,int set2_enum){ ++ ++ int index; ++ int set_enum; ++ ++ /*Find node index*/ ++ index = this->GetNodeIndex(node); ++ ++ /*Output */ ++ int d_nz = 0; ++ int o_nz = 0; ++ ++ /*Loop over all nodes*/ ++ for(int i=0;i<3;i++){ ++ ++ if(!flags[this->nodes[i]->Sid()]){ ++ ++ /*flag current node so that no other element processes it*/ ++ flags[this->nodes[i]->Sid()]=true; ++ ++ /*What set are we interested in?*/ ++ if(i!=index) ++ set_enum=set2_enum; ++ else ++ set_enum=set1_enum; ++ ++ /*if node is clone, we have an off-diagonal non-zero, else it is a diagonal non-zero*/ ++ switch(set2_enum){ ++ case FsetEnum: ++ if(nodes[i]->indexing.fsize){ ++ if(this->nodes[i]->IsClone()) ++ o_nz += 1; ++ else ++ d_nz += 1; ++ } ++ break; ++ case GsetEnum: ++ if(nodes[i]->indexing.gsize){ ++ if(this->nodes[i]->IsClone()) ++ o_nz += 1; ++ else ++ d_nz += 1; ++ } ++ break; ++ case SsetEnum: ++ if(nodes[i]->indexing.ssize){ ++ if(this->nodes[i]->IsClone()) ++ o_nz += 1; ++ else ++ d_nz += 1; ++ } ++ break; ++ default: _error_("not supported"); ++ } ++ } ++ } ++ ++ /*Assign output pointers: */ ++ *pd_nz=d_nz; ++ *po_nz=o_nz; ++} ++/*}}}*/ + /*FUNCTION Tria::CreateKMatrix {{{*/ + void Tria::CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df){ + +Index: ../trunk-jpl/src/c/classes/objects/Elements/Tria.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Tria.h (revision 13859) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Tria.h (revision 13860) +@@ -75,6 +75,7 @@ + void ComputeStressTensor(); + void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); + void SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); ++ void SetwiseNodeConnectivity(int* d_nz,int* o_nz,Node* node,bool* flags,int set1_enum,int set2_enum); + void CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df); + void CreatePVector(Vector* pf); + void CreateJacobianMatrix(Matrix* Jff); +Index: ../trunk-jpl/src/c/classes/objects/Elements/Penta.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Penta.h (revision 13859) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Penta.h (revision 13860) +@@ -79,6 +79,7 @@ + void ComputeStressTensor(); + void Configure(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); + void SetCurrentConfiguration(Elements* elements,Loads* loads,DataSet* nodes,Materials* materials,Parameters* parameters); ++ void SetwiseNodeConnectivity(int* d_nz,int* o_nz,Node* node,bool* flags,int set1_enum,int set2_enum){_error_("not implemented yet");}; + void CreateKMatrix(Matrix* Kff, Matrix* Kfs,Vector* df); + void CreatePVector(Vector* pf); + void CreateJacobianMatrix(Matrix* Jff); Index: /issm/oecreview/Archive/13393-13976/ISSM-13860-13861.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13860-13861.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13860-13861.diff (revision 13980) @@ -0,0 +1,87 @@ +Index: ../trunk-jpl/externalpackages/esmf/doc/ESMF_usrdoc.pdf +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/externalpackages/esmf/doc/ESMF_refdoc.pdf +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/externalpackages/esmf/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/esmf/install.sh (revision 13860) ++++ ../trunk-jpl/externalpackages/esmf/install.sh (revision 13861) +@@ -1,51 +1,38 @@ + #!/bin/bash + set -eu + +-#0: cleanup +-#1: install +-#2: test +- +-install=2 +- + export ESMF_DIR=$ISSM_DIR/externalpackages/esmf/esmf + export ESMF_COMPILER=gfortran + export ESMF_COMM=mpich2 + +-if [[ $install == "0" ]]; then +- #Some cleanup +- rm -rf esmf_5_2_0rp2 +- rm -rf esmf +-fi ++#Some cleanup ++rm -rf esmf_5_2_0rp2 ++rm -rf esmf + +-if [[ $install == "1" ]]; then ++#Download from ISSM server ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/esmf_5_2_0rp2_src.tar.gz' 'esmf_5_2_0rp2_src.tar.gz' ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ESMF_refdoc.pdf' 'ESMF_refdoc.pdf' ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ESMF_usrdoc.pdf' 'ESMF_usrdoc.pdf' + +- #Download from ISSM server +- $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/esmf_5_2_0rp2_src.tar.gz' 'esmf_5_2_0rp2_src.tar.gz' ++#Untar ++tar -zxvf esmf_5_2_0rp2_src.tar.gz + +- #Untar +- tar -zxvf esmf_5_2_0rp2_src.tar.gz + ++#Configure esmf ++cd esmf + +- #Configure esmf +- cd esmf +- +- +- +- #Compile and install esmf +- if [ $# -eq 0 ]; then +- make +- make install +- else +- make -j $1 +- make -j $1 install +- fi ++#Compile and install esmf ++if [ $# -eq 0 ]; then ++ make ++ make install ++else ++ make -j $1 ++ make -j $1 install + fi + +-if [[ $install == "2" ]]; then +- cd esmf +- if [ $# -eq 0 ]; then +- make all_tests +- else +- make -j $1 all_tests +- fi ++cd esmf ++if [ $# -eq 0 ]; then ++ make all_tests ++else ++ make -j $1 all_tests + fi Index: /issm/oecreview/Archive/13393-13976/ISSM-13861-13862.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13861-13862.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13861-13862.diff (revision 13980) @@ -0,0 +1,611 @@ +Index: ../trunk-jpl/src/m/classes/autodiff.py +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.py (revision 13861) ++++ ../trunk-jpl/src/m/classes/autodiff.py (revision 13862) +@@ -1,4 +1,6 @@ + #module imports ++from dependent import * ++from independent import * + from fielddisplay import fielddisplay + from EnumDefinitions import * + from checkfield import * +@@ -13,32 +15,183 @@ + """ + + #properties +- def __init__(self): +- # {{{ Properties +- self.isautodiff = False ++ def __init__(self,*args): # {{{ ++ self.isautodiff = False ++ self.dependents = [] ++ self.independents = [] ++ self.driver = 'fos_forward' + +- #set defaults +- self.setdefaultparameters() ++ if not len(args): ++ self.setdefaultparameters() ++ else: ++ raise RuntimeError("constructor not supported") ++ # }}} + +- #}}} +- def __repr__(self): +- # {{{ Display +- string=' automatic differentiation parameters:' +- string="%s\n%s"%(string,fielddisplay(self,'isautodiff','indicates if the automatic differentiation is activated')) +- return string +- #}}} +- def setdefaultparameters(self): +- # {{{setdefaultparameters ++ def __repr__(self): # {{{ ++ s =" automatic differentiation parameters:" ++ ++ s+="%s\n" % fielddisplay(self,'isautodiff',"indicates if the automatic differentiation is activated") ++ s+="%s\n" % fielddisplay(self,'dependents',"list of dependent variables") ++ s+="%s\n" % fielddisplay(self,'independents',"list of independent variables") ++ s+="%s\n" % fielddisplay(self,'driver',"ADOLC driver ('fos_forward' or 'fov_forward'") ++ ++ return s ++ # }}} ++ ++ def setdefaultparameters(self): # {{{ + return self +- #}}} ++ # }}} + + def checkconsistency(self,md,solution,analyses): # {{{ ++ ++ #Early return ++ if not self.isautodiff: ++ return md ++ ++ #Driver value: ++ md = checkfield(md,'autodiff.driver','values',['fos_forward','fov_forward','fov_forward_all','fos_reverse','fov_reverse','fov_reverse_all']) ++ ++ #go through our dependents and independents and check consistency: ++ for dep in self.dependents: ++ dep.checkconsistency(md,solution,analyses) ++ for i,indep in enumerate(self.independents): ++ indep.checkconsistency(md,i,solution,analyses,self.driver) ++ + return md + # }}} + + def marshall(self,fid): # {{{ + WriteData(fid,'object',self,'fieldname','isautodiff','format','Boolean') +- WriteData(fid,'data',False,'enum',AutodiffMassFluxSegmentsPresentEnum(),'format','Boolean'); +- WriteData(fid,'data',False,'enum',AutodiffKeepEnum(),'format','Boolean'); ++ WriteData(fid,'object',self,'fieldname','driver','format','String') ++ ++ #early return ++ if not self.isautodiff: ++ WriteData(fid,'data',False,'enum',AutodiffMassFluxSegmentsPresentEnum(),'format','Boolean') ++ WriteData(fid,'data',False,'enum',AutodiffKeepEnum(),'format','Boolean') ++ return ++ ++ #process dependent variables {{{ ++ num_dependent_objects=len(self.dependents) ++ WriteData(fid,'data',num_dependent_objects,'enum',AutodiffNumDependentObjectsEnum(),'format','Integer') ++ ++ if num_dependent_objects: ++ names=numpy.zeros(num_dependent_objects) ++ types=numpy.zeros(num_dependent_objects) ++ indices=numpy.zeros(num_dependent_objects) ++ ++ for i,dep in enumerate(self.dependents): ++ names[i]=StringToEnum(dep.name)[0] ++ types[i]=dep.typetoscalar() ++ indices[i]=dep.index ++ ++ WriteData(fid,'data',names,'enum',AutodiffDependentObjectNamesEnum(),'format','IntMat','mattype',3) ++ WriteData(fid,'data',types,'enum',AutodiffDependentObjectTypesEnum(),'format','IntMat','mattype',3) ++ WriteData(fid,'data',indices,'enum',AutodiffDependentObjectIndicesEnum(),'format','IntMat','mattype',3) ++ #}}} ++ ++ #process independent variables {{{ ++ num_independent_objects=len(self.independents) ++ WriteData(fid,'data',num_independent_objects,'enum',AutodiffNumIndependentObjectsEnum(),'format','Integer') ++ ++ if num_independent_objects: ++ names=numpy.zeros(num_independent_objects) ++ types=numpy.zeros(num_independent_objects) ++ ++ for i,indep in enumerate(self.independents): ++ names[i]=StringToEnum(indep.name)[0] ++ types[i]=indep.typetoscalar() ++ ++ WriteData(fid,'data',names,'enum',AutodiffIndependentObjectNamesEnum(),'format','IntMat','mattype',3) ++ WriteData(fid,'data',types,'enum',AutodiffIndependentObjectTypesEnum(),'format','IntMat','mattype',3) ++ #}}} ++ ++ #if driver is fos_forward, build index: {{{ ++ if strcmpi(self.driver,'fos_forward'): ++ index=0 ++ ++ for indep in self.independents: ++ if not isnan(indep.fos_forward_index): ++ index+=indep.fos_forward_index ++ break ++ else: ++ if strcmpi(indep.type,'scalar'): ++ index+=1 ++ else: ++ index+=indep.nods ++ ++ index-=1 #get c-index numbering going ++ WriteData(fid,'data',index,'enum',AutodiffFosForwardIndexEnum(),'format','Integer') ++ #}}} ++ ++ #if driver is fos_reverse, build index: {{{ ++ if strcmpi(self.driver,'fos_reverse'): ++ index=0 ++ ++ for dep in self.dependents: ++ if not isnan(dep.fos_reverse_index): ++ index+=dep.fos_reverse_index ++ break ++ else: ++ if strcmpi(dep.type,'scalar'): ++ index+=1 ++ else: ++ index+=dep.nods ++ ++ index-=1 #get c-index numbering going ++ WriteData(fid,'data',index,'enum',AutodiffFosReverseIndexEnum(),'format','Integer') ++ end ++ #}}} ++ ++ #if driver is fov_forward, build indices: {{{ ++ if strcmpi(self.driver,'fov_forward'): ++ indices=0 ++ ++ for indep in self.independents: ++ if indep.fos_forward_index: ++ indices+=indep.fov_forward_indices ++ break ++ else: ++ if strcmpi(indep.type,'scalar'): ++ indices+=1 ++ else: ++ indices+=indep.nods ++ ++ indices-=1 #get c-indices numbering going ++ WriteData(fid,'data',indices,'enum',AutodiffFovForwardIndicesEnum(),'format','IntMat','mattype',3) ++ end ++ #}}} ++ ++ #deal with mass fluxes: {{{ ++ mass_flux_segments=[dep.segments for dep in self.dependents if strcmpi(dep.name,'MassFlux')] ++ ++ if mass_flux_segments: ++ WriteData(fid,'data',mass_flux_segments,'enum',MassFluxSegmentsEnum(),'format','MatArray') ++ flag=True ++ else: ++ flag=False ++ WriteData(fid,'data',flag,'enum',AutodiffMassFluxSegmentsPresentEnum(),'format','Boolean') ++ #}}} ++ ++ #deal with trace keep on: {{{ ++ keep=False ++ ++ #From ADOLC userdoc: ++ # The optional integer argument keep of trace on determines whether the numerical values of all active variables are ++ # recorded in a buffered temporary array or file called the taylor stack. This option takes effect if keep = 1 and ++ # prepares the scene for an immediately following gradient evaluation by a call to a routine implementing the reverse ++ # mode as described in the Section 4 and Section 5. ++ # ++ ++ if len(self.driver)<=3: ++ keep=False #there is no "_reverse" string within the driver string: ++ else: ++ if strncmpi(self.driver[3:],'_reverse',8): ++ keep=True ++ else: ++ keep=False ++ WriteData(fid,'data',keep,'enum',AutodiffKeepEnum(),'format','Boolean') ++ #}}} ++ ++ return + # }}} + +Index: ../trunk-jpl/src/m/classes/autodiff.m +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.m (revision 13861) ++++ ../trunk-jpl/src/m/classes/autodiff.m (revision 13862) +@@ -54,10 +54,10 @@ + WriteData(fid,'object',obj,'fieldname','driver','format','String'); + + %early return +- if ~obj.isautodiff, +- WriteData(fid,'data',false,'enum',AutodiffMassFluxSegmentsPresentEnum,'format','Boolean'); +- WriteData(fid,'data',false,'enum',AutodiffKeepEnum,'format','Boolean'); +- return; ++ if ~obj.isautodiff, ++ WriteData(fid,'data',false,'enum',AutodiffMassFluxSegmentsPresentEnum(),'format','Boolean'); ++ WriteData(fid,'data',false,'enum',AutodiffKeepEnum(),'format','Boolean'); ++ return; + end + + %process dependent variables {{{ +@@ -117,7 +117,7 @@ + end + end + index=index-1; %get c-index numbering going +- WriteData(fid,'data',index,'enum',AutodiffFosForwardIndexEnum(),'format','Integer'); ++ WriteData(fid,'data',index,'enum',AutodiffFosForwardIndexEnum(),'format','Integer'); + end + %}}} + %if driver is fos_reverse, build index: {{{ +@@ -138,7 +138,7 @@ + end + end + index=index-1; %get c-index numbering going +- WriteData(fid,'data',index,'enum',AutodiffFosReverseIndexEnum(),'format','Integer'); ++ WriteData(fid,'data',index,'enum',AutodiffFosReverseIndexEnum(),'format','Integer'); + end + %}}} + %if driver is fov_forward, build indices: {{{ +@@ -159,8 +159,7 @@ + end + end + indices=indices-1; %get c-indices numbering going +- +- WriteData(fid,'data',indices,'enum',AutodiffFovForwardIndicesEnum,'format','IntMat','mattype',3); ++ WriteData(fid,'data',indices,'enum',AutodiffFovForwardIndicesEnum(),'format','IntMat','mattype',3); + end + %}}} + %deal with mass fluxes: {{{ +@@ -172,12 +171,12 @@ + end + end + if ~isempty(mass_flux_segments), +- WriteData(fid,'data',mass_flux_segments,'enum',MassFluxSegmentsEnum,'format','MatArray'); ++ WriteData(fid,'data',mass_flux_segments,'enum',MassFluxSegmentsEnum(),'format','MatArray'); + flag=true; +- else +- flag=false; ++ else ++ flag=false; + end +- WriteData(fid,'data',flag,'enum',AutodiffMassFluxSegmentsPresentEnum,'format','Boolean'); ++ WriteData(fid,'data',flag,'enum',AutodiffMassFluxSegmentsPresentEnum(),'format','Boolean'); + %}}} + %deal with trace keep on: {{{ + keep=false; +@@ -198,7 +197,7 @@ + keep=false; + end + end +- WriteData(fid,'data',keep,'enum',AutodiffKeepEnum,'format','Boolean'); ++ WriteData(fid,'data',keep,'enum',AutodiffKeepEnum(),'format','Boolean'); + %}}} + + end % }}} +Index: ../trunk-jpl/src/m/classes/dependent.m +=================================================================== +--- ../trunk-jpl/src/m/classes/dependent.m (revision 13861) ++++ ../trunk-jpl/src/m/classes/dependent.m (revision 13862) +@@ -14,35 +14,34 @@ + nods = 0; + end + methods +- function obj= dependent(varargin) % {{{ ++ function obj = dependent(varargin) % {{{ + +- %use provided options to change fields +- options=pairoptions(varargin{:}); ++ %use provided options to change fields ++ options=pairoptions(varargin{:}); + +- obj.name=getfieldvalue(options,'name',''); +- obj.type=getfieldvalue(options,'type',''); +- obj.exp=getfieldvalue(options,'exp',''); +- obj.segments=getfieldvalue(options,'segments',[]); +- obj.index=getfieldvalue(options,'index',-1); +- obj.nods=getfieldvalue(options,'nods',0); ++ obj.name=getfieldvalue(options,'name',''); ++ obj.type=getfieldvalue(options,'type',''); ++ obj.exp=getfieldvalue(options,'exp',''); ++ obj.segments=getfieldvalue(options,'segments',[]); ++ obj.index=getfieldvalue(options,'index',-1); ++ obj.nods=getfieldvalue(options,'nods',0); + +- %if name is mass flux: +- if strcmpi(obj.name,'MassFlux'), +- %make sure that we supplied a file and that it exists! +- if exist(obj.exp)~=2, +- error('dependent checkconsistency: specified ''exp'' file does not exist!'); +- end +- %process the file and retrieve segments +- mesh=getfieldvalue(options,'mesh'); +- obj.segments=MeshProfileIntersection(mesh.elements,mesh.x,mesh.y,obj.exp); +- end +- end +- %}}} ++ %if name is mass flux: ++ if strcmpi(obj.name,'MassFlux'), ++ %make sure that we supplied a file and that it exists! ++ if exist(obj.exp)~=2, ++ error('dependent checkconsistency: specified ''exp'' file does not exist!'); ++ end ++ %process the file and retrieve segments ++ mesh=getfieldvalue(options,'mesh'); ++ obj.segments=MeshProfileIntersection(mesh.elements,mesh.x,mesh.y,obj.exp); ++ end ++ end ++ %}}} + function obj = setdefaultparameters(obj) % {{{ +- %do nothing ++ %do nothing + end % }}} + function md = checkconsistency(obj,md,solution,analyses) % {{{ +- %do nothing for now + if strcmpi(obj.name,'MassFlux'), + if isempty(obj.segments), + error('dependent checkconsistency error: need segments to compute this dependent response'); +@@ -56,14 +55,13 @@ + error('cannot declare a dependent with a fos_reverse_index when the driver is not fos_reverse!'); + end + if obj.nods==0, +- error('ependent checkconsistency error: nods should be set to the size of the independent variable'); ++ error('dependent checkconsistency error: nods should be set to the size of the independent variable'); + end +- + end + + end % }}} + function disp(obj) % {{{ +- disp(sprintf(' dependent variable :')); ++ disp(sprintf(' dependent variable:')); + + fielddisplay(obj,'name','variable name (must match corresponding Enum)'); + fielddisplay(obj,'type','type of variable (''vertex'' or ''scalar'')'); +@@ -78,11 +76,11 @@ + + end % }}} + function scalar=typetoscalar(obj) % {{{ +- if strcmpi(obj.type,'scalar'), +- scalar=0; +- elseif strcmpi(obj.type,'vertex'), +- scalar=1; +- end ++ if strcmpi(obj.type,'scalar'), ++ scalar=0; ++ elseif strcmpi(obj.type,'vertex'), ++ scalar=1; ++ end + + end % }}} + end +Index: ../trunk-jpl/src/m/classes/independent.py +=================================================================== +--- ../trunk-jpl/src/m/classes/independent.py (revision 0) ++++ ../trunk-jpl/src/m/classes/independent.py (revision 13862) +@@ -0,0 +1,75 @@ ++from pairoptions import * ++from MatlabFuncs import * ++from EnumDefinitions import * ++from WriteData import * ++ ++class independent(object): ++ """ ++ INDEPENDENT class definition ++ ++ Usage: ++ independent=independent(); ++ """ ++ ++ def __init__(self,*args): # {{{ ++ self.name = '' ++ self.type = '' ++ self.fos_forward_index = float('NaN') ++ self.fov_forward_indices = numpy.array([]) ++ self.nods = 0 ++ ++ #set defaults ++ self.setdefaultparameters() ++ ++ #use provided options to change fields ++ options=pairoptions(*args) ++ ++ #OK get other fields ++ self=options.AssignObjectFields(self) ++ # }}} ++ ++ def setdefaultparameters(self): # {{{ ++ #do nothing ++ return self ++ # }}} ++ ++ def checkconsistency(self,md,i,solution,analyses,driver): # {{{ ++ if not isnan(self.fos_forward_index): ++ if not strcmpi(driver,'fos_forward'): ++ raise TypeError("cannot declare an independent with a fos_forward_index when the driver is not fos_forward!") ++ if self.nods==0: ++ raise TypeError("independent checkconsistency error: nods should be set to the size of the independent variable") ++ ++ if self.fov_forward_indices: ++ if not strcmpi(driver,'fov_forward'): ++ raise TypeError("cannot declare an independent with fov_forward_indices when the driver is not fov_forward!") ++ if self.nods==0: ++ raise TypeError("independent checkconsistency error: nods should be set to the size of the independent variable") ++ end ++ md = checkfield(md,"autodiff.independents[%d].fov_forward_indices" % i,'>=',1,'<=',self.nods,'size',[float('NaN'),1]) ++ ++ return md ++ # }}} ++ ++ def __repr__(self): # {{{ ++ s =" independent variable:\n" ++ ++ s+="%s\n" % fielddisplay(self,'name',"variable name (must match corresponding Enum)") ++ s+="%s\n" % fielddisplay(self,'type',"type of variable ('vertex' or 'scalar')") ++ if not isnan(self.fos_forward_index): ++ s+="%s\n" % fielddisplay(self,'fos_forward_index',"index for fos_foward driver of ADOLC") ++ if numpy.any(numpy.logical_not(numpy.isnan(self.fov_forward_indices))): ++ s+="%s\n" % fielddisplay(self,'fov_forward_indices',"indices for fov_foward driver of ADOLC") ++ ++ return s ++ # }}} ++ ++ def typetoscalar(self): # {{{ ++ if strcmpi(self.type,'scalar'): ++ scalar=0 ++ elif strcmpi(self.type,'vertex'): ++ scalar=1 ++ ++ return scalar ++ # }}} ++ +Index: ../trunk-jpl/src/m/classes/independent.m +=================================================================== +--- ../trunk-jpl/src/m/classes/independent.m (revision 13861) ++++ ../trunk-jpl/src/m/classes/independent.m (revision 13862) +@@ -12,22 +12,21 @@ + nods = 0; + end + methods +- function obj= independent(varargin) % {{{ ++ function obj = independent(varargin) % {{{ + +- %use provided options to change fields +- options=pairoptions(varargin{:}); ++ %use provided options to change fields ++ options=pairoptions(varargin{:}); + +- %OK get other fields +- obj=AssignObjectFields(pairoptions(varargin{:}),obj); ++ %OK get other fields ++ obj=AssignObjectFields(pairoptions(varargin{:}),obj); + +- end +- %}}} ++ end ++ %}}} + function obj = setdefaultparameters(obj) % {{{ + %do nothing + + end % }}} + function md = checkconsistency(obj,md,i,solution,analyses,driver) % {{{ +- %do nothing for now + if ~isnan(obj.fos_forward_index), + if ~strcmpi(driver,'fos_forward'), + error('cannot declare an independent with a fos_forward_index when the driver is not fos_forward!'); +@@ -41,7 +40,6 @@ + if ~strcmpi(driver,'fov_forward'), + error('cannot declare an independent with fov_forward_indices when the driver is not fov_forward!'); + end +- + if obj.nods==0, + error('independent checkconsistency error: nods should be set to the size of the independent variable'); + end +@@ -50,7 +48,7 @@ + + end % }}} + function disp(obj) % {{{ +- disp(sprintf(' independent variable :')); ++ disp(sprintf(' independent variable:')); + + fielddisplay(obj,'name','variable name (must match corresponding Enum)'); + fielddisplay(obj,'type','type of variable (''vertex'' or ''scalar'')'); +Index: ../trunk-jpl/src/m/classes/dependent.py +=================================================================== +--- ../trunk-jpl/src/m/classes/dependent.py (revision 0) ++++ ../trunk-jpl/src/m/classes/dependent.py (revision 13862) +@@ -0,0 +1,94 @@ ++import os.path ++from pairoptions import * ++from MatlabFuncs import * ++from EnumDefinitions import * ++from WriteData import * ++#from MeshProfileIntersection import * ++ ++class dependent(object): ++ """ ++ DEPENDENT class definition ++ ++ Usage: ++ dependent=dependent(); ++ """ ++ ++ def __init__(self,*args): # {{{ ++ self.name = '' ++ self.type = '' ++ self.fos_reverse_index = float('NaN') ++ self.exp = '' ++ self.segments = [] ++ self.index = -1 ++ self.nods = 0 ++ ++ #set defaults ++ self.setdefaultparameters() ++ ++ #use provided options to change fields ++ options=pairoptions(*args) ++ ++ self.name=options.getfieldvalue('name','') ++ self.type=options.getfieldvalue('type','') ++ self.exp=options.getfieldvalue('exp','') ++ self.segments=options.getfieldvalue('segments',[]) ++ self.index=options.getfieldvalue('index',-1) ++ self.nods=options.getfieldvalue('nods',0) ++ ++ #if name is mass flux: ++ if strcmpi(self.name,'MassFlux'): ++ #make sure that we supplied a file and that it exists! ++ if not os.path.exists(self.exp): ++ raise IOError("dependent checkconsistency: specified 'exp' file does not exist!") ++ #process the file and retrieve segments ++ mesh=options.getfieldvalue('mesh') ++ raise RuntimeError("MeshProfileIntersection is not complete.") ++ self.segments=MeshProfileIntersection(mesh.elements,mesh.x,mesh.y,self.exp) ++ # }}} ++ ++ def setdefaultparameters(self): # {{{ ++ #do nothing ++ return self ++ # }}} ++ ++ def checkconsistency(self,md,solution,analyses): # {{{ ++ if strcmpi(self.name,'MassFlux'): ++ if not self.segments: ++ raise RuntimeError("dependent checkconsistency error: need segments to compute this dependent response") ++ if self.index<0: ++ raise RuntimeError("dependent checkconsistency error: index for segments should be >=0") ++ ++ if not isnan(self.fos_reverse_index): ++ if not strcmpi(driver,'fos_reverse'): ++ raise TypeError("cannot declare a dependent with a fos_reverse_index when the driver is not fos_reverse!") ++ if self.nods==0: ++ raise TypeError("dependent checkconsistency error: nods should be set to the size of the independent variable") ++ ++ return md ++ # }}} ++ ++ def __repr__(self): # {{{ ++ s =" dependent variable:\n" ++ ++ s+="%s\n" % fielddisplay(self,'name',"variable name (must match corresponding Enum)") ++ s+="%s\n" % fielddisplay(self,'type',"type of variable ('vertex' or 'scalar')") ++ ++ if not isnan(self.fos_reverse_index): ++ s+="%s\n" % fielddisplay(self,'fos_reverse_index',"index for fos_reverse driver of ADOLC") ++ end ++ if self.exp: ++ s+="%s\n" % fielddisplay(self,'exp',"file needed to compute dependent variable") ++ s+="%s\n" % fielddisplay(self,'segments',"mass flux segments") ++ ++ return s ++ # }}} ++ ++ def typetoscalar(self): # {{{ ++ if strcmpi(self.type,'scalar'): ++ scalar=0 ++ elif strcmpi(self.type,'vertex'): ++ scalar=1 ++ ++ return scalar ++ # }}} ++ Index: /issm/oecreview/Archive/13393-13976/ISSM-13862-13863.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13862-13863.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13862-13863.diff (revision 13980) @@ -0,0 +1,165 @@ +Index: ../trunk-jpl/src/m/classes/autodiff.py +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.py (revision 13862) ++++ ../trunk-jpl/src/m/classes/autodiff.py (revision 13863) +@@ -28,12 +28,12 @@ + # }}} + + def __repr__(self): # {{{ +- s =" automatic differentiation parameters:" ++ s =" automatic differentiation parameters:\n" + + s+="%s\n" % fielddisplay(self,'isautodiff',"indicates if the automatic differentiation is activated") + s+="%s\n" % fielddisplay(self,'dependents',"list of dependent variables") + s+="%s\n" % fielddisplay(self,'independents',"list of independent variables") +- s+="%s\n" % fielddisplay(self,'driver',"ADOLC driver ('fos_forward' or 'fov_forward'") ++ s+="%s\n" % fielddisplay(self,'driver',"ADOLC driver ('fos_forward' or 'fov_forward')") + + return s + # }}} +@@ -139,7 +139,6 @@ + + index-=1 #get c-index numbering going + WriteData(fid,'data',index,'enum',AutodiffFosReverseIndexEnum(),'format','Integer') +- end + #}}} + + #if driver is fov_forward, build indices: {{{ +@@ -158,7 +157,6 @@ + + indices-=1 #get c-indices numbering going + WriteData(fid,'data',indices,'enum',AutodiffFovForwardIndicesEnum(),'format','IntMat','mattype',3) +- end + #}}} + + #deal with mass fluxes: {{{ +Index: ../trunk-jpl/src/m/classes/autodiff.m +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.m (revision 13862) ++++ ../trunk-jpl/src/m/classes/autodiff.m (revision 13863) +@@ -42,11 +42,11 @@ + + end % }}} + function disp(obj) % {{{ +- disp(sprintf(' automatic differentiation parameters:')); ++ disp(sprintf(' automatic differentiation parameters:')); + fielddisplay(obj,'isautodiff','indicates if the automatic differentiation is activated'); + fielddisplay(obj,'dependents','list of dependent variables'); + fielddisplay(obj,'independents','list of independent variables'); +- fielddisplay(obj,'driver','ADOLC driver (''fos_forward'' or ''fov_forward'''); ++ fielddisplay(obj,'driver','ADOLC driver (''fos_forward'' or ''fov_forward'')'); + end % }}} + function marshall(obj,fid) % {{{ + +Index: ../trunk-jpl/src/m/classes/independent.py +=================================================================== +--- ../trunk-jpl/src/m/classes/independent.py (revision 13862) ++++ ../trunk-jpl/src/m/classes/independent.py (revision 13863) +@@ -1,4 +1,5 @@ + from pairoptions import * ++from fielddisplay import * + from MatlabFuncs import * + from EnumDefinitions import * + from WriteData import * +@@ -28,6 +29,19 @@ + self=options.AssignObjectFields(self) + # }}} + ++ def __repr__(self): # {{{ ++ s =" independent variable:\n" ++ ++ s+="%s\n" % fielddisplay(self,'name',"variable name (must match corresponding Enum)") ++ s+="%s\n" % fielddisplay(self,'type',"type of variable ('vertex' or 'scalar')") ++ if not isnan(self.fos_forward_index): ++ s+="%s\n" % fielddisplay(self,'fos_forward_index',"index for fos_foward driver of ADOLC") ++ if numpy.any(numpy.logical_not(numpy.isnan(self.fov_forward_indices))): ++ s+="%s\n" % fielddisplay(self,'fov_forward_indices',"indices for fov_foward driver of ADOLC") ++ ++ return s ++ # }}} ++ + def setdefaultparameters(self): # {{{ + #do nothing + return self +@@ -45,25 +59,11 @@ + raise TypeError("cannot declare an independent with fov_forward_indices when the driver is not fov_forward!") + if self.nods==0: + raise TypeError("independent checkconsistency error: nods should be set to the size of the independent variable") +- end + md = checkfield(md,"autodiff.independents[%d].fov_forward_indices" % i,'>=',1,'<=',self.nods,'size',[float('NaN'),1]) + + return md + # }}} + +- def __repr__(self): # {{{ +- s =" independent variable:\n" +- +- s+="%s\n" % fielddisplay(self,'name',"variable name (must match corresponding Enum)") +- s+="%s\n" % fielddisplay(self,'type',"type of variable ('vertex' or 'scalar')") +- if not isnan(self.fos_forward_index): +- s+="%s\n" % fielddisplay(self,'fos_forward_index',"index for fos_foward driver of ADOLC") +- if numpy.any(numpy.logical_not(numpy.isnan(self.fov_forward_indices))): +- s+="%s\n" % fielddisplay(self,'fov_forward_indices',"indices for fov_foward driver of ADOLC") +- +- return s +- # }}} +- + def typetoscalar(self): # {{{ + if strcmpi(self.type,'scalar'): + scalar=0 +Index: ../trunk-jpl/src/m/classes/dependent.py +=================================================================== +--- ../trunk-jpl/src/m/classes/dependent.py (revision 13862) ++++ ../trunk-jpl/src/m/classes/dependent.py (revision 13863) +@@ -1,5 +1,6 @@ + import os.path + from pairoptions import * ++from fielddisplay import * + from MatlabFuncs import * + from EnumDefinitions import * + from WriteData import * +@@ -46,6 +47,21 @@ + self.segments=MeshProfileIntersection(mesh.elements,mesh.x,mesh.y,self.exp) + # }}} + ++ def __repr__(self): # {{{ ++ s =" dependent variable:\n" ++ ++ s+="%s\n" % fielddisplay(self,'name',"variable name (must match corresponding Enum)") ++ s+="%s\n" % fielddisplay(self,'type',"type of variable ('vertex' or 'scalar')") ++ ++ if not isnan(self.fos_reverse_index): ++ s+="%s\n" % fielddisplay(self,'fos_reverse_index',"index for fos_reverse driver of ADOLC") ++ if self.exp: ++ s+="%s\n" % fielddisplay(self,'exp',"file needed to compute dependent variable") ++ s+="%s\n" % fielddisplay(self,'segments',"mass flux segments") ++ ++ return s ++ # }}} ++ + def setdefaultparameters(self): # {{{ + #do nothing + return self +@@ -67,22 +83,6 @@ + return md + # }}} + +- def __repr__(self): # {{{ +- s =" dependent variable:\n" +- +- s+="%s\n" % fielddisplay(self,'name',"variable name (must match corresponding Enum)") +- s+="%s\n" % fielddisplay(self,'type',"type of variable ('vertex' or 'scalar')") +- +- if not isnan(self.fos_reverse_index): +- s+="%s\n" % fielddisplay(self,'fos_reverse_index',"index for fos_reverse driver of ADOLC") +- end +- if self.exp: +- s+="%s\n" % fielddisplay(self,'exp',"file needed to compute dependent variable") +- s+="%s\n" % fielddisplay(self,'segments',"mass flux segments") +- +- return s +- # }}} +- + def typetoscalar(self): # {{{ + if strcmpi(self.type,'scalar'): + scalar=0 Index: /issm/oecreview/Archive/13393-13976/ISSM-13863-13864.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13863-13864.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13863-13864.diff (revision 13980) @@ -0,0 +1,93 @@ +Index: ../trunk-jpl/src/wrappers/python/Makefile.am +=================================================================== +--- ../trunk-jpl/src/wrappers/python/Makefile.am (revision 13863) ++++ ../trunk-jpl/src/wrappers/python/Makefile.am (revision 13864) +@@ -32,6 +32,7 @@ + ElementConnectivity.la\ + EnumToString.la\ + InterpFromMeshToMesh2d.la\ ++ MeshProfileIntersection.la\ + NodeConnectivity.la\ + StringToEnum.la\ + TriMesh.la\ +@@ -107,6 +108,10 @@ + ../InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h + InterpFromMeshToMesh2d_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) $(MULTITHREADINGLIB) + ++MeshProfileIntersection_la_SOURCES = ../MeshProfileIntersection/MeshProfileIntersection.cpp\ ++ ../MeshProfileIntersection/MeshProfileIntersection.h ++MeshProfileIntersection_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) ++ + NodeConnectivity_la_SOURCES = ../NodeConnectivity/NodeConnectivity.cpp\ + ../NodeConnectivity/NodeConnectivity.h + NodeConnectivity_la_LIBADD = ${deps} $(MPILIB) $(PETSCLIB) +Index: ../trunk-jpl/src/wrappers/MeshProfileIntersection/MeshProfileIntersection.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/MeshProfileIntersection/MeshProfileIntersection.cpp (revision 13863) ++++ ../trunk-jpl/src/wrappers/MeshProfileIntersection/MeshProfileIntersection.cpp (revision 13864) +@@ -10,7 +10,7 @@ + index,x,y is a triangulation + filename: name of Argus style .exp file containing the segments (can be groups of disconnected segments) + output: +- segments: array made of x1,y1,x2,y2,element_id lines (x1,y1) and (x2,y2) are segment extremitis for a segment ++ segments: array made of x1,y1,x2,y2,element_id lines (x1,y1) and (x2,y2) are segment extremities for a segment + belonging to the elemnt_id element. there are as many lines in segments as there are segments intersecting the + mesh. + */ +@@ -25,7 +25,7 @@ + _printLine_(" index,x,y is a triangulation"); + _printLine_(" filename: name of Argus style .exp file containing the segments (can be groups of disconnected segments)"); + _printLine_(" output:"); +- _printLine_(" segments: array made of x1,y1,x2,y2,element_id lines (x1,y1) and (x2,y2) are segment extremitis for a segment "); ++ _printLine_(" segments: array made of x1,y1,x2,y2,element_id lines (x1,y1) and (x2,y2) are segment extremities for a segment "); + _printLine_(" belonging to the elemnt_id element. there are as many lines in segments as there are segments intersecting the "); + _printLine_(" mesh."); + }/*}}}*/ +@@ -44,7 +44,7 @@ + int dummy; + + //contours +- mxArray* matlabstructure=NULL; ++ DataSet *domain = NULL; + Contour** contours=NULL; + int numcontours; + Contour* contouri=NULL; +@@ -56,12 +56,9 @@ + /*Boot module: */ + MODULEBOOT(); + +- /*checks on arguments on the matlab side: */ +- CheckNumMatlabArguments(nlhs,NLHS,nrhs,NRHS,__FUNCT__,&MeshProfileIntersectionUsage); ++ /*checks on arguments: */ ++ CHECKARGUMENTS(NLHS,NRHS,&MeshProfileIntersectionUsage); + +- /*First, call expread on filename to build a contour array in the matlab workspace: */ +- mexCallMATLAB( 1, &matlabstructure, 1, (mxArray**)&FILENAME, "expread"); +- + /*Fetch inputs: */ + //index + FetchData(&double_index,&nel,&dummy,INDEX); +@@ -77,18 +74,12 @@ + FetchData(&y,&dummy,Y); + + //contours +- numcontours=mxGetNumberOfElements(matlabstructure); ++ FetchData(&domain,FILENAME); ++ // MeshProfileIntersectionx should be modified to take DataSet directly (and perhaps SeqMat and SeqVec). ++ numcontours=domain->Size(); + contours=xNew*>(numcontours); +- for(i=0;i >(1); +- //retrieve dimension of this contour. +- contouri->nods=(int)mxGetScalar(mxGetField(matlabstructure,i,"nods")); +- //set pointers. +- contouri->x=mxGetPr(mxGetField(matlabstructure,i,"x")); +- contouri->y=mxGetPr(mxGetField(matlabstructure,i,"y")); +- *(contours+i)=contouri; +- } ++ for(i=0;i*)domain->GetObjectByOffset(i); + + /* Debugging of contours :{{{1*/ + /*for(i=0;i=0") + +- if not isnan(self.fos_reverse_index): ++ if not numpy.isnan(self.fos_reverse_index): + if not strcmpi(driver,'fos_reverse'): + raise TypeError("cannot declare a dependent with a fos_reverse_index when the driver is not fos_reverse!") + if self.nods==0: Index: /issm/oecreview/Archive/13393-13976/ISSM-13865-13866.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13865-13866.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13865-13866.diff (revision 13980) @@ -0,0 +1,100 @@ +Index: ../trunk-jpl/src/m/classes/verbose.py +=================================================================== +--- ../trunk-jpl/src/m/classes/verbose.py (revision 13865) ++++ ../trunk-jpl/src/m/classes/verbose.py (revision 13866) +@@ -15,7 +15,9 @@ + convergence : convergence criteria + control : control method + qmu : sensitivity analysis ++ autodiff : AD analysis + ++ + Usage: + verbose=verbose(); + verbose=verbose(3); +@@ -35,6 +37,7 @@ + self.convergence = False + self.control = False + self.qmu = False ++ self.autodiff = False + #ENDFIELDS + + if not len(args): +@@ -67,6 +70,23 @@ + raise TypeError("verbose supported field values are logicals only (True or False)") + # }}} + ++ def __repr__(self): # {{{ ++ ++ #BEGINDISP ++ s ="class '%s' = \n" % type(self) ++ s+=" %15s : %s\n" % ('mprocessor',self.mprocessor) ++ s+=" %15s : %s\n" % ('module',self.module) ++ s+=" %15s : %s\n" % ('solution',self.solution) ++ s+=" %15s : %s\n" % ('solver',self.solver) ++ s+=" %15s : %s\n" % ('convergence',self.convergence) ++ s+=" %15s : %s\n" % ('control',self.control) ++ s+=" %15s : %s\n" % ('qmu',self.qmu) ++ s+=" %15s : %s\n" % ('autodiff',self.autodiff) ++ #ENDDISP ++ ++ return s ++ # }}} ++ + def VerboseToBinary(self): # {{{ + + #BEGINVERB2BIN +@@ -85,6 +105,8 @@ + binary=binary | 32 + if self.qmu: + binary=binary | 64 ++ if self.autodiff: ++ binary=binary | 128 + #ENDVERB2BIN + + return binary +@@ -93,13 +115,14 @@ + def BinaryToVerbose(self,binary): # {{{ + + #BEGINBIN2VERB +- self.mprocessor =bool(binary & 1) +- self.module =bool(binary & 2) +- self.solution =bool(binary & 4) +- self.solver =bool(binary & 8) +- self.convergence=bool(binary & 16) +- self.control =bool(binary & 32) +- self.qmu =bool(binary & 64) ++ self.mprocessor =bool(binary & 1) ++ self.module =bool(binary & 2) ++ self.solution =bool(binary & 4) ++ self.solver =bool(binary & 8) ++ self.convergence=bool(binary & 16) ++ self.control =bool(binary & 32) ++ self.qmu =bool(binary & 64) ++ self.autodiff =bool(binary & 128) + #ENDBIN2VERB + # }}} + +@@ -107,22 +130,6 @@ + return md + # }}} + +- def __repr__(self): # {{{ +- +- #BEGINDISP +- s ="class '%s' = \n" % type(self) +- s+=" %15s : %s\n" % ('mprocessor',self.mprocessor) +- s+=" %15s : %s\n" % ('module',self.module) +- s+=" %15s : %s\n" % ('solution',self.solution) +- s+=" %15s : %s\n" % ('solver',self.solver) +- s+=" %15s : %s\n" % ('convergence',self.convergence) +- s+=" %15s : %s\n" % ('control',self.control) +- s+=" %15s : %s\n" % ('qmu',self.qmu) +- #ENDDISP +- +- return s +- # }}} +- + def marshall(self,fid): # {{{ + WriteData(fid,'data',self.VerboseToBinary(),'enum',VerboseEnum(),'format','Integer') + # }}} Index: /issm/oecreview/Archive/13393-13976/ISSM-13866-13867.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13866-13867.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13866-13867.diff (revision 13980) @@ -0,0 +1,49 @@ +Index: ../trunk-jpl/src/m/solve/WriteData.py +=================================================================== +--- ../trunk-jpl/src/m/solve/WriteData.py (revision 13866) ++++ ../trunk-jpl/src/m/solve/WriteData.py (revision 13867) +@@ -100,7 +100,7 @@ + + elif strcmpi(format,'BooleanMat'): # {{{ + +- if isinstance(data,bool): ++ if not isinstance(data,numpy.ndarray): + data=numpy.array([data]) + if len(data.shape) == 1: + if numpy.size(data): +@@ -131,7 +131,7 @@ + + elif strcmpi(format,'IntMat'): # {{{ + +- if isinstance(data,(int,long)): ++ if not isinstance(data,numpy.ndarray): + data=numpy.array([data]) + if len(data.shape) == 1: + if numpy.size(data): +@@ -162,7 +162,7 @@ + + elif strcmpi(format,'DoubleMat'): # {{{ + +- if isinstance(data,(bool,int,long,float)): ++ if not isinstance(data,numpy.ndarray): + data=numpy.array([data]) + if len(data.shape) == 1: + if numpy.size(data): +@@ -196,7 +196,7 @@ + #first get length of record + recordlength=4+4 #number of records + code + for matrix in data: +- if isinstance(matrix,(bool,int,long,float)): ++ if not isinstance(matrix,numpy.ndarray): + matrix=numpy.array([matrix]) + if len(matrix.shape) == 1: + if numpy.size(matrix): +@@ -218,7 +218,7 @@ + + #write each matrix: + for matrix in data: +- if isinstance(matrix,(bool,int,long,float)): ++ if not isinstance(matrix,numpy.ndarray): + matrix=numpy.array([matrix]) + if len(matrix.shape) == 1: + matrix=matrix.reshape(numpy.size(matrix),1) Index: /issm/oecreview/Archive/13393-13976/ISSM-13867-13868.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13867-13868.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13867-13868.diff (revision 13980) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp (revision 13867) ++++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp (revision 13868) +@@ -88,9 +88,6 @@ + _assert_(this->matrix); + MatAssemblyBegin(this->matrix,MAT_FINAL_ASSEMBLY); + MatAssemblyEnd(this->matrix,MAT_FINAL_ASSEMBLY); +- #if _PETSC_MAJOR_ == 2 +- MatCompress(this->matrix); +- #endif + + } + /*}}}*/ Index: /issm/oecreview/Archive/13393-13976/ISSM-13868-13869.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13868-13869.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13868-13869.diff (revision 13980) @@ -0,0 +1,70 @@ +Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp (revision 13868) ++++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp (revision 13869) +@@ -39,7 +39,7 @@ + this->matrix=NewMat(M,N,sparsity,IssmComm::GetComm()); + } + /*}}}*/ +-/*FUNCTION PetscMat(IssmDouble* serial_mat,int M,int N,IssmDouble sparsity){{{*/ ++/*FUNCTION PetscMat::PetscMat(IssmDouble* serial_mat,int M,int N,IssmDouble sparsity){{{*/ + PetscMat::PetscMat(IssmDouble* serial_mat,int M,int N,IssmDouble sparsity){ + + int i; +@@ -76,6 +76,20 @@ + /*}}}*/ + + /*PetscMat specific routines: */ ++/*FUNCTION PetscMat::AllocationInfo{{{*/ ++void PetscMat::AllocationInfo(void){ ++ ++ MatInfo info; ++ MatGetInfo(this->matrix,MAT_GLOBAL_SUM,&info); ++ _pprintLine_("=========================== Stiffness matrix allocation info ==========================="); ++ _pprintLine_(""); ++ _pprintLine_(" nz_allocated: "<pmatrix->AllocationInfo(); ++ #endif ++ } ++ else if(type==SeqMatType){ ++ //this->smatrix->AllocationInfo(); ++ } ++ else _error_("Matrix type: " << type << " not supported yet!"); ++ }/*}}}*/ + /*FUNCTION Assemble{{{*/ + void Assemble(void){ + Index: /issm/oecreview/Archive/13393-13976/ISSM-13869-13870.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13869-13870.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13869-13870.diff (revision 13980) @@ -0,0 +1,83 @@ +Index: ../trunk-jpl/src/m/plot/curvedarrow.m +=================================================================== +--- ../trunk-jpl/src/m/plot/curvedarrow.m (revision 13869) ++++ ../trunk-jpl/src/m/plot/curvedarrow.m (revision 13870) +@@ -9,11 +9,12 @@ + % options can be: + % 'ratio': default .5 (ratio headarrow/length) + % 'widthratio': default is 1/10 of length ++% 'width': if you want to specify an absolute width + + %recover options + options=pairoptions(varargin{:}); + ratio=getfieldvalue(options,'ratio',.1); +- widthratio=getfieldvalue(options,'widthratio',.1); ++ arrowlength=getfieldvalue(options,'arrowlength',1); + color=getfieldvalue(options,'color','k'); + + %transform angle in radians +@@ -22,7 +23,16 @@ + + %compute some values out of (x1,y1) and (x2,y2) + length=distance*angle; +- width=length*widthratio; ++ ++ if exist(options,'widthratio'), ++ widthratio=getfieldvalue(options,'widthratio'); ++ width=length*widthratio; ++ else if exist(options,'width'), ++ width=getfieldvalue(options,'width'); ++ else ++ widthratio=.1; ++ width=length*widthratio; ++ end + + %buidl the arrow itself: + A=[centerx+distance, centery]; +@@ -40,13 +50,19 @@ + %Build arrowhead + E=D+2/3*(D-C); + F=C+2/3*(C-D); ++ + n=(F-E)/norm(F-E,2); + m=[-n(2) n(1)]; + if(angle<0) + m=-m; + end +- d=(distance*angle)*ratio; + ++ if exist(options,'arrowlength'), ++ d=arrowlength; ++ else ++ d=abs((distance*angle)*ratio); ++ end ++ + %G is d distance from middle of E and F: + G=(E+F)/2+d*m; + +Index: ../trunk-jpl/src/m/plot/plot_riftrelvel.m +=================================================================== +--- ../trunk-jpl/src/m/plot/plot_riftrelvel.m (revision 13869) ++++ ../trunk-jpl/src/m/plot/plot_riftrelvel.m (revision 13870) +@@ -78,17 +78,17 @@ + penetration=(vx2-vx1)*normal(1)+(vy2-vy1)*normal(2); + %if penetration is negative, plot in black, positive, plot in red;: ie: if rift is closing, black, if rift is opening, red. + if(penetration>0), +- p2=plot(x(penaltypairs(j,1)) ,y(penaltypairs(j,1)),'*','MarkerSize',markersize); set(p2,'Color',[140 140 140]/255); ++ p2=plot(x(penaltypairs(j,1)) ,y(penaltypairs(j,1)),'.','MarkerSize',markersize); set(p2,'Color',[140 140 140]/255); + isp2=1; + else +- p1=plot(x(penaltypairs(j,1)) ,y(penaltypairs(j,1)),'k*','MarkerSize',markersize); ++ p1=plot(x(penaltypairs(j,1)) ,y(penaltypairs(j,1)),'k.','MarkerSize',markersize); + isp1=1; + end + end + + %point out the tips +- h2=plot(x(md.rifts.riftstruct(i).tips(1)),y(md.rifts.riftstruct(i).tips(1)),'g*','MarkerSize',markersize); +- plot(x(md.rifts.riftstruct(i).tips(2)),y(md.rifts.riftstruct(i).tips(2)),'g*','MarkerSize',markersize); ++ h2=plot(x(md.rifts.riftstruct(i).tips(1)),y(md.rifts.riftstruct(i).tips(1)),'g.','MarkerSize',markersize); ++ plot(x(md.rifts.riftstruct(i).tips(2)),y(md.rifts.riftstruct(i).tips(2)),'g.','MarkerSize',markersize); + segments=md.rifts.riftstruct(i).segments(:,1:2); + end + Index: /issm/oecreview/Archive/13393-13976/ISSM-13870-13871.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13870-13871.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13870-13871.diff (revision 13980) @@ -0,0 +1,10 @@ +Index: ../trunk-jpl/externalpackages/export_fig +=================================================================== +--- ../trunk-jpl/externalpackages/export_fig (revision 13870) ++++ ../trunk-jpl/externalpackages/export_fig (revision 13871) + +Property changes on: ../trunk-jpl/externalpackages/export_fig +___________________________________________________________________ +Added: svn:ignore +## -0,0 +1 ## ++.ignore Index: /issm/oecreview/Archive/13393-13976/ISSM-13871-13872.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13871-13872.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13871-13872.diff (revision 13980) @@ -0,0 +1,39 @@ +Index: ../trunk-jpl/externalpackages/gsl/install-android.sh +=================================================================== +--- ../trunk-jpl/externalpackages/gsl/install-android.sh (revision 13871) ++++ ../trunk-jpl/externalpackages/gsl/install-android.sh (revision 13872) +@@ -24,7 +24,7 @@ + if [[ $step == "2" || $step == "0" ]]; then + cd src + +- autoreconf -iv --force -I $LIBTOOL_DIR/share/aclocal/ ++ autoreconf -iv --force -I $ISSM_DIR/externalpackages/autotools/install/share/aclocal + + ./configure \ + --build="i386-apple-darwin10.8.0" \ +@@ -35,6 +35,7 @@ + + #Compile gsl + if [[ $step == "3" || $step == "0" ]]; then ++ cd src + if [ $# -eq 0 ]; then + make $j + else +@@ -43,3 +44,4 @@ + + make install + fi ++ +Index: ../trunk-jpl/externalpackages/gsl +=================================================================== +--- ../trunk-jpl/externalpackages/gsl (revision 13871) ++++ ../trunk-jpl/externalpackages/gsl (revision 13872) + +Property changes on: ../trunk-jpl/externalpackages/gsl +___________________________________________________________________ +Modified: svn:ignore +## -1,3 +1,4 ## ++install-macosx* + *.gz + install + src Index: /issm/oecreview/Archive/13393-13976/ISSM-13872-13873.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13872-13873.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13872-13873.diff (revision 13980) @@ -0,0 +1,27 @@ +Index: ../trunk-jpl/etc/environment.sh +=================================================================== +--- ../trunk-jpl/etc/environment.sh (revision 13872) ++++ ../trunk-jpl/etc/environment.sh (revision 13873) +@@ -65,9 +65,11 @@ + libpathappend "$MATLAB_DIR/lib" + + MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install" +-export MPI_DIR +-pathprepend "$MPI_DIR/bin" +-libpathappend "$MPI_DIR/lib" ++if [ -d "$MPI_DIR" ]; then ++ export MPI_DIR ++ pathprepend "$MPI_DIR/bin" ++ libpathappend "$MPI_DIR/lib" ++fi + + PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" + export PETSC_DIR +@@ -194,6 +196,7 @@ + + export ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install" + pathappend "$ANDROID_SDK_DIR/" ++pathappend "$ANDROID_DIR/arm-linux-android-4.0/bin/" + + GSL_DIR="$ISSM_DIR/externalpackages/gsl/install" + libpathappend "$GSL_DIR/lib" Index: /issm/oecreview/Archive/13393-13976/ISSM-13873-13874.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13873-13874.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13873-13874.diff (revision 13980) @@ -0,0 +1,452 @@ +Index: ../trunk-jpl/src/c/modules/MinVzx/MinVzx.h +=================================================================== +--- ../trunk-jpl/src/c/modules/MinVzx/MinVzx.h (revision 13873) ++++ ../trunk-jpl/src/c/modules/MinVzx/MinVzx.h (revision 13874) +@@ -1,14 +0,0 @@ +-/*!\file: MinVzx.h +- * \brief header file for inverse methods misfit computation +- */ +- +-#ifndef _MINVZX_H +-#define _MINVZX_H +- +-#include "../../Container/Container.h" +-#include "../../classes/objects/objects.h" +- +-/* local prototypes: */ +-void MinVzx( IssmDouble* pminvz, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units); +- +-#endif /* _MINVZX_H */ +Index: ../trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp (revision 13873) ++++ ../trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp (revision 13874) +@@ -1,42 +0,0 @@ +-/*!\file MinVzx +- */ +- +-#include "./MinVzx.h" +- +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../../toolkits/toolkits.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +- +-void MinVzx( IssmDouble* pminvz, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units){ +- +- int i; +- IssmDouble minvz; +- IssmDouble node_minvz; +- IssmDouble element_minvz; +- +- /*Go through elements, and request velocity: */ +- for(i=0;iSize();i++){ +- Element* element=dynamic_cast(elements->GetObjectByOffset(i)); +- element->MinVz(&element_minvz,process_units); //go pick up the minimum velocity in the inputs +- +- if(i==0)minvz=element_minvz; //initialize minvz +- else{ +- if(element_minvzSize()==0){ +- minvz=INFINITY; +- } +- +- /*Figure out minimum across the cluster: */ +- #ifdef _HAVE_MPI_ +- MPI_Reduce (&minvz,&node_minvz,1,MPI_DOUBLE,MPI_MIN,0,IssmComm::GetComm() ); +- MPI_Bcast(&node_minvz,1,MPI_DOUBLE,0,IssmComm::GetComm()); +- minvz=node_minvz; +- #endif +- +- /*Assign output pointers:*/ +- *pminvz=minvz; +-} +Index: ../trunk-jpl/src/c/modules/MinVelx/MinVelx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/MinVelx/MinVelx.cpp (revision 13873) ++++ ../trunk-jpl/src/c/modules/MinVelx/MinVelx.cpp (revision 13874) +@@ -1,43 +0,0 @@ +-/*!\file MinVelx +- * \brief: compute misfit between observations and model +- */ +- +-#include "./MinVelx.h" +- +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../../toolkits/toolkits.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +- +-void MinVelx( IssmDouble* pminvel, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units){ +- +- int i; +- IssmDouble minvel; +- IssmDouble node_minvel; +- IssmDouble element_minvel; +- +- /*Go through elements, and request velocity: */ +- for(i=0;iSize();i++){ +- Element* element=dynamic_cast(elements->GetObjectByOffset(i)); +- element->MinVel(&element_minvel,process_units); //go pick up the minimum velocity in the inputs +- +- if(i==0)minvel=element_minvel; //initialize minvel +- else{ +- if(element_minvelSize()==0){ +- minvel=INFINITY; +- } +- +- /*Figure out minimum across the cluster: */ +- #ifdef _HAVE_MPI_ +- MPI_Reduce (&minvel,&node_minvel,1,MPI_DOUBLE,MPI_MIN,0,IssmComm::GetComm() ); +- MPI_Bcast(&node_minvel,1,MPI_DOUBLE,0,IssmComm::GetComm()); +- minvel=node_minvel; +- #endif +- +- /*Assign output pointers:*/ +- *pminvel=minvel; +-} +Index: ../trunk-jpl/src/c/modules/MinVelx/MinVelx.h +=================================================================== +--- ../trunk-jpl/src/c/modules/MinVelx/MinVelx.h (revision 13873) ++++ ../trunk-jpl/src/c/modules/MinVelx/MinVelx.h (revision 13874) +@@ -1,14 +0,0 @@ +-/*!\file: MinVelx.h +- * \brief header file for inverse methods misfit computation +- */ +- +-#ifndef _MINVELX_H +-#define _MINVELX_H +- +-#include "../../Container/Container.h" +-#include "../../classes/objects/objects.h" +- +-/* local prototypes: */ +-void MinVelx( IssmDouble* pminvel, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units); +- +-#endif /* _MINVELX_H */ +Index: ../trunk-jpl/src/c/modules/MinVxx/MinVxx.h +=================================================================== +--- ../trunk-jpl/src/c/modules/MinVxx/MinVxx.h (revision 13873) ++++ ../trunk-jpl/src/c/modules/MinVxx/MinVxx.h (revision 13874) +@@ -1,14 +0,0 @@ +-/*!\file: MinVxx.h +- * \brief header file for inverse methods misfit computation +- */ +- +-#ifndef _MINVX_H +-#define _MINVX_H +- +-#include "../../Container/Container.h" +-#include "../../classes/objects/objects.h" +- +-/* local prototypes: */ +-void MinVxx( IssmDouble* pminvx, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units); +- +-#endif /* _MINVX_H */ +Index: ../trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp (revision 13873) ++++ ../trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp (revision 13874) +@@ -1,42 +0,0 @@ +-/*!\file MinVxx +- */ +- +-#include "./MinVxx.h" +- +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../../toolkits/toolkits.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +- +-void MinVxx( IssmDouble* pminvx, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units){ +- +- int i; +- IssmDouble minvx; +- IssmDouble node_minvx; +- IssmDouble element_minvx; +- +- /*Go through elements, and request velocity: */ +- for(i=0;iSize();i++){ +- Element* element=dynamic_cast(elements->GetObjectByOffset(i)); +- element->MinVx(&element_minvx,process_units); //go pick up the minimum velocity in the inputs +- +- if(i==0)minvx=element_minvx; //initialize minvx +- else{ +- if(element_minvxSize()==0){ +- minvx=INFINITY; +- } +- +- /*Figure out minimum across the cluster: */ +- #ifdef _HAVE_MPI_ +- MPI_Reduce (&minvx,&node_minvx,1,MPI_DOUBLE,MPI_MIN,0,IssmComm::GetComm() ); +- MPI_Bcast(&node_minvx,1,MPI_DOUBLE,0,IssmComm::GetComm()); +- minvx=node_minvx; +- #endif +- +- /*Assign output pointers:*/ +- *pminvx=minvx; +-} +Index: ../trunk-jpl/src/c/modules/MinVyx/MinVyx.h +=================================================================== +--- ../trunk-jpl/src/c/modules/MinVyx/MinVyx.h (revision 13873) ++++ ../trunk-jpl/src/c/modules/MinVyx/MinVyx.h (revision 13874) +@@ -1,14 +0,0 @@ +-/*!\file: MinVyx.h +- * \brief header file for inverse methods misfit computation +- */ +- +-#ifndef _MINVYX_H +-#define _MINVYX_H +- +-#include "../../Container/Container.h" +-#include "../../classes/objects/objects.h" +- +-/* local prototypes: */ +-void MinVyx( IssmDouble* pminvy, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units); +- +-#endif /* _MINVYX_H */ +Index: ../trunk-jpl/src/c/modules/MinVyx/MinVyx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/MinVyx/MinVyx.cpp (revision 13873) ++++ ../trunk-jpl/src/c/modules/MinVyx/MinVyx.cpp (revision 13874) +@@ -1,42 +0,0 @@ +-/*!\file MinVyx +- */ +- +-#include "./MinVyx.h" +- +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../../toolkits/toolkits.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +- +-void MinVyx( IssmDouble* pminvy, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units){ +- +- int i; +- IssmDouble minvy; +- IssmDouble node_minvy; +- IssmDouble element_minvy; +- +- /*Go through elements, and request velocity: */ +- for(i=0;iSize();i++){ +- Element* element=dynamic_cast(elements->GetObjectByOffset(i)); +- element->MinVy(&element_minvy,process_units); //go pick up the minimum velocity in the inputs +- +- if(i==0)minvy=element_minvy; //initialize minvy +- else{ +- if(element_minvySize()==0){ +- minvy=INFINITY; +- } +- +- /*Figure out minimum across the cluster: */ +- #ifdef _HAVE_MPI_ +- MPI_Reduce (&minvy,&node_minvy,1,MPI_DOUBLE,MPI_MIN,0,IssmComm::GetComm() ); +- MPI_Bcast(&node_minvy,1,MPI_DOUBLE,0,IssmComm::GetComm()); +- minvy=node_minvy; +- #endif +- +- /*Assign output pointers:*/ +- *pminvy=minvy; +-} +Index: ../trunk-jpl/src/c/modules/modules.h +=================================================================== +--- ../trunk-jpl/src/c/modules/modules.h (revision 13873) ++++ ../trunk-jpl/src/c/modules/modules.h (revision 13874) +@@ -66,10 +66,6 @@ + #include "./Mergesolutionfromftogx/Mergesolutionfromftogx.h" + #include "./MeshPartitionx/MeshPartitionx.h" + #include "./MeshProfileIntersectionx/MeshProfileIntersectionx.h" +-#include "./MinVelx/MinVelx.h" +-#include "./MinVxx/MinVxx.h" +-#include "./MinVyx/MinVyx.h" +-#include "./MinVzx/MinVzx.h" + #include "./SurfaceAbsVelMisfitx/SurfaceAbsVelMisfitx.h" + #include "./SurfaceRelVelMisfitx/SurfaceRelVelMisfitx.h" + #include "./SurfaceLogVelMisfitx/SurfaceLogVelMisfitx.h" +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13873) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13874) +@@ -481,15 +481,7 @@ + ./solutions/balancethickness_core.cpp + #}}} + #Responses sources {{{ +-responses_sources = ./modules/MinVelx/MinVelx.h\ +- ./modules/MinVelx/MinVelx.cpp\ +- ./modules/MinVxx/MinVxx.h\ +- ./modules/MinVxx/MinVxx.cpp\ +- ./modules/MinVyx/MinVyx.h\ +- ./modules/MinVyx/MinVyx.cpp\ +- ./modules/MinVzx/MinVzx.h\ +- ./modules/MinVzx/MinVzx.cpp\ +- ./modules/TotalSmbx/TotalSmbx.h\ ++responses_sources = ./modules/TotalSmbx/TotalSmbx.h\ + ./modules/TotalSmbx/TotalSmbx.cpp\ + ./modules/IceVolumex/IceVolumex.h\ + ./modules/IceVolumex/IceVolumex.cpp\ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13873) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13874) +@@ -404,15 +404,15 @@ + + #ifdef _HAVE_RESPONSES_ + case IceVolumeEnum: IceVolumex( responses, elements,nodes, vertices, loads, materials, parameters,process_units); break; +- case MinVelEnum: MinVelx( responses, elements,nodes, vertices, loads, materials, parameters,process_units); break; ++ case MinVelEnum: this->MinVelx(responses,process_units); break; + case MaxVelEnum: this->MaxVelx( responses,process_units); break; +- case MinVxEnum: MinVxx( responses, elements,nodes, vertices, loads, materials, parameters,process_units); break; ++ case MinVxEnum: this->MinVxx(responses,process_units); break; + case MaxVxEnum: this->MaxVxx( responses,process_units); break; + case MaxAbsVxEnum: this->MaxAbsVxx( responses,process_units); break; +- case MinVyEnum: MinVyx( responses, elements,nodes, vertices, loads, materials, parameters,process_units); break; ++ case MinVyEnum: this->MinVyx(responses,process_units); break; + case MaxVyEnum: this->MaxVyx( responses,process_units); break; + case MaxAbsVyEnum: this->MaxAbsVyx( responses,process_units); break; +- case MinVzEnum: MinVzx( responses, elements,nodes, vertices, loads, materials, parameters,process_units); break; ++ case MinVzEnum: this->MinVzx(responses,process_units); break; + case MaxVzEnum: this->MaxVzx( responses,process_units); break; + case MaxAbsVzEnum: this->MaxAbsVzx( responses,process_units); break; + case MassFluxEnum: this->MassFluxx( responses,process_units); break; +@@ -792,7 +792,111 @@ + *pmaxvz=maxvz; + + }/*}}}*/ ++void FemModel::MinVelx(IssmDouble* pminvel,bool process_units){/*{{{*/ ++ ++ int i; ++ IssmDouble minvel; ++ IssmDouble node_minvel; ++ IssmDouble element_minvel; ++ ++ /*Go through elements, and request velocity: */ ++ minvel=INFINITY; ++ for(i=0;ielements->Size();i++){ ++ Element* element=(Element*)this->elements->GetObjectByOffset(i); ++ element->MinVel(&element_minvel,process_units); ++ if(element_minvelelements->Size();i++){ ++ Element* element=(Element*)this->elements->GetObjectByOffset(i); ++ element->MinVx(&element_minvx,process_units); ++ if(element_minvxelements->Size();i++){ ++ Element* element=(Element*)this->elements->GetObjectByOffset(i); ++ element->MinVy(&element_minvy,process_units); ++ if(element_minvyelements->Size();i++){ ++ Element* element=(Element*)this->elements->GetObjectByOffset(i); ++ element->MinVz(&element_minvz,process_units); ++ if(element_minvzSize();i++){ +- Element* element=dynamic_cast(elements->GetObjectByOffset(i)); +- local_ice_volume+=element->IceVolume(); +- } +- #ifdef _HAVE_MPI_ +- MPI_Reduce(&local_ice_volume,&total_ice_volume,1,MPI_DOUBLE,MPI_SUM,0,IssmComm::GetComm() ); +- MPI_Bcast(&total_ice_volume,1,MPI_DOUBLE,0,IssmComm::GetComm()); +- #else +- total_ice_volume=local_ice_volume; +- #endif +- +- /*Assign output pointers: */ +- *pV=total_ice_volume; +-} +Index: ../trunk-jpl/src/c/modules/IceVolumex/IceVolumex.h +=================================================================== +--- ../trunk-jpl/src/c/modules/IceVolumex/IceVolumex.h (revision 13874) ++++ ../trunk-jpl/src/c/modules/IceVolumex/IceVolumex.h (revision 13875) +@@ -1,14 +0,0 @@ +-/*!\file: IceVolumex.h +- * \brief header file for inverse methods misfit computation +- */ +- +-#ifndef _ICEVOLUMEX_H +-#define _ICEVOLUMEX_H +- +-#include "../../Container/Container.h" +-#include "../../classes/objects/objects.h" +- +-/* local prototypes: */ +-void IceVolumex(IssmDouble* pV, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units); +- +-#endif +Index: ../trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.cpp (revision 13874) ++++ ../trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.cpp (revision 13875) +@@ -1,56 +0,0 @@ +-/*!\file ElementResponsex +- * \brief: compute element input on one element only +- */ +- +-#include "./ElementResponsex.h" +- +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../../toolkits/toolkits.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +- +-void ElementResponsex( IssmDouble* presponse, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,int response_enum,bool process_units){ +- +- int my_rank; +- int i; +- +- int found=0; +- int sumfound=0; +- int cpu_found=-1; +- int index; +- IssmDouble response; +- Element* element=NULL; +- +- /*retrieve element we are interested in: */ +- parameters->FindParam(&index,IndexEnum); +- my_rank=IssmComm::GetRank(); +- +- /*now, go through our elements, and retrieve the one with this id: index: */ +- for(i=0;iSize();i++){ +- element=dynamic_cast(elements->GetObjectByOffset(i)); +- if (element->Id()==index){ +- found=1; +- cpu_found=my_rank; +- break; +- } +- } +- +- /*Broadcast whether we found the element: */ +- #ifdef _HAVE_MPI_ +- MPI_Allreduce ( &found,&sumfound,1,MPI_INT,MPI_SUM,IssmComm::GetComm()); +- if(!sumfound)_error_("could not find material with id" << index << " to compute ElementResponse"); +- #endif +- +- /*Ok, we found the element, compute responseocity: */ +- if(my_rank==cpu_found){ +- element->ElementResponse(&response,response_enum,IuToExtEnum); +- } +- +- /*Broadcast and plug into response: */ +- #ifdef _HAVE_MPI_ +- MPI_Allreduce ( &cpu_found,&cpu_found,1,MPI_INT,MPI_MAX,IssmComm::GetComm()); +- MPI_Bcast(&response,1,MPI_DOUBLE,cpu_found,IssmComm::GetComm()); +- #endif +- +- *presponse=response; +-} +Index: ../trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.h +=================================================================== +--- ../trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.h (revision 13874) ++++ ../trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.h (revision 13875) +@@ -1,14 +0,0 @@ +-/*!\file: ElementResponsex.h +- * \brief header file for computing input average over one element +- */ +- +-#ifndef _ELEMENTRESPONSEX_H +-#define _ELEMENTRESPONSEX_H +- +-#include "../../Container/Container.h" +-#include "../../classes/objects/objects.h" +- +-/* local prototypes: */ +-void ElementResponsex( IssmDouble* presponse, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,int response_enum,bool process_units); +- +-#endif /* _ELEMENTRESPONSEX_H */ +Index: ../trunk-jpl/src/c/modules/TotalSmbx/TotalSmbx.h +=================================================================== +--- ../trunk-jpl/src/c/modules/TotalSmbx/TotalSmbx.h (revision 13874) ++++ ../trunk-jpl/src/c/modules/TotalSmbx/TotalSmbx.h (revision 13875) +@@ -1,14 +0,0 @@ +-/*!\file: TotalSmbx.h +- * \brief header file for inverse methods misfit computation +- */ +- +-#ifndef _TOTALSMBX_H +-#define _TOTALSMBX_H +- +-#include "../../Container/Container.h" +-#include "../../classes/objects/objects.h" +- +-/* local prototypes: */ +-void TotalSmbx(IssmDouble* pSmb, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,bool process_units); +- +-#endif +Index: ../trunk-jpl/src/c/modules/TotalSmbx/TotalSmbx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/TotalSmbx/TotalSmbx.cpp (revision 13874) ++++ ../trunk-jpl/src/c/modules/TotalSmbx/TotalSmbx.cpp (revision 13875) +@@ -1,30 +0,0 @@ +-/*!\file TotalSmbx +- * \brief: compute total ice sheet surface mass balance +- */ +- +-#include "./TotalSmbx.h" +- +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../../toolkits/toolkits.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +- +-void TotalSmbx(IssmDouble* pSmb, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials,Parameters* parameters,bool process_units){ +- +- IssmDouble local_smb = 0; +- IssmDouble total_smb; +- +- for(int i=0;iSize();i++){ +- Element* element=dynamic_cast(elements->GetObjectByOffset(i)); +- local_smb+=element->TotalSmb(); +- } +- #ifdef _HAVE_MPI_ +- MPI_Reduce(&local_smb,&total_smb,1,MPI_DOUBLE,MPI_SUM,0,IssmComm::GetComm() ); +- MPI_Bcast(&total_smb,1,MPI_DOUBLE,0,IssmComm::GetComm()); +- #else +- total_smb=local_smb; +- #endif +- +- /*Assign output pointers: */ +- *pSmb=total_smb; +-} +Index: ../trunk-jpl/src/c/modules/modules.h +=================================================================== +--- ../trunk-jpl/src/c/modules/modules.h (revision 13874) ++++ ../trunk-jpl/src/c/modules/modules.h (revision 13875) +@@ -33,8 +33,6 @@ + #include "./Gradjx/Gradjx.h" + #include "./GroundinglineMigrationx/GroundinglineMigrationx.h" + #include "./HoleFillerx/HoleFillerx.h" +-#include "./TotalSmbx/TotalSmbx.h" +-#include "./IceVolumex/IceVolumex.h" + #include "./InputControlUpdatex/InputControlUpdatex.h" + #include "./InputConvergencex/InputConvergencex.h" + #include "./InputDuplicatex/InputDuplicatex.h" +@@ -62,7 +60,6 @@ + #include "./Kml2Expx/Kml2Expx.h" + #include "./Krigingx/Krigingx.h" + #include "./Shp2Kmlx/Shp2Kmlx.h" +-#include "./ElementResponsex/ElementResponsex.h" + #include "./Mergesolutionfromftogx/Mergesolutionfromftogx.h" + #include "./MeshPartitionx/MeshPartitionx.h" + #include "./MeshProfileIntersectionx/MeshProfileIntersectionx.h" +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13874) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13875) +@@ -480,14 +480,6 @@ + ./modules/ModelProcessorx/Balancethickness/CreateLoadsBalancethickness.cpp\ + ./solutions/balancethickness_core.cpp + #}}} +-#Responses sources {{{ +-responses_sources = ./modules/TotalSmbx/TotalSmbx.h\ +- ./modules/TotalSmbx/TotalSmbx.cpp\ +- ./modules/IceVolumex/IceVolumex.h\ +- ./modules/IceVolumex/IceVolumex.cpp\ +- ./modules/ElementResponsex/ElementResponsex.h\ +- ./modules/ElementResponsex/ElementResponsex.cpp +-#}}} + #Slope sources {{{ + slope_sources = ./modules/ModelProcessorx/BedSlope/UpdateElementsBedSlope.cpp\ + ./modules/ModelProcessorx/BedSlope/CreateNodesBedSlope.cpp \ +@@ -862,10 +854,6 @@ + issm_sources += $(balanced_sources) + endif + +-if RESPONSES +-issm_sources += $(responses_sources) +-endif +- + if SLOPE + issm_sources += $(slope_sources) + endif +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13874) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13875) +@@ -403,7 +403,7 @@ + switch (response_descriptor_enum){ + + #ifdef _HAVE_RESPONSES_ +- case IceVolumeEnum: IceVolumex( responses, elements,nodes, vertices, loads, materials, parameters,process_units); break; ++ case IceVolumeEnum: this->IceVolumex(responses,process_units); break; + case MinVelEnum: this->MinVelx(responses,process_units); break; + case MaxVelEnum: this->MaxVelx( responses,process_units); break; + case MinVxEnum: this->MinVxx(responses,process_units); break; +@@ -415,21 +415,21 @@ + case MinVzEnum: this->MinVzx(responses,process_units); break; + case MaxVzEnum: this->MaxVzx( responses,process_units); break; + case MaxAbsVzEnum: this->MaxAbsVzx( responses,process_units); break; +- case MassFluxEnum: this->MassFluxx( responses,process_units); break; +- case SurfaceAbsVelMisfitEnum: SurfaceAbsVelMisfitx( responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; +- case SurfaceRelVelMisfitEnum: SurfaceRelVelMisfitx( responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; +- case SurfaceLogVelMisfitEnum: SurfaceLogVelMisfitx( responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; +- case SurfaceLogVxVyMisfitEnum: SurfaceLogVxVyMisfitx( responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; ++ case MassFluxEnum: this->MassFluxx( responses,process_units); break; ++ case SurfaceAbsVelMisfitEnum: SurfaceAbsVelMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; ++ case SurfaceRelVelMisfitEnum: SurfaceRelVelMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; ++ case SurfaceLogVelMisfitEnum: SurfaceLogVelMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; ++ case SurfaceLogVxVyMisfitEnum: SurfaceLogVxVyMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; + case SurfaceAverageVelMisfitEnum:SurfaceAverageVelMisfitx( responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; +- case ThicknessAbsMisfitEnum: ThicknessAbsMisfitx( responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; +- case ThicknessAbsGradientEnum: this->ThicknessAbsGradientx( responses, process_units,weight_index); break; +- case ThicknessAlongGradientEnum: ThicknessAlongGradientx( responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; +- case ThicknessAcrossGradientEnum:ThicknessAcrossGradientx( responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; +- case TotalSmbEnum: TotalSmbx( responses, elements,nodes, vertices, loads, materials, parameters,process_units); break; +- case RheologyBbarAbsGradientEnum:RheologyBbarAbsGradientx( responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; ++ case ThicknessAbsMisfitEnum: ThicknessAbsMisfitx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; ++ case ThicknessAbsGradientEnum: this->ThicknessAbsGradientx(responses, process_units,weight_index); break; ++ case ThicknessAlongGradientEnum: ThicknessAlongGradientx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; ++ case ThicknessAcrossGradientEnum:ThicknessAcrossGradientx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; ++ case TotalSmbEnum: this->TotalSmbx(responses,process_units); break; ++ case RheologyBbarAbsGradientEnum:RheologyBbarAbsGradientx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; + case DragCoefficientAbsGradientEnum:DragCoefficientAbsGradientx(responses, elements,nodes, vertices, loads, materials, parameters,process_units,weight_index); break; +- case MaterialsRheologyBbarEnum:ElementResponsex(responses, elements,nodes, vertices, loads, materials, parameters,MaterialsRheologyBbarEnum,process_units); break; +- case VelEnum:ElementResponsex(responses, elements,nodes, vertices, loads, materials, parameters,VelEnum,process_units); break; ++ case MaterialsRheologyBbarEnum: this->ElementResponsex(responses,MaterialsRheologyBbarEnum,process_units); break; ++ case VelEnum: this->ElementResponsex(responses,VelEnum,process_units); break; + case FrictionCoefficientEnum:NodalValuex(responses, FrictionCoefficientEnum,elements,nodes, vertices, loads, materials, parameters,process_units); break; + default: _error_("response descriptor \"" << EnumToStringx(response_descriptor_enum) << "\" not supported yet!"); break; + #else +@@ -896,7 +896,91 @@ + *pminvz=minvz; + + }/*}}}*/ ++void FemModel::TotalSmbx(IssmDouble* pSmb,bool process_units){/*{{{*/ ++ ++ IssmDouble local_smb = 0; ++ IssmDouble total_smb; ++ ++ for(int i=0;ielements->Size();i++){ ++ Element* element=dynamic_cast(this->elements->GetObjectByOffset(i)); ++ local_smb+=element->TotalSmb(); ++ } ++#ifdef _HAVE_MPI_ ++ MPI_Reduce(&local_smb,&total_smb,1,MPI_DOUBLE,MPI_SUM,0,IssmComm::GetComm() ); ++ MPI_Bcast(&total_smb,1,MPI_DOUBLE,0,IssmComm::GetComm()); ++#else ++ total_smb=local_smb; + #endif ++ ++ /*Assign output pointers: */ ++ *pSmb=total_smb; ++ ++}/*}}}*/ ++void FemModel::IceVolumex(IssmDouble* pV,bool process_units){/*{{{*/ ++ ++ IssmDouble local_ice_volume = 0; ++ IssmDouble total_ice_volume; ++ ++ for(int i=0;ielements->Size();i++){ ++ Element* element=dynamic_cast(this->elements->GetObjectByOffset(i)); ++ local_ice_volume+=element->IceVolume(); ++ } ++ #ifdef _HAVE_MPI_ ++ MPI_Reduce(&local_ice_volume,&total_ice_volume,1,MPI_DOUBLE,MPI_SUM,0,IssmComm::GetComm() ); ++ MPI_Bcast(&total_ice_volume,1,MPI_DOUBLE,0,IssmComm::GetComm()); ++ #else ++ total_ice_volume=local_ice_volume; ++ #endif ++ ++ /*Assign output pointers: */ ++ *pV=total_ice_volume; ++ ++}/*}}}*/ ++void FemModel::ElementResponsex(IssmDouble* presponse,int response_enum,bool process_units){/*{{{*/ ++ ++ int found=0; ++ int sumfound=0; ++ int cpu_found=-1; ++ int index; ++ IssmDouble response; ++ Element* element=NULL; ++ ++ /*retrieve element we are interested in: */ ++ this->parameters->FindParam(&index,IndexEnum); ++ int my_rank=IssmComm::GetRank(); ++ ++ /*now, go through our elements, and retrieve the one with this id: index: */ ++ for(int i=0;ielements->Size();i++){ ++ element=dynamic_cast(this->elements->GetObjectByOffset(i)); ++ if (element->Id()==index){ ++ found=1; ++ cpu_found=my_rank; ++ break; ++ } ++ } ++ ++ /*Broadcast whether we found the element: */ ++#ifdef _HAVE_MPI_ ++ MPI_Allreduce ( &found,&sumfound,1,MPI_INT,MPI_SUM,IssmComm::GetComm()); ++ if(!sumfound)_error_("could not find material with id" << index << " to compute ElementResponse"); ++#endif ++ ++ /*Ok, we found the element, compute responseocity: */ ++ if(my_rank==cpu_found){ ++ element->ElementResponse(&response,response_enum,IuToExtEnum); ++ } ++ ++ /*Broadcast and plug into response: */ ++#ifdef _HAVE_MPI_ ++ MPI_Allreduce ( &cpu_found,&cpu_found,1,MPI_INT,MPI_MAX,IssmComm::GetComm()); ++ MPI_Bcast(&response,1,MPI_DOUBLE,cpu_found,IssmComm::GetComm()); ++#endif ++ ++ /*Assign output pointers: */ ++ *presponse=response; ++ ++}/*}}}*/ ++#endif + #ifdef _HAVE_CONTROL_ + void FemModel::ThicknessAbsGradientx( IssmDouble* pJ, bool process_units, int weight_index){/*{{{*/ + +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 13874) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 13875) +@@ -73,6 +73,9 @@ + void MinVxx(IssmDouble* presponse,bool process_units); + void MinVyx(IssmDouble* presponse,bool process_units); + void MinVzx(IssmDouble* presponse,bool process_units); ++ void TotalSmbx(IssmDouble* pSmb,bool process_units); ++ void IceVolumex(IssmDouble* pV,bool process_units); ++ void ElementResponsex(IssmDouble* presponse,int response_enum,bool process_units); + #endif + #ifdef _HAVE_DAKOTA_ + void DakotaResponsesx(double* d_responses,char** responses_descriptors,int numresponsedescriptors,int d_numresponses); Index: /issm/oecreview/Archive/13393-13976/ISSM-13875-13876.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13875-13876.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13875-13876.diff (revision 13980) @@ -0,0 +1,77 @@ +Index: ../trunk-jpl/src/c/modules/SmearFunctionx/SmearFunctionx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/SmearFunctionx/SmearFunctionx.cpp (revision 13875) ++++ ../trunk-jpl/src/c/modules/SmearFunctionx/SmearFunctionx.cpp (revision 13876) +@@ -1,52 +0,0 @@ +-/*!\file SmearFunctionx +- * \brief: create +- */ +- +-#include "./SmearFunctionx.h" +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../../io/io.h" +-#include "../../toolkits/toolkits.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +- +-void SmearFunctionx(Vec* psmearedvector,double (*WeightFunction)(double distance,double radius), int SmearedFieldEnum, double radius,Elements* elements,Nodes* nodes, Parameters* parameters){ +- +- Element *element = NULL; +- Vec x=NULL; +- Vec y=NULL; +- Vec z=NULL; +- Vec smearedvector=NULL; +- int i; +- +- double* x_serial=NULL; +- double* y_serial=NULL; +- double* z_serial=NULL; +- +- /*retrive parameters: */ +- parameters->FindParam(&configuration_type,ConfigurationTypeEnum); +- +- /*allocate: */ +- gsize=nodes->NumberOfDofs(configuration_type,GsetEnum); +- smearedvector=NewVec(gsize,IssmComm::GetComm()); +- +- x=NewVec(gsize,IssmComm::GetComm()); +- y=NewVec(gsize,IssmComm::GetComm()); +- z=NewVec(gsize,IssmComm::GetComm()); +- +- for(i=0;iSize();i++){ +- +- } +- +- /*Fill smearedvector vector: */ +- for (i=0;iSize();i++){ +- element=dynamic_cast(elements->GetObjectByOffset(i)); +- element->SmearFunction(smearedvector,WeightFunction,SmearedFieldEnum,radius); +- } +- +- VecAssemblyBegin(smearedvector); +- VecAssemblyEnd(smearedvector); +- +- /*Assign output pointers: */ +- *psmearedvector=smearedvector; +- +-} +Index: ../trunk-jpl/src/c/modules/SmearFunctionx/SmearFunctionx.h +=================================================================== +--- ../trunk-jpl/src/c/modules/SmearFunctionx/SmearFunctionx.h (revision 13875) ++++ ../trunk-jpl/src/c/modules/SmearFunctionx/SmearFunctionx.h (revision 13876) +@@ -1,15 +0,0 @@ +-/*!\file: SystemMatricesx.h +- * \brief header file for degree of freedoms distribution routines. +- */ +- +-#ifndef _SYSTEMMATRICESX_H +-#define _SYSTEMMATRICESX_H +- +-#include "../../Container/Container.h" +-#include "../../classes/objects/objects.h" +- +-/* local prototypes: */ +-void SystemMatricesx(Mat* pKff, Mat* pKfs, Vec* ppf, Vec* pdf, double* pkmax,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters, +- bool kflag=true,bool pflag=true,bool penalty_kflag=true,bool penalty_pflag=true); +- +-#endif /* _SYSTEMMATRICESX_H */ Index: /issm/oecreview/Archive/13393-13976/ISSM-13876-13877.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13876-13877.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13876-13877.diff (revision 13980) @@ -0,0 +1,460 @@ +Index: ../trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 13876) ++++ ../trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.cpp (revision 13877) +@@ -1,129 +0,0 @@ +-/*!\file SystemMatricesx +- * \brief: create system matrices (stiffness matrix, loads vector) +- */ +- +-#include "./SystemMatricesx.h" +-#include "../../shared/shared.h" +-#include "../../include/include.h" +-#include "../../io/io.h" +-#include "../../toolkits/toolkits.h" +-#include "../../EnumDefinitions/EnumDefinitions.h" +- +-void SystemMatricesx(Matrix** pKff, Matrix** pKfs, Vector** ppf, Vector** pdf, IssmDouble* pkmax,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters,bool kflag,bool pflag,bool penalty_kflag,bool penalty_pflag){ +- +- /*intermediary: */ +- int i; +- int fsize,ssize; +- int connectivity, numberofdofspernode; +- int analysis_type, configuration_type; +- Element *element = NULL; +- Load *load = NULL; +- +- /*output: */ +- Matrix* Kff = NULL; +- Matrix* Kfs = NULL; +- Vector* pf = NULL; +- Vector* df=NULL; +- IssmDouble kmax = 0; +- +- /*Display message*/ +- if(VerboseModule()) _pprintLine_(" Generating matrices"); +- +- /*retrive parameters: */ +- parameters->FindParam(&analysis_type,AnalysisTypeEnum); +- parameters->FindParam(&configuration_type,ConfigurationTypeEnum); +- parameters->FindParam(&connectivity,MeshAverageVertexConnectivityEnum); +- +- /*Get size of matrices: */ +- fsize=nodes->NumberOfDofs(configuration_type,FsetEnum); +- ssize=nodes->NumberOfDofs(configuration_type,SsetEnum); +- +- numberofdofspernode=nodes->MaxNumDofs(configuration_type,GsetEnum); +- +- /*Checks in debugging mode {{{*/ +- if(penalty_kflag)_assert_(kflag); +- if(penalty_pflag)_assert_(pflag); +- /*}}}*/ +- +- /*Compute penalty free mstiffness matrix and load vector*/ +- if(kflag){ +- +- Kff=new Matrix(fsize,fsize,connectivity,numberofdofspernode); +- Kfs=new Matrix(fsize,ssize,connectivity,numberofdofspernode); +- df=new Vector(fsize); +- +- /*Fill stiffness matrix from elements: */ +- for (i=0;iSize();i++){ +- element=dynamic_cast(elements->GetObjectByOffset(i)); +- element->CreateKMatrix(Kff,Kfs,df); +- } +- +- /*Fill stiffness matrix from loads if loads have the current configuration_type: */ +- for (i=0;iSize();i++){ +- load=dynamic_cast(loads->GetObjectByOffset(i)); +- if (load->InAnalysis(configuration_type)) load->CreateKMatrix(Kff,Kfs); +- } +- +- /*Assemble matrix and doftypes and compress matrix to save memory: */ +- Kff->Assemble(); +- Kfs->Assemble(); +- df->Assemble(); +- } +- +- if(pflag){ +- +- pf=new Vector(fsize); +- +- /*Fill right hand side vector, from elements: */ +- for (i=0;iSize();i++){ +- element=dynamic_cast(elements->GetObjectByOffset(i)); +- element->CreatePVector(pf); +- } +- +- /*Fill right hand side from loads if loads have the current configuration_type: */ +- for (i=0;iSize();i++){ +- load=dynamic_cast(loads->GetObjectByOffset(i)); +- if (load->InAnalysis(configuration_type)) load->CreatePVector(pf); +- } +- pf->Assemble(); +- } +- +- /*Now, figure out maximum value of K_gg, so that we can penalize it correctly: */ +- kmax=Kff->Norm(NORM_INF); +- +- /*Now, deal with penalties*/ +- if(penalty_kflag){ +- +- /*Fill stiffness matrix from loads: */ +- for (i=0;iSize();i++){ +- load=dynamic_cast(loads->GetObjectByOffset(i)); +- if (load->InAnalysis(configuration_type)) load->PenaltyCreateKMatrix(Kff,Kfs,kmax); +- } +- +- /*Assemble matrix and compress matrix to save memory: */ +- Kff->Assemble(); +- Kfs->Assemble(); +- } +- +- if(penalty_pflag){ +- +- /*Fill right hand side vector, from loads: */ +- for (i=0;iSize();i++){ +- load=dynamic_cast(loads->GetObjectByOffset(i)); +- if (load->InAnalysis(configuration_type)) load->PenaltyCreatePVector(pf,kmax); +- } +- +- pf->Assemble(); +- } +- +- /*Assign output pointers: */ +- if(pKff) *pKff=Kff; +- else xdelete(&Kff); +- if(pKfs) *pKfs=Kfs; +- else xdelete(&Kfs); +- if(ppf) *ppf=pf; +- else xdelete(&pf); +- if(pdf) *pdf=df; +- else xdelete(&df); +- if(pkmax) *pkmax=kmax; +-} +Index: ../trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.h +=================================================================== +--- ../trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.h (revision 13876) ++++ ../trunk-jpl/src/c/modules/SystemMatricesx/SystemMatricesx.h (revision 13877) +@@ -1,15 +0,0 @@ +-/*!\file: SystemMatricesx.h +- * \brief header file for degree of freedoms distribution routines. +- */ +- +-#ifndef _SYSTEMMATRICESX_H +-#define _SYSTEMMATRICESX_H +- +-#include "../../Container/Container.h" +-#include "../../classes/objects/objects.h" +- +-/* local prototypes: */ +-void SystemMatricesx(Matrix** pKff, Matrix** pKfs, Vector** ppf, Vector** pdf, IssmDouble* pkmax,Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads,Materials* materials, Parameters* parameters, +- bool kflag=true,bool pflag=true,bool penalty_kflag=true,bool penalty_pflag=true); +- +-#endif /* _SYSTEMMATRICESX_H */ +Index: ../trunk-jpl/src/c/modules/modules.h +=================================================================== +--- ../trunk-jpl/src/c/modules/modules.h (revision 13876) ++++ ../trunk-jpl/src/c/modules/modules.h (revision 13877) +@@ -90,7 +90,6 @@ + #include "./Solverx/Solverx.h" + #include "./SpcNodesx/SpcNodesx.h" + #include "./SurfaceAreax/SurfaceAreax.h" +-#include "./SystemMatricesx/SystemMatricesx.h" + #include "./CreateJacobianMatrixx/CreateJacobianMatrixx.h" + #include "./TriaSearchx/TriaSearchx.h" + #include "./TriMeshx/TriMeshx.h" +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 13876) ++++ ../trunk-jpl/src/c/Makefile.am (revision 13877) +@@ -298,8 +298,6 @@ + ./modules/EnumToStringx/EnumToStringx.h\ + ./modules/StringToEnumx/StringToEnumx.cpp\ + ./modules/StringToEnumx/StringToEnumx.h\ +- ./modules/SystemMatricesx/SystemMatricesx.cpp\ +- ./modules/SystemMatricesx/SystemMatricesx.h\ + ./modules/CreateJacobianMatrixx/CreateJacobianMatrixx.cpp\ + ./modules/CreateJacobianMatrixx/CreateJacobianMatrixx.h\ + ./modules/ConstraintsStatex/ConstraintsStatex.cpp\ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13876) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13877) +@@ -517,6 +517,110 @@ + } + } + /*}}}*/ ++void FemModel::SystemMatricesx(Matrix** pKff, Matrix** pKfs, Vector** ppf, Vector** pdf, IssmDouble* pkmax){/*{{{*/ ++ ++ /*intermediary: */ ++ int i; ++ int fsize,ssize; ++ int connectivity, numberofdofspernode; ++ int analysis_type, configuration_type; ++ Element *element = NULL; ++ Load *load = NULL; ++ ++ /*output: */ ++ Matrix *Kff = NULL; ++ Matrix *Kfs = NULL; ++ Vector *pf = NULL; ++ Vector *df = NULL; ++ IssmDouble kmax; ++ ++ /*Display message*/ ++ if(VerboseModule()) _pprintLine_(" Generating matrices"); ++ ++ /*retrive parameters: */ ++ this->parameters->FindParam(&analysis_type,AnalysisTypeEnum); ++ this->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); ++ this->parameters->FindParam(&connectivity,MeshAverageVertexConnectivityEnum); ++ ++ /*Get size of matrices: */ ++ fsize=this->nodes->NumberOfDofs(configuration_type,FsetEnum); ++ ssize=this->nodes->NumberOfDofs(configuration_type,SsetEnum); ++ ++ numberofdofspernode=this->nodes->MaxNumDofs(configuration_type,GsetEnum); ++ ++ /*Compute penalty free mstiffness matrix and load vector*/ ++ Kff=new Matrix(fsize,fsize,connectivity,numberofdofspernode); ++ Kfs=new Matrix(fsize,ssize,connectivity,numberofdofspernode); ++ df =new Vector(fsize); ++ ++ /*Fill stiffness matrix from elements: */ ++ for (i=0;ielements->Size();i++){ ++ element=dynamic_cast(this->elements->GetObjectByOffset(i)); ++ element->CreateKMatrix(Kff,Kfs,df); ++ } ++ ++ /*Fill stiffness matrix from loads if loads have the current configuration_type: */ ++ for (i=0;iloads->Size();i++){ ++ load=dynamic_cast(this->loads->GetObjectByOffset(i)); ++ if (load->InAnalysis(configuration_type)) load->CreateKMatrix(Kff,Kfs); ++ } ++ ++ /*Assemble matrices*/ ++ Kff->Assemble(); ++ Kfs->Assemble(); ++ df->Assemble(); ++ ++ /*Create Load vector*/ ++ pf=new Vector(fsize); ++ ++ /*Fill right hand side vector, from elements: */ ++ for (i=0;ielements->Size();i++){ ++ element=dynamic_cast(this->elements->GetObjectByOffset(i)); ++ element->CreatePVector(pf); ++ } ++ ++ /*Fill right hand side from loads if loads have the current configuration_type: */ ++ for (i=0;iloads->Size();i++){ ++ load=dynamic_cast(this->loads->GetObjectByOffset(i)); ++ if (load->InAnalysis(configuration_type)) load->CreatePVector(pf); ++ } ++ pf->Assemble(); ++ ++ /*Now, figure out maximum value of K_gg, so that we can penalize it correctly: */ ++ kmax=Kff->Norm(NORM_INF); ++ ++ /*Now, deal with penalties*/ ++ /*Fill stiffness matrix from loads: */ ++ for (i=0;iloads->Size();i++){ ++ load=dynamic_cast(this->loads->GetObjectByOffset(i)); ++ if (load->InAnalysis(configuration_type)) load->PenaltyCreateKMatrix(Kff,Kfs,kmax); ++ } ++ ++ /*Assemble matrices*/ ++ Kff->Assemble(); ++ Kfs->Assemble(); ++ ++ /*Fill right hand side vector, from loads: */ ++ for (i=0;iloads->Size();i++){ ++ load=dynamic_cast(this->loads->GetObjectByOffset(i)); ++ if (load->InAnalysis(configuration_type)) load->PenaltyCreatePVector(pf,kmax); ++ } ++ ++ /*Assemble vector*/ ++ pf->Assemble(); ++ ++ /*Assign output pointers: */ ++ if(pKff) *pKff=Kff; ++ else xdelete(&Kff); ++ if(pKfs) *pKfs=Kfs; ++ else xdelete(&Kfs); ++ if(ppf) *ppf=pf; ++ else xdelete(&pf); ++ if(pdf) *pdf=df; ++ else xdelete(&df); ++ if(pkmax) *pkmax=kmax; ++} ++/*}}}*/ + void FemModel::TimeAdaptx(IssmDouble* pdt){/*{{{*/ + + int i; +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 13876) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 13877) +@@ -88,6 +88,7 @@ + void CostFunctionx( IssmDouble* pJ); + void ThicknessAbsGradientx( IssmDouble* pJ, bool process_units,int weight_index); + #endif ++ void SystemMatricesx(Matrix** pKff, Matrix** pKfs, Vector** ppf, Vector** pdf, IssmDouble* pkmax); + void TimeAdaptx(IssmDouble* pdt); + void UpdateConstraintsx(void); + int UpdateVertexPositionsx(void); +Index: ../trunk-jpl/src/c/solvers/solver_nonlinear.cpp +=================================================================== +--- ../trunk-jpl/src/c/solvers/solver_nonlinear.cpp (revision 13876) ++++ ../trunk-jpl/src/c/solvers/solver_nonlinear.cpp (revision 13877) +@@ -23,7 +23,7 @@ + Vector* df = NULL; + Vector* ys = NULL; + +- Loads* loads=NULL; ++ Loads* savedloads=NULL; + bool converged; + int constraints_converged; + int num_unstable_constraints; +@@ -32,7 +32,7 @@ + /*parameters:*/ + int min_mechanical_constraints; + int max_nonlinear_iterations; +- int configuration_type; ++ int configuration_type; + + /*Recover parameters: */ + femmodel->parameters->FindParam(&min_mechanical_constraints,DiagnosticRiftPenaltyThresholdEnum); +@@ -41,14 +41,15 @@ + femmodel->UpdateConstraintsx(); + + /*Were loads requested as output? : */ +- if(conserve_loads) loads=static_cast(femmodel->loads->Copy()); //protect loads from being modified by the solution +- else loads=static_cast(femmodel->loads); //modify loads in this solution ++ if(conserve_loads){ ++ savedloads = static_cast(femmodel->loads->Copy()); ++ } + + count=1; + converged=false; + + /*Start non-linear iteration using input velocity: */ +- GetSolutionFromInputsx(&ug, femmodel->elements, femmodel->nodes, femmodel->vertices, loads, femmodel->materials, femmodel->parameters); ++ GetSolutionFromInputsx(&ug, femmodel->elements, femmodel->nodes, femmodel->vertices,femmodel->loads, femmodel->materials, femmodel->parameters); + Reducevectorgtofx(&uf, ug, femmodel->nodes,femmodel->parameters); + + //Update once again the solution to make sure that vx and vxold are similar (for next step in transient or steadystate) +@@ -61,7 +62,7 @@ + xdelete(&old_ug);old_ug=ug; + xdelete(&old_uf);old_uf=uf; + +- SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,loads,femmodel->materials,femmodel->parameters); ++ femmodel->SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); + Reduceloadx(pf, Kfs, ys); xdelete(&Kfs); + Solverx(&uf, Kff, pf, old_uf, df, femmodel->parameters); +@@ -71,7 +72,7 @@ + InputUpdateFromConstantx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,converged,ConvergedEnum); + InputUpdateFromSolutionx( femmodel->elements,femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,ug); + +- ConstraintsStatex(&constraints_converged, &num_unstable_constraints, femmodel->elements,femmodel->nodes,femmodel->vertices,loads,femmodel->materials,femmodel->parameters); ++ ConstraintsStatex(&constraints_converged, &num_unstable_constraints, femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + if(VerboseConvergence()) _pprintLine_(" number of unstable constraints: " << num_unstable_constraints); + + //rift convergence +@@ -107,7 +108,10 @@ + if(VerboseConvergence()) _pprintLine_("\n total number of iterations: " << count-1); + + /*clean-up*/ +- if(conserve_loads) delete loads; ++ if(conserve_loads){ ++ delete femmodel->loads; ++ femmodel->loads=savedloads; ++ } + xdelete(&uf); + xdelete(&ug); + xdelete(&old_ug); +Index: ../trunk-jpl/src/c/solvers/solver_linear.cpp +=================================================================== +--- ../trunk-jpl/src/c/solvers/solver_linear.cpp (revision 13876) ++++ ../trunk-jpl/src/c/solvers/solver_linear.cpp (revision 13877) +@@ -23,7 +23,7 @@ + femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); + femmodel->UpdateConstraintsx(); + +- SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); ++ femmodel->SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); + Reduceloadx(pf, Kfs, ys); xdelete(&Kfs); + Solverx(&uf, Kff, pf, NULL, df, femmodel->parameters); +Index: ../trunk-jpl/src/c/solvers/solver_newton.cpp +=================================================================== +--- ../trunk-jpl/src/c/solvers/solver_newton.cpp (revision 13876) ++++ ../trunk-jpl/src/c/solvers/solver_newton.cpp (revision 13877) +@@ -55,7 +55,7 @@ + xdelete(&old_uf);old_uf=uf; + + /*Solver forward model*/ +- SystemMatricesx(&Kff,&Kfs,&pf,&df,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); ++ femmodel->SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); + Reduceloadx(pf,Kfs,ys);xdelete(&Kfs); + Solverx(&uf,Kff,pf,old_uf,df,femmodel->parameters);xdelete(&df); +@@ -82,7 +82,7 @@ + } + + /*Prepare next iteration using Newton's method*/ +- SystemMatricesx(&Kff,&Kfs,&pf,NULL,&kmax,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); ++ femmodel->SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); + Reduceloadx(pf,Kfs,ys); xdelete(&Kfs); + +Index: ../trunk-jpl/src/c/solvers/solver_stokescoupling_nonlinear.cpp +=================================================================== +--- ../trunk-jpl/src/c/solvers/solver_stokescoupling_nonlinear.cpp (revision 13876) ++++ ../trunk-jpl/src/c/solvers/solver_stokescoupling_nonlinear.cpp (revision 13877) +@@ -62,7 +62,7 @@ + xdelete(&old_uf_horiz); old_uf_horiz=uf_horiz; + + /*solve: */ +- SystemMatricesx(&Kff_horiz, &Kfs_horiz, &pf_horiz, &df_horiz, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); ++ femmodel->SystemMatricesx(&Kff_horiz, &Kfs_horiz, &pf_horiz, &df_horiz, NULL); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); + Reduceloadx(pf_horiz, Kfs_horiz, ys); xdelete(&Kfs_horiz); + Solverx(&uf_horiz, Kff_horiz, pf_horiz, old_uf_horiz, df_horiz,femmodel->parameters); +@@ -76,7 +76,7 @@ + femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); + + /*solve: */ +- SystemMatricesx(&Kff_vert, &Kfs_vert, &pf_vert, &df_vert,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); ++ femmodel->SystemMatricesx(&Kff_vert, &Kfs_vert, &pf_vert, &df_vert,NULL); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); + Reduceloadx(pf_vert, Kfs_vert, ys); xdelete(&Kfs_vert); + Solverx(&uf_vert, Kff_vert, pf_vert, NULL, df_vert,femmodel->parameters); xdelete(&Kff_vert); xdelete(&pf_vert); xdelete(&df_vert); +Index: ../trunk-jpl/src/c/solvers/solver_thermal_nonlinear.cpp +=================================================================== +--- ../trunk-jpl/src/c/solvers/solver_thermal_nonlinear.cpp (revision 13876) ++++ ../trunk-jpl/src/c/solvers/solver_thermal_nonlinear.cpp (revision 13877) +@@ -52,7 +52,7 @@ + + for(;;){ + +- SystemMatricesx(&Kff, &Kfs, &pf,&df, &melting_offset,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); ++ femmodel->SystemMatricesx(&Kff, &Kfs, &pf,&df, &melting_offset); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); + Reduceloadx(pf, Kfs, ys); xdelete(&Kfs); xdelete(&tf); + Solverx(&tf, Kff, pf,tf_old, df, femmodel->parameters); +Index: ../trunk-jpl/src/c/solvers/solver_adjoint_linear.cpp +=================================================================== +--- ../trunk-jpl/src/c/solvers/solver_adjoint_linear.cpp (revision 13876) ++++ ../trunk-jpl/src/c/solvers/solver_adjoint_linear.cpp (revision 13877) +@@ -25,7 +25,7 @@ + femmodel->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); + femmodel->UpdateConstraintsx(); + +- SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); ++ femmodel->SystemMatricesx(&Kff, &Kfs, &pf, &df, NULL); + CreateNodalConstraintsx(&ys,femmodel->nodes,configuration_type); + Reduceloadx(pf, Kfs, ys,true); xdelete(&Kfs); //true means spc = 0 + Solverx(&uf, Kff, pf, NULL, df, femmodel->parameters); xdelete(&Kff); xdelete(&pf); xdelete(&df); Index: /issm/oecreview/Archive/13393-13976/ISSM-13877-13878.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13877-13878.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13877-13878.diff (revision 13980) @@ -0,0 +1,170 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13877) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13878) +@@ -336,6 +336,48 @@ + /*}}}*/ + + /*Modules:*/ ++void FemModel::AllocateSystemMatrices(Matrix** pKff,Matrix** pKfs,Vector** pdf,Vector** ppf){ /*{{{*/ ++ ++ /*Intermediary*/ ++ int fsize,ssize; ++ int connectivity, numberofdofspernode; ++ int analysis_type, configuration_type; ++ ++ /*output*/ ++ Matrix *Kff = NULL; ++ Matrix *Kfs = NULL; ++ Vector *pf = NULL; ++ Vector *df = NULL; ++ ++ bool oldalloc=true; ++ ++ /*retrieve parameters: */ ++ this->parameters->FindParam(&analysis_type,AnalysisTypeEnum); ++ this->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); ++ this->parameters->FindParam(&connectivity,MeshAverageVertexConnectivityEnum); ++ ++ /*retrieve node info*/ ++ fsize=this->nodes->NumberOfDofs(configuration_type,FsetEnum); ++ ssize=this->nodes->NumberOfDofs(configuration_type,SsetEnum); ++ numberofdofspernode=this->nodes->MaxNumDofs(configuration_type,GsetEnum); ++ ++ if(oldalloc){ ++ Kff=new Matrix(fsize,fsize,connectivity,numberofdofspernode); ++ Kfs=new Matrix(fsize,ssize,connectivity,numberofdofspernode); ++ df =new Vector(fsize); ++ pf =new Vector(fsize); ++ } ++ else{ ++ /*IN PROGRESS*/ ++ } ++ ++ /*Allocate output pointers*/ ++ *pKff = Kff; ++ *pKfs = Kfs; ++ *pdf = df; ++ *ppf = pf; ++} ++/*}}}*/ + int FemModel::UpdateVertexPositionsx(void){ /*{{{*/ + + int i; +@@ -521,9 +563,7 @@ + + /*intermediary: */ + int i; +- int fsize,ssize; +- int connectivity, numberofdofspernode; +- int analysis_type, configuration_type; ++ int configuration_type; + Element *element = NULL; + Load *load = NULL; + +@@ -534,79 +574,58 @@ + Vector *df = NULL; + IssmDouble kmax; + ++ + /*Display message*/ + if(VerboseModule()) _pprintLine_(" Generating matrices"); + + /*retrive parameters: */ +- this->parameters->FindParam(&analysis_type,AnalysisTypeEnum); + this->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); +- this->parameters->FindParam(&connectivity,MeshAverageVertexConnectivityEnum); + +- /*Get size of matrices: */ +- fsize=this->nodes->NumberOfDofs(configuration_type,FsetEnum); +- ssize=this->nodes->NumberOfDofs(configuration_type,SsetEnum); +- +- numberofdofspernode=this->nodes->MaxNumDofs(configuration_type,GsetEnum); +- + /*Compute penalty free mstiffness matrix and load vector*/ +- Kff=new Matrix(fsize,fsize,connectivity,numberofdofspernode); +- Kfs=new Matrix(fsize,ssize,connectivity,numberofdofspernode); +- df =new Vector(fsize); ++ this->AllocateSystemMatrices(&Kff,&Kfs,&df,&pf); + +- /*Fill stiffness matrix from elements: */ ++ /*Fill stiffness matrix from elements and loads */ + for (i=0;ielements->Size();i++){ + element=dynamic_cast(this->elements->GetObjectByOffset(i)); + element->CreateKMatrix(Kff,Kfs,df); + } +- +- /*Fill stiffness matrix from loads if loads have the current configuration_type: */ + for (i=0;iloads->Size();i++){ + load=dynamic_cast(this->loads->GetObjectByOffset(i)); + if (load->InAnalysis(configuration_type)) load->CreateKMatrix(Kff,Kfs); + } + +- /*Assemble matrices*/ +- Kff->Assemble(); +- Kfs->Assemble(); +- df->Assemble(); + +- /*Create Load vector*/ +- pf=new Vector(fsize); +- +- /*Fill right hand side vector, from elements: */ ++ /*Fill right hand side vector, from elements and loads */ + for (i=0;ielements->Size();i++){ + element=dynamic_cast(this->elements->GetObjectByOffset(i)); + element->CreatePVector(pf); + } +- +- /*Fill right hand side from loads if loads have the current configuration_type: */ + for (i=0;iloads->Size();i++){ + load=dynamic_cast(this->loads->GetObjectByOffset(i)); + if (load->InAnalysis(configuration_type)) load->CreatePVector(pf); + } +- pf->Assemble(); + +- /*Now, figure out maximum value of K_gg, so that we can penalize it correctly: */ ++ /*Assemble matrices (required to get kmax)*/ ++ Kff->Assemble(); ++ Kfs->Assemble(); ++ df->Assemble(); ++ ++ /*Now, figure out maximum value of stiffness matrix, so that we can penalize it correctly: */ + kmax=Kff->Norm(NORM_INF); + +- /*Now, deal with penalties*/ +- /*Fill stiffness matrix from loads: */ ++ /*Now that we have kmax, deal with penalties (only in loads)*/ + for (i=0;iloads->Size();i++){ + load=dynamic_cast(this->loads->GetObjectByOffset(i)); + if (load->InAnalysis(configuration_type)) load->PenaltyCreateKMatrix(Kff,Kfs,kmax); + } +- +- /*Assemble matrices*/ +- Kff->Assemble(); +- Kfs->Assemble(); +- +- /*Fill right hand side vector, from loads: */ + for (i=0;iloads->Size();i++){ + load=dynamic_cast(this->loads->GetObjectByOffset(i)); + if (load->InAnalysis(configuration_type)) load->PenaltyCreatePVector(pf,kmax); + } + +- /*Assemble vector*/ ++ /*Assemble matrices and vector*/ ++ Kff->Assemble(); ++ Kfs->Assemble(); + pf->Assemble(); + + /*Assign output pointers: */ +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 13877) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 13878) +@@ -51,6 +51,7 @@ + ~FemModel(); + + /*Methods:*/ ++ void AllocateSystemMatrices(Matrix** pKff,Matrix** pKfs,Vector** pdf,Vector** ppf); + void Echo(); + void InitFromFiles(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int solution_type,const int* analyses,const int nummodels); + void Solve(void); Index: /issm/oecreview/Archive/13393-13976/ISSM-13878-13879.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13878-13879.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13878-13879.diff (revision 13980) @@ -0,0 +1,746 @@ +Index: ../trunk-jpl/test/NightlyRun/test202.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test202.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test202.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test202.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test216.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test216.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test216.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test216.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test426.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test426.m (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test426.m (revision 13879) +@@ -22,7 +22,7 @@ + 'Bed2','Surface2','Thickness2','Floatingice2',... + 'Bed3','Surface3','Thickness3','Floatingice3'}; + field_tolerances={1e-13,1e-13,1e-13,1e-13,... +- 1e-11,1e-11,1e-11,1e-13,... ++ 1e-11,1e-10,1e-11,1e-13,... + 1e-10,1e-10,1e-10,1e-13}; + field_values={... + (md.results.TransientSolution(1).Bed),... +Index: ../trunk-jpl/test/NightlyRun/test211.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test211.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test211.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test211.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test220.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test220.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test220.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test220.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test208.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test208.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test208.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test208.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test108.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test108.m (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test108.m (revision 13879) +@@ -9,7 +9,7 @@ + + %Fields and tolerances to track changes + field_names ={'Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13}; ++field_tolerances={1e-13,1e-5}; + field_values={... + (md.results.ThermalSolution.Temperature),... + (md.results.ThermalSolution.BasalforcingsMeltingRate),... +Index: ../trunk-jpl/test/NightlyRun/test3005.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3005.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test3005.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test3005.m +-Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test203.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test203.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test203.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test203.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test217.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test217.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test217.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test217.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test232.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test232.m (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test232.m (revision 13879) +@@ -15,7 +15,7 @@ + + %Fields and tolerances to track changes + field_names ={'Temperature1','BasalforcingsMeltingRate1','Temperature2','BasalforcingsMeltingRate2','Temperature3','BasalforcingsMeltingRate3','Temperature4','BasalforcingsMeltingRate4'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; ++field_tolerances={1e-13,1e-6,1e-13,1e-6,1e-13,1e-6,1e-13,1e-6}; + field_values={... + (md.results.TransientSolution(1).Temperature),... + (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +Index: ../trunk-jpl/test/NightlyRun/test212.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test212.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test212.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test212.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test207.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test207.m (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test207.m (revision 13879) +@@ -12,7 +12,7 @@ + + %Fields and tolerances to track changes + field_names ={'Temperature1','BasalforcingsMeltingRate1','Temperature2','BasalforcingsMeltingRate2','Temperature3','BasalforcingsMeltingRate3'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; ++field_tolerances={1e-13,1e-6,1e-13,1e-6,1e-13,1e-6}; + field_values={... + (md.results.TransientSolution(1).Temperature),... + (md.results.TransientSolution(1).BasalforcingsMeltingRate),... +Index: ../trunk-jpl/test/NightlyRun/test209.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test209.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test209.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test209.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test3006.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3006.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test3006.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test3006.m +-Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test204.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test204.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test204.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test204.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test406.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test406.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test406.py (revision 13879) +@@ -19,7 +19,7 @@ + + #Fields and tolerances to track changes + field_names =['Temperature','BasalforcingsMeltingRate'] +-field_tolerances=[1e-13,1e-13] ++field_tolerances=[1e-13,1e-5] + field_values=[\ + md.results['ThermalSolution'][1]['Temperature'],\ + md.results['ThermalSolution'][1]['BasalforcingsMeltingRate'],\ +Index: ../trunk-jpl/test/NightlyRun/test3001.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3001.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test3001.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test3001.m +-Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test213.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test213.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test213.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test213.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test415.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test415.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test415.py (revision 13879) +@@ -35,7 +35,7 @@ + + #Fields and tolerances to track changes + field_names =['Gradient','Misfits','FrictionCoefficient','Pressure','Vel','Vx','Vy','Vz','Temperature','BasalforcingsMeltingRate'] +-field_tolerances=[1e-10,1e-10,1e-11,1e-13,1e-10,1e-09,1e-10,1e-8,1e-09,1e-6] ++field_tolerances=[1e-10,1e-9,1e-10,1e-13,1e-10,1e-09,1e-10,1e-8,1e-09,1e-6] + field_values=[\ + md.results['SteadystateSolution'][1]['Gradient1'],\ + md.results['SteadystateSolution'][1]['J'],\ +Index: ../trunk-jpl/test/NightlyRun/test3010.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3010.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test3010.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test3010.m +-Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test3007.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3007.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test3007.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test3007.m +-Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test205.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test205.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test205.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test205.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test219.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test219.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test219.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test219.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test3002.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3002.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test3002.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test3002.m +-Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test214.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test214.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test214.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test214.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test406.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test406.m (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test406.m (revision 13879) +@@ -9,7 +9,7 @@ + + %Fields and tolerances to track changes + field_names ={'Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13}; ++field_tolerances={1e-13,1e-5}; + field_values={... + (md.results.ThermalSolution.Temperature),... + (md.results.ThermalSolution.BasalforcingsMeltingRate),... +Index: ../trunk-jpl/test/NightlyRun/test318.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test318.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test318.py (revision 13879) +@@ -18,7 +18,7 @@ + + #Fields and tolerances to track changes + field_names =['Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'] +-field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_tolerances=[1e-13,1e-13,1e-10,1e-10,1e-13,1e-11,1e-6] + field_values=[\ + md.results['SteadystateSolution'][1]['Vx'],\ + md.results['SteadystateSolution'][1]['Vy'],\ +Index: ../trunk-jpl/test/NightlyRun/test415.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test415.m (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test415.m (revision 13879) +@@ -23,7 +23,7 @@ + + %Fields and tolerances to track changes + field_names ={'Gradient','Misfits','FrictionCoefficient','Pressure','Vel','Vx','Vy','Vz','Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-10,1e-10,1e-11,1e-13,1e-10,1e-09,1e-10,1e-8,1e-09,1e-6}; ++field_tolerances={1e-10,1e-9,1e-10,1e-13,1e-10,1e-09,1e-10,1e-8,1e-09,1e-6}; + field_values={... + (md.results.SteadystateSolution.Gradient1),... + md.results.SteadystateSolution.J,... +Index: ../trunk-jpl/test/NightlyRun/test3008.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3008.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test3008.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test3008.m +-Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test232.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test232.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test232.py (revision 13879) +@@ -25,7 +25,7 @@ + + #Fields and tolerances to track changes + field_names =['Temperature1','BasalforcingsMeltingRate1','Temperature2','BasalforcingsMeltingRate2','Temperature3','BasalforcingsMeltingRate3','Temperature4','BasalforcingsMeltingRate4'] +-field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_tolerances=[1e-13,1e-6,1e-13,1e-6,1e-13,1e-6,1e-13,1e-6] + field_values=[\ + md.results['TransientSolution'][1]['Temperature'],\ + md.results['TransientSolution'][1]['BasalforcingsMeltingRate'],\ +Index: ../trunk-jpl/test/NightlyRun/test206.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test206.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test206.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test206.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test3003.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3003.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test3003.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test3003.m +-Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test215.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test215.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test215.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test215.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test108.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test108.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test108.py (revision 13879) +@@ -18,7 +18,7 @@ + + #Fields and tolerances to track changes + field_names =['Temperature','BasalforcingsMeltingRate'] +-field_tolerances=[1e-13,1e-13] ++field_tolerances=[1e-13,1e-5] + field_values=[\ + md.results['ThermalSolution'][1]['Temperature'],\ + md.results['ThermalSolution'][1]['BasalforcingsMeltingRate'],\ +Index: ../trunk-jpl/test/NightlyRun/test318.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test318.m (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test318.m (revision 13879) +@@ -9,7 +9,7 @@ + + %Fields and tolerances to track changes + field_names ={'Vx','Vy','Vz','Vel','Pressure','Temperature','BasalforcingsMeltingRate'}; +-field_tolerances={1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13}; ++field_tolerances={1e-13,1e-13,1e-10,1e-10,1e-13,1e-11,1e-6}; + field_values={... + (md.results.SteadystateSolution.Vx),... + (md.results.SteadystateSolution.Vy),... +Index: ../trunk-jpl/test/NightlyRun/test210.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test210.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test210.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test210.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test426.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test426.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test426.py (revision 13879) +@@ -32,7 +32,7 @@ + 'Bed2','Surface2','Thickness2','Floatingice2',\ + 'Bed3','Surface3','Thickness3','Floatingice3'] + field_tolerances=[1e-13,1e-13,1e-13,1e-13,\ +- 1e-11,1e-11,1e-11,1e-13,\ ++ 1e-11,1e-10,1e-11,1e-13,\ + 1e-10,1e-10,1e-10,1e-13] + field_values=[\ + md.results['TransientSolution'][1]['Bed'],\ +Index: ../trunk-jpl/test/NightlyRun/test3009.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3009.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test3009.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test3009.m +-Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/NightlyRun/test207.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test207.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test207.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test207.m +-Created on 2012-09-27 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +@@ -32,11 +20,9 @@ + md.transient.isgroundingline=0 + md=solve(md,TransientSolutionEnum()) + +- + # Fields and tolerances to track changes +- + field_names =['Temperature1','BasalforcingsMeltingRate1','Temperature2','BasalforcingsMeltingRate2','Temperature3','BasalforcingsMeltingRate3'] +-field_tolerances=[1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++field_tolerances=[1e-13,1e-6,1e-13,1e-6,1e-13,1e-6] + field_values=[\ + md.results['TransientSolution'][1]['Temperature'],\ + md.results['TransientSolution'][1]['BasalforcingsMeltingRate'],\ +Index: ../trunk-jpl/test/NightlyRun/test3004.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3004.py (revision 13878) ++++ ../trunk-jpl/test/NightlyRun/test3004.py (revision 13879) +@@ -1,15 +1,3 @@ +-""" +-== == == == == == == == == == == == == == == == == == == +-Auto generated python script for ISSM: test3004.m +-Created on 2012-09-25 via translateToPy.py Ver 1.0 by mikep +-== == == == == == == == == == == == == == == == == == == +- +-Matlab script conversion into python +-translateToPy.py Author: Michael Pellegrin +-translateToPy.py Date: 09/24/12 +-== == == == == == == == == == == == == == == == == == == +-""" +- + from MatlabFuncs import * + from model import * + from EnumDefinitions import * +Index: ../trunk-jpl/test/Archives/Archive237.nc +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/13393-13976/ISSM-13879-13880.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13879-13880.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13879-13880.diff (revision 13980) @@ -0,0 +1,221 @@ +Index: ../trunk-jpl/src/c/toolkits/issm/SeqMat.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/issm/SeqMat.h (revision 13879) ++++ ../trunk-jpl/src/c/toolkits/issm/SeqMat.h (revision 13880) +@@ -60,6 +60,15 @@ + if(M*N) this->matrix=xNewZeroInit(pM*pN); + } + /*}}}*/ ++ /*FUNCTION SeqMat(int m,int n,int M,int N,int* d_nnz,int* o_nnz){{{*/ ++ SeqMat(int m,int n,int pM,int pN,int* d_nnz,int* o_nnz){ ++ ++ this->M=pM; ++ this->N=pN; ++ this->matrix=NULL; ++ if(pM*pN) this->matrix=xNewZeroInit(pM*pN); ++ } ++ /*}}}*/ + /*FUNCTION SeqMat(doubletype* serial_mat,int M,int N,doubletype sparsity){{{*/ + SeqMat(doubletype* serial_mat,int pM,int pN,doubletype sparsity){ + +Index: ../trunk-jpl/src/c/toolkits/issm/SeqVec.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/issm/SeqVec.h (revision 13879) ++++ ../trunk-jpl/src/c/toolkits/issm/SeqVec.h (revision 13880) +@@ -48,6 +48,14 @@ + if(this->M) this->vector=xNewZeroInit(pM); + } + /*}}}*/ ++ /*FUNCTION SeqVec(int m,int M){{{*/ ++ SeqVec(int pm,int pM){ ++ ++ this->M=pM; ++ this->vector=NULL; ++ if(this->M) this->vector=xNewZeroInit(pM); ++ } ++ /*}}}*/ + /*FUNCTION SeqVec(int M,bool fromlocalsize){{{*/ + SeqVec(int pM,bool fromlocalsize){ + +Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp (revision 13879) ++++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp (revision 13880) +@@ -39,6 +39,16 @@ + this->matrix=NewMat(M,N,sparsity,IssmComm::GetComm()); + } + /*}}}*/ ++/*FUNCTION PetscMat::PetscMat(int M,int N, IssmDouble sparsity){{{*/ ++PetscMat::PetscMat(int m,int n,int M,int N,int* d_nnz,int* o_nnz){ ++ ++ MatCreate(IssmComm::GetComm(),&this->matrix); ++ MatSetSizes(this->matrix,m,n,M,N); ++ MatSetFromOptions(this->matrix); ++ MatMPIAIJSetPreallocation(this->matrix,0,d_nnz,0,o_nnz); ++ ++} ++/*}}}*/ + /*FUNCTION PetscMat::PetscMat(IssmDouble* serial_mat,int M,int N,IssmDouble sparsity){{{*/ + PetscMat::PetscMat(IssmDouble* serial_mat,int M,int N,IssmDouble sparsity){ + +Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.h (revision 13879) ++++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.h (revision 13880) +@@ -29,14 +29,15 @@ + IssmDouble* avector; + #endif + +- /*PetscVec constructors, destructors {{{*/ ++ /*PetscVec constructors, destructors*/ + PetscVec(); + PetscVec(int M,bool fromlocalsize=false); ++ PetscVec(int m,int M); + PetscVec(IssmDouble* buffer, int M); + PetscVec(Vec petsc_vec); + ~PetscVec(); +- /*}}}*/ +- /*PetscVec specific routines {{{*/ ++ ++ /*PetscVec specific routines*/ + void Echo(void); + void Assemble(void); + void SetValues(int ssize, int* list, IssmDouble* values, InsMode mode); +@@ -54,7 +55,6 @@ + void Scale(IssmDouble scale_factor); + void PointwiseDivide(PetscVec* x,PetscVec* y); + IssmDouble Dot(PetscVec* vector); +- /*}}}*/ + }; + + #endif //#ifndef _PETSCVEC_H_ +Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.h (revision 13879) ++++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.h (revision 13880) +@@ -30,15 +30,16 @@ + IssmDouble* amatrix; + #endif + +- /*PetscMat constructors, destructors {{{*/ ++ /*PetscMat constructors, destructors*/ + PetscMat(); + PetscMat(int M,int N); + PetscMat(int M,int N,IssmDouble sparsity); ++ PetscMat(int m,int n,int M,int N,int* d_nnz,int* o_nnz); + PetscMat(IssmDouble* serial_mat,int M,int N,IssmDouble sparsity); + PetscMat(int M,int N,int connectivity,int numberofdofspernode); + ~PetscMat(); +- /*}}}*/ +- /*PetscMat specific routines {{{*/ ++ ++ /*PetscMat specific routines*/ + void AllocationInfo(void); + void Echo(void); + void Assemble(void); +@@ -50,8 +51,6 @@ + IssmDouble* ToSerial(void); + void SetValues(int m,int* idxm,int n,int* idxn,IssmDouble* values,InsMode mode); + void Convert(MatrixType type); +- /*}}}*/ +- + }; + + #endif //#ifndef _PETSCMAT_H_ +Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.cpp (revision 13879) ++++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.cpp (revision 13880) +@@ -33,6 +33,16 @@ + + } + /*}}}*/ ++/*FUNCTION PetscVec::PetscVec(int m,int M){{{*/ ++PetscVec::PetscVec(int m,int M){ ++ ++ VecCreate(IssmComm::GetComm(),&this->vector); ++ VecSetSizes(this->vector,m,M); ++ VecSetFromOptions(this->vector); ++ VecSet(this->vector,0.0); ++ ++} ++/*}}}*/ + /*FUNCTION PetscVec::PetscVec(Vec petsc_vec){{{*/ + PetscVec::PetscVec(Vec petsc_vec){ + +Index: ../trunk-jpl/src/c/classes/matrix/Vector.h +=================================================================== +--- ../trunk-jpl/src/c/classes/matrix/Vector.h (revision 13879) ++++ ../trunk-jpl/src/c/classes/matrix/Vector.h (revision 13880) +@@ -74,6 +74,33 @@ + + } + /*}}}*/ ++ /*FUNCTION Vector(int m,int M,int in_type){{{*/ ++ #ifdef _HAVE_PETSC_ ++ Vector(int m,int M,int in_type=PetscVecType){ ++ #else ++ Vector(int m,int M,int in_type=SeqVecType){ ++ #endif ++ ++ #ifdef _HAVE_PETSC_ ++ pvector=NULL; ++ #endif ++ svector=NULL; ++ type=in_type; ++ ++ if(type==PetscVecType){ ++ #ifdef _HAVE_PETSC_ ++ this->pvector=new PetscVec(m,M); ++ #else ++ _error_("Petsc matrix format not usable, as Petsc has not been compiled!"); ++ #endif ++ } ++ else if(type==SeqVecType){ ++ this->svector=new SeqVec(m,M); ++ } ++ else _error_("Vector type: " << type << " not supported yet!"); ++ ++ } ++ /*}}}*/ + /*FUNCTION Vector(doubletype* serial_vec,int M,int in_type){{{*/ + #ifdef _HAVE_PETSC_ + Vector(doubletype* serial_vec,int M,int in_type=PetscVecType){ +Index: ../trunk-jpl/src/c/classes/matrix/Matrix.h +=================================================================== +--- ../trunk-jpl/src/c/classes/matrix/Matrix.h (revision 13879) ++++ ../trunk-jpl/src/c/classes/matrix/Matrix.h (revision 13880) +@@ -75,6 +75,33 @@ + + } + /*}}}*/ ++ /*FUNCTION Matrix(int m,int n,int M,int N,int* d_nnz,int* o_nnz,int type){{{*/ ++ #ifdef _HAVE_PETSC_ ++ Matrix(int m,int n,int M,int N,int* d_nnz,int* o_nnz,int in_type=PetscMatType){ ++ #else ++ Matrix(int m,int n,int M,int N,int* d_nnz,int* o_nnz,int in_type=SeqMatType){ ++ #endif ++ ++ #ifdef _HAVE_PETSC_ ++ pmatrix=NULL; ++ #endif ++ smatrix=NULL; ++ type=in_type; ++ ++ if(type==PetscMatType){ ++ #ifdef _HAVE_PETSC_ ++ this->pmatrix=new PetscMat(m,n,M,N,d_nnz,o_nnz); ++ #else ++ _error_("Petsc matrix format not usable, as Petsc has not been compiled!"); ++ #endif ++ } ++ else if(type==SeqMatType){ ++ this->smatrix=new SeqMat(m,n,M,N,d_nnz,o_nnz); ++ } ++ else _error_("Matrix type: " << type << " not supported yet!"); ++ ++ } ++ /*}}}*/ + /*FUNCTION Matrix(int M,int N,IssmDouble sparsity,int in_type){{{*/ + #ifdef _HAVE_PETSC_ + Matrix(int M,int N,double sparsity,int in_type=PetscMatType){ Index: /issm/oecreview/Archive/13393-13976/ISSM-13880-13881.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13880-13881.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13880-13881.diff (revision 13980) @@ -0,0 +1,220 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13880) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13881) +@@ -339,9 +339,12 @@ + void FemModel::AllocateSystemMatrices(Matrix** pKff,Matrix** pKfs,Vector** pdf,Vector** ppf){ /*{{{*/ + + /*Intermediary*/ +- int fsize,ssize; +- int connectivity, numberofdofspernode; +- int analysis_type, configuration_type; ++ int fsize,ssize,flocalsize,slocalsize; ++ int connectivity, numberofdofspernode; ++ int analysis_type,configuration_type; ++ int m,n,M,N; ++ int *d_nnz = NULL; ++ int *o_nnz = NULL; + + /*output*/ + Matrix *Kff = NULL; +@@ -357,8 +360,11 @@ + this->parameters->FindParam(&connectivity,MeshAverageVertexConnectivityEnum); + + /*retrieve node info*/ +- fsize=this->nodes->NumberOfDofs(configuration_type,FsetEnum); +- ssize=this->nodes->NumberOfDofs(configuration_type,SsetEnum); ++ fsize = this->nodes->NumberOfDofs(configuration_type,FsetEnum); ++ ssize = this->nodes->NumberOfDofs(configuration_type,SsetEnum); ++ flocalsize = this->nodes->NumberOfDofsLocal(analysis_type,FsetEnum); ++ slocalsize = this->nodes->NumberOfDofsLocal(analysis_type,SsetEnum); ++ + numberofdofspernode=this->nodes->MaxNumDofs(configuration_type,GsetEnum); + + if(oldalloc){ +@@ -368,7 +374,25 @@ + pf =new Vector(fsize); + } + else{ +- /*IN PROGRESS*/ ++ /*Kff*/ ++ m=flocalsize; n=flocalsize; /*local sizes*/ ++ M=fsize; N=fsize; /*global sizes*/ ++ this->MatrixNonzeros(&d_nnz,&o_nnz,FsetEnum,FsetEnum); ++ Kff=new Matrix(m,n,M,N,d_nnz,o_nnz); ++ xDelete(d_nnz); ++ xDelete(o_nnz); ++ ++ /*Kfs*/ ++ m=flocalsize; n=slocalsize; /*local sizes*/ ++ M=fsize; N=ssize; /*global sizes*/ ++ this->MatrixNonzeros(&d_nnz,&o_nnz,FsetEnum,SsetEnum); ++ Kfs=new Matrix(m,n,M,N,d_nnz,o_nnz); ++ xDelete(d_nnz); ++ xDelete(o_nnz); ++ ++ /*Vectors*/ ++ df =new Vector(flocalsize,fsize); ++ pf =new Vector(flocalsize,fsize); + } + + /*Allocate output pointers*/ +@@ -378,6 +402,136 @@ + *ppf = pf; + } + /*}}}*/ ++void FemModel::MatrixNonzeros(int** pd_nnz,int** po_nnz,int set1enum,int set2enum){/*{{{*/ ++ ++ /*Intermediary*/ ++ int i,j,k,index,count; ++ int analysis_type,configuration_type; ++ int fsize,dim; ++ int d_nz,o_nz; ++ Element *element = NULL; ++ int *head = NULL; ++ int *next = NULL; ++ ++ /*output*/ ++ int *d_nnz = NULL; ++ int *o_nnz = NULL; ++ ++ /*retrive parameters: */ ++ this->parameters->FindParam(&analysis_type,AnalysisTypeEnum); ++ this->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); ++ this->parameters->FindParam(&dim,MeshDimensionEnum); ++ ++ /*Get vector size and number of nodes*/ ++ int numnodes = nodes->NumberOfNodes(analysis_type); ++ int numberofdofspernode = nodes->MaxNumDofs(configuration_type,GsetEnum); ++ int m = nodes->NumberOfDofsLocal(analysis_type,set1enum); ++ ++ /*First, we are building chaining vectors so that we know what nodes are ++ * connected to what elements. These vectors are such that: ++ * for(int i=head[id];i!=-1;i=next[i]) ++ * will loop over all the elements that are connected to the node number ++ * id*/ ++ if(dim==2){ ++ head=xNew(numnodes); for(i=0;i(elements->Size()*3); /*3 = number of nodes per element*/ ++ } ++ else if(dim==3){ ++ head=xNew(numnodes); for(i=0;i(elements->Size()*6); /*6 = number of nodes per element*/ ++ } ++ else{ ++ _error_("dim "<Size();i++){ ++ element=dynamic_cast(elements->GetObjectByOffset(i)); ++ for(int j=0;j<3;j++){ ++ int index =dynamic_cast(element)->nodes[j]->sid;//starts at 0 for a given analysis ++ _assert_(k>=0 && kSize() && index>=0 && index(numnodes); ++ int *d_connectivity = xNewZeroInit(numnodes); ++ int *o_connectivity = xNewZeroInit(numnodes); ++ int *connectivity_clone = xNewZeroInit(numnodes); ++ int *all_connectivity_clone = xNewZeroInit(numnodes); ++ ++ /*Create connectivity vector*/ ++ for(i=0;iSize();i++){ ++ Node* node=dynamic_cast(nodes->GetObjectByOffset(i)); ++ if(node->InAnalysis(analysis_type)){ ++ ++ /*Reinitialize flags to 0*/ ++ for(j=0;jSid()]!=-1); ++ for(j=head[node->Sid()];j!=-1;j=next[j]){ ++ if(dim==2){ ++ index = (int)(double(j)/3); ++ } ++ else if(dim==3){ ++ index = (int)(double(j)/6); ++ } ++ else{ ++ _error_("dim "<(elements->GetObjectByOffset(index)); ++ element->SetwiseNodeConnectivity(&d_nz,&o_nz,node,flags,set1enum,set2enum); ++ if(node->IsClone()){ ++ connectivity_clone[node->Sid()]+=d_nz+o_nz; ++ } ++ else{ ++ d_connectivity[node->Sid()]+=d_nz; ++ o_connectivity[node->Sid()]+=o_nz; ++ } ++ } ++ } ++ } ++ xDelete(flags); ++ xDelete(head); ++ xDelete(next); ++ ++ /*sum over all cpus*/ ++ MPI_Allreduce((void*)connectivity_clone,(void*)all_connectivity_clone,numnodes,MPI_INT,MPI_SUM,IssmComm::GetComm()); ++ xDelete(connectivity_clone); ++ ++ if(set1enum==FsetEnum){ ++ count=0; ++ d_nnz=xNew(m); ++ o_nnz=xNew(m); ++ for(i=0;iSize();i++){ ++ Node* node=dynamic_cast(nodes->GetObjectByOffset(i)); ++ if(node->InAnalysis(analysis_type) && !node->IsClone()){ ++ for(j=0;jindexing.fsize;j++){ ++ _assert_(countSid()] + all_connectivity_clone[node->Sid()]); ++ o_nnz[count]=numberofdofspernode*(o_connectivity[node->Sid()] + all_connectivity_clone[node->Sid()]); ++ if(d_nnz[count]>m) d_nnz[count]=m; ++ if(o_nnz[count]>fsize-m) o_nnz[count]=fsize-m; ++ count++; ++ } ++ } ++ } ++ _assert_(m==count); ++ } ++ else{ ++ _error_("STOP not implemented"); ++ } ++ xDelete(d_connectivity); ++ xDelete(o_connectivity); ++ xDelete(all_connectivity_clone); ++ ++ /*Allocate ouptput pointer*/ ++ *pd_nnz=d_nnz; ++ *po_nnz=o_nnz; ++ ++}/*}}}*/ + int FemModel::UpdateVertexPositionsx(void){ /*{{{*/ + + int i; +@@ -627,6 +781,9 @@ + Kff->Assemble(); + Kfs->Assemble(); + pf->Assemble(); ++ //Kff->AllocationInfo(); ++ //Kfs->AllocationInfo(); ++ //_error_("STOP"); + + /*Assign output pointers: */ + if(pKff) *pKff=Kff; +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 13880) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 13881) +@@ -54,6 +54,7 @@ + void AllocateSystemMatrices(Matrix** pKff,Matrix** pKfs,Vector** pdf,Vector** ppf); + void Echo(); + void InitFromFiles(char* rootpath, char* inputfilename, char* outputfilename, char* petscfilename, char* lockfilename, const int solution_type,const int* analyses,const int nummodels); ++ void MatrixNonzeros(int** pd_nnz,int** po_nnz,int set1enum,int set2enum); + void Solve(void); + void OutputResults(void); + void SetStaticComm(); Index: /issm/oecreview/Archive/13393-13976/ISSM-13881-13882.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13881-13882.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13881-13882.diff (revision 13980) @@ -0,0 +1,40 @@ +Index: ../trunk-jpl/src/android/issm-android-inputfiles/test102.petsc +=================================================================== +--- ../trunk-jpl/src/android/issm-android-inputfiles/test102.petsc (revision 13881) ++++ ../trunk-jpl/src/android/issm-android-inputfiles/test102.petsc (revision 13882) +@@ -1,19 +1,17 @@ + %Petsc options file: test102.petsc written from Matlab solver array + + +NoneAnalysis +--mat_type aij +--ksp_type gmres +--pc_type asm +--sub_pc_type ilu +--pc_asm_overlap 5 +--ksp_max_it 100 +--ksp_rtol 1e-15 ++-mat_type mpiaij ++-ksp_type preonly ++-pc_type lu ++-pc_factor_mat_solver_package mumps ++-mat_mumps_icntl_14 120 ++-pc_factor_shift_positive_definite true + + +DiagnosticVertAnalysis +--mat_type aij +--ksp_type gmres +--pc_type asm +--sub_pc_type ilu +--pc_asm_overlap 5 +--ksp_max_it 100 +--ksp_rtol 1e-15 ++-mat_type mpiaij ++-ksp_type preonly ++-pc_type lu ++-pc_factor_mat_solver_package mumps ++-mat_mumps_icntl_14 120 ++-pc_factor_shift_positive_definite true +Index: ../trunk-jpl/src/android/issm-android-inputfiles/test102.bin +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream Index: /issm/oecreview/Archive/13393-13976/ISSM-13882-13883.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13882-13883.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13882-13883.diff (revision 13980) @@ -0,0 +1,16 @@ +Index: ../trunk-jpl/etc/environment.sh +=================================================================== +--- ../trunk-jpl/etc/environment.sh (revision 13882) ++++ ../trunk-jpl/etc/environment.sh (revision 13883) +@@ -193,10 +193,10 @@ + + export ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install" + pathappend "$ANDROID_NDK_DIR/" ++pathappend "$ANDROID_NDK_DIR/arm-linux-android-install/bin/" + + export ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install" + pathappend "$ANDROID_SDK_DIR/" +-pathappend "$ANDROID_DIR/arm-linux-android-4.0/bin/" + + GSL_DIR="$ISSM_DIR/externalpackages/gsl/install" + libpathappend "$GSL_DIR/lib" Index: /issm/oecreview/Archive/13393-13976/ISSM-13883-13884.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13883-13884.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13883-13884.diff (revision 13980) @@ -0,0 +1,11 @@ +Index: ../trunk-jpl/externalpackages/android/android-ndk/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/android/android-ndk/install.sh (revision 13883) ++++ ../trunk-jpl/externalpackages/android/android-ndk/install.sh (revision 13884) +@@ -27,5 +27,5 @@ + # Create Standalone Development Directory + # Note: API-14 corresponds to Android 4.0. + if [[ $step == "2" || $step == "0" ]]; then +- $ANDROID_NDK_DIR/build/tools/make-standalone-toolchain.sh --platform=android-14 --install-dir=$ANDROID_DIR/arm-linux-android-4.0 ++ $ANDROID_DIR/android-ndk/install/build/tools/make-standalone-toolchain.sh --platform=android-14 --install-dir=$ANDROID_DIR/android-ndk/install/arm-linux-android-install + fi Index: /issm/oecreview/Archive/13393-13976/ISSM-13884-13885.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13884-13885.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13884-13885.diff (revision 13980) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/etc/environment.sh +=================================================================== +--- ../trunk-jpl/etc/environment.sh (revision 13884) ++++ ../trunk-jpl/etc/environment.sh (revision 13885) +@@ -192,8 +192,7 @@ + export ANDROID_DIR="$ISSM_DIR/externalpackages/android" + + export ANDROID_NDK_DIR="$ANDROID_DIR/android-ndk/install" +-pathappend "$ANDROID_NDK_DIR/" +-pathappend "$ANDROID_NDK_DIR/arm-linux-android-install/bin/" ++pathappend "$ANDROID_NDK_DIR/arm-linux-android-install/bin" + + export ANDROID_SDK_DIR="$ANDROID_DIR/android-sdk/install" + pathappend "$ANDROID_SDK_DIR/" Index: /issm/oecreview/Archive/13393-13976/ISSM-13885-13886.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13885-13886.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13885-13886.diff (revision 13980) @@ -0,0 +1,84 @@ +Index: ../trunk-jpl/src/c/classes/objects/Elements/Element.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Element.h (revision 13885) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Element.h (revision 13886) +@@ -34,6 +34,7 @@ + virtual void CreateJacobianMatrix(Matrix* Jff)=0; + virtual void GetSolutionFromInputs(Vector* solution)=0; + virtual int GetNodeIndex(Node* node)=0; ++ virtual int GetNumberOfNodes(void)=0; + virtual int Sid()=0; + virtual bool IsFloating()=0; + virtual bool IsNodeOnShelf()=0; +Index: ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13885) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Tria.cpp (revision 13886) +@@ -1137,6 +1137,19 @@ + _error_("Node provided not found among element nodes"); + } + /*}}}*/ ++/*FUNCTION Tria::GetNumberOfNodes{{{*/ ++int Tria::GetNumberOfNodes(void){ ++ ++ switch(this->element_type){ ++ case P1Enum: ++ return 3; ++ case P1DGEnum: ++ return 3; ++ default: ++ _error_("Element type "<element_type)<<" not supported yet"); ++ } ++} ++/*}}}*/ + /*FUNCTION Tria::GetInputListOnVertices(IssmDouble* pvalue,int enumtype) {{{*/ + void Tria::GetInputListOnVertices(IssmDouble* pvalue,int enumtype){ + +Index: ../trunk-jpl/src/c/classes/objects/Elements/Tria.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Tria.h (revision 13885) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Tria.h (revision 13886) +@@ -81,6 +81,7 @@ + void CreateJacobianMatrix(Matrix* Jff); + void Delta18oParameterization(void); + int GetNodeIndex(Node* node); ++ int GetNumberOfNodes(void); + int Sid(); + bool IsOnBed(); + bool IsFloating(); +Index: ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp (revision 13885) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Penta.cpp (revision 13886) +@@ -890,6 +890,19 @@ + + } + /*}}}*/ ++/*FUNCTION Penta::GetNumberOfNodes{{{*/ ++int Penta::GetNumberOfNodes(void){ ++ ++ switch(this->element_type){ ++ case P1Enum: ++ return 6; ++ case P1DGEnum: ++ return 6; ++ default: ++ _error_("Element type "<element_type)<<" not supported yet"); ++ } ++} ++/*}}}*/ + /*FUNCTION Penta::GetInputListOnVertices(IssmDouble* pvalue,int enumtype) {{{*/ + void Penta::GetInputListOnVertices(IssmDouble* pvalue,int enumtype){ + +Index: ../trunk-jpl/src/c/classes/objects/Elements/Penta.h +=================================================================== +--- ../trunk-jpl/src/c/classes/objects/Elements/Penta.h (revision 13885) ++++ ../trunk-jpl/src/c/classes/objects/Elements/Penta.h (revision 13886) +@@ -86,6 +86,7 @@ + void Delta18oParameterization(void); + void DeleteResults(void); + int GetNodeIndex(Node* node); ++ int GetNumberOfNodes(void); + void GetSolutionFromInputs(Vector* solution); + IssmDouble GetZcoord(GaussPenta* gauss); + void GetVectorFromInputs(Vector* vector,int name_enum); Index: /issm/oecreview/Archive/13393-13976/ISSM-13886-13887.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13886-13887.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13886-13887.diff (revision 13980) @@ -0,0 +1,47 @@ +Index: ../trunk-jpl/src/c/Container/Elements.cpp +=================================================================== +--- ../trunk-jpl/src/c/Container/Elements.cpp (revision 13886) ++++ ../trunk-jpl/src/c/Container/Elements.cpp (revision 13887) +@@ -293,6 +293,30 @@ + delete patch; + } + /*}}}*/ ++/*FUNCTION Elements::MaxNumNodes{{{*/ ++int Elements::MaxNumNodes(void){ ++ ++ int max=0; ++ int allmax; ++ int numnodes=0; ++ ++ /*Now go through all elements, and get how many nodes they own, unless they are clone nodes: */ ++ for(int i=0;iSize();i++){ ++ ++ Element* element=dynamic_cast(this->GetObjectByOffset(i)); ++ numnodes=element->GetNumberOfNodes(); ++ if(numnodes>max)max=numnodes; ++ } ++ ++ /*Grab max of all cpus: */ ++ #ifdef _HAVE_MPI_ ++ MPI_Allreduce((void*)&max,(void*)&allmax,1,MPI_INT,MPI_MAX,IssmComm::GetComm()); ++ max=allmax; ++ #endif ++ ++ return max; ++} ++/*}}}*/ + /*FUNCTION Elements::NumberOfElements{{{*/ + int Elements::NumberOfElements(void){ + +Index: ../trunk-jpl/src/c/Container/Elements.h +=================================================================== +--- ../trunk-jpl/src/c/Container/Elements.h (revision 13886) ++++ ../trunk-jpl/src/c/Container/Elements.h (revision 13887) +@@ -26,6 +26,7 @@ + /*numerics*/ + void Configure(Elements* elements,Loads* loads, Nodes* nodes, Vertices* vertices, Materials* materials,Parameters* parameters); + void DeleteResults(void); ++ int MaxNumNodes(void); + void ProcessResultsUnits(void); + void SetCurrentConfiguration(Elements* elements,Loads* loads, Nodes* nodes, Vertices* vertices, Materials* materials,Parameters* parameters); + void ToResults(Results* results,Parameters* parameters); Index: /issm/oecreview/Archive/13393-13976/ISSM-13887-13888.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13887-13888.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13887-13888.diff (revision 13980) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13887) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13888) +@@ -498,7 +498,9 @@ + xDelete(next); + + /*sum over all cpus*/ ++ #ifdef _HAVE_MPI_ + MPI_Allreduce((void*)connectivity_clone,(void*)all_connectivity_clone,numnodes,MPI_INT,MPI_SUM,IssmComm::GetComm()); ++ #endif + xDelete(connectivity_clone); + + if(set1enum==FsetEnum){ Index: /issm/oecreview/Archive/13393-13976/ISSM-13888-13889.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13888-13889.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13888-13889.diff (revision 13980) @@ -0,0 +1,106 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13888) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 13889) +@@ -405,13 +405,13 @@ + void FemModel::MatrixNonzeros(int** pd_nnz,int** po_nnz,int set1enum,int set2enum){/*{{{*/ + + /*Intermediary*/ +- int i,j,k,index,count; ++ int i,j,k,index,offset,count; + int analysis_type,configuration_type; +- int fsize,dim; + int d_nz,o_nz; +- Element *element = NULL; +- int *head = NULL; +- int *next = NULL; ++ Element *element = NULL; ++ int *head = NULL; ++ int *next = NULL; ++ int *count2offset = NULL; + + /*output*/ + int *d_nnz = NULL; +@@ -420,35 +420,30 @@ + /*retrive parameters: */ + this->parameters->FindParam(&analysis_type,AnalysisTypeEnum); + this->parameters->FindParam(&configuration_type,ConfigurationTypeEnum); +- this->parameters->FindParam(&dim,MeshDimensionEnum); + + /*Get vector size and number of nodes*/ + int numnodes = nodes->NumberOfNodes(analysis_type); + int numberofdofspernode = nodes->MaxNumDofs(configuration_type,GsetEnum); + int m = nodes->NumberOfDofsLocal(analysis_type,set1enum); ++ int numnodesperobject = elements->MaxNumNodes(); + + /*First, we are building chaining vectors so that we know what nodes are + * connected to what elements. These vectors are such that: + * for(int i=head[id];i!=-1;i=next[i]) + * will loop over all the elements that are connected to the node number + * id*/ +- if(dim==2){ +- head=xNew(numnodes); for(i=0;i(elements->Size()*3); /*3 = number of nodes per element*/ +- } +- else if(dim==3){ +- head=xNew(numnodes); for(i=0;i(elements->Size()*6); /*6 = number of nodes per element*/ +- } +- else{ +- _error_("dim "<(numnodes); for(i=0;i(elements->Size()*numnodesperobject); ++ count2offset = xNew(elements->Size()*numnodesperobject); ++ + k=0; + for(i=0;iSize();i++){ + element=dynamic_cast(elements->GetObjectByOffset(i)); +- for(int j=0;j<3;j++){ +- int index =dynamic_cast(element)->nodes[j]->sid;//starts at 0 for a given analysis ++ for(int j=0;j(element)->nodes[j]->sid;//starts at 0 for a given analysis + _assert_(k>=0 && kSize() && index>=0 && indexSid()]!=-1); + for(j=head[node->Sid()];j!=-1;j=next[j]){ +- if(dim==2){ +- index = (int)(double(j)/3); +- } +- else if(dim==3){ +- index = (int)(double(j)/6); +- } +- else{ +- _error_("dim "<(elements->GetObjectByOffset(index)); ++ offset=count2offset[j]; ++ element=dynamic_cast(elements->GetObjectByOffset(offset)); + element->SetwiseNodeConnectivity(&d_nz,&o_nz,node,flags,set1enum,set2enum); + if(node->IsClone()){ + connectivity_clone[node->Sid()]+=d_nz+o_nz; +@@ -494,6 +481,7 @@ + } + } + xDelete(flags); ++ xDelete(count2offset); + xDelete(head); + xDelete(next); + +@@ -514,8 +502,8 @@ + _assert_(countSid()] + all_connectivity_clone[node->Sid()]); + o_nnz[count]=numberofdofspernode*(o_connectivity[node->Sid()] + all_connectivity_clone[node->Sid()]); +- if(d_nnz[count]>m) d_nnz[count]=m; +- if(o_nnz[count]>fsize-m) o_nnz[count]=fsize-m; ++ //if(d_nnz[count]>m) d_nnz[count]=m; ++ //if(o_nnz[count]>fsize-m) o_nnz[count]=fsize-m; + count++; + } + } Index: /issm/oecreview/Archive/13393-13976/ISSM-13889-13890.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13889-13890.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13889-13890.diff (revision 13980) @@ -0,0 +1,594 @@ +Index: ../trunk-jpl/src/android/ISSM/.classpath +=================================================================== +--- ../trunk-jpl/src/android/ISSM/.classpath (revision 0) ++++ ../trunk-jpl/src/android/ISSM/.classpath (revision 13890) +@@ -0,0 +1,8 @@ ++ ++ ++ ++ ++ ++ ++ ++ +Index: ../trunk-jpl/src/android/ISSM/jni/issmlib/include/fac.h +=================================================================== +--- ../trunk-jpl/src/android/ISSM/jni/issmlib/include/fac.h (revision 0) ++++ ../trunk-jpl/src/android/ISSM/jni/issmlib/include/fac.h (revision 13890) +@@ -0,0 +1,5 @@ ++class fac ++{ ++ public: ++ long factorial(long n); ++}; +Index: ../trunk-jpl/src/android/ISSM/jni/issmlib/Android.mk +=================================================================== +--- ../trunk-jpl/src/android/ISSM/jni/issmlib/Android.mk (revision 0) ++++ ../trunk-jpl/src/android/ISSM/jni/issmlib/Android.mk (revision 13890) +@@ -0,0 +1,6 @@ ++LOCAL_PATH:= $(call my-dir) ++include $(CLEAR_VARS) ++LOCAL_MODULE := libISSMCore ++LOCAL_SRC_FILES := libISSMCore.a ++LOCAL_EXPORT_C_INCLUDES := $(LOCAL_PATH)/include ++include $(PREBUILT_STATIC_LIBRARY) +Index: ../trunk-jpl/src/android/ISSM/jni/Main.cpp +=================================================================== +--- ../trunk-jpl/src/android/ISSM/jni/Main.cpp (revision 0) ++++ ../trunk-jpl/src/android/ISSM/jni/Main.cpp (revision 13890) +@@ -0,0 +1,11 @@ ++#include "./issmlib/include/fac.h" ++#include "com_example_issm_FacLib.h" ++#include ++ ++JNIEXPORT jlong JNICALL Java_com_example_issm_FacLib_fac(JNIEnv *env, jclass clazz, jlong n) ++{ ++ fac *f = new fac(); ++ jlong result = (jlong) (f->factorial(n)); ++ delete(f); ++ return (jlong) result; ++} +Index: ../trunk-jpl/src/android/ISSM/jni/Android.mk +=================================================================== +--- ../trunk-jpl/src/android/ISSM/jni/Android.mk (revision 0) ++++ ../trunk-jpl/src/android/ISSM/jni/Android.mk (revision 13890) +@@ -0,0 +1,19 @@ ++LOCAL_PATH:= $(call my-dir) ++my_LOCAL_PATH:=$(LOCAL_PATH) ++ ++#include $(LOCAL_PATH)/issmlib\Android.mk ++include $(call all-subdir-makefiles) ++ ++ ++LOCAL_PATH := $(my_LOCAL_PATH) ++ ++include $(CLEAR_VARS) ++LOCAL_PATH := $(my_LOCAL_PATH) ++LOCAL_ALLOW_UNDEFINED_SYMBOLS := true ++LOCAL_CFLAGS := -Wno-psabi ++LOCAL_LDLIBS := -llog -ldl ++LOCAL_MODULE := FacLib ++LOCAL_SRC_FILES := Main.cpp ++LOCAL_STATIC_LIBRARIES := libISSMCore ++ ++include $(BUILD_SHARED_LIBRARY) +Index: ../trunk-jpl/src/android/ISSM/jni/com_example_issm_FacLib.h +=================================================================== +--- ../trunk-jpl/src/android/ISSM/jni/com_example_issm_FacLib.h (revision 0) ++++ ../trunk-jpl/src/android/ISSM/jni/com_example_issm_FacLib.h (revision 13890) +@@ -0,0 +1,21 @@ ++/* DO NOT EDIT THIS FILE - it is machine generated */ ++#include ++/* Header for class com_example_issm_FacLib */ ++ ++#ifndef _Included_com_example_issm_FacLib ++#define _Included_com_example_issm_FacLib ++#ifdef __cplusplus ++extern "C" { ++#endif ++/* ++ * Class: com_example_issm_FacLib ++ * Method: fac ++ * Signature: (J)J ++ */ ++JNIEXPORT jlong JNICALL Java_com_example_issm_FacLib_fac ++ (JNIEnv *, jclass, jlong); ++ ++#ifdef __cplusplus ++} ++#endif ++#endif +Index: ../trunk-jpl/src/android/ISSM/project.properties +=================================================================== +--- ../trunk-jpl/src/android/ISSM/project.properties (revision 0) ++++ ../trunk-jpl/src/android/ISSM/project.properties (revision 13890) +@@ -0,0 +1,14 @@ ++# This file is automatically generated by Android Tools. ++# Do not modify this file -- YOUR CHANGES WILL BE ERASED! ++# ++# This file must be checked in Version Control Systems. ++# ++# To customize properties used by the Ant build system edit ++# "ant.properties", and override values to adapt the script to your ++# project structure. ++# ++# To enable ProGuard to shrink and obfuscate your code, uncomment this (available properties: sdk.dir, user.home): ++#proguard.config=${sdk.dir}/tools/proguard/proguard-android.txt:proguard-project.txt ++ ++# Project target. ++target=android-15 +Index: ../trunk-jpl/src/android/ISSM/.project +=================================================================== +--- ../trunk-jpl/src/android/ISSM/.project (revision 0) ++++ ../trunk-jpl/src/android/ISSM/.project (revision 13890) +@@ -0,0 +1,33 @@ ++ ++ ++ ISSM ++ ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.ResourceManagerBuilder ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.PreCompilerBuilder ++ ++ ++ ++ ++ org.eclipse.jdt.core.javabuilder ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.ApkBuilder ++ ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.AndroidNature ++ org.eclipse.jdt.core.javanature ++ ++ +Index: ../trunk-jpl/src/android/ISSM/proguard-project.txt +=================================================================== +--- ../trunk-jpl/src/android/ISSM/proguard-project.txt (revision 0) ++++ ../trunk-jpl/src/android/ISSM/proguard-project.txt (revision 13890) +@@ -0,0 +1,20 @@ ++# To enable ProGuard in your project, edit project.properties ++# to define the proguard.config property as described in that file. ++# ++# Add project specific ProGuard rules here. ++# By default, the flags in this file are appended to flags specified ++# in ${sdk.dir}/tools/proguard/proguard-android.txt ++# You can edit the include path and order by changing the ProGuard ++# include property in project.properties. ++# ++# For more details, see ++# http://developer.android.com/guide/developing/tools/proguard.html ++ ++# Add any project specific keep options here: ++ ++# If your project uses WebView with JS, uncomment the following ++# and specify the fully qualified class name to the JavaScript interface ++# class: ++#-keepclassmembers class fqcn.of.javascript.interface.for.webview { ++# public *; ++#} +Index: ../trunk-jpl/src/android/ISSM/AndroidManifest.xml +=================================================================== +--- ../trunk-jpl/src/android/ISSM/AndroidManifest.xml (revision 0) ++++ ../trunk-jpl/src/android/ISSM/AndroidManifest.xml (revision 13890) +@@ -0,0 +1,25 @@ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ +\ No newline at end of file +Index: ../trunk-jpl/src/android/ISSM/src/com/example/issm/FacLib.java +=================================================================== +--- ../trunk-jpl/src/android/ISSM/src/com/example/issm/FacLib.java (revision 0) ++++ ../trunk-jpl/src/android/ISSM/src/com/example/issm/FacLib.java (revision 13890) +@@ -0,0 +1,13 @@ ++package com.example.issm; ++ ++public class FacLib ++{ ++ public static native long fac(long n); ++ static { ++ System.loadLibrary("FacLib"); ++ } ++ public static long facIterative(long n) ++ { ++ return fac(n); ++ } ++} + +Property changes on: ../trunk-jpl/src/android/ISSM/src/com/example/issm/FacLib.java +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +Index: ../trunk-jpl/src/android/ISSM/src/com/example/issm/ISSM.java +=================================================================== +--- ../trunk-jpl/src/android/ISSM/src/com/example/issm/ISSM.java (revision 0) ++++ ../trunk-jpl/src/android/ISSM/src/com/example/issm/ISSM.java (revision 13890) +@@ -0,0 +1,39 @@ ++package com.example.issm; ++ ++import android.os.Bundle; ++import android.app.Activity; ++import android.text.TextUtils; ++import android.view.Menu; ++import android.view.View; ++import android.view.View.OnClickListener; ++import android.widget.Button; ++import android.widget.EditText; ++import android.widget.TextView; ++ ++ ++public class ISSM extends Activity implements OnClickListener { ++ private EditText input; ++ private TextView output; ++ @Override ++ public void onCreate(Bundle savedInstanceState) { ++ super.onCreate(savedInstanceState); ++ setContentView(R.layout.activity_issm); ++ this.input = (EditText) super.findViewById(R.id.input); ++ this.output = (TextView) super.findViewById(R.id.output); ++ Button button = (Button) super.findViewById(R.id.button1); ++ button.setOnClickListener(this); ++ ++ } ++ ++ public void onClick(View view) ++ { ++ // TODO Auto-generated method stub ++ String input = this.input.getText().toString(); ++ if(TextUtils.isEmpty(input)) ++ { ++ return; ++ } ++ long result = FacLib.facIterative(Long.parseLong(input)); ++ this.output.setText("Result = " + result + "\n"); ++ } ++} +Index: ../trunk-jpl/src/android/ISSM/gen/com/example/issm/R.java +=================================================================== +--- ../trunk-jpl/src/android/ISSM/gen/com/example/issm/R.java (revision 0) ++++ ../trunk-jpl/src/android/ISSM/gen/com/example/issm/R.java (revision 13890) +@@ -0,0 +1,43 @@ ++/* AUTO-GENERATED FILE. DO NOT MODIFY. ++ * ++ * This class was automatically generated by the ++ * aapt tool from the resource data it found. It ++ * should not be modified by hand. ++ */ ++ ++package com.example.issm; ++ ++public final class R { ++ public static final class attr { ++ } ++ public static final class dimen { ++ public static final int padding_large=0x7f040002; ++ public static final int padding_medium=0x7f040001; ++ public static final int padding_small=0x7f040000; ++ } ++ public static final class drawable { ++ public static final int ic_action_search=0x7f020000; ++ public static final int ic_launcher=0x7f020001; ++ } ++ public static final class id { ++ public static final int button1=0x7f080001; ++ public static final int input=0x7f080000; ++ public static final int menu_settings=0x7f080003; ++ public static final int output=0x7f080002; ++ } ++ public static final class layout { ++ public static final int activity_issm=0x7f030000; ++ } ++ public static final class menu { ++ public static final int activity_issm=0x7f070000; ++ } ++ public static final class string { ++ public static final int app_name=0x7f050000; ++ public static final int hello_world=0x7f050001; ++ public static final int menu_settings=0x7f050002; ++ public static final int title_activity_issm=0x7f050003; ++ } ++ public static final class style { ++ public static final int AppTheme=0x7f060000; ++ } ++} +Index: ../trunk-jpl/src/android/ISSM/gen/com/example/issm/BuildConfig.java +=================================================================== +--- ../trunk-jpl/src/android/ISSM/gen/com/example/issm/BuildConfig.java (revision 0) ++++ ../trunk-jpl/src/android/ISSM/gen/com/example/issm/BuildConfig.java (revision 13890) +@@ -0,0 +1,6 @@ ++/** Automatically generated file. DO NOT MODIFY */ ++package com.example.issm; ++ ++public final class BuildConfig { ++ public final static boolean DEBUG = true; ++} +\ No newline at end of file +Index: ../trunk-jpl/src/android/ISSM/res/values/styles.xml +=================================================================== +--- ../trunk-jpl/src/android/ISSM/res/values/styles.xml (revision 0) ++++ ../trunk-jpl/src/android/ISSM/res/values/styles.xml (revision 13890) +@@ -0,0 +1,5 @@ ++ ++ ++ +- +- +-
+-

Linux Sysadmin Blog

+- +-
+- +-
+- +-
+-
+- +- +-
+-
+- +-
+- +-

HowTo: Get Started With Amazon EC2 Api Tools

+- +- +-

+- +- +- +- +-Posted by Marius Ducea +- +- - +- +- +- +- +- +- +- +- +- +- +- +- +- +- | Comments +- +-

+- +-
+- +- +-

This article is meant to be a quick quide that will introduce the things needed to get you started with Amazon EC2. +- All this information can be found in the EC2 api docs, and this is not +-meant to be a replacement of the documentation, just trying to show the +-things needed in a clear and short form.

+- +-

Getting Started

+- +-

First of all you will need one Amazon AWS account and enable the EC2 service; in case you don’t have this already now is the time to create your account. Once you do that you can safely return to this doc ;-)

+- +-

Once you have your account working, while still on the aws site, go and create a new X.509 certificate +- (under the AWS Access Identifiers page, in the X.509 certificate +-section near the bottom, click Create New). Once this is done, you will +-want to download locally the private key file and X.509 certificate.

+- +-

EC2 API tools

+- +-

Next you will have to download +- and install the Amazon EC2 api tools on one system (controlling +-machine) that will be used to start your EC2 army of servers, and +-control their usage. You will want to use the latest version (2009-05-15 +- at this time) as it will support all the features Amazon is offering +-for the EC2 service.

+- +-

The only real dependency of the EC2 API tools is java (at +- least version 1.5) so we will want to install that first. If you are +-running debian you can easily do this just by running (for lenny): +-aptitude install sun-java6-jre +-while for etch you will have to use: aptitude install sun-java5-jre +-For other distributions you can either use their internal packaging +-mechanism (in case they provide sun-java packages) or just download the +-binary from sun and install it manually.

+- +-

Extract the EC2 APi tools (it is a zip archive called ec2-api-tools.zip) and move it under a folder of your preferece. I like to use ~/.ec2 for this, but you can use any folder you prefer. Also copy the private key and X.509 certificate in the same directory. Those files will look like cert-xxx.pem and pk-xxx.pem.

+- +-

Next we will have to export some shell variables. A good place to put this is in ~/.bashrc:

+- +-
1
+-2
+-3
+-4
+-5
+-6
+-7
+-8
+-
export EC2_HOME=~/.ec2
+-export PATH=$PATH:$EC2_HOME/bin
+-export EC2_PRIVATE_KEY=$EC2_HOME/pk-xxx.pem
+-export EC2_CERT=$EC2_HOME/cert-xxx.pem
+-#Java home for debian default install path:
+-export JAVA_HOME=/usr
+-#add ec2 tools to default path
+-export PATH=~/.ec2/bin:$PATH
+- +- +-

Finally source the file to have the changes active in your current shell session: +-source ~/.bashrc +-or just open a new shell before starting to use the API tools.

+- +-

EC2 Keypair

+- +-

We will need to create one keypair that will be used to connect using ssh to the EC2 instances we will be using. We will use the ec2-add-keypair utility to create the key and register it with amazon: +-ec2-add-keypair my-keypair +-This will print out the private key that we will have to save in a file: +-`cat > ~/.ec2/id_rsa-my-keypair

+- +-

paste the private key content

+- +-

sudo chmod 600 `~/.ec2/id_rsa-my-keypair

+- +-

Running your first EC2 instance

+- +-

Amazon EC2 uses the concept of AMIs = Amazon Machine +- Images. Any EC2 instance is started from one AMI. You can either use +-standard, public AMIs or create and customize your own private images. +-Creating or modifying existing AMIs is beyond the scope of this article, +- but just as a general information this is done using special AMI tools. +- Also before building your AMI you will want to ensure if you want to +-use a ‘small’ type of image (i386 os) or a ‘large’ type of instance +-(64bit os). These are described under http://aws.amazon.com/ec2/instance-types/

+- +-

For the scope of our article we will find a standard public image and +- start one instance of it to see that all is working properly with the +-EC2 api tools. You can see all the public images using: +-ec2-describe-images -a +-(over 2,300 images ;) ). You should probably grep the result to get any +-useful information. There are many good public images to use, like for +-example the alestic ones (for debian and ubuntu) +-Having the AMI id of the image we want to use we are ready to start our fist EC2 instance: +-ec2-run-instances ami-e348af8a -k my-keypair +-that will start a small instance with a 32bit debian lenny server instance from alestic.com.

+- +-

ec2-describe-instances +-- this will describe the status of all the running instances, with their hostname, instance id, etc.

+- +-

ec2-authorize default -p 22 +-- in order to connect to your instance you will need to customize the +-‘default’ firewall rules for your account. The above rule will allow ssh +- on port 22 from anywhere. If you want to open http traffic you will +-have to add a rule like this: +-ec2-authorize default -p 80

+- +-

Finally we can ssh to the ec2 instance using: +-ssh -i ~/.ec2/id_rsa-my-keypair root@ec2-XXX-XXX-XXX-XXX.z-2.compute-1.amazonaws.com +-where ec2-XXX-XXX-XXX-XXX.z-2.compute-1.amazonaws.com is the actual +-hostname of the instance as obtained from ec2-describe-instances.

+- +-

Note: don’t forget to stop your instance +-when you no longer need it. EC2 is a service paid as you use, hence if +-you forget your instance running you will be billed for it ;-). You can +-do this by running shutdown inside the instance or by using: +-ec2-terminate-instances i-yourinstance +-and verify with ec2-describe-instances that the instance is indeed stopped.

+- +-

Next step is to create/customize your own EC2 AMI images based on +-your needs. This will be covered in a future article. Hopefully you +-found this article useful, and it will get you on track quickly with +-Amazon EC2 api tools.

+-
+- +- +- +-
+- +-
+-

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+- Copyright © 2012 - Promet OPS Team - +- Powered by Octopress +-

+- +-
+- +- +- +- +- +- +-
+- +- +- +- +- +- +- +- +- +- +- +- +- +- +- +\ No newline at end of file +Index: ../trunk-jpl/externalpackages/ec2api/doc/ec2-ug.pdf +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/externalpackages/ec2api/doc/mpi-cluster-with-python-and-amazon-ec2-part-2-of-3.html +=================================================================== +--- ../trunk-jpl/externalpackages/ec2api/doc/mpi-cluster-with-python-and-amazon-ec2-part-2-of-3.html (revision 13947) ++++ ../trunk-jpl/externalpackages/ec2api/doc/mpi-cluster-with-python-and-amazon-ec2-part-2-of-3.html (revision 13948) +@@ -1,1111 +0,0 @@ +- +- +- +- MPI Cluster with Python and Amazon EC2 (part 2 of 3) » Data Wrangling Blog +- +- +- +- +- +- +- +- +- +- +- +- +- +- +- +- +- +- +- +- +- +- +-
+- +- +- +- +- +- +- +- +- +- +-
+-
+-
+-
+-

+- MPI Cluster with Python and Amazon EC2 (part 2 of 3) +-

+-
+-

Posted by Peter Skomoroch on Apr 09, 2007 to cluster computing, python, mpi, amazon ec2, and cloud computing

+-

Today I posted a public AMI which can be used to run a small beowulf cluster on Amazon EC2 and do some parallel computations with C, Fortran, or Python. +- If you prefer another language (Java, Ruby, etc) just install the +-appropriate MPI library and rebundle the EC2 image. The following set +-of Python scripts automate the launch and configuration of an MPI cluster on EC2 (currently limited to 20 nodes while EC2 is in beta):

+- +-

Update (3-19-08): Code for running a cluster with large +-or xlarge 64 bit EC2 instances is now hosted on google code. The new +-images include NFS, ganglia, IPython1, and other useful python packages.

+- +-

http://code.google.com/p/elasticwulf/

+- +-

Update (7-24-07): I've made some important bug fixes to +-the scripts to address issues mentioned in the comments. See the README +- file for details

+- +- +- +- +-

The file contains some quick scripts I threw together using the AWS +-Python example code. This is the approach I'm using to bootstrap an MPI +- cluster until one of the major linux cluster distros is ported to run on EC2. Details on what is included in the public AMI were covered in Part 1 +- of the tutorial, Part 3 will cover cluster operation on EC2 in more +-detail and show how to use Python to carry out some neat parallel +-computations.

+- +-

The cluster launch process is pretty simple once you have an Amazon +-EC2 account and keys, just download the Python scripts and you can be +-running a compute cluster in a few minutes. In a later post I will look +- at cluster bandwidth and performance in detail. If you have only an +-occasional need for running large jobs, $2/hour for a 20 node MPI +-cluster on EC2 is not a bad deal considering the ~ $20K price for +-building your own comparable system.

+- +- +- +- +-

Prerequisites:

+- +-
    +-
  1. Get a valid Amazon EC2 account
    2. +-
  2. Complete the most recent "getting started guide" tutorial on Amazon EC2 and create all needed web service accounts, authorizations, and keypairs
    3. +-
  3. Download and install the Amazon EC2 Python library
    4. +-
  4. Download the Amazon EC2 MPI cluster management scripts
    5. +-
+- +- +-

Launching the EC2 nodes

+- +- +-

First , unzip the cluster management scripts and modify the +-configuration parameters in '''EC2config.py''', substituting your own +-EC2 keys and changing the cluster size if desired:

+- +-
#replace these with your AWS keys
+-AWS_ACCESS_KEY_ID = 'YOUR_KEY_ID_HERE'
+-AWS_SECRET_ACCESS_KEY = 'YOUR_KEY_HERE'
+-#change this to your keypair location (see the EC2 getting started guide tutorial on using ec2-add-keypair)
+-KEYNAME = "gsg-keypair"
+-KEY_LOCATION = "/Users/pskomoroch/id_rsa-gsg-keypair"
+-# remove these next two lines when you've updated your credentials.
+-print "update %s with your AWS credentials" % sys.argv[0]
+-sys.exit()
+-
+-MASTER_IMAGE_ID = "ami-3e836657"
+-IMAGE_ID = "ami-3e836657"
+-
+-DEFAULT_CLUSTER_SIZE = 5
+-
+-
+- +- +-

Launch the EC2 cluster by running the '''ec2-start_cluster.py''' script from your local machine:

+- +-
 
+-peter-skomorochs-computer:~/AmazonEC2_MPI_scripts pskomoroch$ ./ec2-start-cluster.py 
+-
+-image ami-3e836657
+-master image ami-3e836657
+------ starting master -----
+-RESERVATION r-275eb84e  027811143419    default
+-INSTANCE    i-0ed33167  ami-3e836657            pending
+------ starting workers -----
+-RESERVATION r-265eb84f  027811143419    default
+-INSTANCE    i-01d33168  ami-3e836657            pending
+-INSTANCE    i-00d33169  ami-3e836657            pending
+-INSTANCE    i-03d3316a  ami-3e836657            pending
+-INSTANCE    i-02d3316b  ami-3e836657            pending
+-
+- +- +-

Verify the EC2 nodes are running with '''./ec2-check-instances.py''':

+- +-

+-peter-skomorochs-computer:~/AmazonEC2_MPI_scripts pskomoroch$ ./ec2-check-instances.py 
+------ listing instances -----
+-
+-RESERVATION     r-aec420c7      027811143419    default
+-INSTANCE        i-ab41a6c2      ami-3e836657    domU-12-31-33-00-02-5A.usma1.compute.amazonaws.com      running
+-INSTANCE        i-aa41a6c3      ami-3e836657    domU-12-31-33-00-01-E3.usma1.compute.amazonaws.com      running
+-INSTANCE        i-ad41a6c4      ami-3e836657    domU-12-31-33-00-03-AA.usma1.compute.amazonaws.com      running
+-INSTANCE        i-ac41a6c5      ami-3e836657    domU-12-31-33-00-04-19.usma1.compute.amazonaws.com      running
+-INSTANCE        i-af41a6c6      ami-3e836657    domU-12-31-33-00-03-E3.usma1.compute.amazonaws.com      running
+-
+- +- +- +- +-

Cluster Configuration and Booting MPI

+- +- +-

Run '''ec2-mpi-config.py''' to configure MPI on the nodes, this will take a minute or two depending on the number of nodes.

+- +-

+-peter-skomorochs-computer:~/AmazonEC2_MPI_scripts pskomoroch$ ./ec2-mpi-config.py 
+-
+----- MPI Cluster Details ----
+-Numer of nodes = 5
+-Instance= i-ab41a6c2 hostname= domU-12-31-33-00-02-5A.usma1.compute.amazonaws.com state= running
+-Instance= i-aa41a6c3 hostname= domU-12-31-33-00-01-E3.usma1.compute.amazonaws.com state= running
+-Instance= i-ad41a6c4 hostname= domU-12-31-33-00-03-AA.usma1.compute.amazonaws.com state= running
+-Instance= i-ac41a6c5 hostname= domU-12-31-33-00-04-19.usma1.compute.amazonaws.com state= running
+-Instance= i-af41a6c6 hostname= domU-12-31-33-00-03-E3.usma1.compute.amazonaws.com state= running
+-
+-The master node is ec2-72-44-46-78.z-2.compute-1.amazonaws.com 
+-
+-
+-... ...
+-
+-Configuration complete, ssh into the master node as lamuser and boot the cluster:
+-$ ssh lamuser@ec2-72-44-46-78.z-2.compute-1.amazonaws.com 
+-> mpdboot -n 5 -f mpd.hosts 
+-> mpdtrace
+-
+- +- +-

Login to the master node, boot the MPI cluster, and test the connectivity:

+- +-

+-
+-peter-skomorochs-computer:~/AmazonEC2_MPI_scripts pskomoroch$ ssh lamuser@ec2-72-44-46-78.z-2.compute-1.amazonaws.com 
+-
+-
+-
+-Sample Fedora Core 6 + MPICH2 + Numpy/PyMPI compute node image 
+-
+-http://www.datawrangling.com/on-demand-mpi-cluster-with-python-and-ec2-part-1-of-3
+-
+----- Modified From Marcin's Cool Images: Cool Fedora Core 6 Base + Updates Image v1.0 ---
+-
+-see http://developer.amazonwebservices.com/connect/entry.jspa?externalID=554&categoryID=101
+-
+-
+-Like Marcin's image, standard disclaimer applies, use as you please...
+-
+-Amazon EC2 MPI Compute Node Image
+-Copyright (c) 2006 DataWrangling. All rights reserved.
+-
+-Redistribution and use in source and binary forms, with or without
+-modification, are permitted provided that the following conditions are
+-met:
+-
+-    * Redistributions of source code must retain the above copyright
+-       notice, this list of conditions and the following disclaimer.
+-
+-    * Redistributions in binary form must reproduce the above
+-       copyright notice, this list of conditions and the following
+-       disclaimer in the documentation and/or other materials provided
+-       with the distribution.
+-
+-    * Neither the name of the DataWrangling nor the names of any
+-       contributors may be used to endorse or promote products derived
+-       from this software without specific prior written permission.
+-
+-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+-OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+-[lamuser@domU-12-31-33-00-02-5A ~]$ 
+-[lamuser@domU-12-31-33-00-02-5A ~]$ mpdboot -n 5 -f mpd.hosts 
+-[lamuser@domU-12-31-33-00-02-5A ~]$ mpdtrace
+-domU-12-31-33-00-02-5A
+-domU-12-31-33-00-01-E3
+-domU-12-31-33-00-03-E3
+-domU-12-31-33-00-03-AA
+-domU-12-31-33-00-04-19
+-
+-
+- +- +-

The results of the mpdtrace command show we have an MPI cluster +-running on 5 nodes. In the next section, we will verify that we can run +-some basic MPI tasks. For more detailed information on these mpi +-commands (and MPI in general), see the MPICH2 documentation.

+- +-

Testing the MPI Cluster

+- +- +-

Next we execute a sample C program bundled with MPICH2 which estimates pi using the cluster:

+- +-

+-[lamuser@domU-12-31-33-00-02-5A ~]$  mpiexec -n 5 /usr/local/src/mpich2-1.0.5/examples/cpi
+-Process 0 of 5 is on domU-12-31-33-00-02-5A
+-Process 1 of 5 is on domU-12-31-33-00-01-E3
+-Process 2 of 5 is on domU-12-31-33-00-03-E3
+-Process 3 of 5 is on domU-12-31-33-00-03-AA
+-Process 4 of 5 is on domU-12-31-33-00-04-19
+-pi is approximately 3.1415926544231230, Error is 0.0000000008333298
+-wall clock time = 0.007539
+-
+-
+- +- +-

Test the message travel time for the ring of nodes you just created:

+- +-

+-[lamuser@domU-12-31-33-00-02-5A ~]$ mpdringtest 100
+-time for 100 loops = 0.14577794075 seconds
+-
+-
+- +- +-

Verify that the cluster can run a multiprocess job:

+- +-

+-[lamuser@domU-12-31-33-00-02-5A ~]$ mpiexec -l -n 5 hostname
+-3: domU-12-31-33-00-03-AA
+-0: domU-12-31-33-00-02-5A
+-1: domU-12-31-33-00-01-E3
+-4: domU-12-31-33-00-04-19
+-2: domU-12-31-33-00-03-E3
+-
+-
+- +- +- +- +-

Testing PyMPI

+- +- +-

Lets verify that the PyMPI install is working with our running cluster of 5 nodes. Execute the following on the master node:

+- +-

+-[lamuser@domU-12-31-33-00-02-5A ~]$ mpirun -np 5 pyMPI /usr/local/src/pyMPI-2.4b2/examples/fractal.py
+-Starting computation (groan)
+-
+-process 1 done with computation!!
+-process 3 done with computation!!
+-process 4 done with computation!!
+-process 2 done with computation!!
+-process 0 done with computation!!
+-Header length is  54
+-BMP size is  (400, 400)
+-Data length is  480000
+-[lamuser@domU-12-31-33-00-02-5A ~]$ ls
+-hosts  id_rsa.pub  mpd.hosts  output.bmp
+-
+-
+- +- +-

This produced the following fractal image (output.bmp):

+- +-

output.bmp

+- +-

We will show some more examples using PyMPI in the next post.

+- +-

Changing the Cluster Size

+- +- +-

If we want to modify the number of nodes in the cluster we first need to kill the mpi cluster from the master node as follows:

+- +-

+-[lamuser@domU-12-31-33-00-02-5A ~]$ mpdallexit
+-[lamuser@domU-12-31-33-00-02-5A ~]$ mpdcleanup
+-
+- +- +-

Once this is done, you can start additional instances of the public +-AMI from your local machine, then re-run the ec2-mpi-config.py script +-and reboot the cluster.

+- +-

Cluster Shutdown

+- +- +-

Run '''ec2-stop-cluster.py''' to stop all EC2 MPI nodes. If you just want to stop the slave nodes, run ec2-stop-slaves.py

+- +-

+-
+-peter-skomorochs-computer:~/AmazonEC2_MPI_scripts pskomoroch$ ./ec2-stop-cluster.py
+-This will stop all your EC2 MPI images, are you sure (yes/no)? yes
+------ listing instances -----
+-RESERVATION     r-aec420c7      027811143419    default
+-INSTANCE        i-ab41a6c2      ami-3e836657    domU-12-31-33-00-02-5A.usma1.compute.amazonaws.com      running
+-INSTANCE        i-aa41a6c3      ami-3e836657    domU-12-31-33-00-01-E3.usma1.compute.amazonaws.com      running
+-INSTANCE        i-ad41a6c4      ami-3e836657    domU-12-31-33-00-03-AA.usma1.compute.amazonaws.com      running
+-INSTANCE        i-ac41a6c5      ami-3e836657    domU-12-31-33-00-04-19.usma1.compute.amazonaws.com      running
+-INSTANCE        i-af41a6c6      ami-3e836657    domU-12-31-33-00-03-E3.usma1.compute.amazonaws.com      running
+-
+----- Stopping instance Id's ----
+-Stoping Instance Id = i-ab41a6c2 
+-Stoping Instance Id = i-aa41a6c3 
+-Stoping Instance Id = i-ad41a6c4 
+-Stoping Instance Id = i-ac41a6c5 
+-Stoping Instance Id = i-af41a6c6 
+-
+-Waiting for shutdown ....
+------ listing new state of instances -----
+-RESERVATION     r-aec420c7      027811143419    default
+-INSTANCE        i-ab41a6c2      ami-3e836657    domU-12-31-33-00-02-5A.usma1.compute.amazonaws.com      shutting-down
+-INSTANCE        i-aa41a6c3      ami-3e836657    domU-12-31-33-00-01-E3.usma1.compute.amazonaws.com      shutting-down
+-INSTANCE        i-ad41a6c4      ami-3e836657    domU-12-31-33-00-03-AA.usma1.compute.amazonaws.com      shutting-down
+-INSTANCE        i-ac41a6c5      ami-3e836657    domU-12-31-33-00-04-19.usma1.compute.amazonaws.com      shutting-down
+-INSTANCE        i-af41a6c6      ami-3e836657    domU-12-31-33-00-03-E3.usma1.compute.amazonaws.com      shutting-down
+-
+-
+- +- +-
+- +- +- +- +-

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  • Aarthi 8288 3 comments collapsed Collapse Expand

    Hi,

    +- +-

    I was trying to launch a cluster using the given scripts. I got the following error :

    +- +-

    # ./ec2-start-cluster.py
    Traceback (most recent call last):
    File "./ec2-start-cluster.py", line 23, in <module>
    import EC2
    ImportError: No module named EC2

    +- +-

    Can anyone help me out ?
    </module>

  • Adeel Jan 1 comment collapsed Collapse Expand

    I think you need to get python library :)

    +- +-

    Adeel Jan.

  • Lukearron 1 comment collapsed Collapse Expand

    Did +- anyone solve this problem?  I had the same problem, and I +-downloaded and unpacked the libraries, but perhaps the python library +-needs to be _placed_ somewhere?

  • Easwar 1 comment collapsed Collapse Expand

    Dear Sir,

    +- +-

      I am trying to use MPI for
    running Data parallel +-applications. I read this post and on following up, I have few queries. +-Would be great, if I can get answers to them.

    +- +-

    a) As of now, I am choosing AMI using the browser interface of +-Amazon. You have uploaded two AMI's one for master (ami-e813f681) and +-another for slave (ami-eb13f682).
    When I launch an instance, I can only choose one. Which one should I
    choose ? (Or how should I choose both, in case I need to)  ? Do these
    AMI's has OPEMPI implementation ?

    +- +-

    b) Secondly, if I launch multiple instances of a Large CPU (say 3
    instances), +- I would be get many nodes (say m nodes per one instance, hence i would +-have m*3 nodes). Can I communicate between nodes
    of different instances just as we normally do in MPI ?

    +- +-

    c) Are you aware any MPI image with ubuntu ?

    +- +-

    d) I am using browser, since I have to connect through proxy. How/Where
    do set proxy connections, if I need to start cluster using your python
    scripts ?

    +- +-

    Easwar

  • Johnliu 1 comment collapsed Collapse Expand

    Hi,

    +- +-

    Does anyone have this running under cygwin in windows?

    +- +-

    If so, can you please post your code for ec2-mpi-config.py? I tried using the current file but get lots of errors.

    +- +-

    Thanks,
    John

  • Supriyamunshaw 2 comments collapsed Collapse Expand

    I have sucessfully connected to 5 nodes but am having trouble with the ec2-mpi-config.py script. When I run it, I repeatedly get the following:

    +- +-

    ---- MPI Cluster Details ----
    Numer of nodes = 5
    Instance= i-8d2949e7 external_name = ec2-184-72-183-113.compute-1.a... hostname= ip-10-212-239-33.ec2.internal state=
    Instance= i-832949e9 external_name = ec2-174-129-138-43.compute-1.a... hostname= domU-12-31-39-10-6C-13.compute-1.internal state=
    Instance= i-812949eb external_name = ec2-184-72-141-241.compute-1.a... hostname= domU-12-31-39-0B-00-F8.compute-1.internal state=
    Instance= i-872949ed external_name = ec2-174-129-131-171.compute-1.... hostname= domU-12-31-39-09-C4-24.compute-1.internal state=
    Instance= i-852949ef external_name = ec2-174-129-61-151.compute-1.a... hostname= domU-12-31-39-0C-D8-57.compute-1.internal state=
    5

    +- +-

    The master node is ec2-184-72-183-113.compute-1.a...

    +- +-

    Writing out mpd.hosts file

    +- +-

    scp -i id_rsa-gsg-keypair -o "StrictHostKeyChecking no" id_rsa-gsg-keypair root@ec2-184-72-183-113.compute-1.amaz...:~/.ssh/id_rsa-gsg-keypair

    +- +-

    ssh: connect to host ec2-184-72-183-113.compute-1.a... port 22: Connection timed out
    lost connection

    +- +-

    ssh -o "StrictHostKeyChecking no" root@ec2-184-72-183-113.compute-1.amaz... "touch .ssh/authorized_keys"

    +- +-

    ssh: connect to host ec2-184-72-183-113.compute-1.a... port 22: Connection timed out

    +- +-

    ssh -o "StrictHostKeyChecking no" root@ec2-184-72-183-113.compute-1.amaz... "cp -r .ssh /home/lamuser/"

    +- +-

    It seems I'm having a connection problem. Does anyone what I can do about this?

  • Supriyamunshaw 1 comment collapsed Collapse Expand

    ok, i figured it out. the connection was being made through my default security group where port 22 was not open.

  • Henrywang41 1 comment collapsed Collapse Expand

    Can someone please help? mc2-mpi-config.py is giving the following error:

    +- +-

    ---- MPI Cluster Details ----
    Numer of nodes = 2
    Instance= i-bf90f5d5 external_name = ec2-184-73-36-216.compute-1.am... hostname= ip-10-242-1
    18-239.ec2.internal state= running
    Instance= i-bd90f5d7 external_name = ec2-174-129-77-216.compute-1.a... hostname= ip-10-242-
    117-139.ec2.internal state= running

    +- +-

    The master node is ec2-184-73-36-216.compute-1.am...

    +- +-

    Writing out mpd.hosts file
    Traceback (most recent call last):
    File "ec2-mpi-config.py", line 210, in <module>
    sys.exit(main())
    File "ec2-mpi-config.py", line 65, in main
    configure()
    File "ec2-mpi-config.py", line 151, in configure
    rsakeys = open(homedir + "/.ssh/id_rsa", 'r').read()
    IOError: [Errno 2] No such file or directory: 'C:\\Documents and Settings\\Yunzhi Ma/.ssh/id_rsa'

    +- +-

    Could this possibly be due to anything about chunk and parsed_response? I printed out parsedresponse:

    +- +-

    [['RESERVATION', 'r-30733b5b', '219669225938', 'default'], ['INSTANCE', 'i-bf90f5d5', 'ami-e813f681'
    , 'ec2-184-73-36-216.compute-1.am...', 'ip-10-242-118-239.ec2.internal', 'running'], ['RESER
    VATION', 'r-36733b5d', '219669225938', 'default'], ['INSTANCE', 'i-bd90f5d7', 'ami-eb13f682', 'ec2-1
    74-129-77-216.compute-1.amazon...', 'ip-10-242-117-139.ec2.internal', 'running']]

    +- +-

    Thanks so much,
    Henry</module>

  • Henrywang41 1 comment collapsed Collapse Expand

    Hi,

    +- +-

    Amazon just recently (last month) released a cloud computing instance (http://developer.amazonwebserv...

    +- +-

    Does the code and what you describe here work for this new released +-instance for HPC? (It's CentOS HVM AMI, ami-7ea24a17 under U.S. East)

    +- +-

    Thanks,

    +- +-

    Henry

  • Henrywang41 1 comment collapsed Collapse Expand

    Hi,

    +- +-

    Is Elasticwulf and MPI essentially the same thing? I'm trying to run +-some high performance computing using an Amazon EC2 cluster.

    +- +-

    Also, is boto necessary to set up a cluster on amazon EC2? What's the difference between boto and Elasticwulf?

    +- +-

    Thanks,

    +- +-

    Henry

  • Henrywang41 1 comment collapsed Collapse Expand

    Hi,

    +- +-

    What exactly is the difference between Elasticwulf and MPI? Are they +-the same thing? I'm trying to launch a cluster for HPC, which one is +-more suitable?

    +- +-

    Also, is boto necessary too for launching a cluster?

    +- +-

    Thanks,
    Henry

  • bearrito 1 comment collapsed Collapse Expand

    Little late on the thread here but would still like some feedback.

    +- +-

    My issues:

    +- +-

    1. I was also being prompted for my password. I ended up using the solution that Raghave suggested.

    +- +-

    2. I am not seeing /usr/local/src/pyMPI-2.4b2/. That directory +-doesn't appear to be present. I tried to get around this by copying in fractal.py from my local machine. I end up with the following:

    +- +-

    mpirun -np 2 pyMPI /home/lamuser/fractal.py
    pyMPI: can't open file '/home/lamuser/fractal.py': [Errno 2] No such file or directory

    +- +-

    fractal.py is in that directory.

    +- +-

    Advice?

  • miccloud 1 comment collapsed Collapse Expand

    I have a python script that calls a program installed on the master node and slave nodes.
    Can I run it from the master node and get the results with mpirun?

    +- +-

    Thanks a lot.

  • miccloud 1 comment collapsed Collapse Expand

    Can I execute bash script in a node with a job?

    +- +-

    Thanks.

  • Harry 1 comment collapsed Collapse Expand

    Hello everybody,

    +- +-

    I had error with Fortran 77 library in AMI ami-e813f681 (Fedora core 6 +- x86- 64 bit) because of two libraries: libf2c or libg2c in the AMI.
    (....
    checking for f_exit in -lf2c... no
    checking for f_exit in -lg2c... no
    checking for dummy main to link with Fortran 77 libraries... unknown
    configure: error: linking to Fortran libraries from C fails
    )

    +- +-

    Could anybody help me solve the problem? Thanks so much!

    +- +-

    best regards,

    +- +-

    Harry

  • Pete 9 comments collapsed Collapse Expand

    Jeff,


    I'm +- actually working on a new version of Elasticwulf right now. Shoot me +-an email at pete@datawrangling.com and I'll try to include what you need +- for Rmpi. If you have some sample Rmpi code you want to test and that +-you don't mind releasing, we can build that into the AMI to ensure +-everything you need is installed.


    Here are the MPI installs that were included on that Fedora 64 bit image:


    # mpich2 
    
+-
+-
    cd /usr/local/src/
    wget http://www.mcs.anl.gov/researc...
    tar -xzvf mpich2-1.0.6p1.tar.gz
    cd mpich2-1.0.6p1
    ./configure --enable-sharedlibs=gcc --prefix=/usr/local/mpich2
    make
    make install
    
+-
+-
    # openmpi
    
+-
+-
    cd /usr/local/src/
    wget http://www.open-mpi.org/softwa...
    #wget http://www.open-mpi.de/softwar...
    tar -zxf openmpi-1.2.5.tar.gz
    cd openmpi-1.2.5
    ./configure --prefix=/usr/local/openmpi
    make all
    make install
    
+-
+-
    #lam
    cd /usr/local/src/
    wget http://www.lam-mpi.org/downloa...
    tar -xzvf lam-7.1.2.tar.gz
    cd lam-7.1.2
    ./configure --enable-shared --prefix=/usr/local/lam
    make 
    make install
    
+-
+-
    # mpich1
    cd /usr/local/src/
    wget http://www-unix.mcs.anl.gov/mp...
    tar -zxf mpich.tar.gz
    cd mpich-1.2.7p1/
    ./configure --enable-sharedlib --prefix=/usr/local/mpich
    make
    make install

  • Andrew Lonie 8 comments collapsed Collapse Expand

    Hi +- - I'd be very interested in a Elasticwulf cluster that supports R, too. +- Did anything come of this? I'd be happy to be involved.

    +- +-

    Andrew

  • pskomoroch 7 comments collapsed Collapse Expand

    Yes, +- I have a Rails REST web service on github now for spawning MPI clusters +- that support R. Haven't had time yet to finish the docs or write a +-blog post about it. Works fine in operation...

    +- +-

    http://github.com/datawranglin...

  • Soren Macbeth, Chief Data Scientist @yieldbot. Co-founder of @StockTwits 3 comments collapsed Collapse Expand

    Hey Peter,

    +- +-

    Thanks for the awesome ec2cluster project! I forked it on github so +-that I could add the ability to install R packages from CRAN across all +-the nodes in the cluster. Basically I added the following to ubuntu_installs.sh:
    --snip--
    # Custom R packages
    cat <<eof>> /home/ec2cluster/install_custom_packages.R
    install.packages("DEoptim",repos="http://cran.stat.ucla.edu")
    EOF

    R CMD BATCH /home/ec2cluster/install_custom_packages.R
    --snip--

    +- +-

    A bit crude I know, but something people wanting to do things with R will probably find useful.

    +- +-

    To actually run the R code, I was successful with the follow approach:

    +- +-

    1) put your R code in a file and save it as foo.R
    2) add the following line to a shellscript: mpirun -n 1 -hostfile /mnt/ec2cluster/openmpi_hostfile R CMD BATCH foo.R
    3) call the shellscript and grab the produced .Rout file to your S3 bucket!
    </eof>

  • pskomoroch 2 comments collapsed Collapse Expand

    Soren,

    +- +-

    Glad ec2cluster helped, are you guys big R users at StockTwits?

    +- +-

    -Pete

  • Soren Macbeth, Chief Data Scientist @yieldbot. Co-founder of @StockTwits 1 comment collapsed Collapse Expand

    The +- very first StockTwits prototype used R to generate some statistics as +-well as generate charts of the stocks being talked about in tweets :)

  • Andrew Lonie 3 comments collapsed Collapse Expand

    Thanks +- - this is impressive, and a web interface for building clusters would +-be very nice, but maybe I'm after something slightly closer to your +-original solution. You might already know that R has an in-language +-cluster support API built on Rmpi, called SNOW (Simple network of +-workstations). It allows for various script commands like +-clusterExport(data) and clusterApply(vector, function) which let you +-interactively cluster jobs according to the parameter values in a list.
    Would +- this be compatible with your cluster app? I notice that it's more +-schedule-focused and the nodes need to talk to the app; is the app +-acting as the master rather than one of the ec2 nodes? Ideally my +-architecture would be something like master Rmpi node running on ec2 +-talking to arbitrary slave #nodes, accessed through maybe something like +- the Biocep remote R client (http://biocep-distrib.r-forge.... clustering done in-session.

  • pskomoroch 2 comments collapsed Collapse Expand

    Yes, +- this is compatible with the cluster app. One of the bundled examples +-runs some calculations with R and SNOW, another uses Rmpi (see the code +-on Github http://bit.ly/ocKCn ).

    +- +-

    The web interface can be run anywhere, but needs to be https +-accessible to the EC2 nodes. I usually just run it as a small ec2 +-instance as shown in the docs. You can start a job from the API or the +-web console with shutdown_after_complete = false, and the cluster will +-remain live for interactive work, just ssh into the master node like you +- would with Elasticwulf. The app is not acting as the MPI master node, +-but the cluster nodes do talk to the app to handle configuration etc.

  • Andrew Lonie 1 comment collapsed Collapse Expand

    OK thanks I understand. I'll try this out properly; it sounds like exactly what I'm after.

  • Jeff Howbert 1 comment collapsed Collapse Expand

    Hello Pete -


    Thanks +- for putting together your ElsticWulf scripts and AMIs. They have saved +- me a huge amount of time and effort compared with building my own from +-scratch.


    I am interested in parallelizing some machine +-learning algorithms written in R. My interest in ElasticWulf comes +-partly from the fact that R is already bundled with its AMIs. I +-discovered, however, that Rmpi is not one of the installed packages. +-What were your intentions/plans with R in the ElasticWulf environment? +-Did you plan for parallel communication using a mechanism other than +-MPI?


    It wasn't hard to install Rmpi on top of the ElasticWulf +-AMI, but despite a couple of days' struggle, I haven't found a +-combination of Rmpi version and paths to the AMI's existing MPI +-libraries that fully works. The best I've been able to do is spawn an R +- cluster where all the nodes are running on the master node.


    Could +- you tell me what version of R and the various MPI implementations +-(OpenMPI, MPICH, LAM) went into your 64-bit AMI? That might help me +-sort things out. A couple of observations, for what they're worth:


    1) +- Once I have an ElasticWulf cluster up and have run mpdboot, I find that +- mpiexec works, but orterun (the equivalent in OpenMPI) does not.


    2) There has been at least one report of problems between the latest version of Rmpi and OpenMPI:


    https://stat.ethz.ch/pipermail...


    Much thanks.


    Jeff Howbert

  • Ben Racine 1 comment collapsed Collapse Expand

    Hello,


    I +- get the same problem that Michael Creel was having. I am able to start +- the instances and get them "running" successfully, by pointing them to +-my keypair with the KEYNAME variable, but I believe my KEY_LOCATION +-variable in my EC2config.py file must be causing the prompt for a password.


    This is all per the default block of code in EC2config.py:

    +- +-

    change this to your keypair location (see the EC2 getting started guide tutorial on using ec2-add-keypair)

    +- +-

    KEYNAME = "my_keypair"
    KEY_LOCATION = "/Users/pskomoroch/id_rsa-gsg-keypair"


    I +- believe this requires me to go back through the "getting started +-guide", but I just wanted to update my progress in case others are +-seeing the same thing.


    Many thanks for sharing your progress Peter!


    Ben Racine

  • ej 1 comment collapsed Collapse Expand

    @Pete - Feb08



    Can’t get the ec-mpi-config to work. Says list >index out of range for mpi-externalnames[0] on >line 108



    You are right - the output from ec2-describe-instances has changed. Do the following..


    Change


    machine_state.append(chunk[-1])


    to


    machine_state.append(chunk[5])


    in "ec2-mpi-config.py"


    Or, +- if the output changes again - just do an "ec2-describe-instances" and +-match up the required fields to the index on the chunk[] array

  • Pete 1 comment collapsed Collapse Expand

    Joanne,


    Try +- logging in and running your commands as "lamuser" instead of root. The +- default configuration assumes lamuser is running all commands.


    $ ssh lamuser@ec2-72-44-46-78.z-2.compute-1.ama...


    See part 1 of the post for details on changing the configuration to run MPI as root.


    -Pete

  • jjiyunlee 1 comment collapsed Collapse Expand

    Hi,


    Thanks +- for your writeup! It's very helpful. I'm running into an error with +-mpdtrace and was hoping for some of your insight into it. I am running +-mpd as root, with one node for simplicity.


    I can successfully start up mpd on the instance and "mpd &":
    root@...:/etc# mpdboot -n 1 -f mpd.hosts
    root@...:/etc# mpd &
    [1] 2280


    but "mpdtrace -l" gives me an error:
    root@ip-10-251-143-0:/etc# mpdtrace -l
    mpdtrace: unexpected msg from mpd=:{'error_msg': 'invalid secretword to root mpd'}:


    I +- have tried all pairwise combinations of having MPD_SECRETWORD= or +-secretword= in ~/.mpd.conf and /etc/mpd.conf, all of which were set to +-read/write for root only.


    I also can't do "mpdallexit":
    I can't mpdallexit:
    root@...:~# mpdallexit
    mpdallexit: mpd_uncaught_except_tb handling:
    : 'cmd'
    /usr/local/bin/mpich2-install/bin/mpdallexit 53 mpdallexit
    elif msg['cmd'] != 'mpdallexit_ack':
    /usr/local/bin/mpich2-install/bin/mpdallexit 59
    mpdallexit()


    I can also run mpdcheck as a server and have it listen for mpdcheck as a client from the same instance (in a different window).


    Suggestions/help? I'd greatly appreciate any advice you have on this problem. Thanks --


    <ul>
    <li>Joanne</li>
    </ul>

  • Tim Salimans 1 comment collapsed Collapse Expand

    Got it working using OpenSSH, guess PuTTy was the problem after all.

  • Tim Salimans 1 comment collapsed Collapse Expand

    Great +- project and thanks very much for sharing! I do have some trouble +-getting it all to work though. Everything works fine until it tries to +-run the create_hosts.py:


    /////// OUTPUT ///////////////


    Creating hosts file on master node and copying hosts file to compute nodes...


    pscp -scp -i D:\grid\keys\keypair.ppk -q create_hosts.py root@ec2-67-202-19-253.
    compute-1.amazonaws.com:/etc/


    plink -ssh -i D:\grid\keys\keypair.ppk root@ec2-67-202-19-253.compute-1.amazonaw
    s.com "python /etc/create_hosts.py"


    exporting 10.252.31.48:/home/beowulf
    exporting 10.252.31.48:/mnt/data
    @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
    @ WARNING: UNPROTECTED PRIVATE KEY FILE! @
    @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
    Permissions 0644 for '/root/.ssh/id_rsa' are too open.
    It is recommended that your private key files are NOT accessible by others.
    This private key will be ignored.
    bad permissions: ignore key: /root/.ssh/id_rsa
    Permission denied, please try again.
    Permission denied, please try again.
    Permission denied (publickey,gssapi-with-mic,password).
    lost connection
    @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
    @ WARNING: UNPROTECTED PRIVATE KEY FILE! @
    @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
    Permissions 0644 for '/root/.ssh/id_rsa' are too open.
    It is recommended that your private key files are NOT accessible by others.
    This private key will be ignored.
    bad permissions: ignore key: /root/.ssh/id_rsa
    Permission denied, please try again.
    Permission denied, please try again.
    Permission denied (publickey,gssapi-with-mic,password).
    lost connection


    etcetera


    //////////////////////////////////


    As +- you can see I made some small modifications in order to use PuTTy as my +- SSH client, but that does not seem to be the problem... Does anyone +-else have this problem, and does anyone know how to fix it?

  • Pete 4 comments collapsed Collapse Expand

    Magg,


    I +- wouldn't recommend it, the latency would be huge and I'm not sure how +-MPI would handle that. You would also need to open the mpi ports to the +- outside world using the EC2 security group authorize commands.


    An +- alternative is to open an X11 session and connect to the head node or +-maybe VNC in to the instance. The 64 bit elasticwulf images are set up +-for X11 sessions and adding a desktop package would allow you to VNC in +-if you prefer that route.


    -Pete

  • Abhimanyu 3 comments collapsed Collapse Expand

    I am facing the same problem. I am able to set up the ring manually but mpdboot complains:

    +- +-

    mpdboot_domU-blah(handle_mpd_output 414): from mpd on domU-blah-,
    invalid port info:
    no_port

    +- +-

    any word on this?

  • Abhimanyu 1 comment collapsed Collapse Expand

    I +- found the problem. Apparently I had forgotten to include the "chown -R +-user:user /home/user" command. It didnt have access to the id_rsa file. +-As root mpdboot would work. Rather silly error message though.

  • pskomoroch 1 comment collapsed Collapse Expand

    I +- think there are some SGE grid solutions now that allow you to add EC2 +-nodes to your existing cluster, but again the performance of MPI from a +-local network to EC2 would be horrible...

    +- +-

    If you are interested in running MPI on EC2, I have a new project on Github I'll be announcing soon:

    +- +-

    http://github.com/datawranglin...

  • magg 1 comment collapsed Collapse Expand

    Hi Peter,


    Have +- you tried to connect EC2 instances with your local desktops? I am +-trying to do that with mpich2 1.0.7 but I am not successful at all. +-mpdboot complains about invalid port info (no_port) - actually no port +-when I try to do mpdboot -n 2. Even when I tried to mpd& on EC2 +-machine and then mpdtrace -l and then unblock the port and then mpd -h +-ec2-blabla -p ec2-mpdtrace-l-port still I have no luck. Have you faced +-similar problems?


    Thanks
    - magg

  • Pete 1 comment collapsed Collapse Expand

    @Theo,


    I'm attending MMDS this week at Stanford (http://www.stanford.edu/group/mmds/), +- and had a chance to ask James Demmel a few questions. He gave a talk +-titled "Avoiding communication in linear algebra algorithms", which was +-very relevant. His advice for matrix multiplication in a high latency +-environment like EC2 was to try dialing up the block size as much as +-possible in the standard MPI solvers and see how performance was +-affected.


    -Pete

  • Pete 1 comment collapsed Collapse Expand

    I found the secret to avoiding a lot of MPI errors on EC2, but haven't found time to do an additional post...


    The +- secret seems to be that just because Amazon says that an instance is +-"running", doesn't mean that the ssh daemons are available. This caused +- all kinds of intermittent problems setting up the hosts and my old +-scripts would fail silently.


    In my current codebase, I do some checks like the following:


        print "Instance is %s" % BOOTING_INSTANCE
        
        # wait for instance description to return "running" and grab HOSTNAME variable
        print "Polling server status (ec2-describe-instances %s)" % BOOTING_INSTANCE
        while 1:
          print "waiting for instance to boot..."
          HOSTNAME = commands.getoutput("ec2-describe-instances %s | grep running | awk '{print $4}'" % BOOTING_INSTANCE)
          if len(HOSTNAME) > 1:
            print "-------Instance booted, The server is available at %s" % HOSTNAME
            DOM_NAME = commands.getoutput("ec2-describe-instances %s | grep running | awk '{print $5}'" % BOOTING_INSTANCE).split('.')[0]
            break
          time.sleep(1)    
        
        # sometimes it takes a while for the ssh service to start, even when the ec2 api describes an instance as running.
        # A machine in the "running" state may not have finished booting. Try executing a no-op command until a valid response is found
        print "verifying ssh daemon has started..."
        counter=0
        while 1:
          print "Waiting for ssh daemon to start..."
          counter += 1        
          REPLY = commands.getoutput('''ssh %s "root@%s" 'echo "hello"' ''' % (SSH_OPTS, HOSTNAME) )
          if REPLY == 'hello':
            print "-------ssh has started, proceeding with AMI build"
            break
          if counter > 24:
            print "Instance not respoding to SSH hails, aborting..."
            ## sshd should not take more than 2 minutes to launch
            terminate_status = commands.getoutput('ec2-terminate-instances %s' % BOOTING_INSTANCE)
            ec2_launch_failed = True
            print "Base Instance terminated"
            break
          time.sleep(5)
        
        if ec2_launch_failed:
            print "Aborting build"
            return
        
    
+-
+-

  • Patrick 1 comment collapsed Collapse Expand

    Thanks, Peter. The original EC2.py was the problem. I now have the large AMIs up and running. Thanks again for the article and help!


    Patrick

  • Theo 1 comment collapsed Collapse Expand

    Peter:


    I +- am diving into Hadoop with Map/Reduce as we speak. As you know Google +-implemented its environment in C++, so I was a bit disappointed that +-Hadoop had chosen Java VM to do its bidding. Java makes interfacing with +- hardcore numerical operations much harder. The particular problems I am +- looking at are large scale Lanczos solvers to find eigen values/vectors +- of large systems of equations. These systems are of interest in +-advertising, quantitative finance, and sensor networks. Problem is that +-they all are environments in which latency is of the essence. So you +-have a capacity component in terms of the size of the system and a +-latency issue in terms of the data rate coming in and the opportunity +-cost for somebody to get to the answer faster.


    I would be +-interested in working on this particular benchmark problem: pick a big +-eigen value/vector problem and solve it on a cluster, EC2, and via +-Hadoop/Map-reduce. Clearly this is going to be a lot of work so this +-should be publishing worthy. I am sure many folks would be interested in +- this experiment, so let me know if this is something that could invest +-time in.


    Theo

  • Pete 1 comment collapsed Collapse Expand

    Patrick,


    Did you start with a clean install of the 64 bit scripts? I made some changes to EC2.py in the new scripts to handle the new instance types...

  • Patrick 1 comment collapsed Collapse Expand

    Peter,


    Very +- useful tool! I've gotten a cluster up and running using the small +-instance type but am having difficulty launching the _64 AMIs.


    $ ./ec2-start-cluster.py
    m1.large
    image ami-eb13f682
    master image ami-e813f681
    ----- starting master -----
    Traceback (most recent call last):
    File "./ec2-start-cluster.py", line 39, in ?
    +- master_response = conn.run_instances(imageId=MASTER_IMAGE_ID, +-minCount=1, maxCount=1, keyName= KEYNAME, instanceType=INSTANCE_TYPE )
    TypeError: run_instances() got an unexpected keyword argument 'instanceType'


    If I try to start the cluster without passing an INSTANCE_TYPE arg I get the following:
    $ ./ec2-start-cluster.py
    m1.large
    image ami-eb13f682
    master image ami-e813f681
    ----- starting master -----
    InvalidParameterValue: +- The requested instance type's architecture (i386) does not match the +-architecture in the manifest for ami-e813f681 (x86_64)
    ----- starting workers -----
    InvalidParameterValue: +- The requested instance type's architecture (i386) does not match the +-architecture in the manifest for ami-eb13f682 (x86_64)


    Any ideas? Thanks!

  • Pete 1 comment collapsed Collapse Expand

    Raghav,


    You can ssh in as root instead of lamuser, or compile the output file into your home directory.


    Check out the new AMI and managment code:


    http://www.datawrangling.com/pycon-2008-elasticwulf-slides.html


    The +- new AMI includes a preconfigured NFS mounted directory /home/beowulf. +-If you compiled the file there, hellompi would be available on all +-nodes.


    Note that the new images default to the 'large' instance type which charges .40 cents/hour for each node.


    -Pete

  • raghav 1 comment collapsed Collapse Expand

    i am trying to compile a simple c mpi file "hellompi.c" using the command:



    mpicc -o /usr/hellompi /usr/local/src/hellompi.c



    why does it give me the following error?


    /usr/bin/ld: cannot open output file /usr/hellompi: Permission denied
    collect2: ld returned 1 exit status


    how do I get root priveledges?

  • Kurt Grandis 1 comment collapsed Collapse Expand

    Thanks +- Pete. I wish I had made the PyCon session, but these posts have been +-very helpful. The cluster went up pretty quickly and I have already used +- it to crunch a few minor data runs.
    In setting everything up I also +-ran into a similar problem as Raghav and ended up solving it in a +-similar manner by forcing the -i credentials switch. I imagine it has +-something to do with the way I configured and placed my certs.

  • raghav 1 comment collapsed Collapse Expand

    Thanks pete. For your prompt reply!!

  • raghav 1 comment collapsed Collapse Expand

    Hey guys,
    Actually I made a change in the ec2-mpi-cluster.py file. I have no clue about python and I dono why it worked but it worked.


    I modified:


    template = ssh -o "StrictHostKeyChecking no" %(user)s@%(host)s "%(cmd)s"
    to
    template = 'ssh -i "/home/id_rsa-gsg-keypair" %(user)s@%(host)s "%(cmd)s"


    and


    template = '%(cmd)s %(switches)s -o "StrictHostKeyChecking no" %(src)s %(user)s@%(host)s:%(dest)s'
    to
    template = '%(cmd)s %(switches)s -i "/home/id_rsa-gsg-keypair" %(src)s %(user)s@%(host)s:%(dest)s'


    And it started working perfectly fine. I was able to log in to the master node and the pi problem executed perfectly fine.


    Thanks a lot guys


    Cheers,
    Raghav

  • Pete 1 comment collapsed Collapse Expand

    raghav,


    Another suggestion is to make sure the instances are running with ./ec2-check-instances.py and then retry the script, sometimes it takes a while for sshd to start up on EC2.


    -Pete

  • Pete 1 comment collapsed Collapse Expand

    raghav,


    I assume you were able to start the instances with ec2-start-cluster.py? +- The text on the terminal is normal, but it shouldn't ask you for a +-password (I should probably add a verbose option instead of streaming +-out text by default). There was a path issue on windows with an earlier +-version of the scripts, so that may be the problem.


    If you send me the script version number from the README and/or terminal output, I can try to track down what is going on...


    peter.skomoroch@gmail.com


    -Pete

  • raghav 1 comment collapsed Collapse Expand

    Why does it ask me for a password when i try to run the ec2-mpi-config.py file.?
    it says root@xxx password:
    And I get a lot of text on the terminal when I try running the file.

  • Pete 1 comment collapsed Collapse Expand

    No +- problem, thanks for finding the typos. These were meant to be some +-quick hacks, but took on a life of their own after a while.


    I found this worked for configuring LAM, I'll send you more details in an email...


    The contents of bash_profile should be as follows:


     
    -bash-3.1# more .bash_profile 
    # .bash_profile
    
+-
+-
    # Get the aliases and functions
    if [ -f ~/.bashrc ]; then
            . ~/.bashrc
    fi
    
+-
+-
    # User specific environment and startup programs
    
+-
+-
    LAMRSH="ssh -x"
    export LAMRSH
    
+-
+-
    LD_LIBRARY_PATH="/usr/local/lam-7.1.2/lib/"
    export LD_LIBRARY_PATH
    
+-
+-
    MPICH_PORT_RANGE="2000:8000"
    export MPICH_PORT_RANGE
    
+-
+-
    PATH=$PATH:$HOME/bin
    
+-
+-
    PATH=/usr/local/lam-7.1.2/bin:$PATH
    
+-
+-
    MANPATH=/usr/local/lam-7.1.2/man:$MANPATH
    
+-
+-
    export PATH
    export MANPATH

    Launch the cluster on EC2 and try booting LAM manually:


    [lamuser@domU-12-31-33-00-04-4B ~]$ lamboot /etc/mpd.hosts
    
+-
+-
    [lamuser@domU-12-31-33-00-04-4B ~]$ lamnodes
    n0      domU-12-31-33-00-04-4B.usma1.c...:1:origin,this_node
    n1      domU-12-31-33-00-03-35.usma1.c...:1:
    n2      domU-12-31-33-00-03-3C.usma1.c...:1:
    n3      domU-12-31-34-00-00-55.usma2.c...:1:
    
+-
+-
    [lamuser@domU-12-31-33-00-04-4B ~]$ tping N -c3
      1 byte from 3 remote nodes and 1 local node: 0.039 secs
      1 byte from 3 remote nodes and 1 local node: 0.004 secs
      1 byte from 3 remote nodes and 1 local node: 0.002 secs

  • pete 1 comment collapsed Collapse Expand

    Found +- another typo too, ok I'm nit picking. In the stop-cluster script the +-message says Stoping as opposed to stopping. A year ago when you first +-posted this stuff you mentioned that the reason why the non-root user +-was called lamuser was that the scripts were used for LAM in some +-previous incarnation. Since I'm actually trying to use LAM, if you have +-any LAM stuff around that might help me to iron out one or two problems I +- still have.


    Anyway, thanks again,
    Pete

  • Pete 1 comment collapsed Collapse Expand

    pete +- found the error... the image Ids he entered into the config module +-inadvertently contained a capital letter. This doesn’t cause any +-problems for starting images since string case is ignored by Amazon. The +- corresponding image id response string from AWS is always lowercase, so +- the python script comparison on image ID string fails.


    In the +- next version of the scripts, I will handle upper/lowercase differences +-in the ami strings. For now, just make sure to use all lower case or +-call the python .lower() method,


     
    >>> test = 'ami-fE9a7f97'
    >>> test.lower()
    'ami-fe9a7f97'
    >>> 
    
+-
+-

  • pete 1 comment collapsed Collapse Expand

    Can't get the ec-mpi-config to work. Says list index out of range for mpi-externalnames[0] on line 108
    start cluster and check instances are OK so I think that python, EC, elementree
    are OK
    Any +- ideas why? Has AWS changed the format of the response you're parsing +-(yes I have had a look at the python code but since I haven't used +-python before I can't see anything obvious to me)
    BTW you have a typo in mpi config Numer of nodes as opposed to Number of nodes , it even shows in your example above.
    Otherwise I like what you've done, I'd just like it to work for me.
    Thanks,
    Pete

  • Pete 1 comment collapsed Collapse Expand

    Theo,


    Sorry +- for the delay in posting this and responding. I've been working on a +-startup for the past 7 months and was in serious crunch mode. Don't +-read too much into the large gap in posts, it is just me working on this +- as a side-project. I finished moving the blog to another host and +-finally have some time to get back to the EC2 work. This experience has +- taught me to never name a series of blog posts "part 1 of N" :)


    You +- make some excellent points. One thing that has changed since I wrote +-the first post is that EC2 now offers larger 64bit machine images with +-better I/O (you can provision an entire physical server and not be +-limited by sharing network resources in the virtual instance). I'd like +- to see if this improves the network performance. I'm giving a talk on +-this in March, so I'm on the hook to have some benchmarks by then.


    I +- also agree on the mapreduce side. For embarrassingly parallel +-problems, hadoop on ec2 is potentially much more attractive...more +-robust, easier for most people to program. Ideally, I would like to do +-some comparisons between the two approaches and run the numbers.


    The +- performance of an EC2 MPI cluster is definitely going to be worse than +-your own custom hardware, but it still might fit certain niche +-situations. In my case, I needed to run some MPI code for a large +-problem and didn't have access to a large enough cluster. The +-performance on EC2 was nowhere near what you get on a high-end cluster, +-but it got the job done for a reasonable price.


    This discussion on the beowulf list goes into more detail on the pros/cons:


    http://www.beowulf.org/pipermail/beowulf/2008-January/020490.html


    -Pete

  • Theo 1 comment collapsed Collapse Expand

    Does the 5 month hiatus in this project mean that it was a bad idea and you guys have learnt enough to waste no more time on it?


    Given +- the virtualization uncertainty, finding the right +-communication/computation balance for typical MPI programs appears to be +- very unrewarding. Secondly, MPI development and debug and then QA and +-scale out are not addressed, which doesn't bode well. It appears most +-productive to have a local small cluster for development and debug, and +-then do QA and scale out on EC2, but some benchmarking numbers would +-really help.


    If EC2 is only robust for embarrassingly parallel +- problems, then MapReduce style programs are more attractive. There the +-size of the data set and how well it integrates in a distributed file +-system appear to be the problems to focus on. Or BOINC like approaches +-if there is no integrated DFS. Anyone have operational data on these +-approaches?

  • Patrick Ball 1 comment collapsed Collapse Expand


    the first two parts really set the stage ... Part 3?


    :)

  • Soo.. 1 comment collapsed Collapse Expand

    What about that Part 3? :)

  • Pete 1 comment collapsed Collapse Expand

    Update (7-24-07): I’ve made some important bug fixes to the scripts to address issues mentioned in the comments.


    Specific changes made:


    <ul>
    <li>fixed lamuser home directory permissions bug</li>
    <li>fixed section of ec2-mpi-config.py which clobbered existing rsa keys on the client machine</li>
    <li>Updated calls of AWS python EC2 library to use API version 2007-01-19
    http://developer.amazonwebserv...</li>
    <li>fixed mpdboot issue by using amazon internal DNS names in hosts files</li>
    <li>scripts should now work on windows/cygwin client environments</li>
    </ul>

    After +- I run some benchmarks, I'm hoping to find some time to add LAM and +-OpenMPI to the EC2 image along with NFS configuration, C3 cluster tools, +- Ganglia, and a benchmarking package.

  • Pete 1 comment collapsed Collapse Expand

    Ralph,


    More +- good points. I've been tied up with some other projects, but it sounds +-like enough feedback is in to make a revised version of the image and +-scripts. I expect the latency to vary a bit depending on the random EC2 +-network topology when a cluster is launched...(instances on the same box +- vs. over ethernet) that might explain the ringtest. The mutual ssh +-access was set up since we do a lot of file/data shuffling between nodes +- outside of MPI.


    Thanks again, looking forward to hearing how the regression test system works out.


    -Pete

  • Ralph Giles 1 comment collapsed Collapse Expand

    Yeah, that would work better. Some more detailed comments:


    <ul>
    <li>

    Your image has /home/lamuser/.mpd.conf owned by root. I had to chown it to lamuser before I could start mpd.

    </li>
    <li>

    You +- script passes the public dns names for the nodes into mpd.hosts. For +-that to work, a hole has to be opened in the firewall for the ports the +-mpi daemon is using. A simpler solution is to just pass the internal dns +- names. Then all the traffic happens behind the firewall, which probably +- also improves latency. (Although my ringtest was noticably slower than +-yours, averaging 2.2e-3 seconds/loop so who knows?)

    </li>
    <li>

    I +- was surprised that when I originally ran ec2-add-keypair in the EC2 +-tutorial that it uploaded the public key (ok) and printed out the +-private key (ok I guess) but didn't print out the public key locally +-(weird). Your scripts seem to assume the public key is available as +-id_rsa.pub on the client machine. Shouldn't this first be copied either +-from /root/.ssh/authorized_keys on the master node (as installed by +-amazon) or retrieved through the query interface?

    </li>
    </ul>

    Is +- the mutual ssh access required for more than just launching the MPI +-daemon? If all subsequent traffic goes through the mpi daemons, starting +- mpd from the client machine, or automatically from the init scripts +-after pulling mpd.hosts from S3 would save the whole trouble, including +-uploading the private key at all.

  • Pete 1 comment collapsed Collapse Expand

    Ralph,


    Good catch. Thanks for pointing that out. I just lifted those passwordless ssh lines straight from an MPI tutorial.


    This might solve the clobbering as well (from http://www.maclife.com/forums/topic/61520):


    cat id_rsa.pub >> .ssh/authorized_keys


    "The +- above command will create the "authorized_keys" file in the ".ssh" +-directory if that file doesn't already exist, and it will append the new +- id_rsa.pub file to it if it does already exist."


    I'll add +-that change to the scripts. Good luck with the regression cluster, I +-heard Oracle developers do something like that using Condor on otherwise +- idle desktops (see http://www.cs.wisc.edu/condor/doc/nmi-lisa2006-slides.pdf).


    -Pete

  • Ralph Giles 1 comment collapsed Collapse Expand

    ===== DO NOT USE THESE SCRIPTS! =====


    This section of ec2-mpi-config.py is a bit problematic:


    os.system('cp %s ~/id_rsa.pub' % KEY_LOCATION )
    os.system('cp ~/id_rsa.pub ~/.ssh/id_rsa')


    This +- will clobber any existing rsa key on the initiating machine's account, +-and with break normal auth on the next login if you have a different +-default rsa key!


    The script should instead copy the private key directly from KEY_LOCATION to the nodes.


    ===== DO NOT USE THESE SCRIPTS! =====


    Otherwise, +- way cool. Thanks for putting this tutorial together. We're trying EC2 +-clusters out as a way to get quicker feedback from regression tests +-after changes to our software. Unfortunately, with the one hour +-granularity I don't think it will be price competitive. We want 20-100 +-nodes for about 5 minutes at a time.

  • Pete 1 comment collapsed Collapse Expand

    Mike +- Cariaso modified my scripts to fix some path issues and got it working +-on a windows laptop, he might have also fixed some other errors I didn't +- notice. I haven't had a chance to try them yet, but you can download +-the modified scripts here:


    http://mpiblast.pbwiki.com/AmazonEC2

  • Michael Creel 1 comment collapsed Collapse Expand

    Yep, +- I run the mpi-config script right after creating the instances, doing +-just what you suggest. The fact that the instances start up at all seems +- to me to mean that the keypair information is ok. Do you know if anyone +- but you has been able to launch a cluster? Very cool stuff. I'm going +-to be looking into making a Debian AMI that works the same way.

  • Pete 1 comment collapsed Collapse Expand

    Michael,


    I +- haven't had the scripts prompt me for a password before, are you +-running them from your local machine? The mpi-config script expects the +-keyname and keypair location to match what was used to start the +-instance. Take a look at your EC2config.py +- file and make sure the instances were all started with your own keypair +- (i used the gsg keypair I created on my laptop in the Amazon "getting +-started guide" tutorial):





    AWS_ACCESS_KEY_ID = ‘YOUR_KEY_ID_HERE’
    AWS_SECRET_ACCESS_KEY = ‘YOUR_KEY_HERE’
    MASTER_IMAGE_ID = "ami-3e836657"
    IMAGE_ID = "ami-3e836657"
    KEYNAME = "gsg-keypair"
    KEY_LOCATION = "~/id_rsa-gsg-keypair"
    DEFAULT_CLUSTER_SIZE = 5





    I'm +- working on an updated version of the scripts and EC2 image which should +- make things a bit cleaner. Sorry the code is ugly right now in terms +-of error handling...I just wanted to toss something together to get +-people started :)

  • Michael Creel 1 comment collapsed Collapse Expand

    A little report on my trial.
    1) ./ec2-start_cluster.py +- is not always successful in getting the requested number of nodes to +-come up. The instances sometimes have status "terminated" before +-anything is done with them.


    2) When the 5 nodes all come up, I still get a problem with ./ec2-mpi-config.py requesting a root password:


    michael@yosemite:~/ec2/AmazonEC2_MPI_scripts$ ./ec2-mpi-config.py


    ---- MPI Cluster Details ----
    Numer of nodes = 5
    Instance= i-e39c7a8a hostname= ec2-72-44-45-138.z-2.compute-1... state= running
    Instance= i-e29c7a8b hostname= ec2-72-44-45-185.z-2.compute-1... state= running
    Instance= i-e59c7a8c hostname= ec2-72-44-45-186.z-2.compute-1... state= running
    Instance= i-e49c7a8d hostname= ec2-72-44-45-122.z-2.compute-1... state= running
    Instance= i-e79c7a8e hostname= ec2-72-44-45-60.z-2.compute-1.... state= running


    The master node is ec2-72-44-45-138.z-2.compute-1...


    Writing out mpd.hosts file
    nslookup ec2-72-44-45-138.z-2.compute-1...
    (0, 'Server:\t\t158.109.0.1\nAddress:\t158.109.0.1#53\n\nNon-authoritative answer:\nName:\tec2-72-44-45-138.z-2.compute-...\nAddress: 72.44.45.138\n')
    nslookup ec2-72-44-45-185.z-2.compute-1...
    (0, 'Server:\t\t158.109.0.1\nAddress:\t158.109.0.1#53\n\nNon-authoritative answer:\nName:\tec2-72-44-45-185.z-2.compute-...\nAddress: 72.44.45.185\n')
    nslookup ec2-72-44-45-186.z-2.compute-1...
    (0, 'Server:\t\t158.109.0.1\nAddress:\t158.109.0.1#53\n\nNon-authoritative answer:\nName:\tec2-72-44-45-186.z-2.compute-...\nAddress: 72.44.45.186\n')
    nslookup ec2-72-44-45-122.z-2.compute-1...
    (0, 'Server:\t\t158.109.0.1\nAddress:\t158.109.0.1#53\n\nNon-authoritative answer:\nName:\tec2-72-44-45-122.z-2.compute-...\nAddress: 72.44.45.122\n')
    nslookup ec2-72-44-45-60.z-2.compute-1....
    (0, 'Server:\t\t158.109.0.1\nAddress:\t158.109.0.1#53\n\nNon-authoritative answer:\nName:\tec2-72-44-45-60.z-2.compute-1...\nAddress: 72.44.45.60\n')
    Warning: Permanently added 'ec2-72-44-45-138.z-2.compute-1...,72.44.45.138' (RSA) to the list of known hosts.
    id_rsa.pub 100% 1675 1.6KB/s 00:00
    root@ec2-72-44-45-138.z-2.compute-1.am...'s password:


    This is as far as I can get at the moment. Looks like a minor problem. Cheers, M.

  • Michael Creel 1 comment collapsed Collapse Expand

    One question, do you know if something like an NFS shared home directory is possible. Using S3, possibly?

  • Michael Creel 1 comment collapsed Collapse Expand

    Excellent +- stuff! I've gotten started with EC2 and I'll be trying your images out +-soon. I doubt that I'll be trying to make ParallelKnoppix work on EC2, +-because your approach is the right one, I think. PK is designed to use +-when the hardware is not known ahead of time. With EC2, the hardware is +-known, so a tailor-made image is the way to go. Your scripts allow an +-on-demand cluster to be created in minutes, and that's all that PK +-offers, anyway. PK usually needs some remastering so that users can add +-their own packages. Re-bundling an EC2 image is completely analogous. +-I'm planning on doing just that, probably starting with your images, and +- doing some testing of latency on tasks that require different degrees +-of internode communication. Thanks for all this, it'll make the rest an +-easy job.

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+- +- +- +- +- +- +- +- +- +- +- +- +\ No newline at end of file +Index: ../trunk-jpl/externalpackages/ec2api/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/ec2api/install.sh (revision 13947) ++++ ../trunk-jpl/externalpackages/ec2api/install.sh (revision 13948) +@@ -7,6 +7,7 @@ + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/ec2-api-tools.zip' 'ec2-api-tools.zip' ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ec2-ug.pdf' 'ec2-ug.pdf' + + #Untar + unzip ec2-api-tools.zip +Index: ../trunk-jpl/externalpackages/scotch/ptscotch_user5.1.pdf +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/externalpackages/scotch/scotch_user5.1.pdf +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/externalpackages/scotch/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/scotch/install.sh (revision 13947) ++++ ../trunk-jpl/externalpackages/scotch/install.sh (revision 13948) +@@ -11,6 +11,8 @@ + + #Download from ISSM server + $ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/scotch_5.1.6.tar.gz' 'scotch_5.1.6.tar.gz' ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/ptscotch_user5.1.pdf' 'ptscotch_user5.1.pdf' ++$ISSM_DIR/scripts/DownloadExternalPackage.py 'http://issm.jpl.nasa.gov/files/externalpackages/docs/scotch_user5.1.pdf' 'scotch_user5.1.pdf' + + # Untar + tar -xvzf scotch_5.1.6.tar.gz Index: /issm/oecreview/Archive/13393-13976/ISSM-13948-13949.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13948-13949.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13948-13949.diff (revision 13980) @@ -0,0 +1,25 @@ +Index: ../trunk-jpl/externalpackages/matlab/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/matlab/install.sh (revision 13948) ++++ ../trunk-jpl/externalpackages/matlab/install.sh (revision 13949) +@@ -1,3 +1,20 @@ + #!/bin/bash ++set -eu ++ ++#Erase symlink + rm -rf install ++ ++#Select or create a new simlink ++#ln -s /usr/local/pkgs/matlab-7.6/ install ++#ln -s /discover/vis/mathworks/matlab_r2011b/ install ++#ln -s /usr/local/matlab704/ install ++#ln -s /usr/local/matlab711/ install + ln -s /usr/local/matlab712/ install ++ ++# Macintosh (OSX) simlink ++#ln -s /Applications/MATLAB_R2008a/ install ++#ln -s /Applications/MATLAB_R2009a.app/ install ++#ln -s /Applications/MATLAB_R2010a.app/ install ++#ln -s /Applications/MATLAB_R2012a.app/ install ++#ln -s /Applications/MATLAB_R2011a.app/ install ++#ln -s /Applications/MATLAB*.app/ install Index: /issm/oecreview/Archive/13393-13976/ISSM-13949-13950.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13949-13950.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13949-13950.diff (revision 13980) @@ -0,0 +1,61 @@ +Index: ../trunk-jpl/src/m/io/savevars.py +=================================================================== +--- ../trunk-jpl/src/m/io/savevars.py (revision 13949) ++++ ../trunk-jpl/src/m/io/savevars.py (revision 13950) +@@ -31,13 +31,14 @@ + raise TypeError("Missing file name.") + + if len(args) >= 3 and isinstance(args[1],(str,unicode)): # (filename,name,value) +- nvdict[args[1]]=args[2] ++ for i in xrange(1,len(args),2): ++ nvdict[args[i]]=args[i+1] + +- elif len(args) >= 3 and isinstance(args[1],list) and isinstance(args[2],list): # (filename,[names],[values]) ++ elif len(args) == 3 and isinstance(args[1],list) and isinstance(args[2],list): # (filename,[names],[values]) + for name,value in zip(args[1],args[2]): + nvdict[name]=value + +- elif len(args) >= 2 and isinstance(args[1],dict): # (filename,{names:values}) ++ elif len(args) == 2 and isinstance(args[1],dict): # (filename,{names:values}) + nvdict=args[1] + + else: +Index: ../trunk-jpl/src/m/io/loadvars.py +=================================================================== +--- ../trunk-jpl/src/m/io/loadvars.py (revision 13949) ++++ ../trunk-jpl/src/m/io/loadvars.py (revision 13950) +@@ -31,13 +31,14 @@ + raise TypeError("Missing file name.") + + if len(args) >= 2 and isinstance(args[1],(str,unicode)): # (filename,name) +- nvdict[args[1]]=None ++ for name in args[1:]: ++ nvdict[name]=None + +- elif len(args) >= 2 and isinstance(args[1],list): # (filename,[names]) ++ elif len(args) == 2 and isinstance(args[1],list): # (filename,[names]) + for name in args[1]: + nvdict[name]=None + +- elif len(args) >= 2 and isinstance(args[1],dict): # (filename,{names:values}) ++ elif len(args) == 2 and isinstance(args[1],dict): # (filename,{names:values}) + nvdict=args[1] + + elif len(args) == 1: # (filename) +@@ -70,12 +71,13 @@ + my_shelf.close() + + if len(args) >= 2 and isinstance(args[1],(str,unicode)): # (value) +- return nvdict[args[1]] ++ value=[nvdict[name] for name in args[1:]] ++ return value + +- elif len(args) >= 2 and isinstance(args[1],list): # ([values]) ++ elif len(args) == 2 and isinstance(args[1],list): # ([values]) + value=[nvdict[name] for name in args[1]] + return value + +- elif (len(args) >= 2 and isinstance(args[1],dict)) or (len(args) == 1): # ({names:values}) ++ elif (len(args) == 2 and isinstance(args[1],dict)) or (len(args) == 1): # ({names:values}) + return nvdict + Index: /issm/oecreview/Archive/13393-13976/ISSM-13950-13951.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13950-13951.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13950-13951.diff (revision 13980) @@ -0,0 +1,34 @@ +Index: ../trunk-jpl/src/m/classes/mesh.py +=================================================================== +--- ../trunk-jpl/src/m/classes/mesh.py (revision 13950) ++++ ../trunk-jpl/src/m/classes/mesh.py (revision 13951) +@@ -131,12 +131,12 @@ + md = checkfield(md,'mesh.x','NaN',1,'size',[md.mesh.numberofvertices]) + md = checkfield(md,'mesh.y','NaN',1,'size',[md.mesh.numberofvertices]) + md = checkfield(md,'mesh.z','NaN',1,'size',[md.mesh.numberofvertices]) +- md = checkfield(md,'mesh.elements','NaN',1,'>',0,'values',range(1,md.mesh.numberofvertices+1)) ++ md = checkfield(md,'mesh.elements','NaN',1,'>',0,'values',numpy.arange(1,md.mesh.numberofvertices+1)) + if md.mesh.dimension==2: + md = checkfield(md,'mesh.elements','size',[md.mesh.numberofelements,3]) + else: + md = checkfield(md,'mesh.elements','size',[md.mesh.numberofelements,6]) +- if numpy.any(numpy.logical_not(ismember(range(1,md.mesh.numberofvertices+1),md.mesh.elements))): ++ if numpy.any(numpy.logical_not(ismember(numpy.arange(1,md.mesh.numberofvertices+1),md.mesh.elements))): + md.checkmessage("orphan nodes have been found. Check the mesh outline") + md = checkfield(md,'mesh.dimension','values',[2,3]) + md = checkfield(md,'mesh.numberoflayers','>=',0) +Index: ../trunk-jpl/src/m/classes/flowequation.py +=================================================================== +--- ../trunk-jpl/src/m/classes/flowequation.py (revision 13950) ++++ ../trunk-jpl/src/m/classes/flowequation.py (revision 13951) +@@ -67,8 +67,8 @@ + md = checkfield(md,'flowequation.vertex_equation','size',[md.mesh.numberofvertices],'values',[1,2]) + md = checkfield(md,'flowequation.element_equation','size',[md.mesh.numberofelements],'values',[1,2]) + else: +- md = checkfield(md,'flowequation.vertex_equation','size',[md.mesh.numberofvertices],'values',range(0,7+1)) +- md = checkfield(md,'flowequation.element_equation','size',[md.mesh.numberofelements],'values',range(0,7+1)) ++ md = checkfield(md,'flowequation.vertex_equation','size',[md.mesh.numberofvertices],'values',numpy.arange(0,7+1)) ++ md = checkfield(md,'flowequation.element_equation','size',[md.mesh.numberofelements],'values',numpy.arange(0,7+1)) + if not (self.ismacayealpattyn or self.ishutter or self.isstokes or self.isl1l2): + md.checkmessage("no element types set for this model. At least one of ismacayealpattyn, ishutter or isstokes need to be =1") + Index: /issm/oecreview/Archive/13393-13976/ISSM-13951-13952.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13951-13952.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13951-13952.diff (revision 13980) @@ -0,0 +1,67 @@ +Index: ../trunk-jpl/src/m/plot/radarpower.m +=================================================================== +--- ../trunk-jpl/src/m/plot/radarpower.m (revision 13951) ++++ ../trunk-jpl/src/m/plot/radarpower.m (revision 13952) +@@ -31,14 +31,14 @@ + %figure out if we should go look for Greenland or Antarctica geotiff, or if user provided one. + if ~exist(options,'overlay_image'), + if strcmpi(md.mesh.hemisphere,'n'), +- %if ~exist([jplsvn() '/projects/ModelData/MOG/mog150_greenland_map.jpg']), +- % error(['radarpower error message: file ' jplsvn() '/projects/ModelData/MOG/mog150_greenland_map.jpg not found.']); ++ %if ~exist(['/u/astrid-r1b/ModelData/MOG/mog150_greenland_map.jpg']), ++ % error(['radarpower error message: file ' '/u/astrid-r1b/ModelData/MOG/mog150_greenland_map.jpg not found.']); + %end + %name = 'mog150_greenland_map'; + %name = 'mog100_hp1_v10'; + %%name = 'mog500_hp1_v10'; +- %jpgim=[jplsvn() '/projects/ModelData/MOG/' name '.jpg']; +- %geom=load([jplsvn() '/projects/ModelData/MOG/' name '.jpgw'],'ascii'); ++ %jpgim=['/u/astrid-r1b/ModelData/MOG/' name '.jpg']; ++ %geom=load(['/u/astrid-r1b/ModelData/MOG/' name '.jpgw'],'ascii'); + %%jpgim='/u/astrid-r1b/morlighe/issmjpl/projects/MorlighemGRL2012/Data/Mosaic_amp_asar2010.jpg'; + %%geom=load('/u/astrid-r1b/morlighe/issmjpl/projects/MorlighemGRL2012/Data/Mosaic_amp_asar2010.jpgw'); + %jpgim='/u/astrid-r1b/morlighe/issmjpl/projects/MorlighemGRL2012/Data/Russel_asar2010.png'; +@@ -64,15 +64,15 @@ + %md.radaroverlay.x=(xmin:(xmax-xmin)/(size(md.radaroverlay.pwr,2)-1):xmax); + %md.radaroverlay.y=(ymin:(ymax-ymin)/(size(md.radaroverlay.pwr,1)-1):ymax); + if highres, +- if ~exist([jplsvn() '/projects/ModelData/MOG/mog100_r2_hp1.tif']), +- error(['radarpower error message: file ' jplsvn() '/projects/ModelData/MOG/mog100_r2_hp1.tif not found.']); ++ if ~exist(['/u/astrid-r1b/ModelData/MOG/mog100_r2_hp1.tif']), ++ error(['radarpower error message: file ' '/u/astrid-r1b/ModelData/MOG/mog100_r2_hp1.tif not found.']); + end +- geotiff_name=[jplsvn() '/projects/ModelData/MOG/mog100_r2_hp1.tif']; ++ geotiff_name=['/u/astrid-r1b/ModelData/MOG/mog100_r2_hp1.tif']; + else +- if ~exist([jplsvn() '/projects/ModelData/MOG/mog500_r2_hp1.tif']), +- error(['radarpower error message: file ' jplsvn() '/projects/ModelData/MOG/mog500_r2_hp1.tif not found.']); ++ if ~exist(['/u/astrid-r1b/ModelData/MOG/mog500_r2_hp1.tif']), ++ error(['radarpower error message: file ' '/u/astrid-r1b/ModelData/MOG/mog500_r2_hp1.tif not found.']); + end +- geotiff_name=[jplsvn() '/projects/ModelData/MOG/mog500_r2_hp1.tif']; ++ geotiff_name=['/u/astrid-r1b/ModelData/MOG/mog500_r2_hp1.tif']; + end + + %Name of image +@@ -91,15 +91,15 @@ + + elseif strcmpi(md.mesh.hemisphere,'s'), + if highres, +- if ~exist([jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif']), +- error(['radarpower error message: file ' jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif not found.']); ++ if ~exist(['/u/astrid-r1b/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif']), ++ error(['radarpower error message: file ' '/u/astrid-r1b/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif not found.']); + end +- geotiff_name=[jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif']; ++ geotiff_name=['/u/astrid-r1b/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif']; + else +- if ~exist([jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif']), +- error(['radarpower error message: file ' jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif not found.']); ++ if ~exist(['/u/astrid-r1b/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif']), ++ error(['radarpower error message: file ' '/u/astrid-r1b/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif not found.']); + end +- geotiff_name=[jplsvn() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif']; ++ geotiff_name=['/u/astrid-r1b/ModelData/MosaicTiffRsat/amm125m_v2_1km.tif']; + end + + %Name of image Index: /issm/oecreview/Archive/13393-13976/ISSM-13952-13953.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13952-13953.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13952-13953.diff (revision 13980) @@ -0,0 +1,39 @@ +Index: ../trunk-jpl/src/m/classes/organizer.py +=================================================================== +--- ../trunk-jpl/src/m/classes/organizer.py (revision 13952) ++++ ../trunk-jpl/src/m/classes/organizer.py (revision 13953) +@@ -4,6 +4,7 @@ + from loadvars import * + from loadmodel import * + from savevars import * ++from model import model + + class organizer(object): + """ +@@ -43,7 +44,7 @@ + + #Get repository + repository=options.getfieldvalue('repository','./') +- if not isinstance(repository(str,unicode)): ++ if not isinstance(repository,(str,unicode)): + raise TypeError("repository is not a string") + if not os.path.isdir(repository): + raise IOError("Directory '%s' not found" % repository) +@@ -55,7 +56,7 @@ + #Get trunk prefix (only if provided by user) + if options.exist('trunkprefix'): + trunkprefix=options.getfieldvalue('trunkprefix','') +- if not isinstance(trunkprefix(str,unicode)): ++ if not isinstance(trunkprefix,(str,unicode)): + raise TypeError("trunkprefix is not a string") + if not strcmp(trunkprefix,trunkprefix.strip()) or len(trunkprefix.split()) > 1: + raise TypeError("trunkprefix should not have any white space") +@@ -136,7 +137,7 @@ + self._currentstep+=1 + + #if requestedsteps = 0, print all steps in self +- if any(self.requestedsteps==0): ++ if 0 in self.requestedsteps: + if self._currentstep==1: + print " prefix: %s" % self.prefix + print " step #%2i : %s" % (self.steps[self._currentstep-1]['id'],self.steps[self._currentstep-1]['string']) Index: /issm/oecreview/Archive/13393-13976/ISSM-13953-13954.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13953-13954.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13953-13954.diff (revision 13980) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/solutions/issm.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutions/issm.cpp (revision 13953) ++++ ../trunk-jpl/src/c/solutions/issm.cpp (revision 13954) +@@ -25,7 +25,7 @@ + delete femmodel; + + /*Finalize environment:*/ +- //EnvironmentFinalize(); ++ EnvironmentFinalize(); + + /*Finalize exception trapping: */ + ExceptionTrapEnd(); Index: /issm/oecreview/Archive/13393-13976/ISSM-13954-13955.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13954-13955.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13954-13955.diff (revision 13980) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/src/m/classes/organizer.py +=================================================================== +--- ../trunk-jpl/src/m/classes/organizer.py (revision 13954) ++++ ../trunk-jpl/src/m/classes/organizer.py (revision 13955) +@@ -132,7 +132,7 @@ + + #Add step + self.steps.append(OrderedDict()) +- self.steps[-1]['id']=len(self.steps)+1 ++ self.steps[-1]['id']=len(self.steps) + self.steps[-1]['string']=string + self._currentstep+=1 + +@@ -140,7 +140,7 @@ + if 0 in self.requestedsteps: + if self._currentstep==1: + print " prefix: %s" % self.prefix +- print " step #%2i : %s" % (self.steps[self._currentstep-1]['id'],self.steps[self._currentstep-1]['string']) ++ print " step #%i : %s" % (self.steps[self._currentstep-1]['id'],self.steps[self._currentstep-1]['string']) + + #Ok, now if _currentstep is a member of steps, return true + if self._currentstep in self.requestedsteps: Index: /issm/oecreview/Archive/13393-13976/ISSM-13955-13956.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13955-13956.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13955-13956.diff (revision 13980) @@ -0,0 +1,46 @@ +Index: ../trunk-jpl/src/android/ISSM/jni/Main_nojavah.cpp +=================================================================== +--- ../trunk-jpl/src/android/ISSM/jni/Main_nojavah.cpp (revision 0) ++++ ../trunk-jpl/src/android/ISSM/jni/Main_nojavah.cpp (revision 13956) +@@ -0,0 +1,40 @@ ++#include ++#include "../../../c/android/fac.h" ++namespace com_example_issm ++{ ++ static jlong factorial(JNIEnv *env, jclass clazz, jlong n) ++ { ++ fac *f = new fac(); ++ jlong result = (jlong) (f->factorial(n)); ++ delete(f); ++ return (jlong) result; ++ } ++//------------------------------------------------------------------------------------ ++ static JNINativeMethod method_table[] = { ++ {"fac" ,"(J)J" , (void *) factorial}, ++ }; ++} ++ ++using namespace com_example_issm; ++ ++extern "C" jint JNI_OnLoad(JavaVM* vm, void* reserved) ++{ ++ JNIEnv* env; ++ if (vm->GetEnv(reinterpret_cast(&env), JNI_VERSION_1_6) != JNI_OK) { ++ return -1; ++ } ++ else ++ { ++ jclass clazz = env->FindClass("com/example/issm/IssmJni"); ++ if(clazz) ++ { ++ env->RegisterNatives(clazz, method_table, 1); ++ env->DeleteLocalRef(clazz); ++ return JNI_VERSION_1_6; ++ } ++ else return -1; ++ } ++ ++ // Get jclass with env->FindClass. ++ // Register methods with env->RegisterNatives. ++} +\ No newline at end of file Index: /issm/oecreview/Archive/13393-13976/ISSM-13956-13957.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13956-13957.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13956-13957.diff (revision 13980) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/src/m/plot/processdata.py +=================================================================== +--- ../trunk-jpl/src/m/plot/processdata.py (revision 13956) ++++ ../trunk-jpl/src/m/plot/processdata.py (revision 13957) +@@ -37,7 +37,7 @@ + if npy.ndim(data)==1: + datasize=npy.array([len(data),1]) + else: +- datasize=shape(data) ++ datasize=npy.shape(data) + + #process NaN's if any + if options.exist('nan'): +Index: ../trunk-jpl/src/m/plot/applyoptions.py +=================================================================== +--- ../trunk-jpl/src/m/plot/applyoptions.py (revision 13956) ++++ ../trunk-jpl/src/m/plot/applyoptions.py (revision 13957) +@@ -151,7 +151,7 @@ + #wrapping + + #colorbar {{{ +- if 'on' in options.getfieldvalue('colorbar','on'): ++ if 'on' in options.getfieldvalue('colorbar','off'): + p.colorbar() + #}}} + Index: /issm/oecreview/Archive/13393-13976/ISSM-13957-13958.diff =================================================================== --- /issm/oecreview/Archive/13393-13976/ISSM-13957-13958.diff (revision 13980) +++ /issm/oecreview/Archive/13393-13976/ISSM-13957-13958.diff (revision 13980) @@ -0,0 +1,1163 @@ +Index: ../trunk-jpl/src/android/ISSM_Visual/.classpath +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/.classpath (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/.classpath (revision 13958) +@@ -0,0 +1,8 @@ ++ ++ ++ ++ ++ ++ ++ ++ +Index: ../trunk-jpl/src/android/ISSM_Visual/project.properties +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/project.properties (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/project.properties (revision 13958) +@@ -0,0 +1,14 @@ ++# This file is automatically generated by Android Tools. ++# Do not modify this file -- YOUR CHANGES WILL BE ERASED! ++# ++# This file must be checked in Version Control Systems. ++# ++# To customize properties used by the Ant build system edit ++# "ant.properties", and override values to adapt the script to your ++# project structure. ++# ++# To enable ProGuard to shrink and obfuscate your code, uncomment this (available properties: sdk.dir, user.home): ++#proguard.config=${sdk.dir}/tools/proguard/proguard-android.txt:proguard-project.txt ++ ++# Project target. ++target=android-16 +Index: ../trunk-jpl/src/android/ISSM_Visual/.project +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/.project (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/.project (revision 13958) +@@ -0,0 +1,33 @@ ++ ++ ++ ISSM_Visual ++ ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.ResourceManagerBuilder ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.PreCompilerBuilder ++ ++ ++ ++ ++ org.eclipse.jdt.core.javabuilder ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.ApkBuilder ++ ++ ++ ++ ++ ++ com.android.ide.eclipse.adt.AndroidNature ++ org.eclipse.jdt.core.javanature ++ ++ +Index: ../trunk-jpl/src/android/ISSM_Visual/proguard-project.txt +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/proguard-project.txt (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/proguard-project.txt (revision 13958) +@@ -0,0 +1,20 @@ ++# To enable ProGuard in your project, edit project.properties ++# to define the proguard.config property as described in that file. ++# ++# Add project specific ProGuard rules here. ++# By default, the flags in this file are appended to flags specified ++# in ${sdk.dir}/tools/proguard/proguard-android.txt ++# You can edit the include path and order by changing the ProGuard ++# include property in project.properties. ++# ++# For more details, see ++# http://developer.android.com/guide/developing/tools/proguard.html ++ ++# Add any project specific keep options here: ++ ++# If your project uses WebView with JS, uncomment the following ++# and specify the fully qualified class name to the JavaScript interface ++# class: ++#-keepclassmembers class fqcn.of.javascript.interface.for.webview { ++# public *; ++#} +Index: ../trunk-jpl/src/android/ISSM_Visual/AndroidManifest.xml +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/AndroidManifest.xml (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/AndroidManifest.xml (revision 13958) +@@ -0,0 +1,25 @@ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ +\ No newline at end of file +Index: ../trunk-jpl/src/android/ISSM_Visual/src/com/example/issm_visual/ISSMVisual.java +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/src/com/example/issm_visual/ISSMVisual.java (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/src/com/example/issm_visual/ISSMVisual.java (revision 13958) +@@ -0,0 +1,99 @@ ++package com.example.issm_visual; ++ ++ ++import android.app.Activity; ++import android.content.Context; ++import android.opengl.GLES20; ++import android.opengl.GLSurfaceView; ++import android.opengl.GLSurfaceView.Renderer; ++import android.os.Bundle; ++import android.util.AttributeSet; ++import android.view.Menu; ++import android.view.View; ++import android.view.View.OnClickListener; ++import android.widget.Button; ++import android.widget.FrameLayout; ++import android.widget.RelativeLayout; ++import android.widget.SeekBar; ++import android.widget.SeekBar.OnSeekBarChangeListener; ++import android.widget.TextView; ++import android.widget.Toast; ++import java.nio.ByteBuffer; ++import java.nio.ByteOrder; ++import java.nio.FloatBuffer; ++import java.nio.ShortBuffer; ++import javax.microedition.khronos.egl.EGLConfig; ++import javax.microedition.khronos.opengles.GL10; ++ ++public class ISSMVisual extends Activity implements OnSeekBarChangeListener ++{ ++ private SeekBar bar; ++ private TextView txtStatus, txtValue; ++ private GLSurfaceView mGLView; ++ private FrameLayout frame; ++ @Override ++ public void onCreate(Bundle savedInstanceState) { ++ super.onCreate(savedInstanceState); ++ setContentView(R.layout.activity_issmvisual); ++ ++ bar = (SeekBar)findViewById(R.id.seekBar); // make seekbar object ++ bar.setOnSeekBarChangeListener(this); // set seekbar listener ++ txtValue = (TextView)findViewById(R.id.value); ++ txtStatus = (TextView)findViewById(R.id.status); ++ ++ mGLView = new MyGLSurfaceView(this); ++ frame = (FrameLayout)findViewById(R.id.frame); ++ frame.addView(mGLView); ++ } ++ ++ ++ @Override ++ public void onProgressChanged(SeekBar seekBar, int val, ++ boolean fromUser) ++ { ++ // change progress text label with current Seekbar value ++ txtValue.setText("Value: " + val); ++ txtStatus.setText("Status: changing"); ++ } ++ ++ @Override ++ public void onStartTrackingTouch(SeekBar seekBar) ++ { ++ txtStatus.setText("Status: Starting to track touch"); ++ ++ } ++ ++ @Override ++ public void onStopTrackingTouch(SeekBar seekBar) ++ { ++ seekBar.setSecondaryProgress(seekBar.getProgress()); // set the shade of the previous value. ++ txtStatus.setText("Status: Ended tracking touch"); ++ } ++ ++ @Override ++ protected void onPause() { ++ super.onPause(); ++ // The following call pauses the rendering thread. ++ // If your OpenGL application is memory intensive, ++ // you should consider de-allocating objects that ++ // consume significant memory here. ++ mGLView.onPause(); ++ } ++ ++ @Override ++ protected void onResume() { ++ super.onResume(); ++ // The following call resumes a paused rendering thread. ++ // If you de-allocated graphic objects for onPause() ++ // this is a good place to re-allocate them. ++ mGLView.onResume(); ++ } ++ ++ ++ @Override ++ public boolean onCreateOptionsMenu(Menu menu) ++ { ++ getMenuInflater().inflate(R.menu.activity_issmvisual, menu); ++ return true; ++ } ++} +Index: ../trunk-jpl/src/android/ISSM_Visual/src/com/example/issm_visual/MyGLRenderer.java +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/src/com/example/issm_visual/MyGLRenderer.java (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/src/com/example/issm_visual/MyGLRenderer.java (revision 13958) +@@ -0,0 +1,248 @@ ++/* ++ * Copyright (C) 2012 The Android Open Source Project ++ * ++ * Licensed under the Apache License, Version 2.0 (the "License"); ++ * you may not use this file except in compliance with the License. ++ * You may obtain a copy of the License at ++ * ++ * http://www.apache.org/licenses/LICENSE-2.0 ++ * ++ * Unless required by applicable law or agreed to in writing, software ++ * distributed under the License is distributed on an "AS IS" BASIS, ++ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. ++ * See the License for the specific language governing permissions and ++ * limitations under the License. ++ */ ++ ++package com.example.issm_visual; ++import java.nio.ByteBuffer; ++import java.nio.ByteOrder; ++import java.nio.FloatBuffer; ++ ++import javax.microedition.khronos.egl.EGLConfig; ++import javax.microedition.khronos.opengles.GL10; ++ ++import android.opengl.GLES20; ++import android.opengl.GLSurfaceView; ++ ++public class MyGLRenderer implements GLSurfaceView.Renderer { ++ ++ private Triangle mTriangle1, mTriangle2, mTriangle3; ++ ++ @Override ++ public void onSurfaceCreated(GL10 unused, EGLConfig config) { ++ ++ // Set the background frame color ++ GLES20.glClearColor(1.0f, 1.0f, 1.0f, 1.0f); ++ ++ mTriangle1 = new Triangle( ++ 0.0f, 0.6f, 0.0f, // top ++ -0.5f, -0.3f, 0.0f, // bottom left ++ 0.5f, -0.3f, 0.0f, ++ 0.0f, 0.0f, 1.0f, 1.0f); // bottom right ++ //mTriangle = new Triangle(); ++ ++ mTriangle2 = new Triangle( ++ -0.5f, -0.3f, 0.0f, ++ 0.0f, -1.0f, 0.0f, ++ 0.5f, -0.3f, 0.0f, ++ 1.0f, 0.0f, 0.0f, 1.0f); ++ ++ mTriangle3 = new Triangle( ++ 0.0f, 0.6f, 0.0f, ++ 0.5f, -0.3f, 0.0f, ++ 1.0f, 0.6f, 0.0f, ++ 1.0f, 1.0f, 0.0f, 1.0f); ++ } ++ ++ @Override ++ public void onDrawFrame(GL10 unused) { ++ ++ // Draw background color ++ GLES20.glClear(GLES20.GL_COLOR_BUFFER_BIT); ++ ++ // Draw triangle ++ mTriangle1.draw(); ++ mTriangle2.draw(); ++ mTriangle3.draw(); ++ } ++ ++ @Override ++ public void onSurfaceChanged(GL10 unused, int width, int height) { ++ // Adjust the viewport based on geometry changes, ++ // such as screen rotation ++ GLES20.glViewport(0, 0, width, height); ++ } ++ ++ public static int loadShader(int type, String shaderCode){ ++ ++ // create a vertex shader type (GLES20.GL_VERTEX_SHADER) ++ // or a fragment shader type (GLES20.GL_FRAGMENT_SHADER) ++ int shader = GLES20.glCreateShader(type); ++ ++ // add the source code to the shader and compile it ++ GLES20.glShaderSource(shader, shaderCode); ++ GLES20.glCompileShader(shader); ++ ++ return shader; ++ } ++ ++} ++ ++class Triangle ++{ ++ ++ private final String vertexShaderCode = ++ "attribute vec4 vPosition;" + ++ "void main() {" + ++ " gl_Position = vPosition;" + ++ "}"; ++ ++ private final String fragmentShaderCode = ++ "precision mediump float;" + ++ "uniform vec4 vColor;" + ++ "void main() {" + ++ " gl_FragColor = vColor;" + ++ "}"; ++ ++ private final FloatBuffer vertexBuffer; ++ private final int mProgram; ++ private int mPositionHandle; ++ private int mColorHandle; ++ ++ // number of coordinates per vertex in this array ++ static final int COORDS_PER_VERTEX = 3; ++ float triangleCoords[] ; /*){ // in counterclockwise order: ++ 0.0f, 0.6f, 0.0f, // top ++ -0.5f, -0.3f, 0.0f, // bottom left ++ 0.5f, -0.3f, 0.0f}; */ // bottom right ++ ++ /* -0.55f, -0.35f, 0.0f, ++ 0.0f, -1.2f, 0.0f, ++ 0.55f, -0.35f, 0.0f ++ };*/ ++ ++ private final int vertexCount = 9 / COORDS_PER_VERTEX; ++ private final int vertexStride = COORDS_PER_VERTEX * 4; // bytes per vertex ++ ++ // Set color with red, green, blue and alpha (opacity) values ++ float color[]; ++ //private final FloatBuffer colorBuffer; ++ private final int colorCount = 4/COORDS_PER_VERTEX; ++ ++ public Triangle() ++ { ++ // initialize vertex byte buffer for shape coordinates ++ ByteBuffer bb = ByteBuffer.allocateDirect( ++ // (number of coordinate values * 4 bytes per float) ++ triangleCoords.length * 4); ++ // use the device hardware's native byte order ++ bb.order(ByteOrder.nativeOrder()); ++ ++ // create a floating point buffer from the ByteBuffer ++ vertexBuffer = bb.asFloatBuffer(); ++ // add the coordinates to the FloatBuffer ++ vertexBuffer.put(triangleCoords); ++ // set the buffer to read the first coordinate ++ vertexBuffer.position(0); ++ ++ /*ByteBuffer bb1 = ByteBuffer.allocateDirect(color.length*4); ++ bb1.order(ByteOrder.nativeOrder()); ++ colorBuffer = bb1.asFloatBuffer(); ++ colorBuffer.put(color); ++ colorBuffer.position(0);*/ ++ ++ //GLES20.glEnableVertexAttribArray(1); ++ //GLES20.glBindBuffer(GLES20.GL_ARRAY_BUFFER, colorBuffer); ++ ++ // prepare shaders and OpenGL program ++ int vertexShader = MyGLRenderer.loadShader(GLES20.GL_VERTEX_SHADER, ++ vertexShaderCode); ++ int fragmentShader = MyGLRenderer.loadShader(GLES20.GL_FRAGMENT_SHADER, ++ fragmentShaderCode); ++ ++ mProgram = GLES20.glCreateProgram(); // create empty OpenGL Program ++ GLES20.glAttachShader(mProgram, vertexShader); // add the vertex shader to program ++ GLES20.glAttachShader(mProgram, fragmentShader); // add the fragment shader to program ++ GLES20.glLinkProgram(mProgram); // create OpenGL program executables ++ } ++ public Triangle(float x1, float y1, float z1, ++ float x2, float y2, float z2, ++ float x3, float y3, float z3, ++ float c1, float c2, float c3, float c4) ++ { ++ triangleCoords = new float[9]; ++ color = new float[4]; ++ triangleCoords[0] = x1; ++ triangleCoords[1] = y1; ++ triangleCoords[2] = z1; ++ triangleCoords[3] = x2; ++ triangleCoords[4] = y2; ++ triangleCoords[5] = z2; ++ triangleCoords[6] = x3; ++ triangleCoords[7] = y3; ++ triangleCoords[8] = z3; ++ color[0] = c1; ++ color[1] = c2; ++ color[2] = c3; ++ color[3] = c4; ++ // initialize vertex byte buffer for shape coordinates ++ ByteBuffer bb = ByteBuffer.allocateDirect( ++ // (number of coordinate values * 4 bytes per float) ++ triangleCoords.length * 4); ++ // use the device hardware's native byte order ++ bb.order(ByteOrder.nativeOrder()); ++ ++ // create a floating point buffer from the ByteBuffer ++ vertexBuffer = bb.asFloatBuffer(); ++ // add the coordinates to the FloatBuffer ++ vertexBuffer.put(triangleCoords); ++ // set the buffer to read the first coordinate ++ vertexBuffer.position(0); ++ ++ /*ByteBuffer bb1 = ByteBuffer.allocateDirect(color.length*4); ++ bb1.order(ByteOrder.nativeOrder()); ++ colorBuffer = bb1.asFloatBuffer(); ++ colorBuffer.put(color); ++ colorBuffer.position(0);*/ ++ ++ // prepare shaders and OpenGL program ++ int vertexShader = MyGLRenderer.loadShader(GLES20.GL_VERTEX_SHADER, ++ vertexShaderCode); ++ int fragmentShader = MyGLRenderer.loadShader(GLES20.GL_FRAGMENT_SHADER, ++ fragmentShaderCode); ++ ++ mProgram = GLES20.glCreateProgram(); // create empty OpenGL Program ++ GLES20.glAttachShader(mProgram, vertexShader); // add the vertex shader to program ++ GLES20.glAttachShader(mProgram, fragmentShader); // add the fragment shader to program ++ GLES20.glLinkProgram(mProgram); // create OpenGL program executables ++ } ++ ++ public void draw() ++ { ++ // Add program to OpenGL environment ++ GLES20.glUseProgram(mProgram); ++ ++ // get handle to vertex shader's vPosition member ++ mPositionHandle = GLES20.glGetAttribLocation(mProgram, "vPosition"); ++ ++ // Enable a handle to the triangle vertices ++ GLES20.glEnableVertexAttribArray(mPositionHandle); ++ ++ // Prepare the triangle coordinate data ++ GLES20.glVertexAttribPointer(mPositionHandle, COORDS_PER_VERTEX, ++ GLES20.GL_FLOAT, false, ++ vertexStride, vertexBuffer); ++ ++ // get handle to fragment shader's vColor member ++ mColorHandle = GLES20.glGetUniformLocation(mProgram, "vColor"); ++ ++ // Set color for drawing the triangle ++ //GLES20.glUniform4fv(mColorHandle, 0, color, 0); ++ //GLES20.glVertexAttrib4f(0, 0.5f, 0.5f, 0.0f, 1.0f); ++ //GLES20.glVertexAttribPointer(mPositionHandle, 4, GLES20.GL_FLOAT, false, stride, offset) ++ GLES20.glUniform4fv(mColorHandle, 1, color, 0); ++ // Draw the triangle ++ GLES20.glDrawArrays(GLES20.GL_TRIANGLES, 0, vertexCount); ++ } ++} +Index: ../trunk-jpl/src/android/ISSM_Visual/src/com/example/issm_visual/MyGLSurfaceView.java +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/src/com/example/issm_visual/MyGLSurfaceView.java (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/src/com/example/issm_visual/MyGLSurfaceView.java (revision 13958) +@@ -0,0 +1,21 @@ ++package com.example.issm_visual; ++ ++import android.content.Context; ++import android.opengl.GLSurfaceView; ++ ++ ++class MyGLSurfaceView extends GLSurfaceView { ++ ++ public MyGLSurfaceView(Context context) { ++ super(context); ++ ++ // Create an OpenGL ES 2.0 context. ++ setEGLContextClientVersion(2); ++ ++ // Set the Renderer for drawing on the GLSurfaceView ++ setRenderer(new MyGLRenderer()); ++ ++ // Render the view only when there is a change in the drawing data ++ setRenderMode(GLSurfaceView.RENDERMODE_WHEN_DIRTY); ++ } ++} +\ No newline at end of file +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/AndroidManifest.xml +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/AndroidManifest.xml (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/AndroidManifest.xml (revision 13958) +@@ -0,0 +1,25 @@ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ +\ No newline at end of file +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/ISSM_Visual.apk +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/ISSM_Visual.apk +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/ISSM_Visual.apk (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/ISSM_Visual.apk (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/ISSM_Visual.apk +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/resources.ap_ +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/resources.ap_ +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/resources.ap_ (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/resources.ap_ (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/resources.ap_ +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-hdpi/ic_launcher.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-hdpi/ic_launcher.png +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-hdpi/ic_launcher.png (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-hdpi/ic_launcher.png (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-hdpi/ic_launcher.png +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-hdpi/ic_action_search.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-hdpi/ic_action_search.png +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-hdpi/ic_action_search.png (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-hdpi/ic_action_search.png (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-hdpi/ic_action_search.png +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-ldpi/ic_launcher.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-ldpi/ic_launcher.png +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-ldpi/ic_launcher.png (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-ldpi/ic_launcher.png (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-ldpi/ic_launcher.png +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-mdpi/ic_launcher.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-mdpi/ic_launcher.png +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-mdpi/ic_launcher.png (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-mdpi/ic_launcher.png (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-mdpi/ic_launcher.png +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-mdpi/ic_action_search.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-mdpi/ic_action_search.png +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-mdpi/ic_action_search.png (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-mdpi/ic_action_search.png (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-mdpi/ic_action_search.png +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-xhdpi/ic_launcher.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-xhdpi/ic_launcher.png +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-xhdpi/ic_launcher.png (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-xhdpi/ic_launcher.png (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-xhdpi/ic_launcher.png +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-xhdpi/ic_action_search.png +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-xhdpi/ic_action_search.png +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-xhdpi/ic_action_search.png (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-xhdpi/ic_action_search.png (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/res/drawable-xhdpi/ic_action_search.png +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/jarlist.cache +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/jarlist.cache (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/jarlist.cache (revision 13958) +@@ -0,0 +1,3 @@ ++# cache for current jar dependecy. DO NOT EDIT. ++# format is ++# Encoding is UTF-8 +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes.dex +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes.dex +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes.dex (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes.dex (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes.dex +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/MyGLSurfaceView.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/MyGLSurfaceView.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/MyGLSurfaceView.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/MyGLSurfaceView.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/MyGLSurfaceView.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$string.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$string.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$string.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$string.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$string.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/ISSMVisual.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/ISSMVisual.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/ISSMVisual.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/ISSMVisual.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/ISSMVisual.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/MyGLRenderer.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/MyGLRenderer.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/MyGLRenderer.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/MyGLRenderer.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/MyGLRenderer.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$attr.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$attr.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$attr.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$attr.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$attr.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$id.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$id.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$id.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$id.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$id.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$layout.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$layout.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$layout.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$layout.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$layout.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/BuildConfig.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/BuildConfig.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/BuildConfig.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/BuildConfig.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/BuildConfig.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/Triangle.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/Triangle.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/Triangle.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/Triangle.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/Triangle.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$style.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$style.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$style.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$style.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$style.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$drawable.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$drawable.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$drawable.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$drawable.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$drawable.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$menu.class +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$menu.class +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$menu.class (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$menu.class (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/bin/classes/com/example/issm_visual/R$menu.class +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/gen/com/example/issm_visual/R.java +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/gen/com/example/issm_visual/R.java (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/gen/com/example/issm_visual/R.java (revision 13958) +@@ -0,0 +1,40 @@ ++/* AUTO-GENERATED FILE. DO NOT MODIFY. ++ * ++ * This class was automatically generated by the ++ * aapt tool from the resource data it found. It ++ * should not be modified by hand. ++ */ ++ ++package com.example.issm_visual; ++ ++public final class R { ++ public static final class attr { ++ } ++ public static final class drawable { ++ public static final int ic_action_search=0x7f020000; ++ public static final int ic_launcher=0x7f020001; ++ } ++ public static final class id { ++ public static final int frame=0x7f070003; ++ public static final int menu_settings=0x7f070005; ++ public static final int relativeLay=0x7f070000; ++ public static final int seekBar=0x7f070001; ++ public static final int status=0x7f070002; ++ public static final int value=0x7f070004; ++ } ++ public static final class layout { ++ public static final int activity_issmvisual=0x7f030000; ++ } ++ public static final class menu { ++ public static final int activity_issmvisual=0x7f060000; ++ } ++ public static final class string { ++ public static final int app_name=0x7f040000; ++ public static final int hello_world=0x7f040001; ++ public static final int menu_settings=0x7f040002; ++ public static final int title_activity_issmvisual=0x7f040003; ++ } ++ public static final class style { ++ public static final int AppTheme=0x7f050000; ++ } ++} +Index: ../trunk-jpl/src/android/ISSM_Visual/gen/com/example/issm_visual/BuildConfig.java +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/gen/com/example/issm_visual/BuildConfig.java (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/gen/com/example/issm_visual/BuildConfig.java (revision 13958) +@@ -0,0 +1,6 @@ ++/** Automatically generated file. DO NOT MODIFY */ ++package com.example.issm_visual; ++ ++public final class BuildConfig { ++ public final static boolean DEBUG = true; ++} +\ No newline at end of file +Index: ../trunk-jpl/src/android/ISSM_Visual/libs/android-support-v4.jar +=================================================================== +Cannot display: file marked as a binary type. +svn:mime-type = application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/libs/android-support-v4.jar +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/libs/android-support-v4.jar (revision 13957) ++++ ../trunk-jpl/src/android/ISSM_Visual/libs/android-support-v4.jar (revision 13958) + +Property changes on: ../trunk-jpl/src/android/ISSM_Visual/libs/android-support-v4.jar +___________________________________________________________________ +Added: svn:mime-type +## -0,0 +1 ## ++application/octet-stream +Index: ../trunk-jpl/src/android/ISSM_Visual/res/values/styles.xml +=================================================================== +--- ../trunk-jpl/src/android/ISSM_Visual/res/values/styles.xml (revision 0) ++++ ../trunk-jpl/src/android/ISSM_Visual/res/values/styles.xml (revision 13958) +@@ -0,0 +1,5 @@ ++ ++ ++