Index: /issm/oecreview/Archive/23185-23389/Date.tex =================================================================== --- /issm/oecreview/Archive/23185-23389/Date.tex (revision 23390) +++ /issm/oecreview/Archive/23185-23389/Date.tex (revision 23390) @@ -0,0 +1,1 @@ +Oct-5-2018 Index: /issm/oecreview/Archive/23185-23389/ISSM-23190-23191.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23190-23191.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23190-23191.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/configure.ac +=================================================================== +--- ../trunk-jpl/configure.ac (revision 23190) ++++ ../trunk-jpl/configure.ac (revision 23191) +@@ -1,7 +1,7 @@ + # Process this file with autoconf to produce a configure script. + + #AUTOCONF +-AC_INIT([Ice Sheet System Model (ISSM)],[4.14],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure ++AC_INIT([Ice Sheet System Model (ISSM)],[4.15],[issm@jpl.nasa.gov],[issm],[http://issm.jpl.nasa.gov]) #Initializing configure + AC_CONFIG_AUX_DIR([./aux-config]) #Put config files in aux-config + AC_CONFIG_MACRO_DIR([m4]) #m4 macros are located in m4 + m4_include([m4/issm_options.m4]) Index: /issm/oecreview/Archive/23185-23389/ISSM-23191-23192.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23191-23192.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23191-23192.diff (revision 23390) @@ -0,0 +1,52 @@ +Index: ../trunk-jpl/src/m/modules/Triangle.py +=================================================================== +--- ../trunk-jpl/src/m/modules/Triangle.py (revision 23191) ++++ ../trunk-jpl/src/m/modules/Triangle.py (nonexistent) +@@ -1,21 +0,0 @@ +-from Triangle_python import Triangle_python +- +-def Triangle(domainoutlinefilename,rifts,mesh_area): +- """ +- TRIMESH - Mesh a domain using an .exp file +- +- Usage: +- [index,x,y,segments,segmentmarkers]=Triangle(domainoutlinefilename,rifts,mesh_area); +- +- index,x,y: defines a triangulation +- segments: An array made of exterior segments to the mesh domain outline +- segmentmarkers: An array flagging each segment +- +- domainoutlinefilename: an Argus domain outline file +- mesh_area: The maximum area desired for any element of the resulting mesh +- """ +- # Call mex module +- index,x,y,segments,segmentmarkers=Triangle_python(domainoutlinefilename,rifts,mesh_area) +- # Return +- return index,x,y,segments,segmentmarkers +- +Index: ../trunk-jpl/src/m/mesh/triangle2dvertical.m +=================================================================== +--- ../trunk-jpl/src/m/mesh/triangle2dvertical.m (revision 23191) ++++ ../trunk-jpl/src/m/mesh/triangle2dvertical.m (revision 23192) +@@ -24,7 +24,7 @@ + area=resolution^2; + + %Mesh using Triangle +-[elements,x,z,segments,segmentmarkers]=Triangle(domainname,'',area); ++[elements,x,z,segments,segmentmarkers]=Triangle_matlab(domainname,'',area); + + %check that all the created nodes belong to at least one element + orphan=find(~ismember([1:length(x)],sort(unique(elements(:))))); +Index: ../trunk-jpl/src/m/mesh/triangle.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/triangle.py (revision 23191) ++++ ../trunk-jpl/src/m/mesh/triangle.py (revision 23192) +@@ -49,7 +49,7 @@ + + #Mesh using Triangle + md.mesh=mesh2d() +- md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers=Triangle(domainname,riftname,area) ++ md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers=Triangle_python(domainname,riftname,area) + md.mesh.elements=md.mesh.elements.astype(int) + md.mesh.segments=md.mesh.segments.astype(int) + md.mesh.segmentmarkers=md.mesh.segmentmarkers.astype(int) Index: /issm/oecreview/Archive/23185-23389/ISSM-23192-23193.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23192-23193.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23192-23193.diff (revision 23390) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/NightlyRun/test421.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test421.py (revision 23192) ++++ ../trunk-jpl/test/NightlyRun/test421.py (revision 23193) +@@ -19,7 +19,7 @@ + + #Fields and tolerances to track changes + field_names =['Vx','Vy','Vz','Vel','Pressure'] +-field_tolerances=[1e-06,9e-07,2e-05,2e-06,2e-06] ++field_tolerances=[2e-06,9e-07,2e-05,2e-06,2e-06] + field_values=[\ + md.results.StressbalanceSolution.Vx,\ + md.results.StressbalanceSolution.Vy,\ +Index: ../trunk-jpl/test/NightlyRun/test421.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test421.m (revision 23192) ++++ ../trunk-jpl/test/NightlyRun/test421.m (revision 23193) +@@ -9,7 +9,7 @@ + + %Fields and tolerances to track changes + field_names ={'Vx','Vy','Vz','Vel','Pressure'}; +-field_tolerances={1e-06,9e-07,2e-05,2e-06,2e-06}; ++field_tolerances={2e-06,9e-07,2e-05,2e-06,2e-06}; + field_values={... + (md.results.StressbalanceSolution.Vx),... + (md.results.StressbalanceSolution.Vy),... Index: /issm/oecreview/Archive/23185-23389/ISSM-23193-23194.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23193-23194.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23193-23194.diff (revision 23390) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/m/mesh/triangle.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/triangle.py (revision 23193) ++++ ../trunk-jpl/src/m/mesh/triangle.py (revision 23194) +@@ -4,6 +4,7 @@ + from Triangle import Triangle + from NodeConnectivity import NodeConnectivity + from ElementConnectivity import ElementConnectivity ++from Triangle_python import Triangle_python + import MatlabFuncs as m + + def triangle(md,domainname,*args): Index: /issm/oecreview/Archive/23185-23389/ISSM-23197-23198.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23197-23198.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23197-23198.diff (revision 23390) @@ -0,0 +1,37 @@ +Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_nonlinear.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_nonlinear.cpp (revision 23197) ++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_nonlinear.cpp (revision 23198) +@@ -20,10 +20,6 @@ + Vector* df = NULL; + Vector* ys = NULL; + +- Vec res; +- double resNorm; +- +- + Loads* savedloads=NULL; + bool converged; + int constraints_converged; +@@ -74,21 +70,6 @@ + Solverx(&uf, Kff, pf, old_uf, df, femmodel->parameters); + femmodel->profiler->Stop(SOLVER); + +- +-// VecDuplicate(uf->pvector->vector,&res); +-// VecCopy(uf->pvector->vector,res); +-// VecAssemblyBegin(res); +-// VecAssemblyEnd(res); +-// VecScale(pf->pvector->vector,-1.); +-// MatMultAdd(Kff->pmatrix->matrix,uf->pvector->vector,pf->pvector->vector,res); +-// VecScale(pf->pvector->vector,-1.); +-// VecView(pf->pvector->vector,PETSC_VIEWER_STDOUT_WORLD); +-// VecNorm(res,NORM_INFINITY,&resNorm); +-// PetscPrintf(PETSC_COMM_WORLD,"Count = %d, Res. norm: %g\n", count,resNorm); +- +- +- +- + Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);delete ys; + + convergence(&converged,Kff,pf,uf,old_uf,eps_res,eps_rel,eps_abs); delete Kff; delete pf; delete df; Index: /issm/oecreview/Archive/23185-23389/ISSM-23198-23199.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23198-23199.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23198-23199.diff (revision 23390) @@ -0,0 +1,93 @@ +Index: ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.h +=================================================================== +--- ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.h (revision 23198) ++++ ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.h (revision 23199) +@@ -74,6 +74,7 @@ + ElementMatrix* CreateKMatrixFSViscousLA(Element* element); + ElementMatrix* CreateKMatrixFSViscousXTH(Element* element); + ElementMatrix* CreatePressureMassMatrix(Element* element); ++ ElementMatrix* CreateSchurPrecondMatrix(Element* element); + ElementVector* CreatePVectorFS(Element* element); + ElementVector* CreatePVectorFSFriction(Element* element); + ElementVector* CreatePVectorFSFront(Element* element); +Index: ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp (revision 23198) ++++ ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp (revision 23199) +@@ -944,9 +944,11 @@ + #ifdef _HAVE_PETSC_ + int solver_type; + PetscOptionsDetermineSolverType(&solver_type); ++ + if(solver_type==FSSolverEnum) is_schur_cg_solver = true; + #endif + ++ + if(is_schur_cg_solver) + solutionsequence_schurcg(femmodel); + else if (fe_FS==XTaylorHoodEnum) +@@ -3288,6 +3290,64 @@ + xDelete(pbasis); + return Ke; + }/*}}}*/ ++ElementMatrix* StressbalanceAnalysis::CreateSchurPrecondMatrix(Element* element){/*{{{*/ ++ ++ /*Intermediaries*/ ++ int i,dim; ++ IssmDouble viscosity,FSreconditioning,Jdet; ++ IssmDouble *xyz_list = NULL; ++ ++ /*Get problem dimension*/ ++ element->FindParam(&dim,DomainDimensionEnum); ++ ++ /*Fetch number of nodes and dof for this finite element*/ ++ int vnumnodes = element->NumberofNodesVelocity(); ++ int pnumnodes = element->NumberofNodesPressure(); ++ int numdof = vnumnodes*dim + pnumnodes; ++ ++ /*Initialize Element matrix and vectors*/ ++ ElementMatrix* Ke = element->NewElementMatrix(FSvelocityEnum); ++ IssmDouble* pbasis = xNew(pnumnodes); ++ ++ /*Retrieve all inputs and parameters*/ ++ element->GetVerticesCoordinates(&xyz_list); ++ //element->FindParam(&FSreconditioning,StressbalanceFSreconditioningEnum); ++ Input* vx_input=element->GetInput(VxEnum); _assert_(vx_input); ++ Input* vy_input=element->GetInput(VyEnum); _assert_(vy_input); ++ Input* vz_input = NULL; ++ if(dim==3){vz_input=element->GetInput(VzEnum); _assert_(vz_input);} ++ ++ ++ /* Start looping on the number of gaussian points: */ ++ Gauss* gauss = element->NewGauss(5); ++ for(int ig=gauss->begin();igend();ig++){ ++ gauss->GaussPoint(ig); ++ ++ element->JacobianDeterminant(&Jdet,xyz_list,gauss); ++ element->NodalFunctionsPressure(pbasis,gauss); ++ element->material->ViscosityFS(&viscosity,dim,xyz_list,gauss,vx_input,vy_input,vz_input); ++ ++ ++ if(dim==3){ ++ /*Pressure mass matrix*/ ++ for(int k=0;kvalues[(3*vnumnodes+k)*numdof+3*vnumnodes+j] += gauss->weight*1./viscosity*Jdet*(pbasis[j]*pbasis[k]); ++ } ++ } ++ } ++ else{ ++ _error_("STOP"); ++ } ++ } ++ ++ /*Clean up and return*/ ++ delete gauss; ++ xDelete(xyz_list); ++ xDelete(pbasis); ++ return Ke; ++}/*}}}*/ ++ + ElementMatrix* StressbalanceAnalysis::CreateKMatrixFSViscousLA(Element* element){/*{{{*/ + + /*Intermediaries*/ Index: /issm/oecreview/Archive/23185-23389/ISSM-23204-23205.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23204-23205.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23204-23205.diff (revision 23390) @@ -0,0 +1,369 @@ +Index: ../trunk-jpl/src/c/solutionsequences/convergence.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutionsequences/convergence.cpp (revision 23204) ++++ ../trunk-jpl/src/c/solutionsequences/convergence.cpp (revision 23205) +@@ -6,7 +6,7 @@ + #include "../modules/modules.h" + #include "../shared/shared.h" + +-void convergence(bool* pconverged, Matrix* Kff,Vector* pf,Vector* uf,Vector* old_uf,IssmDouble eps_res,IssmDouble eps_rel,IssmDouble eps_abs){ ++void convergence(bool* pconverged, Matrix* Kff,Vector* pf,Vector* uf,Vector* old_uf,IssmDouble eps_res,IssmDouble eps_rel,IssmDouble eps_abs){/*{{{*/ + + /*output*/ + bool converged=false; +@@ -33,9 +33,12 @@ + return; + } + ++ + /*Display solver caracteristics*/ + if (VerboseConvergence()){ + ++ ++ + /*compute KUF = KU - F = K*U - F*/ + KU=uf->Duplicate(); Kff->MatMult(uf,KU); + KUF=KU->Duplicate(); KU->Copy(KUF); KUF->AYPX(pf,-1.0); +@@ -135,4 +138,6 @@ + + /*assign output*/ + *pconverged=converged; +-} ++}/*}}}*/ ++ ++ +Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_schurcg.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_schurcg.cpp (revision 23204) ++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_schurcg.cpp (revision 23205) +@@ -11,12 +11,13 @@ + + + #ifdef _HAVE_PETSC_ +-void SchurCGSolver(Vector** puf,Mat Kff,Mat Iff,Vec pf, Vec uf0,Vec df,Parameters* parameters){/*{{{*/ + ++ ++void SchurCGSolver(Vector** puf,Mat Kff,Vec pf, Vec uf0,IS isv,IS isp,Parameters* parameters){/*{{{*/ ++ + Mat A, B, BT; /* Saddle point block matrices */ + Mat IP; /* Preconditioner matrix */ +- IS isv=NULL; /* Index set free velocity nodes */ +- IS isp=NULL; /* Index set free pressure nodes */ ++ Mat IP2; + int nu, np; /* No of. free nodes in velocity / pressure space */ + Vec p,uold,unew; /* Solution vectors for pressure / vel. */ + Vec tmpu, tmpp, rhsu,rhsp; /* temp. vectors, arbitrary RHS in vel. / pressure space */ +@@ -37,16 +38,6 @@ + /*Initialize output*/ + Vector* out_uf=new Vector(uf0); + +- /* Get velocity and pressure index sets for extraction */ +- #if _PETSC_MAJOR_==3 +- /*Make indices out of doftypes: */ +- if(!df)_error_("need doftypes for FS solver!\n"); +- DofTypesToIndexSet(&isv,&isp,df,FSSolverEnum); +- #else +- _error_("Petsc 3.X required"); +- #endif +- +- + /* Extract block matrices from the saddle point matrix */ + /* [ A B ] = Kff + * [ B^T 0 ] +@@ -56,8 +47,8 @@ + MatGetSubMatrix(Kff,isp,isv,MAT_INITIAL_MATRIX,&BT); + + /* Extract preconditioner matrix on the pressure space*/ +- MatGetSubMatrix(Iff,isp,isp,MAT_INITIAL_MATRIX,&IP); +- ++ MatGetSubMatrix(Kff,isp,isp,MAT_INITIAL_MATRIX,&IP); ++ + /* Get number of velocity / pressure nodes */ + MatGetSize(B,&nu,&np); + +@@ -229,9 +220,12 @@ + break; + else if(rnorm > 100*initRnorm) + _error_("Solver diverged. This shouldn't happen\n"); +- else +- PetscPrintf(PETSC_COMM_WORLD,"rel. residual at step %d: %g, at TOL = %g\n",count,rnorm/initRnorm,TOL); +- ++ //else ++ // PetscPrintf(PETSC_COMM_WORLD,"rel. residual at step %d: %g, at TOL = %g\n",count,rnorm/initRnorm,TOL); ++ ++ ++ ++ + if(count > np-1) break; + + +@@ -273,6 +267,194 @@ + VecDestroy(&thetanew);VecDestroy(&thetaold); + + }/*}}}*/ ++void convergence_schurcg(bool* pconverged, Matrix* Kff,Vector* pf,Vector* uf,Vector* old_uf,IssmDouble eps_res,IssmDouble eps_rel,IssmDouble eps_abs,IS isv,IS isp){/*{{{*/ ++ ++ /*output*/ ++ bool converged=false; ++ ++ /*intermediary*/ ++ //Vector* KU=NULL; ++ //Vector* KUF=NULL; ++ //Vector* KUold=NULL; ++ //Vector* KUoldF=NULL; ++ Vector* duf=NULL; ++ IssmDouble ndu,nduinf,nu; ++ IssmDouble nKUF; ++ IssmDouble nKUoldF; ++ IssmDouble nF; ++ IssmDouble solver_residue,res; ++ int analysis_type; ++ ++ Mat A, B, BT; ++ Vec u,p,uold,pold,f1,f2,tmp,res1,res2; ++ int n_u,n_p; ++ double rnorm1, rnorm2; ++ ++ ++ if(VerboseModule()) _printf0_(" checking convergence\n"); ++ ++ /*If uf is NULL in input, f-set is nil, model is fully constrained, therefore converged from ++ * the get go: */ ++ if(uf->IsEmpty()){ ++ *pconverged=true; ++ return; ++ } ++ ++ /* Note: SchurCG also constructs the Schur preconditioner and stores it in the free block of Kff */ ++ /* [A B] ++ * Kff = | | ++ * [B^T IP] ++ /* To calculate the residual, only the necessary blocks need to be extracted */ ++ ++ /*Extract A, B, B^T */ ++ MatGetSubMatrix(Kff->pmatrix->matrix,isv,isv,MAT_INITIAL_MATRIX,&A); ++ MatGetSubMatrix(Kff->pmatrix->matrix,isv,isp,MAT_INITIAL_MATRIX,&B); ++ MatGetSubMatrix(Kff->pmatrix->matrix,isp,isv,MAT_INITIAL_MATRIX,&BT); ++ ++ /*no. of free nodes in velocity/pressure space*/ ++ MatGetSize(B,&n_u,&n_p); ++ ++ /*Extract values corresponding to the free velocity/pressure nodes*/ ++ VecCreate(IssmComm::GetComm(),&p);VecSetSizes(p,PETSC_DECIDE,n_p);VecSetFromOptions(p); ++ VecAssemblyBegin(p);VecAssemblyEnd(p); ++ VecCreate(IssmComm::GetComm(),&u);VecSetSizes(u,PETSC_DECIDE,n_u);VecSetFromOptions(u); ++ VecAssemblyBegin(u);VecAssemblyEnd(u); ++ ++ VecGetSubVector(uf->pvector->vector,isv,&u); ++ VecGetSubVector(uf->pvector->vector,isp,&p); ++ ++ ++ /*Extract values of the RHS corresponding to the first/second block*/ ++ VecDuplicate(u,&f1);VecSet(f1,1.0); ++ VecDuplicate(p,&f2);VecSet(f2,1.0); ++ VecGetSubVector(pf->pvector->vector,isv,&f1); ++ VecGetSubVector(pf->pvector->vector,isp,&f2); ++ ++ /*Allocate intermediaries*/ ++ VecDuplicate(u,&res1);VecSet(res1,1.0); ++ VecDuplicate(u,&tmp);VecSet(tmp,1.0); ++ VecDuplicate(p,&res2);VecSet(res2,1.0); ++ ++ ++ /*Display solver caracteristics*/ ++ if (VerboseConvergence()){ ++ ++ /*Calculate res1 = A*u + B*p - f1*/ ++ VecScale(f1,-1.);MatMultAdd(A,u,f1,tmp);MatMultAdd(B,p,tmp,res1);VecScale(f1,-1.); ++ /*Calculate res2 = B^T * u - f2*/ ++ VecScale(f2,-1.);MatMultAdd(BT,u,f2,res2);VecScale(f2,-1.); ++ ++ ++ /*compute norm(res1), norm(res2), norm(F) and residue*/ ++ VecNorm(res1,NORM_2,&rnorm1);VecNorm(res2,NORM_2,&rnorm2); ++ nKUF=sqrt(rnorm1*rnorm1 + rnorm2*rnorm2); ++ nF=pf->Norm(NORM_TWO); ++ solver_residue=nKUF/nF; ++ _printf0_("\n" << " solver residue: norm(KU-F)/norm(F)=" << solver_residue << "\n"); ++ if(xIsNan(solver_residue)){ ++ //Kff->Echo(); ++ } ++ ++ } ++ /*clean up*/ ++ VecRestoreSubVector(uf->pvector->vector,isv,&u); ++ VecRestoreSubVector(uf->pvector->vector,isp,&p); ++ ++ /*Extract values corresponding to velocity/pressure on the old solution*/ ++ VecGetSubVector(old_uf->pvector->vector,isv,&uold); ++ VecGetSubVector(old_uf->pvector->vector,isp,&pold); ++ ++ ++ /*Force equilibrium (Mandatory)*/ ++ ++ /*Calculate res1 = A*uold + B*pold - f1*/ ++ VecScale(f1,-1.);MatMultAdd(A,uold,f1,tmp);MatMultAdd(B,pold,tmp,res1);VecScale(f1,-1.); ++ /*Calculate res2 = B^T * uold - f2*/ ++ VecScale(f2,-1.);MatMultAdd(BT,uold,f2,res2);VecScale(f2,-1.); ++ ++ /*compute norm(res1), norm(res2), norm(F) and residue*/ ++ VecNorm(res1,NORM_2,&rnorm1);VecNorm(res2,NORM_2,&rnorm2); ++ nKUoldF=sqrt(rnorm1*rnorm1 + rnorm2*rnorm2); ++ nF=pf->Norm(NORM_TWO); ++ res=nKUoldF/nF; ++ if (xIsNan(res)){ ++ _printf0_("norm nf = " << nF << "f and norm kuold = " << nKUoldF << "f\n"); ++ _error_("mechanical equilibrium convergence criterion is NaN!"); ++ } ++ ++ MatDestroy(&A);MatDestroy(&B);MatDestroy(&BT); ++ VecRestoreSubVector(pf->pvector->vector,isv,&f1); ++ VecRestoreSubVector(pf->pvector->vector,isp,&f2); ++ VecDestroy(&res1);VecDestroy(&res2);VecDestroy(&tmp); ++ VecRestoreSubVector(old_uf->pvector->vector,isv,&uold); ++ VecRestoreSubVector(old_uf->pvector->vector,isp,&pold); ++ ++ ++ ++ //print ++ if(res "<(eps_rel) || (VerboseConvergence())){ ++ ++ //compute norm(du)/norm(u) ++ duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); ++ ndu=duf->Norm(NORM_TWO); nu=old_uf->Norm(NORM_TWO); ++ ++ if (xIsNan(ndu) || xIsNan(nu)) _error_("convergence criterion is NaN!"); ++ ++ //clean up ++ delete duf; ++ ++ //print ++ if (!xIsNan(eps_rel)){ ++ if((ndu/nu) " << eps_rel*100 << " %\n"); ++ converged=false; ++ } ++ } ++ else _printf0_(setw(50) << left << " Convergence criterion: norm(du)/norm(u)" << ndu/nu*100 << " %\n"); ++ ++ } ++ ++ /*Absolute criterion (Optional) = max(du)*/ ++ if (!xIsNan(eps_abs) || (VerboseConvergence())){ ++ ++ //compute max(du) ++ duf=old_uf->Duplicate(); old_uf->Copy(duf); duf->AYPX(uf,-1.0); ++ ndu=duf->Norm(NORM_TWO); nduinf=duf->Norm(NORM_INF); ++ if (xIsNan(ndu) || xIsNan(nu)) _error_("convergence criterion is NaN!"); ++ ++ //clean up ++ delete duf; ++ ++ //print ++ if (!xIsNan(eps_abs)){ ++ if ((nduinf) " << eps_abs << "\n"); ++ converged=false; ++ } ++ } ++ else _printf0_(setw(50) << left << " Convergence criterion: max(du)" << nduinf << "\n"); ++ ++ } ++ ++ /*assign output*/ ++ *pconverged=converged; ++}/*}}}*/ + void solutionsequence_schurcg(FemModel* femmodel){/*{{{*/ + + /*intermediary: */ +@@ -284,7 +466,6 @@ + Vector* pf = NULL; + Vector* df = NULL; + Vector* ys = NULL; +- Matrix* Iff = NULL; + + + /*parameters:*/ +@@ -323,19 +504,29 @@ + Reduceloadx(pf, Kfs, ys); delete Kfs; + + /*Create mass matrix*/ +- int fsize; Kff->GetSize(&fsize,&fsize); +- Iff=new Matrix(fsize,fsize,300,4); + StressbalanceAnalysis* analysis = new StressbalanceAnalysis(); + /*Get complete stiffness matrix without penalties*/ + for(int i=0;ielements->Size();i++){ + Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); + ElementMatrix* Ie = analysis->CreateSchurPrecondMatrix(element); +- if(Ie) Ie->AddToGlobal(Iff,NULL); ++ if(Ie) Ie->AddToGlobal(Kff,NULL); + delete Ie; + } +- Iff->Assemble(); ++ Kff->Assemble(); + delete analysis; + ++ /*Obtain index sets for velocity and pressure components */ ++ IS isv = NULL; ++ IS isp = NULL; ++ #if _PETSC_MAJOR_==3 ++ /*Make indices out of doftypes: */ ++ if(!(df->pvector->vector))_error_("need doftypes for FS solver!\n"); ++ DofTypesToIndexSet(&isv,&isp,df->pvector->vector,FSSolverEnum); ++ #else ++ _error_("Petsc 3.X required"); ++ #endif ++ ++ + /*Solve*/ + femmodel->profiler->Start(SOLVER); + _assert_(Kff->type==PetscMatType); +@@ -342,19 +533,19 @@ + + SchurCGSolver(&uf, + Kff->pmatrix->matrix, +- Iff->pmatrix->matrix, + pf->pvector->vector, + old_uf->pvector->vector, +- df->pvector->vector, ++ isv, ++ isp, + femmodel->parameters); + femmodel->profiler->Stop(SOLVER); +- delete Iff; +- ++ ++ + /*Merge solution from f set to g set*/ + Mergesolutionfromftogx(&ug, uf,ys,femmodel->nodes,femmodel->parameters);delete ys; + + /*Check for convergence and update inputs accordingly*/ +- convergence(&converged,Kff,pf,uf,old_uf,eps_res,eps_rel,eps_abs); delete Kff; delete pf; delete df; ++ convergence_schurcg(&converged,Kff,pf,uf,old_uf,eps_res,eps_rel,eps_abs,isv,isp); delete Kff; delete pf; delete df; + count++; + + if(count>=max_nonlinear_iterations){ +@@ -379,6 +570,7 @@ + delete old_uf; + + }/*}}}*/ ++ + #else + void solutionsequence_schurcg(FemModel* femmodel){_error_("PETSc needs to be installed");} + #endif Index: /issm/oecreview/Archive/23185-23389/ISSM-23205-23206.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23205-23206.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23205-23206.diff (revision 23390) @@ -0,0 +1,32 @@ +Index: ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp (revision 23205) ++++ ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp (revision 23206) +@@ -3278,6 +3278,13 @@ + Ke->values[(3*vnumnodes+k)*numdof+3*vnumnodes+j] += gauss->weight*Jdet*(pbasis[j]*pbasis[k]); + } + } ++ }else if(dim==2){ ++ /*Pressure mass matrix*/ ++ for(int k=0;kvalues[(2*vnumnodes+k)*numdof+2*vnumnodes+j] += gauss->weight*Jdet*(pbasis[j]*pbasis[k]); ++ } ++ } + } + else{ + _error_("STOP"); +@@ -3335,6 +3342,13 @@ + Ke->values[(3*vnumnodes+k)*numdof+3*vnumnodes+j] += gauss->weight*1./viscosity*Jdet*(pbasis[j]*pbasis[k]); + } + } ++ }else if(dim==2){ ++ /*Pressure mass matrix*/ ++ for(int k=0;kvalues[(2*vnumnodes+k)*numdof+2*vnumnodes+j] += gauss->weight*1./viscosity*Jdet*(pbasis[j]*pbasis[k]); ++ } ++ } + } + else{ + _error_("STOP"); Index: /issm/oecreview/Archive/23185-23389/ISSM-23206-23207.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23206-23207.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23206-23207.diff (revision 23390) @@ -0,0 +1,56 @@ +Index: ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp (revision 23206) ++++ ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp (revision 23207) +@@ -3271,22 +3271,14 @@ + element->JacobianDeterminant(&Jdet,xyz_list,gauss); + element->NodalFunctionsPressure(pbasis,gauss); + +- if(dim==3){ ++ if(dim==3 || dim==2){ + /*Pressure mass matrix*/ + for(int k=0;kvalues[(3*vnumnodes+k)*numdof+3*vnumnodes+j] += gauss->weight*Jdet*(pbasis[j]*pbasis[k]); ++ Ke->values[(dim*vnumnodes+k)*numdof+dim*vnumnodes+j] += gauss->weight*Jdet*(pbasis[j]*pbasis[k]); + } + } +- }else if(dim==2){ +- /*Pressure mass matrix*/ +- for(int k=0;kvalues[(2*vnumnodes+k)*numdof+2*vnumnodes+j] += gauss->weight*Jdet*(pbasis[j]*pbasis[k]); +- } +- } +- } +- else{ ++ }else{ + _error_("STOP"); + } + } +@@ -3335,22 +3327,14 @@ + element->material->ViscosityFS(&viscosity,dim,xyz_list,gauss,vx_input,vy_input,vz_input); + + +- if(dim==3){ ++ if(dim==3 || dim==2){ + /*Pressure mass matrix*/ + for(int k=0;kvalues[(3*vnumnodes+k)*numdof+3*vnumnodes+j] += gauss->weight*1./viscosity*Jdet*(pbasis[j]*pbasis[k]); ++ Ke->values[(dim*vnumnodes+k)*numdof+dim*vnumnodes+j] += gauss->weight*1./viscosity*Jdet*(pbasis[j]*pbasis[k]); + } + } +- }else if(dim==2){ +- /*Pressure mass matrix*/ +- for(int k=0;kvalues[(2*vnumnodes+k)*numdof+2*vnumnodes+j] += gauss->weight*1./viscosity*Jdet*(pbasis[j]*pbasis[k]); +- } +- } +- } +- else{ ++ }else{ + _error_("STOP"); + } + } Index: /issm/oecreview/Archive/23185-23389/ISSM-23210-23211.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23210-23211.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23210-23211.diff (revision 23390) @@ -0,0 +1,331 @@ +Index: ../trunk-jpl/src/m/contrib/defleurian/paraview/enveloppeVTK.py +=================================================================== +--- ../trunk-jpl/src/m/contrib/defleurian/paraview/enveloppeVTK.py (revision 23210) ++++ ../trunk-jpl/src/m/contrib/defleurian/paraview/enveloppeVTK.py (revision 23211) +@@ -8,13 +8,13 @@ + function exportVTK(filename,model) + creates a directory with the vtk files for displays in paraview + (only work for triangle and wedges based on their number of nodes) +- +- Give only the results for nw but could be extended to geometry, mask... +- +- input: filename destination ++ ++ Give only the results for nw but could be extended to geometry, mask... ++ ++ input: filename destination + (string) + ------------------------------------------------------------------ +-model this is md ++model this is md + ------------------------------------------------------------------ + By default only the results are exported, you can add whichever + field you need as a string: +@@ -39,24 +39,40 @@ + else: + os.mkdir(filename) + +- IsEnveloppe=np.where(model.mesh.vertexonbase | model.mesh.vertexonsurface) +- #get the element related variables ++ # {{{get the element related variables + if 'z' in dict.keys(model.mesh.__dict__): +- points=np.column_stack((model.mesh.x,model.mesh.y,model.mesh.z)) +- num_of_elt=np.size(np.isnan(model.mesh.lowerelements))+np.size(np.isnan(model.mesh.upperelements)) +- low_elt_num=np.size(np.isnan(model.mesh.lowerelements)) +- top_elt_num=np.size(np.isnan(model.mesh.upperelements)) ++ is_enveloppe=np.logical_or(model.mesh.vertexonbase,model.mesh.vertexonsurface) ++ enveloppe_index=np.where(is_enveloppe)[0] ++ convert_index=np.nan*np.ones(np.shape(model.mesh.x)) ++ convert_index=np.asarray([[i,np.where(enveloppe_index==i)[0][0]] for i,val in enumerate(convert_index) if any(enveloppe_index==i)]) ++ points=np.column_stack((model.mesh.x[enveloppe_index], ++ model.mesh.y[enveloppe_index], ++ model.mesh.z[enveloppe_index])) ++ low_elt_num=np.size(np.where(np.isnan(model.mesh.lowerelements))) ++ top_elt_num=np.size(np.where(np.isnan(model.mesh.upperelements))) ++ num_of_elt=low_elt_num+top_elt_num ++ connect=model.mesh.elements[np.where(is_enveloppe[model.mesh.elements-1])].reshape(int(num_of_elt),3)-1 ++ for elt in range(0, num_of_elt): ++ connect[elt,0]=convert_index[np.where(convert_index==connect[elt,0])[0],1][0] ++ connect[elt,1]=convert_index[np.where(convert_index==connect[elt,1])[0],1][0] ++ connect[elt,2]=convert_index[np.where(convert_index==connect[elt,2])[0],1][0] ++ + else: +- points=np.column_stack((model.mesh.x,model.mesh.y,np.zeros(np.shape(model.mesh.x)))) ++ points=np.column_stack((model.mesh.x, ++ model.mesh.y, ++ np.zeros(np.shape(model.mesh.x)))) + num_of_elt=np.shape(model.mesh.elements)[0] +- +- num_of_points=np.size(points)[0] +- dim=np.size(points)[1] +- point_per_elt=np.shape(model.mesh.elements)[1] +- ++ connect=model.mesh.elements-1 ++ enveloppe_index=np.arange(0,np.size(model.mesh.x)) ++ ++ every_nodes=np.size(model.mesh.x) ++ num_of_points=np.size(enveloppe_index) ++ dim=3 ++ point_per_elt=3 + celltype=5 #triangles +- +- #this is the result structure ++ ++ # }}} ++ # {{{this is the result structure + res_struct=model.results + if (len(res_struct.__dict__)>0): + #Getting all the solutions of the model +@@ -63,7 +79,7 @@ + solnames=(dict.keys(res_struct.__dict__)) + num_of_sols=len(solnames) + num_of_timesteps=1 +- #%building solutionstructure ++ #%building solutionstructure + for solution in solnames: + #looking for multiple time steps + if (np.size(res_struct.__dict__[solution])>num_of_timesteps): +@@ -71,7 +87,8 @@ + num_of_timesteps=int(num_of_timesteps)+1 + else: + num_of_timesteps=1 +- ++ # }}} ++ # {{{write header and mesh + for step in range(0,num_of_timesteps): + timestep=step + fid=open((filename +'/Timestep.vtk'+str(timestep)+'.vtk'),'w+') +@@ -82,26 +99,21 @@ + fid.write('POINTS %d float\n' % num_of_points) + for point in points: + fid.write('%f %f %f \n'%(point[0], point[1], point[2])) +- ++ + fid.write('CELLS %d %d\n' %(num_of_elt, num_of_elt*(point_per_elt+1))) + +- # if exist('low_elt_num') +- # triaconnect=zeros(num_of_elt,3); +- # triaconnect(1:low_elt_num,:)=model.mesh.elements(find(isnan(model.mesh.lowerelements)),1:3); +- # upshift=-min(min(model.mesh.elements(find(isnan(model.mesh.upperelements)),4:6)))+1+max(max(model.mesh.elements(find(isnan(model.mesh.lowerelements)),1:3))); +- # triaconnect(1+low_elt_num:num_of_elt,:)=model.mesh.elements(find(isnan(model.mesh.upperelements)),4:6)+upshift; +- # fprintf(fid,s,[(3)*ones(num_of_elt,1) triaconnect-1]'); + for elt in range(0, num_of_elt): +- +- fid.write('3 %d %d %d\n' %(model.mesh.elements[elt,0]-1,model.mesh.elements[elt,1]-1,model.mesh.elements[elt,2]-1)) +- ++ fid.write('3 %d %d %d\n' %(connect[elt,0], ++ connect[elt,1], ++ connect[elt,2])) ++ + fid.write('CELL_TYPES %d\n' %num_of_elt) + for elt in range(0, num_of_elt): + fid.write('%d\n' %celltype) + + fid.write('POINT_DATA %s \n' %str(num_of_points)) +- +- #loop over the different solution structures ++ # }}} ++ # {{{loop over the different solution structures + if 'solnames' in locals(): + for sol in solnames: + #dealing with results on different timesteps +@@ -109,7 +121,7 @@ + timestep = step + else: + timestep = np.size(res_struct.__dict__[sol]) +- ++ + #getting the fields in the solution + if(np.size(res_struct.__dict__[sol])>1): + fieldnames=dict.keys(res_struct.__dict__[sol].__getitem__(timestep-1).__dict__) +@@ -122,36 +134,37 @@ + else: + fieldstruct=res_struct.__dict__[sol].__dict__[field] + +- if ((np.size(fieldstruct))==num_of_points): ++ if ((np.size(fieldstruct))==every_nodes): + fid.write('SCALARS %s float 1 \n' % field) + fid.write('LOOKUP_TABLE default\n') + for node in range(0,num_of_points): + #paraview does not like NaN, replacing +- if np.isnan(fieldstruct[node]): ++ if np.isnan(fieldstruct[enveloppe_index[node]]): + fid.write('%e\n' % -9999.9999) + #also checking for verry small value that mess up +- elif (abs(fieldstruct[node])<1.0e-20): ++ elif (abs(fieldstruct[enveloppe_index[node]])<1.0e-20): + fid.write('%e\n' % 0.0) + else: +- fid.write('%e\n' % fieldstruct[node]) +- +- #loop on arguments, if something other than result is asked, do +- #it now ++ fid.write('%e\n' % fieldstruct[enveloppe_index[node]]) ++ # }}} ++ # {{{loop on arguments, if something other than result is asked, do it now ++ + for other in args: + other_struct=model.__dict__[other] + othernames=(dict.keys(other_struct.__dict__)) + for field in othernames: +-# fprintf(fid,s,res_struct.(fieldnames{k})(IsEnveloppe)); +- if ((np.size(other_struct.__dict__[field]))==num_of_points): ++ if ((np.size(other_struct.__dict__[field]))==every_nodes): + fid.write('SCALARS %s float 1 \n' % field) + fid.write('LOOKUP_TABLE default\n') + for node in range(0,num_of_points): + #paraview does not like NaN, replacing +- if np.isnan(other_struct.__dict__[field][node]): ++ if np.isnan(other_struct.__dict__[field][enveloppe_index[node]]): + fid.write('%e\n' % -9999.9999) + #also checking for verry small value that mess up +- elif (abs(other_struct.__dict__[field][node])<1.0e-20): ++ elif (abs(other_struct.__dict__[field][enveloppe_index[node]])<1.0e-20): + fid.write('%e\n' % 0.0) + else: +- fid.write('%e\n' % other_struct.__dict__[field][node]) ++ fid.write('%e\n' % other_struct.__dict__[field][enveloppe_index[node]]) ++ ++ # }}} + fid.close(); +Index: ../trunk-jpl/src/m/contrib/defleurian/paraview/exportVTK.py +=================================================================== +--- ../trunk-jpl/src/m/contrib/defleurian/paraview/exportVTK.py (revision 23210) ++++ ../trunk-jpl/src/m/contrib/defleurian/paraview/exportVTK.py (revision 23211) +@@ -8,13 +8,13 @@ + function exportVTK(filename,model) + creates a directory with the vtk files for displays in paraview + (only work for triangle and wedges based on their number of nodes) +- +- Give only the results for nw but could be extended to geometry, mask... +- +- input: filename destination ++ ++ Give only the results for nw but could be extended to geometry, mask... ++ ++ input: filename destination + (string) + ------------------------------------------------------------------ +-model this is md ++model this is md + ------------------------------------------------------------------ + By default only the results are exported, you can add whichever + field you need as a string: +@@ -66,7 +66,7 @@ + solnames=(dict.keys(res_struct.__dict__)) + num_of_sols=len(solnames) + num_of_timesteps=1 +- #%building solutionstructure ++ #%building solutionstructure + for solution in solnames: + #looking for multiple time steps + if (np.size(res_struct.__dict__[solution])>num_of_timesteps): +@@ -90,9 +90,9 @@ + elif(dim==2): + for point in points: + fid.write('%f %f %f \n'%(point[0], point[1], point[2])) +- ++ + fid.write('CELLS %d %d\n' %(num_of_elt, num_of_elt*(point_per_elt+1))) +- ++ + if point_per_elt==3: + for elt in range(0, num_of_elt): + fid.write('3 %d %d %d\n' %(model.mesh.elements[elt,0]-1,model.mesh.elements[elt,1]-1,model.mesh.elements[elt,2]-1)) +@@ -116,7 +116,7 @@ + timestep = step + else: + timestep = np.size(res_struct.__dict__[sol]) +- ++ + #getting the fields in the solution + if(np.size(res_struct.__dict__[sol])>1): + fieldnames=dict.keys(res_struct.__dict__[sol].__getitem__(timestep).__dict__) +@@ -186,13 +186,16 @@ + fid.write('%e\n' % current_force[node]) + # reloaded variable are generally of dim 2 + elif np.shape(other_struct.__dict__[field])[0]==num_of_points: ++ # we want only vector ++ if np.shape(other_struct.__dict__[field])[1]==1: + fid.write('SCALARS %s float 1 \n' % field) + fid.write('LOOKUP_TABLE default\n') + for node in range(0,num_of_points): + #paraview does not like NaN, replacing ++ print other_struct.__dict__[field][node] + if np.isnan(other_struct.__dict__[field][node]): + fid.write('%e\n' % -9999.9999) +- #also checking for verry small value that mess up ++ #also checking for verry small value that mess up + elif (abs(other_struct.__dict__[field][node])<1.0e-20): + fid.write('%e\n' % 0.0) + else: +Index: ../trunk-jpl/src/m/contrib/defleurian/netCDF/export_netCDF.py +=================================================================== +--- ../trunk-jpl/src/m/contrib/defleurian/netCDF/export_netCDF.py (revision 23210) ++++ ../trunk-jpl/src/m/contrib/defleurian/netCDF/export_netCDF.py (revision 23211) +@@ -17,7 +17,7 @@ + else: + print ('New file name is {}'.format(newname)) + filename=newname +- ++ + NCData=Dataset(filename, 'w', format='NETCDF4') + NCData.description = 'Results for run' + md.miscellaneous.name + NCData.history = 'Created ' + time.ctime(time.time()) +@@ -99,12 +99,12 @@ + Subgroup=NCgroup.createGroup(str(field)) + Subgroup.__setattr__('classtype',md.__dict__[group].__class__.__name__) + subfields=dict.keys(md.__dict__[group].__dict__[field].__dict__) +- ++ + for subfield in subfields: + if str(subfield)!='outlog': + Var=md.__dict__[group].__dict__[field].__dict__[subfield] + DimDict=CreateVar(NCData,Var,subfield,Subgroup,DimDict) +- ++ + NCData.close() + + #============================================================================ +@@ -129,11 +129,12 @@ + np.int64:'i8', + str:str, + dict:str} +- ++ + val_dim=np.shape(val_shape)[0] ++ + #Now define and fill up variable + #treating scalar string or bool as atribute +- if val_type==str or val_type==unicode or val_type==bool: ++ if val_type in [str,unicode,bool]: + Group.__setattr__(str(field).swapcase(), str(var)) + #treating list as string table + elif val_type==list: +@@ -146,7 +147,7 @@ + ncvar = Group.createVariable(str(field),nctype,dimensions,zlib=True) + if val_shape==0: + ncvar= [] +- else: ++ else: + for elt in range(0,val_shape[0]): + ncvar[elt] = var[elt] + #treating bool tables as string tables +@@ -163,7 +164,7 @@ + ncvar[elt,0]=dict.keys(var)[elt] + ncvar[elt,1]=str(dict.values(var)[elt]) #converting to str to avoid potential problems + #Now dealing with numeric variables +- else: ++ elif val_type in [float,'float64',np.float64,int,'int64']: + dimensions,DimDict=GetDim(NCData,var,val_shape,DimDict,val_dim) + ncvar = Group.createVariable(str(field),TypeDict[val_type],dimensions,zlib=True) + try: +@@ -174,6 +175,8 @@ + ncvar[:] = var + except TypeError: #type does not accept nan, get vallue of the variable + ncvar[:] = var ++ else: ++ print('WARNING type "{}" is unknown for "{}.{}"'.format(val_type,Group.name,field)) + return DimDict + + #============================================================================ Index: /issm/oecreview/Archive/23185-23389/ISSM-23211-23212.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23211-23212.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23211-23212.diff (revision 23390) @@ -0,0 +1,28 @@ +Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_schurcg.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_schurcg.cpp (revision 23211) ++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_schurcg.cpp (revision 23212) +@@ -88,7 +88,11 @@ + + /* Create KSP context */ + KSPCreate(IssmComm::GetComm(),&kspu); ++ #if (_PETSC_MAJOR_==3) && (_PETSC_MINOR_>=5) + KSPSetOperators(kspu,A,A); ++ #else ++ KSPSetOperators(kspu,A,A,DIFFERENT_NONZERO_PATTERN); ++ #endif + KSPSetType(kspu,KSPCG); + KSPSetInitialGuessNonzero(kspu,PETSC_TRUE); + //KSPSetTolerances(kspu,1e-12,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT); +@@ -119,7 +123,11 @@ + + /* Create KSP context */ + KSPCreate(IssmComm::GetComm(),&kspp); ++ #if (_PETSC_MAJOR_==3) && (_PETSC_MINOR_>=5) + KSPSetOperators(kspp,IP,IP); ++ #else ++ KSPSetOperators(kspp,IP,IP,DIFFERENT_NONZERO_PATTERN); ++ #endif + + /* Create RHS */ + /* RHS = BT * uold - F2 */ Index: /issm/oecreview/Archive/23185-23389/ISSM-23214-23215.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23214-23215.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23214-23215.diff (revision 23390) @@ -0,0 +1,37 @@ +Index: ../trunk-jpl/src/c/cores/adjointstressbalance_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/adjointstressbalance_core.cpp (revision 23214) ++++ ../trunk-jpl/src/c/cores/adjointstressbalance_core.cpp (revision 23215) +@@ -30,9 +30,20 @@ + + if(VerboseSolution()) _printf0_(" computing velocities\n"); + femmodel->SetCurrentConfiguration(StressbalanceAnalysisEnum); ++ ++ bool is_schur_cg_solver = false; ++ #ifdef _HAVE_PETSC_ ++ int solver_type; ++ PetscOptionsDetermineSolverType(&solver_type); ++ ++ if(solver_type==FSSolverEnum) is_schur_cg_solver = true; ++ #endif ++ + if(isFS){ + if (fe_FS==LATaylorHoodEnum || fe_FS==LACrouzeixRaviartEnum) + solutionsequence_la(femmodel); ++ else if(is_schur_cg_solver) ++ solutionsequence_schurcg(femmodel); + else + solutionsequence_nonlinear(femmodel,conserve_loads); + } +Index: ../trunk-jpl/src/c/cores/stressbalance_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/stressbalance_core.cpp (revision 23214) ++++ ../trunk-jpl/src/c/cores/stressbalance_core.cpp (revision 23215) +@@ -36,7 +36,6 @@ + if(numoutputs) femmodel->parameters->FindParam(&requested_outputs,&numoutputs,StressbalanceRequestedOutputsEnum); + + if(VerboseSolution()) _printf0_(" computing new velocity\n"); +- + /*Compute slopes if necessary */ + if(isSIA || (isFS && domaintype==Domain2DverticalEnum)) surfaceslope_core(femmodel); + if(isFS){ Index: /issm/oecreview/Archive/23185-23389/ISSM-23215-23216.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23215-23216.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23215-23216.diff (revision 23390) @@ -0,0 +1,917 @@ +Index: ../trunk-jpl/m4/issm_options.m4 +=================================================================== +--- ../trunk-jpl/m4/issm_options.m4 (revision 23215) ++++ ../trunk-jpl/m4/issm_options.m4 (revision 23216) +@@ -8,7 +8,7 @@ + + dnl ISSM's internal options + dnl Build info{{{ +- ++ + dnl build date + AC_PATH_PROGS(DATE, date) + AC_MSG_CHECKING(for build date) +@@ -152,7 +152,7 @@ + [WRAPPERS_VALUE="yes"]) dnl action if not given + AC_MSG_CHECKING(for wrappers compilation) + AM_CONDITIONAL([WRAPPERS], [test x$WRAPPERS_VALUE = xyes]) +- AC_MSG_RESULT($WRAPPERS_VALUE) ++ AC_MSG_RESULT($WRAPPERS_VALUE) + dnl }}} + dnl Extensions{{{ + ISSMEXT=".exe" +@@ -250,7 +250,7 @@ + AC_MSG_ERROR([unknown compiler vendor!]) + fi + fi +- AC_SUBST([OSLIBS]) ++ AC_SUBST([OSLIBS]) + AC_MSG_RESULT(done) + dnl }}} + dnl matlab{{{ +@@ -280,23 +280,23 @@ + if test "x$HAVE_MATLAB" = "xyes"; then + + AC_DEFINE([_HAVE_MATLAB_],[1],[with matlab in ISSM src]) +- ++ + dnl 4. get MEXLIB MEXLINK and MEXEXT (experimental) except for windows + AC_MSG_CHECKING([matlab's mex compilation flags]) + case "${host_os}" in +- *cygwin*) ++ *cygwin*) + if test $VENDOR = intel-win7-32; then +- MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" ++ MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" + MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win32/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" + MEXEXT=`$MATLAB_ROOT/bin/mexext.bat` + MEXEXT=".$MEXEXT" + elif test $VENDOR = intel-win7-64; then +- MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" +- MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" ++ MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" ++ MEXLINK="-Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" + MEXEXT=".mexw64" + elif test $VENDOR = MSVC-Win64 || test $VENDOR = MSVC-Win64-par; then +- MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" +- MEXLINK="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" ++ MEXLIB="-Wl,libmx.lib -Wl,libmex.lib -Wl,libmat.lib ${OSLIBS} -Wl,libf2cblas.lib -Wl,libf2clapack.lib" ++ MEXLINK="-Wl,/link -Wl,/LIBPATH:`cygpath -m ${MATLAB_ROOT}/extern/lib/win64/microsoft` -Wl,/link -Wl,/EXPORT:mexFunction -Wl,/DLL" + MATLABINCL="-I`cygpath -m $MATLAB_ROOT/extern/include/`" + MEXEXT=".mexw64" + fi +@@ -310,7 +310,7 @@ + if test "x$MEXEXT" = "x" ; then + echo "#include " > conftest.cpp + echo "void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]){}" >> conftest.cpp +- $MATLAB_ROOT/bin/mex -v -lmex conftest.cpp > conftest.tmp 2>&1 ++ $MATLAB_ROOT/bin/mex -v -lmex conftest.cpp > conftest.tmp 2>&1 + rm -f conftest.cpp + MEXLINK=$(cat conftest.tmp | grep LDFLAGS | sed -e "s/LDFLAGS ://g") + MEXLIB=$( cat conftest.tmp | grep LINKLIBS | sed -e "s/LINKLIBS ://g") +@@ -332,7 +332,7 @@ + AC_SUBST([MATLABINCL]) + MATLABWRAPPEREXT=$MEXEXT + AC_SUBST([MATLABWRAPPEREXT]) +- AC_SUBST([MEXLIB]) ++ AC_SUBST([MEXLIB]) + AC_SUBST([MEXLINK]) + fi + dnl }}} +@@ -344,7 +344,7 @@ + dnl javascript{{{ + AC_ARG_WITH([javascript], + AS_HELP_STRING([--with-javascript], [compile javascript wrappers? default is no.]), +- [JAVASCRIPT=$withval],[JAVASCRIPT="no"]) ++ [JAVASCRIPT=$withval],[JAVASCRIPT="no"]) + + dnl Check whether javascript wrappers are desired + AC_MSG_CHECKING([for javascript]) +@@ -363,7 +363,7 @@ + dnl triangle {{{ + AC_ARG_WITH([triangle-dir], + AS_HELP_STRING([--with-triangle-dir=DIR], [triangle root directory.]), +- [TRIANGLE_ROOT=$withval],[TRIANGLE_ROOT="no"]) ++ [TRIANGLE_ROOT=$withval],[TRIANGLE_ROOT="no"]) + + dnl Check whether triangle is enabled + AC_MSG_CHECKING([for triangle]) +@@ -393,7 +393,7 @@ + TRIANGLELIB=$TRIANGLE_ROOT/triangle.a + if test "x$HAVE_JAVASCRIPT" = "xyes"; then + dnl go to the bit code, not the library. +- TRIANGLELIB=$TRIANGLE_ROOT/triangle.o ++ TRIANGLELIB=$TRIANGLE_ROOT/triangle.o + else + TRIANGLELIB=$TRIANGLE_ROOT/triangle.a + fi +@@ -401,7 +401,7 @@ + *darwin*) + if test "x$HAVE_JAVASCRIPT" = "xyes"; then + dnl go to the bit code, not the library. +- TRIANGLELIB=$TRIANGLE_ROOT/triangle.o ++ TRIANGLELIB=$TRIANGLE_ROOT/triangle.o + else + TRIANGLELIB=$TRIANGLE_ROOT/triangle.a + fi +@@ -415,7 +415,7 @@ + dnl boost{{{ + AC_ARG_WITH([boost-dir], + AS_HELP_STRING([--with-boost-dir=DIR], [boost root directory.]), +- [BOOST_ROOT=$withval],[BOOST_ROOT="no"]) ++ [BOOST_ROOT=$withval],[BOOST_ROOT="no"]) + + dnl Check whether boost is enabled + AC_MSG_CHECKING([for boost]) +@@ -442,8 +442,8 @@ + dnl dakota{{{ + AC_ARG_WITH([dakota-dir], + AS_HELP_STRING([--with-dakota-dir=DIR], [dakota root directory.]), +- [DAKOTA_ROOT=$withval],[DAKOTA_ROOT="no"]) +- ++ [DAKOTA_ROOT=$withval],[DAKOTA_ROOT="no"]) ++ + dnl Check whether dakota is enabled + AC_MSG_CHECKING([for dakota]) + if test "x$DAKOTA_ROOT" = "xno" ; then +@@ -572,7 +572,7 @@ + dnl python{{{ + AC_ARG_WITH([python-dir], + AS_HELP_STRING([--with-python-dir=DIR], [python root directory.]), +- [PYTHON_ROOT=$withval],[PYTHON_ROOT="no"]) ++ [PYTHON_ROOT=$withval],[PYTHON_ROOT="no"]) + + dnl Check whether python is enabled + AC_MSG_CHECKING([for python]) +@@ -596,7 +596,7 @@ + PYTHON_VERSION=$($PYTHON_ROOT/bin/python -c "import sys; print sys.version[[:3]]") + AC_MSG_RESULT($PYTHON_VERSION) + +- dnl recover major ++ dnl recover major + PYTHON_MAJOR=${PYTHON_VERSION%.*} + AC_DEFINE_UNQUOTED([_PYTHON_MAJOR_],$PYTHON_MAJOR,[python version major]) + if test "x$PYTHON_MAJOR" = "x3"; then +@@ -642,8 +642,8 @@ + dnl python-numpy{{{ + AC_ARG_WITH([python-numpy-dir], + AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory.]), +- [PYTHON_NUMPY_ROOT=$withval],[PYTHON_NUMPY_ROOT="no"]) +- ++ [PYTHON_NUMPY_ROOT=$withval],[PYTHON_NUMPY_ROOT="no"]) ++ + dnl Check whether numpy is enabled + AC_MSG_CHECKING(for python-numpy) + if test "x$PYTHON_NUMPY_ROOT" = "xno" ; then +@@ -666,8 +666,8 @@ + dnl chaco{{{ + AC_ARG_WITH([chaco-dir], + AS_HELP_STRING([--with-chaco-dir=DIR], [chaco root directory.]), +- [CHACO_ROOT=$withval],[CHACO_ROOT="no"]) +- ++ [CHACO_ROOT=$withval],[CHACO_ROOT="no"]) ++ + dnl Check whether chaco is enabled + AC_MSG_CHECKING([for chaco]) + if test "x$CHACO_ROOT" = "xno" ; then +@@ -693,7 +693,7 @@ + dnl scotch{{{ + AC_ARG_WITH([scotch-dir], + AS_HELP_STRING([--with-scotch-dir=DIR], [scotch root directory.]), +- [SCOTCH_ROOT=$withval],[SCOTCH_ROOT="no"]) ++ [SCOTCH_ROOT=$withval],[SCOTCH_ROOT="no"]) + + dnl Check whether scotch is enabled + AC_MSG_CHECKING([for scotch]) +@@ -707,7 +707,7 @@ + fi + AC_MSG_RESULT($HAVE_SCOTCH) + AM_CONDITIONAL([SCOTCH],[test x$HAVE_SCOTCH = xyes]) +- ++ + dnl scotch libraries + if test "x$HAVE_SCOTCH" = "xyes"; then + SCOTCHINCL="-DNOFILEIO -I$SCOTCH_ROOT/include -DSCOTCH_VERSION=\\\"UNKNOWN\\\"" +@@ -720,7 +720,7 @@ + dnl esmf{{{ + AC_ARG_WITH([esmf-dir], + AS_HELP_STRING([--with-esmf-dir=DIR], [esmf root directory.]), +- [ESMF_ROOT=$withval],[ESMF_ROOT="no"]) ++ [ESMF_ROOT=$withval],[ESMF_ROOT="no"]) + + dnl Check whether esmf is enabled + AC_MSG_CHECKING([for esmf]) +@@ -733,7 +733,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_ESMF) +- ++ + dnl esmf headers and libraries + if test "x$HAVE_ESMF" == "xyes"; then + ESMFINCL="-I$ESMF_ROOT/include" +@@ -747,7 +747,7 @@ + dnl adolc{{{ + AC_ARG_WITH([adolc-dir], + AS_HELP_STRING([--with-adolc-dir=DIR], [adolc root directory.]), +- [ADOLC_ROOT=$withval],[ADOLC_ROOT="no"]) ++ [ADOLC_ROOT=$withval],[ADOLC_ROOT="no"]) + + dnl Check whether adolc is enabled + AC_MSG_CHECKING([for adolc]) +@@ -760,7 +760,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_ADOLC) +- ++ + dnl adolc headers and libraries + if test "x$HAVE_ADOLC" == "xyes"; then + ADOLCINCL="-I$ADOLC_ROOT/include" +@@ -777,8 +777,8 @@ + dnl adolc-version{{{ + AC_ARG_WITH([adolc-version], + AS_HELP_STRING([--with-adolc-version=number], [adolc version.]), +- [ADOLC_VERSION=$withval],[ADOLC_VERSION=2]) +- AC_MSG_CHECKING(for adolc-version) ++ [ADOLC_VERSION=$withval],[ADOLC_VERSION=2]) ++ AC_MSG_CHECKING(for adolc-version) + + AC_DEFINE_UNQUOTED([_ADOLC_VERSION_],$ADOLC_VERSION,[ADOLC version]) + AC_MSG_RESULT($ADOLC_VERSION) +@@ -786,7 +786,7 @@ + dnl adic2{{{ + AC_ARG_WITH([adic2-dir], + AS_HELP_STRING([--with-adic2-dir=DIR], [adic2 root directory.]), +- [ADIC2_ROOT=$withval],[ADIC2_ROOT="no"]) ++ [ADIC2_ROOT=$withval],[ADIC2_ROOT="no"]) + + dnl Check whether adic2 is enabled + AC_MSG_CHECKING([for adic2]) +@@ -814,7 +814,7 @@ + AC_ARG_WITH([atlas-dir], + AS_HELP_STRING([--with-atlas-dir=DIR],[atlas root directory]), + [ATLAS_ROOT=$withval],[ATLAS_ROOT="no"]) +- ++ + dnl Check whether atlas is enabled + AC_MSG_CHECKING(for atlas and cblas libraries) + if test "x$ATLAS_ROOT" = "xno" ; then +@@ -835,10 +835,10 @@ + ATLASLIB="-L`cygpath -m $ATLAS_ROOT` -Wl,libatlas.lib -Wl,libcblas.lib" + ;; + *linux*) +- ATLASLIB=-L"$ATLAS_ROOT/lib -lcblas -latlas -lm " ++ ATLASLIB=-L"$ATLAS_ROOT/lib -lcblas -latlas -lm " + ;; + *darwin*) +- ATLASLIB=-L"$ATLAS_ROOT/lib -lcblas -latlas -lm" ++ ATLASLIB=-L"$ATLAS_ROOT/lib -lcblas -latlas -lm" + ;; + esac + AC_DEFINE([_HAVE_ATLAS_],[1],[with ATLAS in ISSM src]) +@@ -848,7 +848,7 @@ + dnl gsl{{{ + AC_ARG_WITH([gsl-dir], + AS_HELP_STRING([--with-gsl-dir=DIR], [gsl root directory.]), +- [GSL_ROOT=$withval],[GSL_ROOT="no"]) ++ [GSL_ROOT=$withval],[GSL_ROOT="no"]) + + dnl Check whether gsl is enabled + AC_MSG_CHECKING([for gsl]) +@@ -861,7 +861,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_GSL) +- ++ + dnl gsl headers and libraries + if test "x$HAVE_GSL" == "xyes"; then + GSLINCL="-I$GSL_ROOT/include" +@@ -879,7 +879,7 @@ + dnl adjoinable-mpi{{{ + AC_ARG_WITH([ampi-dir], + AS_HELP_STRING([--with-ampi-dir=DIR], [adjoinable mpi root directory.]), +- [AMPI_ROOT=$withval],[AMPI_ROOT="no"]) ++ [AMPI_ROOT=$withval],[AMPI_ROOT="no"]) + + dnl Check whether ampi is enabled + AC_MSG_CHECKING([for ampi]) +@@ -892,7 +892,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_AMPI) +- ++ + dnl ampi headers and libraries + if test "x$HAVE_AMPI" == "xyes"; then + AMPIINCL="-I$AMPI_ROOT/include" +@@ -914,7 +914,7 @@ + dnl rose{{{ + AC_ARG_WITH([rose-dir], + AS_HELP_STRING([--with-rose-dir=DIR], [rose root directory.]), +- [ROSE_ROOT=$withval],[ROSE_ROOT="no"]) ++ [ROSE_ROOT=$withval],[ROSE_ROOT="no"]) + + dnl Check whether rose is enabled + AC_MSG_CHECKING([for rose]) +@@ -940,7 +940,7 @@ + dnl }}} + dnl mpi{{{ + AC_MSG_CHECKING(for mpi) +- ++ + AC_ARG_WITH([mpi-include], + AS_HELP_STRING([--with-mpi-include=DIR],[mpi include directory, necessary for parallel build]), + [MPI_INCLUDE=$withval],[MPI_INCLUDE=""]) +@@ -953,7 +953,7 @@ + AS_HELP_STRING([--with-mpi-libflags=LIBS],[mpi libraries to be used, necessary for parallel build]), + [MPI_LIBFLAGS=$withval],[MPI_LIBFLAGS=""]) + +- ++ + if test -z "$MPI_INCLUDE" ; then + HAVE_MPI=no + else +@@ -979,7 +979,7 @@ + + if test x$IS_WINDOWS = xyes; then + MPIINCL=/I"$MPI_INCLUDE" +- else ++ else + MPIINCL=-I"$MPI_INCLUDE" + fi + +@@ -995,7 +995,7 @@ + AC_ARG_WITH([petsc-dir], + AS_HELP_STRING([--with-petsc-dir=DIR],[PETSc root directory, necessary for parallel build]), + [PETSC_ROOT=$withval],[PETSC_ROOT="no"]) +- ++ + dnl Check whether petsc is enabled + AC_MSG_CHECKING([for petsc]) + if test "x$PETSC_ROOT" = "xno" ; then +@@ -1032,7 +1032,7 @@ + else + AC_MSG_RESULT(no) + fi +- ++ + AC_ARG_WITH([petsc-arch], + AS_HELP_STRING([--with-petsc-arch=DIR],[PETSc arch, necessary for PETSc < 3.0]), + [PETSC_ARCH=$withval],[PETSC_ARCH=""]) +@@ -1049,7 +1049,7 @@ + if test "x$PETSC_ARCH" != "x" && test -d "$PETSC_ROOT/include/$PETSC_ARCH"; then + PETSCINCL+=" $PETSC_ROOT/include/$PETSC_ARCH" + fi +- ++ + case "${host_os}" in + *cygwin*) + if test $PETSC_MAJOR -lt 3 ; then +@@ -1068,7 +1068,7 @@ + fi + if test "x$host_os_version" = "x3.0.101-0.31.1_1.0502.8394-cray_gem_s" ; then + PETSCLIB="-L$PETSC_ROOT/lib -lcraypetsc_gnu_real -lmetis" +- fi ++ fi + ;; + *darwin*) + if test $PETSC_MAJOR -lt 3 ; then +@@ -1121,10 +1121,10 @@ + fi + + if test "$METIS_VERSION" = "4" ; then +- METISINCL=-I"$METIS_ROOT/Lib" ++ METISINCL=-I"$METIS_ROOT/Lib" + case "${host_os}" in + *cygwin*) +- METISINCL="/I`cygpath -m $METIS_ROOT/Lib`" ++ METISINCL="/I`cygpath -m $METIS_ROOT/Lib`" + METISLIB="-Wl,/link -Wl,/LIBPATH:`cygpath -m $METIS_ROOT` -Wl,libmetis.lib" + ;; + *linux*) +@@ -1149,7 +1149,7 @@ + METISLIB=-L"$METIS_ROOT/lib -lmetis" + ;; + esac +- METISINCL=-I"$METIS_ROOT/include" ++ METISINCL=-I"$METIS_ROOT/include" + AC_DEFINE([_METIS_VERSION_],[5],[ Metis version number]) + fi + +@@ -1163,7 +1163,7 @@ + dnl tao{{{ + AC_ARG_WITH([tao-dir], + AS_HELP_STRING([--with-tao-dir=DIR], [tao root directory.]), +- [TAO_ROOT=$withval],[TAO_ROOT="no"]) ++ [TAO_ROOT=$withval],[TAO_ROOT="no"]) + + dnl Check whether tao is enabled + AC_MSG_CHECKING([for tao]) +@@ -1198,7 +1198,7 @@ + dnl m1qn3{{{ + AC_ARG_WITH([m1qn3-dir], + AS_HELP_STRING([--with-m1qn3-dir=DIR], [m1qn3 root directory.]), +- [M1QN3_ROOT=$withval],[M1QN3_ROOT="no"]) ++ [M1QN3_ROOT=$withval],[M1QN3_ROOT="no"]) + + dnl Check whether m1qn3 is enabled + AC_MSG_CHECKING([for m1qn3]) +@@ -1211,10 +1211,10 @@ + fi + fi + AC_MSG_RESULT($HAVE_M1QN3) +- ++ + dnl m1qn3 headers and libraries + if test "x$HAVE_M1QN3" == "xyes"; then +- M1QN3LIB="$M1QN3_ROOT/libm1qn3.a $M1QN3_ROOT//libddot.a" ++ M1QN3LIB="$M1QN3_ROOT/libm1qn3.a $M1QN3_ROOT/libddot.a" + AC_DEFINE([_HAVE_M1QN3_],[1],[with M1QN3 in ISSM src]) + AC_SUBST([M1QN3LIB]) + fi +@@ -1222,7 +1222,7 @@ + dnl proj.4{{{ + AC_ARG_WITH([proj4-dir], + AS_HELP_STRING([--with-proj4-dir=DIR], [proj4 root directory.]), +- [PROJ4_ROOT=$withval],[PROJ4_ROOT="no"]) ++ [PROJ4_ROOT=$withval],[PROJ4_ROOT="no"]) + + dnl Check whether proj4 is enabled + AC_MSG_CHECKING([for proj.4]) +@@ -1235,7 +1235,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_PROJ4) +- ++ + dnl proj4 headers and libraries + if test "x$HAVE_PROJ4" == "xyes"; then + PROJ4INCL="-I$PROJ4_ROOT/include " +@@ -1250,7 +1250,7 @@ + AC_ARG_WITH([slepc-dir], + AS_HELP_STRING([--with-slepc-dir=DIR],[slepc root directory]), + [SLEPC_ROOT=$withval],[SLEPC_ROOT="no"]) +- ++ + dnl Check whether slepc is enabled + AC_MSG_CHECKING([for slepc]) + if test "x$SLEPC_ROOT" = "xno" ; then +@@ -1262,7 +1262,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_SLEPC) +- ++ + dnl slepc headers and libraries + if test "x$HAVE_SLEPC" == "xyes"; then + SLEPCINCL=-I"$SLEPC_ROOT/include" +@@ -1276,7 +1276,7 @@ + AC_ARG_WITH([shapelib-dir], + AS_HELP_STRING([--with-shapelib-dir=DIR], [shapelib root directory]), + [SHAPELIB_ROOT=$withval],[SHAPELIB_ROOT="no"]) +- ++ + dnl Check whether shapelib is enabled + AC_MSG_CHECKING([for shapelib]) + if test "x$SHAPELIB_ROOT" = "xno" ; then +@@ -1288,7 +1288,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_SHAPELIB) +- ++ + dnl shapelib headers and libraries + if test "x$HAVE_SHAPELIB" == "xyes"; then + SHAPELIBINCL=-I"$SHAPELIB_ROOT/include" +@@ -1308,7 +1308,7 @@ + AC_ARG_WITH([scalapack-lib], + AS_HELP_STRING([--with-scalapack-lib=LIBS],[scalapack libraries to include]), + [SCALAPACKLIB=$withval],[SCALAPACKLIB="no"]) +- ++ + dnl Check whether scalapack is enabled + AC_MSG_CHECKING([for scalapack]) + if test "x$SCALAPACK_ROOT" = "xno" && test "x$SCALAPACKLIB" = "xno"; then +@@ -1328,7 +1328,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_SCALAPACK) +- ++ + dnl scalapack headers and libraries + if test "x$HAVE_SCALAPACK" = "xyes"; then + AC_DEFINE([_HAVE_SCALAPACK_],[1],[with Scalapack in ISSM src]) +@@ -1339,7 +1339,7 @@ + AC_ARG_WITH([blas-lapack-dir], + AS_HELP_STRING([--with-blas-lapack-dir=DIR],[blas-lapack root directory]), + [BLASLAPACK_ROOT=$withval],[BLASLAPACK_ROOT="no"]) +- ++ + dnl Check whether blas-lapack is enabled + AC_MSG_CHECKING([for blas-lapack]) + if test "x$BLASLAPACK_ROOT" = "xno" ; then +@@ -1351,7 +1351,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_BLASLAPACK) +- ++ + dnl blas-lapack headers and libraries + if test "x$HAVE_BLASLAPACK" == "xyes"; then + BLASLAPACKINCL="" +@@ -1361,10 +1361,10 @@ + BLASLAPACKLIB="-L`cygpath -m $BLASLAPACK_ROOT` -Wl,libf2cblas.lib -Wl,libf2clapack.lib" + ;; + *linux*) +- BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " ++ BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " + ;; + *darwin*) +- BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " ++ BLASLAPACKLIB=-L"$BLASLAPACK_ROOT/lib -lflapack -lfblas " + ;; + esac + AC_DEFINE([_HAVE_BLASLAPACK_],[1],[with blas lapack in ISSM src]) +@@ -1392,19 +1392,19 @@ + dnl }}} + dnl plapack{{{ + AC_MSG_CHECKING(for plapack) +- ++ + AC_ARG_WITH([plapack-lib], + AS_HELP_STRING([--with-plapack-lib = lib],[plapack library]), + [PLAPACK_LIB=$withval],[PLAPACK_LIB=""]) +- ++ + AC_ARG_WITH([plapack-include], + AS_HELP_STRING([--with-plapack-include = include], + [plapack include ]), + [PLAPACK_INCLUDE=$withval],[PLAPACK_INCLUDE=""]) +- ++ + if test -n "$PLAPACK_LIB"; then + if test -n "$PLAPACK_INCLUDE"; then +- ++ + HAVE_PLAPACK=yes + PLAPACKINCL="$PLAPACK_INCLUDE" + PLAPACKLIB="$PLAPACK_LIB" +@@ -1423,7 +1423,7 @@ + AC_ARG_WITH([mumps-dir], + AS_HELP_STRING([--with-mumps-dir=DIR],[mumps root directory]), + [MUMPS_ROOT=$withval],[MUMPS_ROOT="no"]) +- ++ + dnl Check whether mumps is enabled + AC_MSG_CHECKING([for mumps]) + if test "x$MUMPS_ROOT" = "xno" ; then +@@ -1435,7 +1435,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_MUMPS) +- ++ + dnl mumps headers and libraries + if test "x$HAVE_MUMPS" == "xyes"; then + MUMPSINCL=-I"$MUMPS_ROOT/include" +@@ -1454,7 +1454,7 @@ + dnl mumps2{{{ + if test "x$HAVE_MUMPS" != "xyes"; then + AC_MSG_CHECKING(for mumps2 (stand alone)) +- ++ + AC_ARG_WITH([mumps2-include], + AS_HELP_STRING([--with-mumps2-include=DIR],[mumps2 include directory, necessary for parallel build]), + [MUMPS_INCLUDE=$withval],[MUMPS_INCLUDE=""]) +@@ -1463,7 +1463,7 @@ + AS_HELP_STRING([--with-mumps2-libflags=LIBS],[mumps2 libraries to be used, necessary for parallel build]), + [MUMPS_LIBFLAGS=$withval],[MUMPS_LIBFLAGS=""]) + +- ++ + if test -z "$MUMPS_INCLUDE" ; then + HAVE_MUMPS=no + else +@@ -1489,7 +1489,7 @@ + AC_ARG_WITH([blacs-dir], + AS_HELP_STRING([--with-blacs-dir=DIR],[blacs root directory]), + [BLACS_ROOT=$withval],[BLACS_ROOT="no"]) +- ++ + dnl Check whether blacs is enabled + AC_MSG_CHECKING([for blacs]) + if test "x$BLACS_ROOT" = "xno" ; then +@@ -1501,7 +1501,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_BLACS) +- ++ + dnl blacs headers and libraries + if test "x$HAVE_BLACS" == "xyes"; then + BLACSINCL="" +@@ -1515,7 +1515,7 @@ + AC_ARG_WITH([hypre-dir], + AS_HELP_STRING([--with-hypre-dir=DIR],[hypre root directory]), + [HYPRE_ROOT=$withval],[HYPRE_ROOT="no"]) +- ++ + dnl Check whether hypre is enabled + AC_MSG_CHECKING([for hypre]) + if test "x$HYPRE_ROOT" = "xno" ; then +@@ -1589,7 +1589,7 @@ + AC_SUBST([SPAILIB]) + fi + dnl }}} +-dnl superlu{{{ ++dnl superlu{{{ + AC_ARG_WITH([superlu-dir], + AS_HELP_STRING([--with-superlu-dir=DIR],[superlu root directory]), + [SUPERLU_ROOT=$withval],[SUPERLU_ROOT="no"]) +@@ -1605,7 +1605,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_SUPERLU) +- ++ + dnl superlu headers and libraries + if test "x$HAVE_SUPERLU" == "xyes"; then + SUPERLUINCL=-I"$SUPERLU_ROOT/include" +@@ -1615,7 +1615,7 @@ + AC_SUBST([SUPERLULIB]) + fi + dnl }}} +-dnl spooles{{{ ++dnl spooles{{{ + AC_ARG_WITH([spooles-dir], + AS_HELP_STRING([--with-spooles-dir=DIR],[spooles root directory]), + [SPOOLES_ROOT=$withval],[SPOOLES_ROOT="no"]) +@@ -1631,7 +1631,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_SPOOLES) +- ++ + dnl spooles headers and libraries + if test "x$HAVE_SPOOLES" == "xyes"; then + SPOOLESINCL=-I"$SPOOLES_ROOT/include" +@@ -1641,7 +1641,7 @@ + AC_SUBST([SPOOLESLIB]) + fi + dnl }}} +-dnl pastix{{{ ++dnl pastix{{{ + AC_ARG_WITH([pastix-dir], + AS_HELP_STRING([--with-pastix-dir=DIR],[pastix root directory]), + [PASTIX_ROOT=$withval],[PASTIX_ROOT="no"]) +@@ -1657,7 +1657,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_PASTIX) +- ++ + dnl pastix headers and libraries + if test "x$HAVE_PASTIX" == "xyes"; then + PASTIXINCL=-I"$PASTIX_ROOT/include" +@@ -1671,7 +1671,7 @@ + AC_ARG_WITH([ml-dir], + AS_HELP_STRING([--with-ml-dir=DIR],[ml root directory]), + [ML_ROOT=$withval],[ML_ROOT="no"]) +- ++ + dnl Check whether ml is enabled + AC_MSG_CHECKING([for ml]) + if test "x$ML_ROOT" = "xno" ; then +@@ -1683,7 +1683,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_ML) +- ++ + dnl ml headers and libraries + if test "x$HAVE_ML" == "xyes"; then + MLINCL=-I"$ML_ROOT/include" +@@ -1697,7 +1697,7 @@ + AC_ARG_WITH([umfpack-dir], + AS_HELP_STRING([--with-umfpack-dir=DIR],[UMFPACK root directory]), + [UMFPACK_ROOT=$withval],[UMFPACK_ROOT="no"]) +- ++ + dnl Check whether umfpack is enabled + AC_MSG_CHECKING([for umfpack]) + if test "x$UMFPACK_ROOT" = "xno" ; then +@@ -1709,7 +1709,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_UMFPACK) +- ++ + dnl umfpack headers and libraries + if test "x$HAVE_UMFPACK" == "xyes"; then + UMFPACKINCL="" +@@ -1737,8 +1737,8 @@ + dnl math77{{{ + AC_ARG_WITH([math77-dir], + AS_HELP_STRING([--with-math77-dir=DIR], [math77 root directory.]), +- [MATH77_ROOT=$withval],[MATH77_ROOT="no"]) +- ++ [MATH77_ROOT=$withval],[MATH77_ROOT="no"]) ++ + dnl Check whether math77 is enabled + AC_MSG_CHECKING([for math77]) + if test "x$MATH77_ROOT" = "xno" ; then +@@ -1750,7 +1750,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_MATH77) +- ++ + dnl math77 headers and libraries + if test "x$HAVE_MATH77" == "xyes"; then + MATH77LIB="-L$MATH77_ROOT/ -lmath77" +@@ -1761,7 +1761,7 @@ + dnl fortran{{{ + AC_ARG_WITH([fortran], + AS_HELP_STRING([--with-fortran = YES], [do we compile fortran code (default is yes)]), +- [FORTRAN=$withval],[FORTRAN=yes]) ++ [FORTRAN=$withval],[FORTRAN=yes]) + AC_MSG_CHECKING(for fortran compilation) + if test "x$FORTRAN" = "xyes"; then + dnl defaults +@@ -1829,7 +1829,7 @@ + dnl meteoio{{{ + AC_ARG_WITH([meteoio-dir], + AS_HELP_STRING([--with-meteoio-dir=DIR], [use meteoio in conjunction with snowpack model.]), +- [METEOIO_ROOT=$withval],[METEOIO_ROOT="no"]) ++ [METEOIO_ROOT=$withval],[METEOIO_ROOT="no"]) + + dnl Check whether meteoio is enabled + AC_MSG_CHECKING([for meteoio]) +@@ -1842,7 +1842,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_METEOIO) +- ++ + dnl meteoio headers and libraries + if test "x$HAVE_METEOIO" == "xyes"; then + METEOIOINCL="-I$METEOIO_ROOT/include" +@@ -1857,7 +1857,7 @@ + dnl snowpack{{{ + AC_ARG_WITH([snowpack-dir], + AS_HELP_STRING([--with-snowpack-dir=DIR], [use snowpack for surface mass balance model.]), +- [SNOWPACK_ROOT=$withval],[SNOWPACK_ROOT="no"]) ++ [SNOWPACK_ROOT=$withval],[SNOWPACK_ROOT="no"]) + + dnl Check whether snowpack is enabled + AC_MSG_CHECKING([for snowpack]) +@@ -1870,7 +1870,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_SNOWPACK) +- ++ + dnl snowpack headers and libraries + if test "x$HAVE_SNOWPACK" == "xyes"; then + SNOWPACKINCL="-I$SNOWPACK_ROOT/include" +@@ -1885,7 +1885,7 @@ + dnl neopz{{{ + AC_ARG_WITH([neopz-dir], + AS_HELP_STRING([--with-neopz-dir=DIR], [neopz root directory.]), +- [NEOPZ_ROOT=$withval],[NEOPZ_ROOT="no"]) ++ [NEOPZ_ROOT=$withval],[NEOPZ_ROOT="no"]) + + dnl Check whether neopz is enabled + AC_MSG_CHECKING([for neopz]) +@@ -1898,7 +1898,7 @@ + fi + fi + AC_MSG_RESULT($HAVE_NEOPZ) +- ++ + dnl neopz headers and libraries + if test "x$HAVE_NEOPZ" == "xyes"; then + NEOPZLIB="$NEOPZ_ROOT/lib/libpz.a" +@@ -1937,7 +1937,7 @@ + dnl with-bamg{{{ + AC_ARG_WITH([bamg], + AS_HELP_STRING([--with-bamg = YES],[compile with bamg capabilities (default is yes)]), +- [BAMG=$withval],[BAMG=yes]) ++ [BAMG=$withval],[BAMG=yes]) + AC_MSG_CHECKING(for bamg capability compilation) + + HAVE_BAMG=no +@@ -1951,7 +1951,7 @@ + dnl with-ocean{{{ + AC_ARG_WITH([ocean], + AS_HELP_STRING([--with-ocean = YES],[compile with ice/ocean coupling (default is no)]), +- [OCEAN=$withval],[OCEAN=no]) ++ [OCEAN=$withval],[OCEAN=no]) + AC_MSG_CHECKING(for ice/ocean capability compilation) + + HAVE_OCEAN=no +@@ -1965,7 +1965,7 @@ + dnl with-kml{{{ + AC_ARG_WITH([kml], + AS_HELP_STRING([--with-kml = YES],[compile with kml capabilities (default is no)]), +- [KML=$withval],[KML=no]) ++ [KML=$withval],[KML=no]) + AC_MSG_CHECKING(for kml capability compilation) + + HAVE_KML=no +@@ -1979,7 +1979,7 @@ + dnl with-kriging{{{ + AC_ARG_WITH([kriging], + AS_HELP_STRING([--with-kriging = YES],[compile with kriging capabilities (default is yes)]), +- [KRIGING=$withval],[KRIGING=yes]) ++ [KRIGING=$withval],[KRIGING=yes]) + AC_MSG_CHECKING(for kriging capability compilation) + + HAVE_KRIGING=no +@@ -1996,7 +1996,7 @@ + dnl with-ios{{{ + AC_ARG_WITH([ios], + AS_HELP_STRING([--with-ios = YES], [compile with iOS capabilities (default is no, alternatives are yes)]), +- [IOS=$withval],[IOS=no]) ++ [IOS=$withval],[IOS=no]) + AC_MSG_CHECKING(for iOS compilation) + + if test "x$IOS" = "xyes"; then +@@ -2015,7 +2015,7 @@ + dnl with-android{{{ + AC_ARG_WITH([android], + AS_HELP_STRING([--with-android = EXE], [compile with android capabilities (default is no, alternatives are exe and jni)]), +- [ANDROID=$withval],[ANDROID=no]) ++ [ANDROID=$withval],[ANDROID=no]) + AC_MSG_CHECKING(for android capability compilation) + + if test "x$ANDROID" = "xjni"; then +@@ -2042,9 +2042,9 @@ + dnl with-android-ndk{{{ + AC_ARG_WITH([android-ndk], + AS_HELP_STRING([--with-android-ndk=DIR], [android-ndk root directory.]), +- [ANDROID_NDK_ROOT=$withval],[ANDROID_NDK_ROOT=""]) ++ [ANDROID_NDK_ROOT=$withval],[ANDROID_NDK_ROOT=""]) + AC_MSG_CHECKING(with android ndk) +- ++ + if test -d "$ANDROID_NDK_ROOT"; then + dnl defaults + HAVE_ANDROID_NDK=yes +@@ -2060,10 +2060,10 @@ + + dnl other options + dnl optimization{{{ +- dnl bypass standard optimization -g -O2 ? ++ dnl bypass standard optimization -g -O2 ? + AC_ARG_WITH([cxxoptflags], + AS_HELP_STRING([--with-cxxoptflags = CXXOPTFLAGS], [optimization using CXX flags, ex: --with-cxxoptflags=-march=opteron -O3]), +- [CXXOPTFLAGS=$withval],[CXXOPTFLAGS="-g -O2 -fPIC"]) ++ [CXXOPTFLAGS=$withval],[CXXOPTFLAGS="-g -O2 -fPIC"]) + AC_MSG_CHECKING(for c++ optimization flags) + AC_SUBST([CXXOPTFLAGS]) + AC_MSG_RESULT(done) +@@ -2078,7 +2078,7 @@ + MULTITHREADING=no + MULTITHREADINLIB="" + if test "$NUMTHREADS_VALUE" != "1"; then +- ++ + MULTITHREADINGLIB="-lpthread -lrt" + case "${host_os}" in + *cygwin*) +@@ -2095,12 +2095,12 @@ + fi + AC_DEFINE_UNQUOTED([_NUMTHREADS_],[$NUMTHREADS_VALUE],[number of threads]) + AC_SUBST([MULTITHREADINGLIB]) +- AC_MSG_RESULT($NUMTHREADS_VALUE) ++ AC_MSG_RESULT($NUMTHREADS_VALUE) + dnl }}} + dnl 64bit {{{ + AC_ARG_WITH([64bit-indices], + AS_HELP_STRING([--with-64bit-indices = bool], [use 64 bit integers, default 0, ex: --with-64bit-indices=1]), +- [USE_64BIT_INDICES=$withval],[USE_64BIT_INDICES=0]) ++ [USE_64BIT_INDICES=$withval],[USE_64BIT_INDICES=0]) + AC_MSG_CHECKING(for 64 bit indices) + + if test "$USE_64BIT_INDICES" == "1"; then +@@ -2131,7 +2131,7 @@ + if test "$HAVE_GIAIVINS" = "yes" && test "$HAVE_FORTRAN" = "no" ; then + AC_MSG_ERROR([need fortran compiler to compile GiaIvins (or use --without-GiaIvins )]); + fi +- ++ + dnl check that fortran is provided if Love is on + if test "$HAVE_LOVE" = "yes" && test "$HAVE_FORTRAN" = "no" ; then + AC_MSG_ERROR([need fortran compiler to compile Love (or use --without-Love)]); +@@ -2141,7 +2141,7 @@ + if test "$HAVE_METIS" = "yes" && test "$HAVE_MPI" = "no" ; then + AC_MSG_ERROR([need mpi if using the metis partitioner!]); + fi +- ++ + dnl check that if we run adolc, we don't compile krigging.exe + if test "$HAVE_ADOLC" = "yes" && test "$HAVE_KRIGING" = "yes" ; then + AC_MSG_ERROR([cannot compile kriging.exe under adolc conditions!]); Index: /issm/oecreview/Archive/23185-23389/ISSM-23216-23217.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23216-23217.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23216-23217.diff (revision 23390) @@ -0,0 +1,37 @@ +Index: ../trunk-jpl/src/c/cores/control_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/control_core.cpp (revision 23216) ++++ ../trunk-jpl/src/c/cores/control_core.cpp (revision 23217) +@@ -142,7 +142,8 @@ + + /*Update control input*/ + SetControlInputsFromVectorx(femmodel,X); +- ++ ++ + /*solve forward: */ + switch(solution_type){ + case SteadystateSolutionEnum: +@@ -151,8 +152,20 @@ + break; + case StressbalanceSolutionEnum: + femmodel->SetCurrentConfiguration(StressbalanceAnalysisEnum); +- solutionsequence_nonlinear(femmodel,conserve_loads); +- break; ++ ++ bool is_schur_cg_solver = false; ++ #ifdef _HAVE_PETSC_ ++ int solver_type; ++ PetscOptionsDetermineSolverType(&solver_type); ++ if(solver_type==FSSolverEnum) is_schur_cg_solver = true; ++ #endif ++ ++ if(is_schur_cg_solver){ ++ solutionsequence_schurcg(femmodel); ++ }else{ ++ solutionsequence_nonlinear(femmodel,conserve_loads); ++ } ++ break; + case BalancethicknessSolutionEnum: + femmodel->SetCurrentConfiguration(BalancethicknessAnalysisEnum); + solutionsequence_linear(femmodel); Index: /issm/oecreview/Archive/23185-23389/ISSM-23217-23218.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23217-23218.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23217-23218.diff (revision 23390) @@ -0,0 +1,21 @@ +Index: ../trunk-jpl/src/c/cores/control_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/control_core.cpp (revision 23217) ++++ ../trunk-jpl/src/c/cores/control_core.cpp (revision 23218) +@@ -150,7 +150,7 @@ + femmodel->SetCurrentConfiguration(StressbalanceAnalysisEnum); + stressbalance_core(femmodel); //We need a 3D velocity!! (vz is required for the next thermal run) + break; +- case StressbalanceSolutionEnum: ++ case StressbalanceSolutionEnum:{ + femmodel->SetCurrentConfiguration(StressbalanceAnalysisEnum); + + bool is_schur_cg_solver = false; +@@ -165,6 +165,7 @@ + }else{ + solutionsequence_nonlinear(femmodel,conserve_loads); + } ++ } + break; + case BalancethicknessSolutionEnum: + femmodel->SetCurrentConfiguration(BalancethicknessAnalysisEnum); Index: /issm/oecreview/Archive/23185-23389/ISSM-23218-23219.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23218-23219.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23218-23219.diff (revision 23390) @@ -0,0 +1,42 @@ +Index: ../trunk-jpl/etc/environment.sh +=================================================================== +--- ../trunk-jpl/etc/environment.sh (revision 23218) ++++ ../trunk-jpl/etc/environment.sh (revision 23219) +@@ -74,20 +74,12 @@ + libpathappend "$GMT_DIR/lib" + fi + +-#legacy mpich2 (To be removed) +-MPI_DIR="$ISSM_DIR/externalpackages/mpich2/install" +-if [ -d "$MPI_DIR" ]; then +- export MPI_DIR +- pathprepend "$MPI_DIR/bin" +- libpathappend "$MPI_DIR/lib" +-fi +- + MPI_DIR="$ISSM_DIR/externalpackages/mpich/install" + if [ -d "$MPI_DIR" ]; then + export MPI_DIR + export MPI_INC_DIR="$MPI_DIR/include" +- pathprepend "$MPI_DIR/bin" +- libpathappend "$MPI_DIR/lib" ++ pathprepend "$MPI_DIR/bin" ++ libpathprepend "$MPI_DIR/lib" + fi + + PETSC_DIR="$ISSM_DIR/externalpackages/petsc/install" +@@ -233,14 +225,6 @@ + GMAKE_DIR="$ISSM_DIR/externalpackages/gmake/install" + pathprepend "$GMAKE_DIR/bin" + +-PYTHON_DIR="$ISSM_DIR/externalpackages/python/install" +-if [ -d "$PYTHON_DIR" ]; then +- export PYTHONPATH="$PYTHONPATH:$ISSM_DIR/lib" +- pathprepend "$PYTHON_DIR/bin" +- libpathprepend "$PYTHON_DIR/lib" +- libpathprepend "$ISSM_DIR/lib" +-fi +- + MODELE_DIR="$ISSM_DIR/externalpackages/modelE/install" + pathappend "$MODELE_DIR/src/exec" + Index: /issm/oecreview/Archive/23185-23389/ISSM-23219-23220.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23219-23220.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23219-23220.diff (revision 23390) @@ -0,0 +1,47 @@ +Index: ../trunk-jpl/src/c/solutionsequences/solutionsequence_schurcg.cpp +=================================================================== +--- ../trunk-jpl/src/c/solutionsequences/solutionsequence_schurcg.cpp (revision 23219) ++++ ../trunk-jpl/src/c/solutionsequences/solutionsequence_schurcg.cpp (revision 23220) +@@ -42,12 +42,22 @@ + /* [ A B ] = Kff + * [ B^T 0 ] + * */ ++ #if (_PETSC_MAJOR_==3) && (_PETSC_MINOR_>=8) ++ MatCreateSubMatrix(Kff,isv,isv,MAT_INITIAL_MATRIX,&A); ++ MatCreateSubMatrix(Kff,isv,isp,MAT_INITIAL_MATRIX,&B); ++ MatCreateSubMatrix(Kff,isp,isv,MAT_INITIAL_MATRIX,&BT); ++ #else + MatGetSubMatrix(Kff,isv,isv,MAT_INITIAL_MATRIX,&A); + MatGetSubMatrix(Kff,isv,isp,MAT_INITIAL_MATRIX,&B); + MatGetSubMatrix(Kff,isp,isv,MAT_INITIAL_MATRIX,&BT); ++ #endif + + /* Extract preconditioner matrix on the pressure space*/ ++ #if (_PETSC_MAJOR_==3) && (_PETSC_MINOR_>=8) ++ MatCreateSubMatrix(Kff,isp,isp,MAT_INITIAL_MATRIX,&IP); ++ #else + MatGetSubMatrix(Kff,isp,isp,MAT_INITIAL_MATRIX,&IP); ++ #endif + + /* Get number of velocity / pressure nodes */ + MatGetSize(B,&nu,&np); +@@ -312,12 +322,18 @@ + /* [A B] + * Kff = | | + * [B^T IP] +- /* To calculate the residual, only the necessary blocks need to be extracted */ ++ * To calculate the residual, only the necessary blocks need to be extracted */ + + /*Extract A, B, B^T */ ++ #if (_PETSC_MAJOR_==3) && (_PETSC_MINOR_>=8) ++ MatCreateSubMatrix(Kff->pmatrix->matrix,isv,isv,MAT_INITIAL_MATRIX,&A); ++ MatCreateSubMatrix(Kff->pmatrix->matrix,isv,isp,MAT_INITIAL_MATRIX,&B); ++ MatCreateSubMatrix(Kff->pmatrix->matrix,isp,isv,MAT_INITIAL_MATRIX,&BT); ++ #else + MatGetSubMatrix(Kff->pmatrix->matrix,isv,isv,MAT_INITIAL_MATRIX,&A); + MatGetSubMatrix(Kff->pmatrix->matrix,isv,isp,MAT_INITIAL_MATRIX,&B); + MatGetSubMatrix(Kff->pmatrix->matrix,isp,isv,MAT_INITIAL_MATRIX,&BT); ++ #endif + + /*no. of free nodes in velocity/pressure space*/ + MatGetSize(B,&n_u,&n_p); Index: /issm/oecreview/Archive/23185-23389/ISSM-23220-23221.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23220-23221.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23220-23221.diff (revision 23390) @@ -0,0 +1,257 @@ +Index: ../trunk-jpl/src/c/cores/masstransport_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/masstransport_core.cpp (revision 23220) ++++ ../trunk-jpl/src/c/cores/masstransport_core.cpp (revision 23221) +@@ -11,6 +11,9 @@ + + void masstransport_core(FemModel* femmodel){ + ++ /*Start profiler*/ ++ femmodel->profiler->Start(MASSTRANSPORTCORE); ++ + /*parameters: */ + int numoutputs,domaintype; + bool save_results; +@@ -80,4 +83,7 @@ + + /*Free ressources:*/ + if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} ++ ++ /*profiler*/ ++ femmodel->profiler->Stop(MASSTRANSPORTCORE); + } +Index: ../trunk-jpl/src/c/cores/stressbalance_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/stressbalance_core.cpp (revision 23220) ++++ ../trunk-jpl/src/c/cores/stressbalance_core.cpp (revision 23221) +@@ -12,6 +12,9 @@ + + void stressbalance_core(FemModel* femmodel){ + ++ /*Start profiler*/ ++ femmodel->profiler->Start(STRESSBALANCECORE); ++ + /*parameters: */ + bool dakota_analysis,control_analysis; + int domaintype; +@@ -85,4 +88,7 @@ + + /*Free ressources:*/ + if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} ++ ++ /*End profiler*/ ++ femmodel->profiler->Stop(STRESSBALANCECORE); + } +Index: ../trunk-jpl/src/c/classes/Profiler.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Profiler.cpp (revision 23220) ++++ ../trunk-jpl/src/c/classes/Profiler.cpp (revision 23221) +@@ -14,7 +14,7 @@ + + /*Profiler constructors and destructors:*/ + Profiler::Profiler(){/*{{{*/ +- for(int i=0;itime[i] = 0.; + this->time_start[i] = 0.; + this->flops[i] = 0.; +@@ -22,6 +22,7 @@ + this->memory[i] = 0.; + this->memory_start[i] = 0.; + this->running[i] = false; ++ this->used[i] = false; + } + } /*}}}*/ + Profiler::~Profiler(){/*{{{*/ +@@ -31,7 +32,7 @@ + /*First do simple copy: */ + Profiler* output=new Profiler(); + +- for(int i=0;itime[i] =this->time[i]; + output->flops[i] =this->flops[i]; + output->memory[i]=this->memory[i]; +@@ -48,7 +49,7 @@ + void Profiler::Echo(void){/*{{{*/ + + _printf_("Profiler:\n"); +- for(int i=0;iflops[i]<<"\n"); + _printf_(" memory: "<memory[i]<<"\n"); +@@ -69,13 +70,13 @@ + + MARSHALLING_ENUM(ProfilerEnum); + pointer = &this->time[0]; +- MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXIMUMSIZE); ++ MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXPROFSIZE); + pointer = &this->flops[0]; +- MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXIMUMSIZE); ++ MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXPROFSIZE); + pointer = &this->memory[0]; +- MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXIMUMSIZE); ++ MARSHALLING_DYNAMIC(pointer,IssmPDouble,MAXPROFSIZE); + bpointer = &this->running[0]; +- MARSHALLING_DYNAMIC(bpointer,bool,MAXIMUMSIZE); ++ MARSHALLING_DYNAMIC(bpointer,bool,MAXPROFSIZE); + + } /*}}}*/ + int Profiler::ObjectEnum(void){/*{{{*/ +@@ -87,7 +88,7 @@ + + /*Get tag*/ + _assert_(tag>=0); +- _assert_(tagrunning[tag]) _error_("Tag "<flops[tag]; +@@ -96,7 +97,7 @@ + + /*Get tag*/ + _assert_(tag>=0); +- _assert_(tagrunning[tag]) _error_("Tag "<=0); +- _assert_(tagrunning[tag]) _error_("Tag "<memory[tag]; +@@ -139,7 +140,7 @@ + + /*Check tag*/ + _assert_(tag>=0); +- _assert_(tagrunning[tag]) _error_("Tag "<time: */ + _assert_(tag>=0); +- _assert_(tagtime_start[tag] = t; + this->flops_start[tag] = f; + this->memory_start[tag] = m; +@@ -173,12 +174,13 @@ + + /*turn on running*/ + this->running[tag] = true; ++ this->used[tag] = true; + }/*}}}*/ + void Profiler::Stop(int tag,bool dontmpisync){/*{{{*/ + + /*Check tag*/ + _assert_(tag>=0); +- _assert_(tagrunning[tag]) _error_("Tag "<time: */ + _assert_(tag>=0); +- _assert_(tagtime[tag] += t - this->time_start[tag]; + this->flops[tag] += f - this->flops_start[tag]; + this->memory[tag] += m - this->memory_start[tag]; +@@ -213,3 +215,10 @@ + /*turn off running*/ + this->running[tag] = false; + }/*}}}*/ ++bool Profiler::Used(int tag){/*{{{*/ ++ ++ /*Check tag*/ ++ _assert_(tag>=0); ++ _assert_(tagused[tag]; ++}/*}}}*/ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23220) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23221) +@@ -253,10 +253,16 @@ + + /*Before we delete the profiler, report statistics for this run: */ + profiler->Stop(TOTAL); //final tagging ++ + _printf0_("\n"); +- _printf0_(" "<TotalTime(MPROCESSOR) << "\n"); +- _printf0_(" "<TotalTime(CORE) << "\n"); +- _printf0_(" "<TotalTime(SOLVER) << "\n"); ++ _printf0_(" "<TotalTime(MPROCESSOR) << "\n"); ++ /*Total times*/ ++ _printf0_(" "<TotalTime(CORE) << "\n"); ++ /*Individual cores*/ ++ if(profiler->Used(STRESSBALANCECORE)) _printf0_(" "<TotalTime(STRESSBALANCECORE) << "\n"); ++ if(profiler->Used(MASSTRANSPORTCORE)) _printf0_(" "<TotalTime(MASSTRANSPORTCORE) << "\n"); ++ /*Linear solver only*/ ++ _printf0_(" "<TotalTime(SOLVER) << " ("<TotalTime(SOLVER)/profiler->TotalTime(CORE)*100.<<"%)\n"); + _printf0_("\n"); + _printf0_(" Total elapsed time: " + <TotalTimeModHour(TOTAL)<<" hrs " +Index: ../trunk-jpl/src/c/classes/Profiler.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Profiler.h (revision 23220) ++++ ../trunk-jpl/src/c/classes/Profiler.h (revision 23221) +@@ -10,23 +10,26 @@ + #include "../datastructures/datastructures.h" + + /*Macros*/ +-#define TOTAL 0 /*Profiling Total time */ +-#define MPROCESSOR 1 /*Profiling Model processor*/ +-#define CORE 2 /*Profiling solution */ +-#define SOLVER 3 /*Profiling solution */ +-#define ADCORE 4 /*Profiling AD */ +-#define MAXIMUMSIZE 5 ++#define TOTAL 0 /*Profiling Total time */ ++#define MPROCESSOR 1 /*Profiling Model processor*/ ++#define CORE 2 /*Profiling solution */ ++#define SOLVER 3 /*Profiling solution */ ++#define ADCORE 4 /*Profiling AD */ ++#define STRESSBALANCECORE 5 /*Profiling AD */ ++#define MASSTRANSPORTCORE 6 /*Profiling AD */ ++#define MAXPROFSIZE 7 /*Used to initialize static arrays*/ + + class Profiler: public Object{ + + public: +- IssmPDouble flops[MAXIMUMSIZE]; +- IssmPDouble flops_start[MAXIMUMSIZE]; +- IssmPDouble memory[MAXIMUMSIZE]; +- IssmPDouble memory_start[MAXIMUMSIZE]; +- IssmPDouble time[MAXIMUMSIZE]; +- IssmPDouble time_start[MAXIMUMSIZE]; +- bool running[MAXIMUMSIZE]; ++ IssmPDouble flops[MAXPROFSIZE]; ++ IssmPDouble flops_start[MAXPROFSIZE]; ++ IssmPDouble memory[MAXPROFSIZE]; ++ IssmPDouble memory_start[MAXPROFSIZE]; ++ IssmPDouble time[MAXPROFSIZE]; ++ IssmPDouble time_start[MAXPROFSIZE]; ++ bool running[MAXPROFSIZE]; ++ bool used[MAXPROFSIZE]; + + /*Profiler constructors, destructors */ + Profiler(); +@@ -49,6 +52,7 @@ + IssmPDouble Memory(int tag); + void Start(int tagenum,bool dontmpisync=false); + void Stop(int tagenum,bool dontmpisync=false); ++ bool Used(int tagenum); + }; + + #endif /* _PROFILER_H_ */ Index: /issm/oecreview/Archive/23185-23389/ISSM-23221-23222.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23221-23222.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23221-23222.diff (revision 23390) @@ -0,0 +1,73 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23221) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23222) +@@ -258,9 +258,7 @@ + _printf0_(" "<TotalTime(MPROCESSOR) << "\n"); + /*Total times*/ + _printf0_(" "<TotalTime(CORE) << "\n"); +- /*Individual cores*/ +- if(profiler->Used(STRESSBALANCECORE)) _printf0_(" "<TotalTime(STRESSBALANCECORE) << "\n"); +- if(profiler->Used(MASSTRANSPORTCORE)) _printf0_(" "<TotalTime(MASSTRANSPORTCORE) << "\n"); ++ + /*Linear solver only*/ + _printf0_(" "<TotalTime(SOLVER) << " ("<TotalTime(SOLVER)/profiler->TotalTime(CORE)*100.<<"%)\n"); + _printf0_("\n"); +@@ -858,10 +856,16 @@ + solution_flops=profiler->TotalFlops(CORE); + solution_memory=profiler->Memory(CORE); + +- _printf0_("Core solution elapsed time : " << solution_time << " Seconds\n"); +- _printf0_("Core solution number of flops : " << solution_flops << " Flops\n"); +- _printf0_("Core solution memory used : " << solution_memory << " Bytes\n"); ++ _printf0_("\nCore solution profiling\n"); ++ _printf0_(" elapsed time : " << solution_time << " Seconds\n"); ++ _printf0_(" number of flops : " << solution_flops << " Flops\n"); ++ _printf0_(" memory used : " << solution_memory << " Bytes\n"); + ++ /*Individual cores*/ ++ _printf0_("Individual core profiling\n"); ++ if(profiler->Used(STRESSBALANCECORE)) _printf0_(" "<TotalTime(STRESSBALANCECORE) << " sec\n"); ++ if(profiler->Used(MASSTRANSPORTCORE)) _printf0_(" "<TotalTime(MASSTRANSPORTCORE) << " sec\n"); ++ + /*Add to results: */ + results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingSolutionTimeEnum, solution_time)); + results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentMemEnum, solution_memory)); +@@ -868,14 +872,16 @@ + results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentFlopsEnum, solution_flops)); + + #ifdef _HAVE_ADOLC_ +- solution_time=profiler->TotalTime(ADCORE); +- solution_flops=profiler->TotalFlops(ADCORE); +- solution_memory=profiler->Memory(ADCORE); ++ solution_time = profiler->TotalTime(ADCORE); ++ solution_flops = profiler->TotalFlops(ADCORE); ++ solution_memory = profiler->Memory(ADCORE); + +- _printf0_("AD Solution elapsed time : " << solution_time << " Seconds\n"); +- _printf0_("AD Solution number of flops : " << solution_flops << " Flops\n"); +- _printf0_("AD Solution memory used : " << solution_memory << " Bytes\n"); ++ _printf0_("AD profiling\n"); ++ _printf0_(" elapsed time : " << solution_time << " Seconds\n"); ++ _printf0_(" number of flops : " << solution_flops << " Flops\n"); ++ _printf0_(" memory used : " << solution_memory << " Bytes\n"); + #endif ++ _printf0_("\n"); + + } + } +Index: ../trunk-jpl/src/c/classes/Profiler.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Profiler.h (revision 23221) ++++ ../trunk-jpl/src/c/classes/Profiler.h (revision 23222) +@@ -50,8 +50,8 @@ + int TotalTimeModMin(int tag); + int TotalTimeModSec(int tag); + IssmPDouble Memory(int tag); +- void Start(int tagenum,bool dontmpisync=false); +- void Stop(int tagenum,bool dontmpisync=false); ++ void Start(int tagenum,bool dontmpisync=true); /*Do not call MPI barrier by default to save some ms*/ ++ void Stop(int tagenum, bool dontmpisync=true); /*Do not call MPI barrier by default to save some ms*/ + bool Used(int tagenum); + }; + Index: /issm/oecreview/Archive/23185-23389/ISSM-23222-23223.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23222-23223.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23222-23223.diff (revision 23390) @@ -0,0 +1,47 @@ +Index: ../trunk-jpl/test/NightlyRun/test2084.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test2084.m (revision 23222) ++++ ../trunk-jpl/test/NightlyRun/test2084.m (revision 23223) +@@ -1,5 +1,5 @@ + +-%Test Name: GiaCaron. ++%Test Name: GiaCaron. + %Forward Love number solution for a viscoelastic earth, model M3-L70-V01 from + %Spada, G., Barletta, V. R., Klemann, V., Riva, R. E. M., Martinec, Z., + %Gasperini, P., Lund, B., Wolf, D., Vermeersen, L. L. A. and King, M. A. +@@ -56,7 +56,7 @@ + + %Fields and tolerances to track changes + field_names ={field_names{:},'LoveH_loading_realpart','LoveK_loading_realpart','LoveL_loading_realpart','LoveH_loading_imagpart','LoveK_loading_imagpart','LoveL_loading_imagpart'}; +-field_tolerances={field_tolerances{:},7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10}; ++field_tolerances={field_tolerances{:},5e-7,5e-7,5e-7,5e-7,5e-7,5e-7}; + field_values={field_values{:},... + (md.results.LoveSolution.LoveHr(:,:)),... + (md.results.LoveSolution.LoveKr(:,:)),... +@@ -74,7 +74,7 @@ + + %tidal love numbers + field_names ={field_names{:},'LoveH_tidal_elastic','LoveK_tidal_elastic','LoveL_tidal_elastic','LoveH_tidal_realpart','LoveK_tidal_realpart','LoveL_tidal_realpart','LoveH_tidal_imagpart','LoveK_tidal_imagpart','LoveL_tidal_imagpart'}; +-field_tolerances={field_tolerances{:},7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10}; ++field_tolerances={field_tolerances{:},3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6}; + field_values={field_values{:},... + (md.results.LoveSolution.LoveHr(:,1)),... + (md.results.LoveSolution.LoveKr(:,1)),... +@@ -114,7 +114,7 @@ + %md=solve(md,'lv'); + % + %field_names ={field_names{:},'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'}; +-%field_tolerances={field_tolerances{:},7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10}; ++%field_tolerances={field_tolerances{:},2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7}; + %field_values={field_values{:},... + % (md.results.LoveSolution.LoveHr(:,1)),... + % (md.results.LoveSolution.LoveKr(:,1)),... +@@ -146,7 +146,7 @@ + md.love.nfreq=length(md.love.frequencies); + + field_names ={field_names{:},'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'}; +-field_tolerances={field_tolerances{:},7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10,7.0e-10}; ++field_tolerances={field_tolerances{:},2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7}; + field_values={field_values{:},... + (md.results.LoveSolution.LoveHr(:,1)),... + (md.results.LoveSolution.LoveKr(:,1)),... Index: /issm/oecreview/Archive/23185-23389/ISSM-23223-23224.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23223-23224.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23223-23224.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/test/NightlyRun/test2084.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test2084.m (revision 23223) ++++ ../trunk-jpl/test/NightlyRun/test2084.m (revision 23224) +@@ -146,7 +146,7 @@ + md.love.nfreq=length(md.love.frequencies); + + field_names ={field_names{:},'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'}; +-field_tolerances={field_tolerances{:},2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7}; ++field_tolerances={field_tolerances{:},6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7}; + field_values={field_values{:},... + (md.results.LoveSolution.LoveHr(:,1)),... + (md.results.LoveSolution.LoveKr(:,1)),... Index: /issm/oecreview/Archive/23185-23389/ISSM-23227-23228.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23227-23228.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23227-23228.diff (revision 23390) @@ -0,0 +1,43 @@ +Index: ../trunk-jpl/src/c/cores/thermal_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/thermal_core.cpp (revision 23227) ++++ ../trunk-jpl/src/c/cores/thermal_core.cpp (revision 23228) +@@ -11,7 +11,10 @@ + #include "../solutionsequences/solutionsequences.h" + + void thermal_core(FemModel* femmodel){ +- ++ ++ /*Start profiler*/ ++ femmodel->profiler->Start(THERMALCORE); ++ + /*intermediary*/ + bool save_results,isenthalpy; + bool dakota_analysis; +@@ -51,5 +54,7 @@ + + /*Free ressources:*/ + if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} +- ++ ++ /*End profiler*/ ++ femmodel->profiler->Stop(THERMALCORE); + } +Index: ../trunk-jpl/src/c/classes/Profiler.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Profiler.h (revision 23227) ++++ ../trunk-jpl/src/c/classes/Profiler.h (revision 23228) +@@ -15,9 +15,10 @@ + #define CORE 2 /*Profiling solution */ + #define SOLVER 3 /*Profiling solution */ + #define ADCORE 4 /*Profiling AD */ +-#define STRESSBALANCECORE 5 /*Profiling AD */ +-#define MASSTRANSPORTCORE 6 /*Profiling AD */ +-#define MAXPROFSIZE 7 /*Used to initialize static arrays*/ ++#define THERMALCORE 5 /*Profiling THERMAL */ ++#define STRESSBALANCECORE 6 /*Profiling STRESSBALANCE */ ++#define MASSTRANSPORTCORE 7 /*Profiling MASSTRANSPORT */ ++#define MAXPROFSIZE 8 /*Used to initialize static arrays*/ + + class Profiler: public Object{ + Index: /issm/oecreview/Archive/23185-23389/ISSM-23228-23229.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23228-23229.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23228-23229.diff (revision 23390) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23228) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23229) +@@ -863,8 +863,10 @@ + + /*Individual cores*/ + _printf0_("Individual core profiling\n"); ++ if(profiler->Used(THERMALCORE)) _printf0_(" "<TotalTime(THERMALCORE) << " sec\n"); + if(profiler->Used(STRESSBALANCECORE)) _printf0_(" "<TotalTime(STRESSBALANCECORE) << " sec\n"); + if(profiler->Used(MASSTRANSPORTCORE)) _printf0_(" "<TotalTime(MASSTRANSPORTCORE) << " sec\n"); ++ + + /*Add to results: */ + results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingSolutionTimeEnum, solution_time)); Index: /issm/oecreview/Archive/23185-23389/ISSM-23229-23230.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23229-23230.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23229-23230.diff (revision 23390) @@ -0,0 +1,254 @@ +Index: ../trunk-jpl/src/m/classes/clusters/stallo.py +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/stallo.py (revision 23229) ++++ ../trunk-jpl/src/m/classes/clusters/stallo.py (revision 23230) +@@ -50,7 +50,7 @@ + self=stallo_settings(self) + #OK get other fields + self=options.AssignObjectFields(self) +- self.np=self.numnodes*self.cpuspernode ++ self.np=self.numnodes*self.cpuspernode + # }}} + + def __repr__(self): +@@ -60,7 +60,7 @@ + s = "%s\n%s"%(s,fielddisplay(self,'name','name of the cluster')) + s = "%s\n%s"%(s,fielddisplay(self,'login','login')) + s = "%s\n%s"%(s,fielddisplay(self,'numnodes','number of nodes')) +- s = "%s\n%s"%(s,fielddisplay(self,'cpuspernode','number of nodes per CPUs')) ++ s = "%s\n%s"%(s,fielddisplay(self,'cpuspernode','number of CPUs per nodes')) + s = "%s\n%s"%(s,fielddisplay(self,'mem','memory per CPU')) + s = "%s\n%s"%(s,fielddisplay(self,'queue','name of the queue (normal (D), short,singlenode,multinode,devel)')) + s = "%s\n%s"%(s,fielddisplay(self,'time','walltime requested in minutes')) +@@ -119,9 +119,9 @@ + m,s=divmod(timeobj.total_seconds(), 60) + h,m=divmod(m, 60) + d,h=divmod(h, 60) +- timestring="%02d-%02d:%02d:%02d" % (d, h, m, s) +- fid.write('#SBATCH --time=%s\n' % timestring) #walltime is minutes +- fid.write('#SBATCH --mem-per-cpu=%iGB\n' % self.mem)# mem is in GB ++# timestring="%02d-%02d:%02d:%02d" % (d, h, m, s) ++ fid.write('#SBATCH --time={}\n'.format(timestring)) #walltime is minutes ++ fid.write('#SBATCH --mem-per-cpu={}MB\n'.format(1000*self.mem))# mem is in MB (to keep it integral) + if (np.mod(self.np,16)+np.mod(self.np,20))==0: + fid.write('#SBATCH --ntask=%i\n' % self.np) + fid.write('#SBATCH --account=%s\n' % self.accountname) +Index: ../trunk-jpl/src/m/classes/clusters/stallo.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/stallo.m (nonexistent) ++++ ../trunk-jpl/src/m/classes/clusters/stallo.m (revision 23230) +@@ -0,0 +1,214 @@ ++% Stallo cluster class definition ++% This is a SLURM queue ++% The priorities are given to: ++% - Large jobs ++% - Short jobs ++% - small number of job per user ++% ++% There are some 20cpu nodes and 16cpu nodes, with 32GB (a few with 128GB) mem per node, you can ask for part of a node if you need more memory.(1 node, 2 CPUS and 10GB per cpu for example) ++ ++% Usage: ++% cluster=stallo(); ++% cluster=stallo('np',3); ++% cluster=stallo('np',3,'login','username'); ++ ++%node task and cpu must be defined, ask andreas for his stallo.py? ++ ++classdef stallo ++ properties (SetAccess=public) ++ % {{{ ++ name = 'stallo'; ++ login = ''; ++ numnodes = 2; ++ cpuspernode = 10; ++ mem = 1.5; ++ queue = 'normal'; ++ time = 2*60; ++ codepath = ''; ++ executionpath = ''; ++ interactive = 0; ++ port = []; ++ accountname = ''; ++ profiling = 0; ++ bbftp = 0; ++ % }}} ++ end ++ methods ++ function cluster=stallo(varargin) % {{{ ++ ++ %initialize cluster using default settings if provided ++ if (exist('stallo_settings')==2), stallo_settings; end ++ ++ %use provided options to change fields ++ cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); ++ end ++ %}}} ++ function disp(cluster) % {{{ ++ % display the object ++ disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); ++ disp(sprintf(' name: %s',cluster.name)); ++ disp(sprintf(' login: %s',cluster.login)); ++ disp(sprintf(' accountname: %s',cluster.accountname)); ++ disp(sprintf(' numnodes: %i',cluster.numnodes)); ++ disp(sprintf(' cpuspernode: %i, cpu per nodes',cluster.cpuspernode)); ++ disp(sprintf(' queue: %s, name of the queue (normal (D), short,singlenode,multinode,devel)',cluster.queue)); ++ disp(sprintf(' codepath: %s',cluster.codepath)); ++ disp(sprintf(' executionpath: %s',cluster.executionpath)); ++ disp(sprintf(' interactive: %i',cluster.interactive)); ++ disp(sprintf(' time: %i, walltime requested in minutes',cluster.time)); ++ disp(sprintf(' memory: %i, memory per CPU',cluster.mem)); ++ disp(sprintf(' profiling: %i, enable profiling if 1 default is 0',cluster.profiling)); ++ end ++ %}}} ++ function md = checkconsistency(cluster,md,solution,analyses) % {{{ ++ ++ available_queues={'short','normal','singlenode','multinode','devel'}; ++ queue_requirements_time=[60 2*24*60 28*24*60 28*24*60 4*60]; ++ queue_requirements_np=[2048 2048 20 2048 2048]; ++ ++ QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,1) ++ ++ %Miscelaneous ++ if isempty(cluster.login), md = checkmessage(md,'login empty'); end ++ if isempty(cluster.accountname), md = checkmessage(md,'accountname empty'); end ++ if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end ++ if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end ++ ++ end ++ %}}} ++ function numprocs=np(cluster) % {{{ ++ %compute number of processors ++ numprocs=cluster.numnodes*cluster.cpuspernode; ++ end ++ %}}} ++ function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ ++ ++ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end ++ if(isgprof), disp('gprof not supported by cluster, ignoring...'); end ++ ++ executable='issm.exe'; ++ if isdakota, ++ version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3)); ++ if (version>=6), ++ executable='issm_dakota.exe'; ++ end ++ end ++ if isoceancoupling, ++ executable='issm_ocean.exe'; ++ end ++ ++ %write queuing script ++ fid=fopen([modelname '.queue'],'w'); ++ fprintf(fid,'#!/bin/bash -l\n'); ++ fprintf(fid,'#SBATCH --job-name=%s \n',modelname); ++ fprintf(fid,'#SBATCH --qos %s \n',cluster.queue); ++ fprintf(fid,'#SBATCH --nodes=%i \n',cluster.numnodes); ++ fprintf(fid,'#SBATCH --ntasks-per-node=%i \n',cluster.cpuspernode); ++ fprintf(fid,'#SBATCH --time=%02i-%02i:%02i:00 \n',floor(cluster.time/(3600*24)),floor(cluster.time/3600),floor(mod(cluster.time,60))); ++ fprintf(fid,'#SBATCH --mem-per-cpu=%iMB\n',1000*cluster.mem); ... ++ % mem in MB ++ if (mod(cluster.np,16)+mod(cluster.np,20))==0, ++ fprintf(fid,'#SBATCH --ntask=%i\n',cluster.np); ++ end ++ fprintf(fid,'#SBATCH --account=%s\n',cluster.accountname); ++ fprintf(fid,'#SBATCH --output %s/%s/%s.outlog \n',cluster.executionpath,dirname,modelname); ++ fprintf(fid,'#SBATCH --error %s/%s/%s.errlog \n\n',cluster.executionpath,dirname,modelname); ++ fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath);%FIXME ++ fprintf(fid,'module purge\n'); ++ fprintf(fid,'module load CMake/3.8.0-GCCcore-6.3.0\n'); ++ fprintf(fid,'module load Automake/1.15.1-GCCcore-6.3.0\n'); ++ fprintf(fid,'module load libtool/2.4.6\n'); ++ fprintf(fid,'module load OpenSSL/1.1.0e-intel-2017a\n'); ++ fprintf(fid,'module load PETSc/3.7.5-intel-2017a-downloaded-deps\n'); ++ ++ fprintf(fid,'cd %s/%s/\n\n',cluster.executionpath,dirname); ++ if cluster.profiling==1, ++ fprintf(fid,'module load perf-report\n'); ++ fprintf(fid,'perf-report mpirun -np %i %s/%s %s %s/%s %s\n',cluster.np,cluster.codepath,executable,solution,cluster.executionpath,dirname,modelname); ++ else ++ fprintf(fid,'mpirun -np %i %s/%s %s %s/%s %s\n',cluster.np,cluster.codepath,executable,solution,cluster.executionpath,dirname,modelname); ++ end ++ %}}} ++ if ~io_gather, %concatenate the output files: ++ fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); ++ end ++ fclose(fid); ++ ++ %in interactive mode, create a run file, and errlog and outlog file ++ if cluster.interactive, ++ fid=fopen([modelname '.run'],'w'); ++ fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); ++ if ~io_gather, %concatenate the output files: ++ fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); ++ end ++ fclose(fid); ++ fid=fopen([modelname '.errlog'],'w'); ++ fclose(fid); ++ fid=fopen([modelname '.outlog'],'w'); ++ fclose(fid); ++ end ++ end ++ ++ ++ function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{ ++ ++ %compress the files into one zip. ++ compressstring=['tar -zcf ' dirname '.tar.gz ']; ++ for i=1:numel(filelist), ++ compressstring = [compressstring ' ' filelist{i}]; ++ end ++ if cluster.interactive, ++ compressstring = [compressstring ' ' modelname '.run ' modelname '.errlog ' modelname '.outlog ']; ++ end ++ system(compressstring); ++ disp('uploading input file and queueing script'); ++ if cluster.interactive==10, ++ directory=[pwd() '/run/']; ++ elseif cluster.interactive, ++ directory=[cluster.executionpath '/Interactive' num2str(cluster.interactive)]; ++ else ++ directory=cluster.executionpath; ++ end ++ ++ if ~cluster.bbftp, ++ issmscpout(cluster.name,directory,cluster.login,cluster.port,{[dirname '.tar.gz']}); ++ else ++ issmbbftpout(cluster.name,directory,cluster.login,cluster.port,cluster.numstreams,{[dirname '.tar.gz']}); ++ ++ end ++ end %}}} ++ function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{ ++ ++ %lauch command, to be executed via ssh ++ if ~cluster.interactive, ++ if ~isempty(restart) ++ launchcommand=['cd ' cluster.executionpath ' && cd ' dirname ' && qsub ' modelname '.queue ']; ++ else ++ launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ... ++ ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && qsub ' modelname '.queue ']; ++ end ++ else ++ if ~isempty(restart) ++ launchcommand=['cd ' cluster.executionpath '/Interactive' num2str(cluster.interactive)]; ++ else ++ if cluster.interactive==10, ++ launchcommand=['cd ' pwd() '/run && tar -zxf ' dirname '.tar.gz']; ++ else ++ launchcommand=['cd ' cluster.executionpath '/Interactive' num2str(cluster.interactive) ' && tar -zxf ' dirname '.tar.gz']; ++ end ++ end ++ end ++ ++ disp('launching solution sequence on remote cluster'); ++ issmssh(cluster.name,cluster.login,cluster.port,launchcommand); ++ end ++ %}}} ++ function Download(cluster,dirname,filelist)% {{{ ++ ++ %copy files from cluster to current directory ++ directory=[cluster.executionpath '/' dirname '/']; ++ issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist); ++ ++ end %}}} ++ end ++end Index: /issm/oecreview/Archive/23185-23389/ISSM-23230-23231.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23230-23231.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23230-23231.diff (revision 23390) @@ -0,0 +1,1000 @@ +Index: ../trunk-jpl/test/NightlyRun/test413.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test413.py (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test413.py (revision 23231) +@@ -0,0 +1,66 @@ ++#Test Name: SquareSheetShelfDiadSSA3dDakotaPart ++import numpy as np ++from model import * ++from socket import gethostname ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++from partitioner import * ++from importancefactors import * ++ ++md = triangle(model(),'../Exp/Square.exp',150000.) ++md = setmask(md,'../Exp/SquareShelf.exp','') ++md = parameterize(md,'../Par/SquareSheetShelf.py') ++md = setflowequation(md,'SSA','all') ++md.cluster = generic('name',gethostname(),'np',3) ++ ++#Dakota options ++ ++#dakota version ++version = IssmConfig('_DAKOTA_VERSION_') ++version = float(version[0]) ++ ++#partitioning ++md.qmu.numberofpartitions = 20 ++md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') ++md.qmu.partition = md.qmu.partition-1 ++ ++#variables ++md.qmu.variables.rho_ice = normal_uncertain.normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01) ++md.qmu.variables.drag_coefficient = normal_uncertain.normal_uncertain('scaled_FrictionCoefficient',1,0.01) ++ ++#responses ++md.qmu.responses.MaxVel = response_function.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.dakota_method('nond_l') ++ ++#parameters ++md.qmu.params.direct = True ++md.qmu.params.interval_type = 'forward' ++ ++if version >= 6: ++ md.qmu.params.analysis_driver = 'matlab' ++ md.qmu.params.evaluation_scheduling = 'master' ++ md.qmu.params.processors_per_evaluation = 2 ++else: ++ md.qmu.params.analysis_driver = 'stressbalance' ++ md.qmu.params.evaluation_concurrency = 1 ++ ++ ++#imperative! ++md.stressbalance.reltol = 10**-5 #tighten for qmu analyses ++md.qmu.isdakota = 1 ++ ++#solve ++md.verbose = verbose('000000000') # this line is recommended ++md = solve(md,'Stressbalance','overwrite','y') ++ ++#Fields and tolerances to track changes ++md.qmu.results = md.results.dakota ++md.results.dakota.importancefactors = importancefactors(md,'scaled_FrictionCoefficient','MaxVel').T ++field_names = ['importancefactors'] ++field_tolerances = [1e-10] ++field_values = [md.results.dakota.importancefactors] +Index: ../trunk-jpl/test/NightlyRun/test234.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test234.py (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test234.py (revision 23231) +@@ -0,0 +1,101 @@ ++#Test Name: SquareShelfTranForceNeg2dDakotaSamp ++import numpy as np ++import scipy.io as spio ++from os import getcwd ++from model import * ++from socket import gethostname ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++from SMBgemb import * ++from partitioner import * ++from dmeth_params_set import * ++ ++md = triangle(model(),'../Exp/Square.exp',180000.) ++md = setmask(md,'all','') ++md = parameterize(md,'../Par/SquareShelf.py') ++md = setflowequation(md,'SSA','all') ++md.cluster = generic('name',gethostname(),'np',3) ++ ++md.timestepping.time_step = 1 ++md.settings.output_frequency = 1 ++md.timestepping.final_time = 4 ++ ++smb = np.ones((md.mesh.numberofvertices,))*3.6 ++smb = np.array([smb,smb*-1]).T ++ ++md.smb.mass_balance = smb ++md.smb.mass_balance = np.concatenate((md.smb.mass_balance,[[1.5,3]])) ++md.transient.isthermal = 0 ++ ++#Dakota options ++ ++#dakota version ++version = IssmConfig('_DAKOTA_VERSION_') ++version = float(version[0]) ++ ++#partitioning ++md.qmu.numberofpartitions = 20 ++md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') ++md.qmu.partition = md.qmu.partition - 1 ++ ++#variables ++md.qmu.variables.surface_mass_balance = normal_uncertain.normal_uncertain('scaled_SmbMassBalance',1,0.1) ++ ++#responses ++md.qmu.responses.MaxVel = response_function.response_function('MaxVel',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.IceVolume = response_function.response_function('IceVolume',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux1 = response_function.response_function('indexed_MassFlux_1',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux2 = response_function.response_function('indexed_MassFlux_2',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux3 = response_function.response_function('indexed_MassFlux_3',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux4 = response_function.response_function('indexed_MassFlux_4',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux5 = response_function.response_function('indexed_MassFlux_5',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.massFlux6 = response_function.response_function('indexed_MassFlux_6',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++ ++#mass flux profiles ++md.qmu.mass_flux_profiles = ['../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp'] ++md.qmu.mass_flux_profile_directory = getcwd() ++ ++## nond_sampling study ++md.qmu.method = dakota_method.dakota_method('nond_samp') ++md.qmu.method = dmeth_params_set(md.qmu.method,'seed',1234,'samples',20,'sample_type','lhs') ++dver = str(version) ++if ((int(dver[0]) == 4 and int(dver[2])>2) or int(dver[0])>4): ++ md.qmu.method = dmeth_params_set(md.qmu.method,'rng','rnum2') ++ ++#parameters ++md.qmu.params.direct = True ++md.qmu.params.analysis_components = '' ++md.qmu.params.interval_type = 'forward' ++md.qmu.params.tabular_graphics_data = True ++md.qmu.isdakota = 1 ++ ++if version >= 6: ++ md.qmu.params.analysis_driver = 'matlab' ++ md.qmu.params.evaluation_scheduling = 'master' ++ md.qmu.params.processors_per_evaluation = 2 ++else: ++ md.qmu.params.analysis_driver = 'stressbalance' ++ md.qmu.params.evaluation_concurrency = 1 ++ ++md.stressbalance.reltol = 10**-5 #tighten for qmu analyses ++md.transient.requested_outputs = ['IceVolume'] ++ ++#solve ++md.verbose = verbose('000000000') # this line is recommended ++md = solve(md,'Transient','overwrite','y') ++md.qmu.results = md.results.dakota ++ ++#Fields and tolerances to track changes ++md.results.dakota.moments = [] ++for i in range(8): ++ md.results.dakota.moments.append(md.results.dakota.dresp_out[i].mean) ++ ++for i in range(8): ++ md.results.dakota.moments.append(md.results.dakota.dresp_out[i].stddev) ++ ++field_names = ['moments'] ++field_tolerances = [1e-11] ++field_values = [md.results.dakota.moments] +Index: ../trunk-jpl/test/NightlyRun/test414.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test414.py (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test414.py (revision 23231) +@@ -0,0 +1,92 @@ ++#Test Name: SquareSheetShelfDiadSSA3dDakotaMassFlux ++import numpy as np ++from os import getcwd ++from model import * ++from socket import gethostname ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++from partitioner import * ++ ++md = triangle(model(),'../Exp/Square.exp',150000.) ++md = setmask(md,'../Exp/SquareShelf.exp','') ++md = parameterize(md,'../Par/SquareSheetShelf.py') ++md = setflowequation(md,'SSA','all') ++md.cluster = generic('name',gethostname(),'np',3) ++md.materials.rho_ice = 10**7 #involved in the mass flux, make it easy ++md.geometry.thickness[:] = 1 #make it easy ++md.geometry.surface = md.geometry.base+md.geometry.thickness ++ ++#constrain all velocities to 1 m/yr, in the y-direction ++md.stressbalance.spcvx = np.zeros((md.mesh.numberofvertices,)) ++md.stressbalance.spcvy = np.ones((md.mesh.numberofvertices,)) ++md.stressbalance.spcvz = np.zeros((md.mesh.numberofvertices,)) ++ ++#Dakota options ++ ++#dakota version ++version = IssmConfig('_DAKOTA_VERSION_') ++version = float(version[0]) ++ ++#partitioning ++md.qmu.numberofpartitions = 20 ++md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') ++md.qmu.partition = md.qmu.partition-1 ++ ++#variables ++md.qmu.variables.drag_coefficient = normal_uncertain.normal_uncertain('scaled_FrictionCoefficient',1,0.01) ++ ++#responses ++md.qmu.responses.MaxVel = response_function.response_function('MaxVel',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux1 = response_function.response_function('indexed_MassFlux_1',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux2 = response_function.response_function('indexed_MassFlux_2',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux3 = response_function.response_function('indexed_MassFlux_3',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux4 = response_function.response_function('indexed_MassFlux_4',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux5 = response_function.response_function('indexed_MassFlux_5',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux6 = response_function.response_function('indexed_MassFlux_6',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux7 = response_function.response_function('indexed_MassFlux_7',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++ ++#mass flux profiles ++md.qmu.mass_flux_profiles = ['../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp','../Exp/Square.exp'] ++md.qmu.mass_flux_profile_directory = getcwd() ++ ++#method ++md.qmu.method = dakota_method.dakota_method('nond_l') ++ ++#parameters ++md.qmu.params.direct = True ++md.qmu.params.interval_type = 'forward' ++md.qmu.isdakota = 1 ++md.stressbalance.reltol = 10**-5 #tighten for qmu analyses ++ ++if version >= 6: ++ md.qmu.params.analysis_driver = 'matlab' ++ md.qmu.params.evaluation_scheduling = 'master' ++ md.qmu.params.processors_per_evaluation = 2 ++else: ++ md.qmu.params.analysis_driver = 'stressbalance' ++ md.qmu.params.evaluation_concurrency = 1 ++ ++#solve ++md.verbose = verbose('000000000') # this line is recommended ++md = solve(md,'Stressbalance','overwrite','y') ++md.qmu.results = md.results.dakota ++ ++#Fields and tolerances to track changes ++#ok, mass flux of 3 profiles should be -3 Gt/yr -3 Gt/yr and the sum, which is -6 Gt/yr ++#we recover those mass fluxes through the mean of the response. ++#also, we recover the max velo, which should be 1m/yr. ++#we put all that data in the moments, which we will use to test for success. ++#also, check that the stddev are 0. ++md.results.dakota.moments = [] ++for i in range(8): ++ md.results.dakota.moments.append(md.results.dakota.dresp_out[i].mean) ++ ++for i in range(8): ++ md.results.dakota.moments.append(md.results.dakota.dresp_out[i].stddev) ++ ++field_names = ['moments'] ++field_tolerances = [1e-11] ++field_values = [md.results.dakota.moments] +Index: ../trunk-jpl/test/NightlyRun/test235.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test235.py (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test235.py (revision 23231) +@@ -0,0 +1,97 @@ ++#Test Name: SquareShelfTranForceNeg2dDakotaLocal ++import numpy as np ++import scipy.io as spio ++from os import getcwd ++from model import * ++from socket import gethostname ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++from SMBgemb import * ++from partitioner import * ++from dmeth_params_set import * ++ ++md = triangle(model(),'../Exp/Square.exp',180000.) ++md = setmask(md,'all','') ++md = parameterize(md,'../Par/SquareShelf.py') ++md = setflowequation(md,'SSA','all') ++md.cluster = generic('name',gethostname(),'np',3) ++ ++md.timestepping.time_step = 1 ++md.settings.output_frequency = 1 ++md.timestepping.final_time = 4 ++ ++smb = np.ones((md.mesh.numberofvertices,))*3.6 ++smb = np.array([smb,smb*-1]).T ++ ++md.smb.mass_balance = smb ++md.smb.mass_balance = np.concatenate((md.smb.mass_balance,[[1.5,3]])) ++md.transient.isthermal = 0 ++ ++#Dakota options ++ ++#dakota version ++version = IssmConfig('_DAKOTA_VERSION_') ++version = float(version[0]) ++ ++#partitioning ++md.qmu.numberofpartitions = 20 ++md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') ++md.qmu.partition = md.qmu.partition - 1 ++ ++#variables ++md.qmu.variables.surface_mass_balance = normal_uncertain.normal_uncertain('scaled_SmbMassBalance',1,100) ++ ++#responses ++md.qmu.responses.MaxVel = response_function.response_function('MaxVel',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.IceVolume = response_function.response_function('IceVolume',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux1 = response_function.response_function('indexed_MassFlux_1',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux2 = response_function.response_function('indexed_MassFlux_2',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux3 = response_function.response_function('indexed_MassFlux_3',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux4 = response_function.response_function('indexed_MassFlux_4',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux5 = response_function.response_function('indexed_MassFlux_5',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.massFlux6 = response_function.response_function('indexed_MassFlux_6',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++ ++#mass flux profiles ++md.qmu.mass_flux_profiles = ['../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp'] ++md.qmu.mass_flux_profile_directory = getcwd() ++ ++#method ++md.qmu.method = dakota_method.dakota_method('nond_l') ++ ++#parameters ++md.qmu.params.direct = True ++md.qmu.params.analysis_components = '' ++md.qmu.params.interval_type = 'forward' ++md.qmu.params.fd_gradient_step_size = '0.1' ++md.qmu.isdakota = 1 ++ ++if version >= 6: ++ md.qmu.params.analysis_driver = 'matlab' ++ md.qmu.params.evaluation_scheduling = 'master' ++ md.qmu.params.processors_per_evaluation = 2 ++else: ++ md.qmu.params.analysis_driver = 'stressbalance' ++ md.qmu.params.evaluation_concurrency = 1 ++ ++md.stressbalance.reltol = 10**-5 #tighten for qmu analyses ++md.transient.requested_outputs = ['IceVolume'] ++ ++#solve ++md.verbose = verbose('000000000') # this line is recommended ++md = solve(md,'Transient','overwrite','y') ++md.qmu.results = md.results.dakota ++ ++#Fields and tolerances to track changes ++md.results.dakota.moments = [] ++for i in range(8): ++ md.results.dakota.moments.append(md.results.dakota.dresp_out[i].mean) ++ ++for i in range(8): ++ md.results.dakota.moments.append(md.results.dakota.dresp_out[i].stddev) ++ ++field_names = ['moments'] ++field_tolerances = [1e-11] ++field_values = [md.results.dakota.moments] +Index: ../trunk-jpl/test/NightlyRun/test417.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test417.py (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test417.py (revision 23231) +@@ -0,0 +1,106 @@ ++#Test Name: SquareSheetShelfDiadSSA3dDakotaSamp ++import numpy as np ++from os import getcwd ++from model import * ++from socket import gethostname ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++from partitioner import * ++from dmeth_params_set import * ++ ++md = triangle(model(),'../Exp/Square.exp',150000.) ++md = setmask(md,'../Exp/SquareShelf.exp','') ++md = parameterize(md,'../Par/SquareSheetShelf.py') ++md = setflowequation(md,'SSA','all') ++md.cluster = generic('name',gethostname(),'np',3) ++md.materials.rho_ice = 10**7 #involved in the mass flux, make it easy ++md.geometry.thickness[:] = 1 #make it easy ++md.geometry.surface = md.geometry.base+md.geometry.thickness ++ ++#constrain all velocities to 1 m/yr, in the y-direction ++md.stressbalance.spcvx[:] = 0 ++md.stressbalance.spcvy[:] = 1 ++md.stressbalance.spcvz[:] = 0 ++ ++#Dakota options ++ ++#dakota version ++version = IssmConfig('_DAKOTA_VERSION_') ++version = float(version[0]) ++ ++#partitioning ++md.qmu.numberofpartitions = 20 ++md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') ++md.qmu.partition = md.qmu.partition-1 ++ ++#variables ++md.qmu.variables.drag_coefficient = normal_uncertain.normal_uncertain('scaled_FrictionCoefficient',1,0.01) ++ ++#responses ++md.qmu.responses.MaxVel = response_function.response_function('MaxVel',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux1 = response_function.response_function('indexed_MassFlux_1',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux2 = response_function.response_function('indexed_MassFlux_2',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux3 = response_function.response_function('indexed_MassFlux_3',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux4 = response_function.response_function('indexed_MassFlux_4',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux5 = response_function.response_function('indexed_MassFlux_5',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux6 = response_function.response_function('indexed_MassFlux_6',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.MassFlux7 = response_function.response_function('indexed_MassFlux_7',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++ ++#mass flux profiles ++md.qmu.mass_flux_profiles = ['../Exp/MassFlux1.exp','../Exp/MassFlux2.exp','../Exp/MassFlux3.exp','../Exp/MassFlux4.exp','../Exp/MassFlux5.exp','../Exp/MassFlux6.exp','../Exp/Square.exp'] ++md.qmu.mass_flux_profile_directory = getcwd() ++ ++#method ++md.qmu.method = dakota_method.dakota_method('nond_samp') ++md.qmu.method = dmeth_params_set(md.qmu.method,'seed',1234,'samples',20,'sample_type','lhs') ++ ++#parameters ++md.qmu.params.direct = True ++md.qmu.params.analysis_components = '' ++md.qmu.params.tabular_graphics_data = True; ++ ++if version >= 6: ++ md.qmu.params.analysis_driver = 'matlab' ++ md.qmu.params.evaluation_scheduling = 'master' ++ md.qmu.params.processors_per_evaluation = 2 ++else: ++ md.qmu.params.analysis_driver = 'stressbalance' ++ md.qmu.params.evaluation_concurrency = 1 ++ ++#partitioning ++md.qmu.numberofpartitions = 20 ++md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') ++md.qmu.partition = md.qmu.partition-1 ++md.qmu.isdakota = 1 ++ ++md.stressbalance.reltol = 10**-5 #tighten for qmu analyses ++ ++#solve ++md.verbose = verbose('000000000') # this line is recommended ++ ++# There may be a pair of numpy warnings in the function true_divide, ++# this is normal and will not affect the results ++# See src/m/qmu/dakota_out_parse.py, function "dak_tab_out" for details ++md = solve(md,'Stressbalance','overwrite','y') ++ ++#Fields and tolerances to track changes ++md.qmu.results = md.results.dakota; ++ ++#ok, mass flux of 3 profiles should be -3 Gt/yr -3 Gt/yr and the sum, which is -6 Gt/yr ++#we recover those mass fluxes through the mean of the response. ++#also, we recover the max velo, which should be 1m/yr. ++#we put all that data in the montecarlo field, which we will use to test for success. ++#also, check that the stddev are 0. ++md.results.dakota.montecarlo = [] ++for i in range(8): ++ md.results.dakota.montecarlo.append(md.results.dakota.dresp_out[i].mean) ++ ++for i in range(8): ++ md.results.dakota.montecarlo.append(md.results.dakota.dresp_out[i].stddev) ++ ++field_names = ['moments'] ++field_tolerances = [1e-11] ++field_values = [md.results.dakota.montecarlo] +Index: ../trunk-jpl/test/NightlyRun/test444.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test444.py (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test444.py (revision 23231) +@@ -0,0 +1,127 @@ ++#Test Name: SquareShelfTranForceNeg2dDakotaLocal ++import numpy as np ++from os import getcwd ++from model import * ++from socket import gethostname ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++from SMBgemb import * ++from partitioner import * ++from dmeth_params_set import * ++from ContourToMesh import * ++from regionaloutput import * ++ ++#model not consistent: equality thickness=surface-base violated ++ ++md = triangle(model(),'../Exp/Square.exp',150000.) ++md = setmask(md,'../Exp/SquareShelf.exp','') ++md = parameterize(md,'../Par/SquareSheetShelf.py') ++md.geometry.bed = md.geometry.base.copy() ++pos = np.where(md.mask.groundedice_levelset < 0) ++md.geometry.bed[pos] = md.geometry.base[pos]-10 ++md.friction.coefficient = 20. * np.ones((md.mesh.numberofvertices,)) ++md.friction.p = np.ones((md.mesh.numberofelements,)) ++md.friction.q = np.ones((md.mesh.numberofelements,)) ++md.transient.isthermal = 0 ++md.transient.isgroundingline = 1 ++md.groundingline.migration = 'AggressiveMigration' ++ ++md.settings.output_frequency = 3 ++md = setflowequation(md,'SSA','all') ++md.cluster = generic('name',oshostname(),'np',3) ++ ++regionalmask = np.zeros((md.mesh.numberofvertices,)) ++c_in = ContourToMesh(md.mesh.elements,md.mesh.x,md.mesh.y,'../Exp/SquareHalfRight.exp','node',1) ++regionalmask[np.where(c_in)] = 1 ++md.transient.requested_outputs = ['default','GroundedArea','FloatingArea','IceVolumeAboveFloatation','GroundedArea1','FloatingArea1','TotalFloatingBmb1','TotalGroundedBmb1','TotalSmb1', ++ 'IceMass1','IceVolume1','IceVolumeAboveFloatation1','IceVolumeAboveFloatation'] ++md.outputdefinition.definitions.append(regionaloutput('name','GroundedArea1','outputnamestring','GroundedArea','mask',regionalmask, ++ 'definitionstring','Outputdefinition1')) ++md.outputdefinition.definitions.append(regionaloutput('name','FloatingArea1','outputnamestring','FloatingArea','mask',regionalmask, ++ 'definitionstring','Outputdefinition2')) ++md.outputdefinition.definitions.append(regionaloutput('name','TotalFloatingBmb1','outputnamestring','TotalFloatingBmb','mask',regionalmask, ++ 'definitionstring','Outputdefinition3')) ++md.outputdefinition.definitions.append(regionaloutput('name','TotalGroundedBmb1','outputnamestring','TotalGroundedBmb','mask',regionalmask, ++ 'definitionstring','Outputdefinition4')) ++md.outputdefinition.definitions.append(regionaloutput('name','IceMass1','outputnamestring','IceMass','mask',regionalmask, ++ 'definitionstring','Outputdefinition5')) ++md.outputdefinition.definitions.append(regionaloutput('name','IceVolume1','outputnamestring','IceVolume','mask',regionalmask, ++ 'definitionstring','Outputdefinition6')) ++md.outputdefinition.definitions.append(regionaloutput('name','IceVolumeAboveFloatation1','outputnamestring','IceVolumeAboveFloatation','mask',regionalmask, ++ 'definitionstring','Outputdefinition7')) ++md.outputdefinition.definitions.append(regionaloutput('name','TotalSmb1','outputnamestring','TotalSmb','mask',regionalmask, ++ 'definitionstring','Outputdefinition8')) ++md.outputdefinition.definitions.append(regionaloutput('name','TotalSmb2','outputnamestring','TotalSmb','mask',regionalmask, ++ 'definitionstring','Outputdefinition9')) ++ ++md.extrude(3,1.) ++md.collapse() ++ ++#Dakota options ++ ++#dakota version ++version = IssmConfig('_DAKOTA_VERSION_') ++version = float(version[0]) ++ ++#variables ++md.qmu.variables.drag_coefficient = normal_uncertain.normal_uncertain('scaled_BasalforcingsFloatingiceMeltingRate',1,0.1) ++ ++#responses ++md.qmu.responses.IceMass1 = response_function.response_function('Outputdefinition5',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.IceVolume1 = response_function.response_function('Outputdefinition6',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.IceVolumeAboveFloatation1 = response_function.response_function('Outputdefinition7',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.IceVolumeAboveFloatation = response_function.response_function('IceVolumeAboveFloatation',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.GroundedArea1 = response_function.response_function('Outputdefinition1',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.FloatingArea1 = response_function.response_function('Outputdefinition2',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.TotalFloatingBmb1 = response_function.response_function('Outputdefinition3',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.TotalGroundedBmb1 = response_function.response_function('Outputdefinition4',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.TotalSmb1 = response_function.response_function('Outputdefinition8',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.TotalSmb2 = response_function.response_function('Outputdefinition9',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++md.qmu.responses.FloatingArea = response_function.response_function('FloatingArea',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++ ++#method ++md.qmu.method = dakota_method.dakota_method('nond_samp') ++md.qmu.method = dmeth_params_set(md.qmu.method,'seed',1234,'samples',20,'sample_type','random') ++ ++#parameters ++md.qmu.params.direct = True ++md.qmu.params.analysis_components = '' ++md.qmu.params.tabular_graphics_data = True ++ ++if version >= 6: ++ md.qmu.params.analysis_driver = 'matlab' ++ md.qmu.params.evaluation_scheduling = 'master' ++ md.qmu.params.processors_per_evaluation = 2 ++else: ++ md.qmu.params.analysis_driver = 'stressbalance' ++ md.qmu.params.evaluation_concurrency = 1 ++ ++#partitioning ++md.qmu.numberofpartitions = 10 ++md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions,'weighting','on') ++md.qmu.partition = md.qmu.partition-1 ++md.qmu.isdakota = 1 ++ ++md.stressbalance.reltol = 10**-5 #tighten for qmu analyses ++ ++#solve ++md.verbose = verbose('000000000') # this line is recommended ++md = solve(md,'Transient','overwrite','y') ++ ++#Fields and tolerances to track changes ++md.qmu.results = md.results.dakota ++ ++#we put all the mean and stdev data in the montecarlo field, which we will use to test for success. ++md.results.dakota.montecarlo = [] ++for i in range(11): ++ md.results.dakota.montecarlo.append(md.results.dakota.dresp_out[i].mean) ++ ++for i in range(11): ++ md.results.dakota.montecarlo.append(md.results.dakota.dresp_out[i].stddev) ++ ++field_names = ['montecarlo'] ++field_tolerances = [1e-11] ++field_values = [md.results.dakota.montecarlo] +Index: ../trunk-jpl/src/m/modules/Chaco.py +=================================================================== +--- ../trunk-jpl/src/m/modules/Chaco.py (revision 23230) ++++ ../trunk-jpl/src/m/modules/Chaco.py (revision 23231) +@@ -4,7 +4,7 @@ + '''CHACO + + Usage: +- [assgn] = Chaco(A,vwgts,ewgts,x,y,z,options,nparts,goal); ++ assgn = Chaco(A,vwgts,ewgts,x,y,z,options,nparts,goal); + + A: Input adjacency matrix + vwgts: weights for all vertices +Index: ../trunk-jpl/src/m/modules/Scotch.py +=================================================================== +--- ../trunk-jpl/src/m/modules/Scotch.py (revision 23230) ++++ ../trunk-jpl/src/m/modules/Scotch.py (revision 23231) +@@ -1,7 +1,7 @@ + from Scotch_python import Scotch_python + + def Scotch(*varargin): +-'''SCOTCH - Scotch partitioner ++ '''SCOTCH - Scotch partitioner + + Usage: + maptab=Scotch(adjmat,vertlb,vertwt,edgewt,archtyp,archpar,Scotch-specific parameters) +Index: ../trunk-jpl/src/m/partition/partitioner.py +=================================================================== +--- ../trunk-jpl/src/m/partition/partitioner.py (revision 23230) ++++ ../trunk-jpl/src/m/partition/partitioner.py (revision 23231) +@@ -2,10 +2,11 @@ + from pairoptions import * + import MatlabFuncs as m + from adjacency import * +-#from Chaco import * ++from Chaco import * + #from Scotch import * +-#from MeshPartition import * ++from MeshPartition import * + from project3d import * ++from mesh2d import * + + def partitioner(md,*varargin): + help =''' +@@ -59,30 +60,31 @@ + print 'skipping adjacency matrix computation as requested in the options' + + if m.strcmpi(package,'chaco'): +- raise RuntimeError('Chaco is not currently supported for this function') ++ #raise RuntimeError('Chaco is not currently supported for this function') + + # default method (from chaco.m) +- #method=np.array([1,1,0,0,1,1,50,0,.001,7654321]).reshape(-1,1) +- #method[0]=3 # global method (3=inertial (geometric)) +- #method[2]=0 # vertex weights (0=off, 1=on) ++ method=np.array([1,1,0,0,1,1,50,0,.001,7654321]) ++ method[0]=3 # global method (3=inertial (geometric)) ++ method[2]=0 # vertex weights (0=off, 1=on) + + #specify bisection +- #method[5]=options.getfieldvalue('section')# ndims (1=bisection, 2=quadrisection, 3=octasection) ++ method[5]=options.getfieldvalue('section')# ndims (1=bisection, 2=quadrisection, 3=octasection) + + #are we using weights? +- #if m.strcmpi(options.getfieldvalue('weighting'),'on'): +- #weights=np.floor(md.qmu.vertex_weight/min(md.qmu.vertex_weight)) +- #method[2]=1 +- #else: +- #weights=[] ++ if m.strcmpi(options.getfieldvalue('weighting'),'on'): ++ weights=np.floor(md.qmu.vertex_weight/min(md.qmu.vertex_weight)) ++ method[2]=1 ++ else: ++ weights=[] + ++ method = method.reshape(-1,1) # transpose to 1x10 instead of 10 ++ + # partition into nparts +- #if isinstance(md.mesh,mesh2d): +- #part=Chaco(md.qmu.adjacency,weights,[],md.mesh.x, md.mesh.y,np.zeros((md.mesh.numberofvertices,)),method,npart,[]).T+1 #index partitions from 1 up. like metis. +- #else: +- #part=Chaco(md.qmu.adjacency,weights,[],md.mesh.x, md.mesh.y,md.mesh.z,method,npart,[]).T+1 #index partitions from 1 up. like metis. ++ if isinstance(md.mesh,mesh2d): ++ part=np.array(Chaco(md.qmu.adjacency,weights,np.array([]),md.mesh.x, md.mesh.y,np.zeros((md.mesh.numberofvertices,)),method,npart,np.array([]))).T+1 #index partitions from 1 up. like metis. ++ else: ++ part=np.array(Chaco(md.qmu.adjacency,weights,np.array([]),md.mesh.x, md.mesh.y,md.mesh.z,method,npart,np.array([]))).T+1 #index partitions from 1 up. like metis. + +- + elif m.strcmpi(package,'scotch'): + raise RuntimeError('Scotch is not currently supported for this function') + +Index: ../trunk-jpl/src/m/qmu/dakota_out_parse.py +=================================================================== +--- ../trunk-jpl/src/m/qmu/dakota_out_parse.py (revision 23230) ++++ ../trunk-jpl/src/m/qmu/dakota_out_parse.py (revision 23231) +@@ -240,6 +240,17 @@ + dmin95 =prctile_issm(data,5,0) + dmax95 =prctile_issm(data,95,0) + ++ # Note: the following line may cause the following warning ++ # (should not crash or invalidate results) when one of ++ # the inputs does not change with respect to the ++ # other/s causing an internal divide-by-zero error ++ ++ #/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py:3163: ++ # RuntimeWarning: invalid value encountered in true_divide ++ # c /= stddev[:,None] ++ ++ # (and/or the same but with "c /= stddev[None, :]") ++ + dcorrel=np.corrcoef(data.T) + + # divide the data into structures for consistency +Index: ../trunk-jpl/src/m/qmu/dakota_in_write.py +=================================================================== +--- ../trunk-jpl/src/m/qmu/dakota_in_write.py (revision 23230) ++++ ../trunk-jpl/src/m/qmu/dakota_in_write.py (revision 23231) +@@ -61,7 +61,7 @@ + + filei2=fullfile(pathstr,name+ext) + +- print 'Opening Dakota input file \''+filei2 + '\'' ++ print 'Opening Dakota input file \''+filei2 + '\'.' + try: + with open(filei2,'w+') as fidi: + +Index: ../trunk-jpl/src/m/qmu/process_qmu_response_data.m +=================================================================== +--- ../trunk-jpl/src/m/qmu/process_qmu_response_data.m (revision 23230) ++++ ../trunk-jpl/src/m/qmu/process_qmu_response_data.m (revision 23231) +@@ -42,9 +42,7 @@ + + %ok, process the domains named in qmu_mass_flux_profiles, to build a list of segments (MatArray) + md.qmu.mass_flux_segments=cell(num_mass_flux,1); +- md.qmu.mass_flux_segments + for i=1:num_mass_flux, + md.qmu.mass_flux_segments{i}=MeshProfileIntersection(md.mesh.elements,md.mesh.x,md.mesh.y,[md.qmu.mass_flux_profile_directory '/' md.qmu.mass_flux_profiles{i}]); + end +- md.qmu.mass_flux_segments + end +Index: ../trunk-jpl/src/wrappers/Chaco/Chaco.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/Chaco/Chaco.cpp (revision 23230) ++++ ../trunk-jpl/src/wrappers/Chaco/Chaco.cpp (revision 23231) +@@ -46,15 +46,15 @@ + + /*Fetch Data*/ + FetchChacoData(&nvtxs,&adjacency,&start,&ewgts,A_IN,EWGTS_IN); +- FetchData(&vwgts,&nterms,VWGTS_IN); +- FetchData(&x,&nterms,X_IN); +- FetchData(&y,&nterms,Y_IN); +- FetchData(&z,&nterms,Z_IN); +- FetchData(&in_options,&nterms,OPTNS_IN); ++ FetchData(&vwgts,&nterms,VWGTS_IN); ++ FetchData(&x,&nterms,X_IN); ++ FetchData(&y,&nterms,Y_IN); ++ FetchData(&z,&nterms,Z_IN); ++ FetchData(&in_options,&nterms,OPTNS_IN); + for (i=0;i<(nterms<10?nterms:10);i++) options[i]=in_options[i]; //copy in_options into default options +- FetchData(&npart,NPARTS_IN); ++ FetchData(&npart,NPARTS_IN); + //int * nparts=xNew(1); nparts[0]=npart; //weird Chacox interface ain't it? +- FetchData(&goal,&nterms,GOAL_IN); ++ FetchData(&goal,&nterms,GOAL_IN); + + /*Allocate output: */ + short* assignment = xNewZeroInit(nvtxs); +Index: ../trunk-jpl/src/wrappers/python/io/pythonio.h +=================================================================== +--- ../trunk-jpl/src/wrappers/python/io/pythonio.h (revision 23230) ++++ ../trunk-jpl/src/wrappers/python/io/pythonio.h (revision 23231) +@@ -50,6 +50,9 @@ + void FetchData(Contours** pcontours,PyObject* py_list); + void FetchChacoData(int* pnvtxs,int** padjacency,int** pstart,float** pewgts,PyObject* A_IN,PyObject* EWGTS_IN); + ++void pyGetJc(double* a, int nvtxs, int* Jc); ++void pyGetIr(double* a, int nvtxs, int nzmax, int* Ir); ++ + int CheckNumPythonArguments(PyObject* inputs,int NRHS, void (*function)( void )); + + /*Utils*/ +Index: ../trunk-jpl/src/wrappers/python/io/FetchPythonData.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/python/io/FetchPythonData.cpp (revision 23230) ++++ ../trunk-jpl/src/wrappers/python/io/FetchPythonData.cpp (revision 23231) +@@ -31,7 +31,7 @@ + #endif + } + else if (PyInt_Check(py_float)) +- dscalar=(double)PyInt_AsLong(py_float); ++ dscalar=(double)PyInt_AsLong(py_float); + else if (PyBool_Check(py_float)) + dscalar=(double)PyLong_AsLong(py_float); + else if (PyTuple_Check(py_float) && (int)PyTuple_Size(py_float)==1) +@@ -131,7 +131,8 @@ + /*output: */ + double* dmatrix=NULL; + double* matrix=NULL; +- int M,N; ++ int M=0; ++ int N=0; + int ndim; + npy_intp* dims=NULL; + +@@ -235,7 +236,8 @@ + + /*output: */ + int* matrix=NULL; +- int M,N; ++ int M=0; ++ int N=0; + int ndim; + npy_intp* dims=NULL; + +@@ -324,7 +326,8 @@ + /*output: */ + bool* bmatrix=NULL; + bool* matrix=NULL; +- int M,N; ++ int M=0; ++ int N=0; + int ndim; + npy_intp* dims=NULL; + +@@ -410,7 +413,7 @@ + /*output: */ + double* dvector=NULL; + double* vector=NULL; +- int M; ++ int M=0; + int ndim; + npy_intp* dims=NULL; + +@@ -498,7 +501,7 @@ + + /*output: */ + float* vector=NULL; +- int M; ++ int M=0; + int ndim; + npy_intp* dims=NULL; + +@@ -538,7 +541,7 @@ + + /*transform into int vector: */ + vector=xNew(M); +- for(i=0;i(M); +- for(i=0;i(contourname); + *pcontours=contours; + } ++ ++void FetchChacoData(int* pnvtxs,int** padjacency,int** pstart,float** pewgts,PyObject* A_IN, PyObject* EWGTS_IN){/*{{{*/ ++ ++ double* a = ((double*)PyArray_DATA((PyArrayObject*)A_IN)); ++ int ndim = PyArray_NDIM((PyArrayObject*)A_IN); ++ int nzmax = PyArray_CountNonzero((PyArrayObject*)A_IN); ++ ++ /*Fetch adjacency matrix:*/ ++ int nvtxs = PyArray_DIMS((PyArrayObject*)A_IN)[1]; ++ ++ int* mwstart = xNewZeroInit(nvtxs+1); ++ pyGetJc(a,nvtxs,mwstart); ++ ++ int* mwadjacency = xNewZeroInit(nzmax); ++ pyGetIr(a,nvtxs,nzmax,mwadjacency); ++ ++ int* start = xNew(nvtxs+1); ++ for(int i=0;i(nzmax); ++ for(int i=0; i(nedges); ++ for(int i = 0; i= 3 + /*FUNCTION FetchData(char** pstring,PyObject* py_unicode){{{*/ Index: /issm/oecreview/Archive/23185-23389/ISSM-23231-23232.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23231-23232.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23231-23232.diff (revision 23390) @@ -0,0 +1,237 @@ +Index: ../trunk-jpl/src/c/cores/gia_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/gia_core.cpp (revision 23231) ++++ ../trunk-jpl/src/c/cores/gia_core.cpp (revision 23232) +@@ -10,6 +10,9 @@ + #include "../solutionsequences/solutionsequences.h" + void gia_core(FemModel* femmodel){ + ++ /*Start profiler*/ ++ femmodel->profiler->Start(GIACORE); ++ + Vector *wg = NULL; + Vector *dwdtg = NULL; + IssmDouble *x = NULL; +@@ -55,4 +58,7 @@ + + xDelete(x); + xDelete(y); ++ ++ /*End profiler*/ ++ femmodel->profiler->Stop(GIACORE); + } +Index: ../trunk-jpl/src/c/cores/transient_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/transient_core.cpp (revision 23231) ++++ ../trunk-jpl/src/c/cores/transient_core.cpp (revision 23232) +@@ -400,6 +400,10 @@ + } + + if(isgroundingline){ ++ ++ /*Start profiler*/ ++ femmodel->profiler->Start(GROUNDINGLINECORE); ++ + if(VerboseSolution()) _printf0_(" computing new grounding line position\n"); + GroundinglineMigrationx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + +@@ -409,6 +413,9 @@ + extrudefrombase_core(femmodel); + femmodel->parameters->SetParam(SurfaceEnum,InputToExtrudeEnum); + extrudefrombase_core(femmodel); ++ ++ /*Stop profiler*/ ++ femmodel->profiler->Stop(GROUNDINGLINECORE); + + if(save_results){ + int outputs[3] = {SurfaceEnum,BaseEnum,MaskGroundediceLevelsetEnum}; +Index: ../trunk-jpl/src/c/cores/esa_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/esa_core.cpp (revision 23231) ++++ ../trunk-jpl/src/c/cores/esa_core.cpp (revision 23232) +@@ -11,6 +11,9 @@ + + void esa_core(FemModel* femmodel){ /*{{{*/ + ++ /*Start profiler*/ ++ femmodel->profiler->Start(ESACORE); ++ + Vector *U_radial = NULL; + Vector *U_north = NULL; + Vector *U_east = NULL; +@@ -111,6 +114,9 @@ + delete U_y; + if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} + } ++ ++ /*End profiler*/ ++ femmodel->profiler->Stop(ESACORE); + + } + /*}}}*/ +Index: ../trunk-jpl/src/c/cores/movingfront_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/movingfront_core.cpp (revision 23231) ++++ ../trunk-jpl/src/c/cores/movingfront_core.cpp (revision 23232) +@@ -10,6 +10,9 @@ + #include "../modules/modules.h" + + void movingfront_core(FemModel* femmodel){ ++ ++ /*Start profiler*/ ++ femmodel->profiler->Start(MOVINGFRONTCORE); + + /* intermediaries */ + bool save_results,isstressbalance,ismasstransport,isthermal,isenthalpy,islevelset,ismovingfront; +@@ -97,4 +100,7 @@ + int outputs[1] = {IceMaskNodeActivationEnum}; + femmodel->RequestedOutputsx(&femmodel->results,&outputs[0],1); + } ++ ++ /*End profiler*/ ++ femmodel->profiler->Stop(MOVINGFRONTCORE); + } +Index: ../trunk-jpl/src/c/cores/damage_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/damage_core.cpp (revision 23231) ++++ ../trunk-jpl/src/c/cores/damage_core.cpp (revision 23232) +@@ -10,7 +10,10 @@ + #include "../solutionsequences/solutionsequences.h" + + void damage_core(FemModel* femmodel){ +- ++ ++ /*Start profiler*/ ++ femmodel->profiler->Start(DAMAGECORE); ++ + /*intermediary*/ + bool save_results; + bool dakota_analysis = false; +@@ -47,4 +50,7 @@ + } + xDelete(requested_outputs); + } ++ ++ /*End profiler*/ ++ femmodel->profiler->Stop(DAMAGECORE); + } +Index: ../trunk-jpl/src/c/cores/hydrology_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/hydrology_core.cpp (revision 23231) ++++ ../trunk-jpl/src/c/cores/hydrology_core.cpp (revision 23232) +@@ -11,6 +11,9 @@ + + void hydrology_core(FemModel* femmodel){ + ++ /*Start profiler*/ ++ femmodel->profiler->Start(HYDROLOGYCORE); ++ + /*intermediary*/ + int hydrology_model; + int solution_type; +@@ -149,4 +152,7 @@ + } + xDelete(requested_outputs); + } ++ ++ /*End profiler*/ ++ femmodel->profiler->Stop(HYDROLOGYCORE); + } +Index: ../trunk-jpl/src/c/cores/smb_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/smb_core.cpp (revision 23231) ++++ ../trunk-jpl/src/c/cores/smb_core.cpp (revision 23232) +@@ -10,7 +10,10 @@ + #include "../solutionsequences/solutionsequences.h" + + void smb_core(FemModel* femmodel){ +- ++ ++ /*Start profiler*/ ++ femmodel->profiler->Start(SMBCORE); ++ + /*parameters: */ + Analysis* analysis=NULL; + int smb_model; +@@ -44,4 +47,7 @@ + + /*Free ressources:*/ + if(numoutputs){for(int i=0;i(requested_outputs[i]);} xDelete(requested_outputs);} ++ ++ /*End profiler*/ ++ femmodel->profiler->Stop(SMBCORE); + } +Index: ../trunk-jpl/src/c/cores/sealevelrise_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/sealevelrise_core.cpp (revision 23231) ++++ ../trunk-jpl/src/c/cores/sealevelrise_core.cpp (revision 23232) +@@ -12,6 +12,9 @@ + /*cores:*/ + void sealevelrise_core(FemModel* femmodel){ /*{{{*/ + ++ /*Start profiler*/ ++ femmodel->profiler->Start(SLRCORE); ++ + /*Parameters, variables:*/ + bool save_results; + bool isslr=0; +@@ -53,6 +56,9 @@ + + /*requested dependents: */ + if(solution_type==SealevelriseSolutionEnum)femmodel->RequestedDependentsx(); ++ ++ /*End profiler*/ ++ femmodel->profiler->Stop(SLRCORE); + } + /*}}}*/ + void geodetic_core(FemModel* femmodel){ /*{{{*/ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23231) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23232) +@@ -864,10 +864,17 @@ + /*Individual cores*/ + _printf0_("Individual core profiling\n"); + if(profiler->Used(THERMALCORE)) _printf0_(" "<TotalTime(THERMALCORE) << " sec\n"); ++ if(profiler->Used(HYDROLOGYCORE)) _printf0_(" "<TotalTime(HYDROLOGYCORE) << " sec\n"); + if(profiler->Used(STRESSBALANCECORE)) _printf0_(" "<TotalTime(STRESSBALANCECORE) << " sec\n"); ++ if(profiler->Used(DAMAGECORE)) _printf0_(" "<TotalTime(DAMAGECORE) << " sec\n"); ++ if(profiler->Used(MOVINGFRONTCORE)) _printf0_(" "<TotalTime(MOVINGFRONTCORE) << " sec\n"); + if(profiler->Used(MASSTRANSPORTCORE)) _printf0_(" "<TotalTime(MASSTRANSPORTCORE) << " sec\n"); ++ if(profiler->Used(SMBCORE)) _printf0_(" "<TotalTime(SMBCORE) << " sec\n"); ++ if(profiler->Used(GROUNDINGLINECORE)) _printf0_(" "<TotalTime(GROUNDINGLINECORE) << " sec\n"); ++ if(profiler->Used(GIACORE)) _printf0_(" "<TotalTime(GIACORE) << " sec\n"); ++ if(profiler->Used(ESACORE)) _printf0_(" "<TotalTime(ESACORE) << " sec\n"); ++ if(profiler->Used(SLRCORE)) _printf0_(" "<TotalTime(SLRCORE) << " sec\n"); + +- + /*Add to results: */ + results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingSolutionTimeEnum, solution_time)); + results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentMemEnum, solution_memory)); +Index: ../trunk-jpl/src/c/classes/Profiler.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Profiler.h (revision 23231) ++++ ../trunk-jpl/src/c/classes/Profiler.h (revision 23232) +@@ -15,10 +15,18 @@ + #define CORE 2 /*Profiling solution */ + #define SOLVER 3 /*Profiling solution */ + #define ADCORE 4 /*Profiling AD */ +-#define THERMALCORE 5 /*Profiling THERMAL */ +-#define STRESSBALANCECORE 6 /*Profiling STRESSBALANCE */ +-#define MASSTRANSPORTCORE 7 /*Profiling MASSTRANSPORT */ +-#define MAXPROFSIZE 8 /*Used to initialize static arrays*/ ++#define THERMALCORE 5 /*Profiling THERMAL */ ++#define HYDROLOGYCORE 6 /*Profiling HYDROLOGY */ ++#define STRESSBALANCECORE 7 /*Profiling STRESSBALANCE */ ++#define DAMAGECORE 8 /*Profiling DAMAGE */ ++#define MOVINGFRONTCORE 9 /*Profiling MOVINGFRONT */ ++#define MASSTRANSPORTCORE 10 /*Profiling MASSTRANSPORT */ ++#define SMBCORE 11 /*Profiling SMB */ ++#define GROUNDINGLINECORE 12 /*Profiling GROUDINGLINE MIGRATION */ ++#define GIACORE 13 /*Profiling GIA */ ++#define ESACORE 14 /*Profiling ESA */ ++#define SLRCORE 15 /*Profiling SLR */ ++#define MAXPROFSIZE 16 /*Used to initialize static arrays*/ + + class Profiler: public Object{ + Index: /issm/oecreview/Archive/23185-23389/ISSM-23232-23233.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23232-23233.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23232-23233.diff (revision 23390) @@ -0,0 +1,37 @@ +Index: ../trunk-jpl/externalpackages/adjointmpi/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/adjointmpi/install.sh (nonexistent) ++++ ../trunk-jpl/externalpackages/adjointmpi/install.sh (revision 23233) +@@ -0,0 +1,25 @@ ++#!/bin/bash ++set -eu ++ ++#Some cleanup ++rm -rf install ++ ++#Almost the same as adjoinable mpi but some adaptations to CoDiPack https://github.com/michel2323/AdjointMPI ++svn co https://github.com/michel2323/AdjointMPI.git/trunk src ++mkdir install ++ ++cd src ++autoreconf -fi ++ ./configure \ ++ --prefix="$ISSM_DIR/externalpackages/adjointmpi/install" \ ++ --with-mpi-root="$ISSM_DIR/externalpackages/mpich/install" \ ++ CXXFLAGS="-O2 -fPIC" CFLAGS="-O2 -fPIC" ++ ++#Compile adjoinablempi ++make clean ++if [ $# -eq 0 ]; then ++ make ++else ++ make -j $1 ++fi ++make install + +Property changes on: ../trunk-jpl/externalpackages/adjointmpi/install.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property Index: /issm/oecreview/Archive/23185-23389/ISSM-23233-23234.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23233-23234.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23233-23234.diff (revision 23390) @@ -0,0 +1,29 @@ +Index: ../trunk-jpl/jenkins/linux64_ross_dakota +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_dakota (revision 23233) ++++ ../trunk-jpl/jenkins/linux64_ross_dakota (revision 23234) +@@ -10,6 +10,8 @@ + ISSM_CONFIG='--prefix=$ISSM_DIR\ + --disable-static \ + --with-matlab-dir=$MATLAB_PATH \ ++ --with-python-dir=/usr \ ++ --with-python-numpy-dir=/home/jenkins/.local/lib/python2.7/site-packages/numpy \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpicxx -lmpifort" \ +@@ -29,7 +31,7 @@ + + #PYTHON and MATLAB testing + MATLAB_TEST=1 +-PYTHON_TEST=0 ++PYTHON_TEST=1 + + #-----------------------------------# + # 3: External packages installation # +@@ -62,5 +64,5 @@ + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-PYTHON_NROPTIONS="--exclude 243 701 702 435" ++PYTHON_NROPTIONS="--exclude 243 701 702 435 --include_name 'Dakota'" + MATLAB_NROPTIONS="'exclude',[243,701,702,435]" Index: /issm/oecreview/Archive/23185-23389/ISSM-23234-23235.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23234-23235.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23234-23235.diff (revision 23390) @@ -0,0 +1,132 @@ +Index: ../trunk-jpl/test/NightlyRun/test2084.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test2084.m (revision 23234) ++++ ../trunk-jpl/test/NightlyRun/test2084.m (revision 23235) +@@ -1,5 +1,4 @@ +- +-%Test Name: GiaCaron. ++%Test Name: GiaCaron + %Forward Love number solution for a viscoelastic earth, model M3-L70-V01 from + %Spada, G., Barletta, V. R., Klemann, V., Riva, R. E. M., Martinec, Z., + %Gasperini, P., Lund, B., Wolf, D., Vermeersen, L. L. A. and King, M. A. +@@ -38,7 +37,7 @@ + %Fields and tolerances to track changes + %loading love numbers + field_names ={'LoveH_loading_elastic','LoveK_loading_elastic','LoveL_loading_elastic'}; +-field_tolerances={7.0e-10,7.0e-10,7.0e-10}; ++field_tolerances={4.3e-9,4.3e-9,4.3e-9}; + field_values={... + (md.results.LoveSolution.LoveHr(:,1)),... + (md.results.LoveSolution.LoveKr(:,1)),... +@@ -56,7 +55,7 @@ + + %Fields and tolerances to track changes + field_names ={field_names{:},'LoveH_loading_realpart','LoveK_loading_realpart','LoveL_loading_realpart','LoveH_loading_imagpart','LoveK_loading_imagpart','LoveL_loading_imagpart'}; +-field_tolerances={field_tolerances{:},5e-7,5e-7,5e-7,5e-7,5e-7,5e-7}; ++field_tolerances={field_tolerances{:},4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9}; + field_values={field_values{:},... + (md.results.LoveSolution.LoveHr(:,:)),... + (md.results.LoveSolution.LoveKr(:,:)),... +@@ -74,7 +73,7 @@ + + %tidal love numbers + field_names ={field_names{:},'LoveH_tidal_elastic','LoveK_tidal_elastic','LoveL_tidal_elastic','LoveH_tidal_realpart','LoveK_tidal_realpart','LoveL_tidal_realpart','LoveH_tidal_imagpart','LoveK_tidal_imagpart','LoveL_tidal_imagpart'}; +-field_tolerances={field_tolerances{:},3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6}; ++field_tolerances={field_tolerances{:},4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9}; + field_values={field_values{:},... + (md.results.LoveSolution.LoveHr(:,1)),... + (md.results.LoveSolution.LoveKr(:,1)),... +@@ -114,7 +113,7 @@ + %md=solve(md,'lv'); + % + %field_names ={field_names{:},'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'}; +-%field_tolerances={field_tolerances{:},2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7,2e-7}; ++%field_tolerances={field_tolerances{:},4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9}; + %field_values={field_values{:},... + % (md.results.LoveSolution.LoveHr(:,1)),... + % (md.results.LoveSolution.LoveKr(:,1)),... +@@ -146,7 +145,7 @@ + md.love.nfreq=length(md.love.frequencies); + + field_names ={field_names{:},'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'}; +-field_tolerances={field_tolerances{:},6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7}; ++field_tolerances={field_tolerances{:},4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9}; + field_values={field_values{:},... + (md.results.LoveSolution.LoveHr(:,1)),... + (md.results.LoveSolution.LoveKr(:,1)),... +Index: ../trunk-jpl/test/NightlyRun/test2084.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test2084.py (revision 23234) ++++ ../trunk-jpl/test/NightlyRun/test2084.py (revision 23235) +@@ -1,9 +1,10 @@ +-#Test Name: GiaCaron. Forward Love number solution for a viscoelastic earth, +-# model M3-L70-V01 from Spada, G., Barletta, V. R., Klemann, V., Riva, R. E. M., +-# Martinec, Z., Gasperini, P., Lund, B., Wolf, D., Vermeersen, L. L. A. +-# and King, M. A. (2011), A benchmark study for glacial isostatic +-# adjustment codes. Geophysical Journal International, +-# 185: 106-132. doi:10.1111/j.1365-246X.2011.04952.x ++#Test Name: GiaCaron ++#Forward Love number solution for a viscoelastic earth, ++#model M3-L70-V01 from Spada, G., Barletta, V. R., Klemann, V., Riva, R. E. M., ++#Martinec, Z., Gasperini, P., Lund, B., Wolf, D., Vermeersen, L. L. A. ++#and King, M. A. (2011), A benchmark study for glacial isostatic ++#adjustment codes. Geophysical Journal International, ++#185: 106-132. doi:10.1111/j.1365-246X.2011.04952.x + + from model import * + from socket import gethostname +@@ -47,8 +48,8 @@ + + #Fields and tolerances to track changes + #loading love numbers +-field_names=['LoveHe','LoveKe','LoveLe'] +-field_tolerances=[3.7e-9,3.7e-9,3.7e-9] ++field_names=['LoveH_loading_elastic','LoveK_loading_elastic','LoveL_loading_elastic'] ++field_tolerances=[4.3e-9,4.3e-9,4.3e-9] + field_values=[ + np.array(md.results.LoveSolution.LoveHr)[:,0], + np.array(md.results.LoveSolution.LoveKr)[:,0], +@@ -66,8 +67,8 @@ + + #Fields and tolerances to track changes + #loading love numbers +-field_names+=['LoveHlr','LoveKlr','LoveLlr','LoveHli','LoveKli','LoveLli'] +-field_tolerances+=[3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9] ++field_names+=['LoveH_loading_realpart','LoveK_loading_realpart','LoveL_loading_realpart','LoveH_loading_imagpart','LoveK_loading_imagpart','LoveL_loading_imagpart'] ++field_tolerances+=[4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9] + field_values+=[ + np.array(md.results.LoveSolution.LoveHr), + np.array(md.results.LoveSolution.LoveKr), +@@ -86,8 +87,8 @@ + md=solve(md,'lv') + + #tidal love numbers, check +-field_names+=['LoveHtr','LoveKtr','LoveLtr','LoveHti','LoveKti','LoveLti'] +-field_tolerances+=[3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9] ++field_names+=['LoveH_tidal_elastic','LoveK_tidal_elastic','LoveL_tidal_elastic','LoveH_tidal_realpart','LoveK_tidal_realpart','LoveL_tidal_realpart','LoveH_tidal_imagpart','LoveK_tidal_imagpart','LoveL_tidal_imagpart'] ++field_tolerances+=[4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9] + field_values+=[ + np.array(md.results.LoveSolution.LoveHr)[:,0], + np.array(md.results.LoveSolution.LoveKr)[:,0], +@@ -126,8 +127,8 @@ + #md.materials.numlayers=len(md.materials.viscosity) + #md=solve(md,'lv') + # +-#field_names=[field_names,'LoveHmr','LoveKmr','LoveLmr','LoveHmi','LoveKmi','LoveLmi'] +-#field_tolerances=[field_tolerances,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13,1e-13] ++#field_names=[field_names,'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'] ++#field_tolerances=[field_tolerances,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9] + #field_values=[field_values,\ + # (md.results.LoveSolution.LoveHr[:][0]),\ + # (md.results.LoveSolution.LoveKr[:][0]),\ +@@ -185,8 +186,8 @@ + -1])*2*pi).reshape(-1,1)/cst + md.love.nfreq=len(md.love.frequencies) + +-field_names+=['LoveHmr','LoveKmr','LoveLmr','LoveHmi','LoveKmi','LoveLmi'] +-field_tolerances+=[3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9,3.7e-9] ++field_names+=['LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'] ++field_tolerances+=[4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9,4.3e-9] + field_values+=[ + np.array(md.results.LoveSolution.LoveHr)[:,0], + np.array(md.results.LoveSolution.LoveKr)[:,0], Index: /issm/oecreview/Archive/23185-23389/ISSM-23235-23236.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23235-23236.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23235-23236.diff (revision 23390) @@ -0,0 +1,40 @@ +Index: ../trunk-jpl/src/m/classes/numberedcostfunction.m +=================================================================== +--- ../trunk-jpl/src/m/classes/numberedcostfunction.m (revision 23235) ++++ ../trunk-jpl/src/m/classes/numberedcostfunction.m (revision 23236) +@@ -1,4 +1,4 @@ +-%M1QN3INVERSION class definition ++%NUMBEREDCOSTFUNCTION class definition + % + % Usage: + % numberedcostfunction=numberedcostfunction(); +@@ -43,20 +43,20 @@ + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + +- num_costfunc=size(md.inversion.cost_functions,2); ++ num_costfunc=size(self.cost_functions,2); + +- md = checkfield(md,'fieldname','inversion.cost_functions','size',[1 num_costfunc],'values',supportedcostfunctions()); +- md = checkfield(md,'fieldname','inversion.cost_functions_coefficients','size',[md.mesh.numberofvertices num_costfunc],'>=',0); +- ++ md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.dependent{X}.cost_functions','field',self.cost_functions,'size',[1 num_costfunc],'values',supportedcostfunctions()); ++ md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.cost_functions_coefficients','field',self.cost_functions_coefficients,'size',[md.mesh.numberofvertices numel(self.cost_functions)],'>=',0); ++ + if strcmp(solution,'BalancethicknessSolution') +- md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); +- md = checkfield(md,'fieldname','inversion.surface_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.thickness_obs','field',self.thickness_obs,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.surface_obs','field',self.surface_obs,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); + elseif strcmp(solution,'BalancethicknessSoftSolution') +- md = checkfield(md,'fieldname','inversion.thickness_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.thickness_obs','field',self.thickness_obs,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); + else +- md = checkfield(md,'fieldname','inversion.vx_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.vx_obs','field',self.vx_obs,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); + if ~strcmp(domaintype(md.mesh),'2Dvertical'), +- md = checkfield(md,'fieldname','inversion.vy_obs','size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); ++ md = checkfield(md,'fieldname','md.outputdefinition.definition{X}.vy_obs','field',self.vy_obs,'size',[md.mesh.numberofvertices 1],'NaN',1,'Inf',1); + end + end + end % }}} Index: /issm/oecreview/Archive/23185-23389/ISSM-23236-23237.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23236-23237.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23236-23237.diff (revision 23390) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/src/c/toolkits/issm/IssmToolkitUtils.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/issm/IssmToolkitUtils.cpp (revision 23236) ++++ ../trunk-jpl/src/c/toolkits/issm/IssmToolkitUtils.cpp (revision 23237) +@@ -85,18 +85,17 @@ + } /*}}}*/ + int IssmSolverTypeFromToolkitOptions(void){ /*{{{*/ + +- char* solver_type=NULL; + int solver_type_enum; +- int num_procs=0; + bool isparallel=false; + + /*first, figure out if we are running in parallel: */ +- num_procs=IssmComm::GetSize(); ++ int num_procs=IssmComm::GetSize(); + if(num_procs>1)isparallel=true; + + /*retrieve solver type as a string, from the Toolkits Options database, similar to what Petsc does. Actually, + *we try and stick with the Petsc vector types: */ +- solver_type=ToolkitOptions::GetToolkitOptionValue("solver_type"); ++ char* solver_type=ToolkitOptions::GetToolkitOptionValue("solver_type"); ++ if(!solver_type) _error_("Solver not set"); + + if (strcmp(solver_type,"mumps")==0){ + solver_type_enum=MumpsEnum; Index: /issm/oecreview/Archive/23185-23389/ISSM-23237-23238.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23237-23238.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23237-23238.diff (revision 23390) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/m/mesh/triangle.py +=================================================================== +--- ../trunk-jpl/src/m/mesh/triangle.py (revision 23237) ++++ ../trunk-jpl/src/m/mesh/triangle.py (revision 23238) +@@ -1,7 +1,6 @@ + import os.path + import numpy as np + from mesh2d import mesh2d +-from Triangle import Triangle + from NodeConnectivity import NodeConnectivity + from ElementConnectivity import ElementConnectivity + from Triangle_python import Triangle_python Index: /issm/oecreview/Archive/23185-23389/ISSM-23238-23239.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23238-23239.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23238-23239.diff (revision 23390) @@ -0,0 +1,108 @@ +Index: ../trunk-jpl/m4/issm_options.m4 +=================================================================== +--- ../trunk-jpl/m4/issm_options.m4 (revision 23238) ++++ ../trunk-jpl/m4/issm_options.m4 (revision 23239) +@@ -744,6 +744,45 @@ + fi + AM_CONDITIONAL([ESMF], [test x$HAVE_ESMF = xyes]) + dnl }}} ++ dnl codipack{{{ ++ AC_ARG_WITH([codipack-dir], ++ AS_HELP_STRING([--with-codipack-dir=DIR], [CoDiPack root directory.]), ++ [CODIPACK_ROOT=$withval],[CODIPACK_ROOT="no"]) ++ ++ dnl Check whether codipack is enabled ++ AC_MSG_CHECKING([for CoDiPack]) ++ if test "x$CODIPACK_ROOT" = "xno" ; then ++ HAVE_CODIPACK=no ++ else ++ HAVE_CODIPACK=yes ++ if ! test -d "$CODIPACK_ROOT"; then ++ AC_MSG_ERROR([codipack directory provided ($CODIPACK_ROOT) does not exist]); ++ fi ++ fi ++ AC_MSG_RESULT($HAVE_CODIPACK) ++ ++ dnl codipack headers and libraries ++ if test "x$HAVE_CODIPACK" == "xyes"; then ++ CODIPACKINCL="-I$CODIPACK_ROOT/include" ++ AC_DEFINE([_HAVE_CODIPACK_],[1],[with codipack in ISSM src]) ++ AC_DEFINE([_HAVE_AD_],[1],[with AD in ISSM src]) ++ AC_SUBST([CODIPACKINCL]) ++ fi ++ AM_CONDITIONAL([CODIPACK], [test x$HAVE_CODIPACK = xyes]) ++ AM_COND_IF(CODIPACK,[CXXFLAGS+=" -std=c++11"]) ++ dnl }}} ++ dnl tapeallocation {{{ ++ AC_ARG_ENABLE([tape-alloc], dnl feature ++ AS_HELP_STRING([--enable-tape-alloc],[turn tape allocation support on]), ++ [enable_tape_alloc=$enableval], [enable_tape_alloc=no]) ++ ++ dnl check whether enabled ++ AC_MSG_CHECKING(for tape memory allocation) ++ if test "x$enable_tape_alloc" = xyes; then ++ AC_DEFINE([_AD_TAPE_ALLOC_],[1],[Macro to enable a priori tape allocation for AD]) ++ fi ++ AC_MSG_RESULT($enable_tape_alloc) ++ dnl }}} + dnl adolc{{{ + AC_ARG_WITH([adolc-dir], + AS_HELP_STRING([--with-adolc-dir=DIR], [adolc root directory.]), +@@ -772,7 +811,7 @@ + AC_SUBST([ADOLCLIB]) + fi + AM_CONDITIONAL([ADOLC], [test x$HAVE_ADOLC = xyes]) +- AM_COND_IF(ADOLC,[CXXFLAGS+=" -std=c++11"]) ++ AM_COND_IF(ADOLC,[CXXFLAGS+=" -std=c++11"]) + dnl }}} + dnl adolc-version{{{ + AC_ARG_WITH([adolc-version], +@@ -876,7 +915,7 @@ + fi + AM_CONDITIONAL([GSL], [test x$HAVE_GSL = xyes]) + dnl }}} +- dnl adjoinable-mpi{{{ ++ dnl ampi (ADOLC){{{ + AC_ARG_WITH([ampi-dir], + AS_HELP_STRING([--with-ampi-dir=DIR], [adjoinable mpi root directory.]), + [AMPI_ROOT=$withval],[AMPI_ROOT="no"]) +@@ -911,6 +950,39 @@ + fi + AM_CONDITIONAL([AMPI], [test x$HAVE_AMPI = xyes]) + dnl }}} ++ dnl adjointmpi (CoDiPack){{{ ++ AC_ARG_WITH([adjointmpi-dir], ++ AS_HELP_STRING([--with-adjointmpi-dir=DIR], [adjoinable mpi root directory.]), ++ [ADJOINTMPI_ROOT=$withval],[ADJOINTMPI_ROOT="no"]) ++ ++ dnl Check whether adjointmpi is enabled ++ AC_MSG_CHECKING([for adjointmpi]) ++ if test "x$ADJOINTMPI_ROOT" = "xno" ; then ++ HAVE_ADJOINTMPI=no ++ else ++ HAVE_ADJOINTMPI=yes ++ if ! test -d "$ADJOINTMPI_ROOT"; then ++ AC_MSG_ERROR([adjointmpi directory provided ($ADJOINTMPI_ROOT) does not exist]); ++ fi ++ fi ++ AC_MSG_RESULT($HAVE_ADJOINTMPI) ++ ++ dnl adjointmpi headers and libraries ++ if test "x$HAVE_ADJOINTMPI" == "xyes"; then ++ if test "x$CODIPACK_ROOT" == "xno"; then ++ AC_MSG_ERROR([cannot run adjoint mpi without CoDiPack]); ++ fi ++ ADJOINTMPIINCL="-I$ADJOINTMPI_ROOT/include" ++ ADJOINTMPILIB="-L$ADJOINTMPI_ROOT/lib -lAMPI" ++ dnl Also set _HAVE_AMPI_, because the interface is (almost) the ++ dnl same as for adjoinable mpi... ++ AC_DEFINE([_HAVE_AMPI_],[1],[with adjoint mpi in ISSM src]) ++ AC_DEFINE([_HAVE_ADJOINTMPI_],[1],[with adjoint mpi in ISSM src]) ++ AC_SUBST([ADJOINTMPIINCL]) ++ AC_SUBST([ADJOINTMPILIB]) ++ fi ++ AM_CONDITIONAL([ADJOINTMPI], [test x$HAVE_ADJOINTMPI = xyes]) ++ dnl }}} + dnl rose{{{ + AC_ARG_WITH([rose-dir], + AS_HELP_STRING([--with-rose-dir=DIR], [rose root directory.]), Index: /issm/oecreview/Archive/23185-23389/ISSM-23239-23240.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23239-23240.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23239-23240.diff (revision 23390) @@ -0,0 +1,123 @@ +Index: ../trunk-jpl/src/c/shared/MemOps/MemOps.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/MemOps/MemOps.cpp (revision 23239) ++++ ../trunk-jpl/src/c/shared/MemOps/MemOps.cpp (revision 23240) +@@ -15,7 +15,7 @@ + + #if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) + template <> adouble* xNew(unsigned int size, const char* const contig) { +- if (*contig == 't') ++ if (contig[0] == 't' || contig[0] == 'c') + ensureContiguousLocations(size); + + adouble* aT_p=new adouble[size]; +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.h +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.h (revision 23239) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.h (revision 23240) +@@ -18,6 +18,7 @@ + void CreateParametersDakota(Parameters* parameters,IoModel* iomodel,char* rootpath); + void CreateOutputDefinitions(Elements* elements, Parameters* parameters,IoModel* iomodel); + void UpdateElementsAndMaterialsControl(Elements* elements,Parameters* parameters,Materials* materials, IoModel* iomodel); ++void UpdateElementsAndMaterialsControlAD(Elements* elements,Parameters* parameters,Materials* materials, IoModel* iomodel); + void UpdateElementsAndMaterialsDakota(Elements* elements,Materials* materials, IoModel* iomodel); + void UpdateElementsTransient(Elements* elements,Parameters* parameters,IoModel* iomodel,int analysis_type); + void CreateNodes(Nodes*nodes, IoModel* iomodel,int analysis,int finite_element,int approximation=NoneApproximationEnum); +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp (revision 23239) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp (revision 23240) +@@ -8,7 +8,6 @@ + #include "../../MeshPartitionx/MeshPartitionx.h" + #include "../ModelProcessorx.h" + +-#if !defined(_HAVE_ADOLC_) + void UpdateElementsAndMaterialsControl(Elements* elements,Parameters* parameters,Materials* materials, IoModel* iomodel){ + /*Intermediary*/ + bool control_analysis; +@@ -21,6 +20,14 @@ + char **cost_functions = NULL; + + /*Fetch parameters: */ ++ bool isautodiff; ++ iomodel->FindConstant(&isautodiff,"md.autodiff.isautodiff"); ++ if(isautodiff){ ++ UpdateElementsAndMaterialsControlAD(elements,parameters,materials,iomodel); ++ return; ++ } ++ ++ /*Fetch parameters: */ + iomodel->FindConstant(&control_analysis,"md.inversion.iscontrol"); + if(control_analysis) iomodel->FindConstant(&num_controls,"md.inversion.num_control_parameters"); + +@@ -125,9 +132,9 @@ + for(int i=0;i(controls[i]); + xDelete(controls); + } +-#else +-void UpdateElementsAndMaterialsControl(Elements* elements,Parameters* parameters,Materials* materials, IoModel* iomodel){ ++void UpdateElementsAndMaterialsControlAD(Elements* elements,Parameters* parameters,Materials* materials, IoModel* iomodel){ + ++ #if defined(_HAVE_ADOLC_) + /*Intermediaries*/ + int num_independent_objects,M,N,M_par,N_par; + char** names = NULL; +@@ -224,5 +231,7 @@ + /*Step2: create cost functions (dependents)*/ + + return; ++#else ++ _error_("ADOLC not compiled"); ++#endif + } +-#endif +Index: ../trunk-jpl/src/c/toolkits/issm/IssmMpiSparseMat.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/issm/IssmMpiSparseMat.h (revision 23239) ++++ ../trunk-jpl/src/c/toolkits/issm/IssmMpiSparseMat.h (revision 23240) +@@ -263,10 +263,10 @@ + } + + for(i=0;i ++#else ++#error "Cannot compile without HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#if defined(_HAVE_CODIPACK_) ++#include "codi.hpp" ++ ++template ++inline void getVectorPrimal(const Real* vec, Passive* pasVec, int n) { ++ for(int i = 0; i < n; ++i) { ++ pasVec[i]=vec[i].getValue(); ++ } ++} ++ ++template ++inline void setVectorPrimal(Real* vec, const Passive* pasVec, int n) { ++ for(int i = 0; i < n; ++i) { ++ vec[i].value() = pasVec[i]; ++ } ++} ++ ++template ++inline void getVectorGradData(const Real* vec, Data* dataVec, int n) { ++ for(int i = 0; i < n; ++i) { ++ dataVec[i]=vec[i].getGradientData(); ++ } ++} ++ ++template ++inline void getVectorPrimalAndGradData(const Real* vec, Passive* pasVec, Data* dataVec, int n) { ++ for(int i = 0; i < n; ++i) { ++ pasVec[i]=vec[i].getValue(); ++ dataVec[i]=vec[i].getGradientData(); ++ } ++} ++ ++template ++inline void getPrimalAndGradData(const Real& value, Passive& pas, Data& data) { ++ pas=value.getValue(); ++ data=value.getGradientData(); ++} ++ ++template ++inline void registerVector(Real* vec, Data* dataVec, int n) { ++ typename Real::TapeType& tape = Real::getGlobalTape(); ++ ++ for(int i = 0; i < n; ++i) { ++ tape.registerInput(vec[i]); ++ dataVec[i]=vec[i].getGradientData(); ++ } ++} ++ ++template ++inline void getVectorAdjoint(Tape& tape, const Data* dataVec, Adjoint* adjVec, int n) { ++ for(int i = 0; i < n; ++i) { ++ Data index = dataVec[i]; ++ adjVec[i] = tape.getGradient(index); ++ tape.gradient(index) = 0.0; ++ } ++} ++ ++template ++inline void updateVectorAdjoint(Tape& tape, const Data* dataVec, const Adjoint* adjVec, int n) { ++ for(int i = 0; i < n; ++i) { ++ Data index = dataVec[i]; ++ tape.gradient(index) += adjVec[i]; ++ } ++} ++ ++template ++inline void updateAdjoint(Tape& tape, const Data& data, const Adjoint& adj) { ++ Data index = data; ++ tape.gradient(index) += adj; ++} ++ ++#endif ++ ++#endif + +Property changes on: ../trunk-jpl/src/c/toolkits/codipack/CoDiPackCommon.hpp +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property +Index: ../trunk-jpl/src/c/toolkits/codipack/CoDiPackGlobal.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/codipack/CoDiPackGlobal.h (nonexistent) ++++ ../trunk-jpl/src/c/toolkits/codipack/CoDiPackGlobal.h (revision 23241) +@@ -0,0 +1,40 @@ ++/* ++ * CoDiPackGlobal.h ++ * ++ * Created on: Jul 20, 2016 ++ * Author: a_h_ck ++ */ ++ ++#ifndef SRC_C_TOOLKITS_CODIPACK_CODIPACKGLOBAL_H_ ++#define SRC_C_TOOLKITS_CODIPACK_CODIPACKGLOBAL_H_ ++ ++#ifdef HAVE_CONFIG_H ++ #include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#if defined(_HAVE_CODIPACK_) ++ ++#include ++#include ++ ++struct CoDi_global { ++ std::vector input_indices; ++ std::vector output_indices; ++ ++ void print(std::ostream& out) const { ++ out << "-------------------------------------\nCoDi_global:\n in = [ "; ++ for(auto& in_index : input_indices) { ++ out << in_index << " "; ++ } ++ out << "]\n out = [ "; ++ for(auto& out_index : output_indices) { ++ out << out_index << " "; ++ } ++ out << "]\n-------------------------------------\n"; ++ } ++}; ++ ++#endif /* _HAVE_CODIPACK_ */ ++#endif /* SRC_C_TOOLKITS_CODIPACK_CODIPACKGLOBAL_H_ */ + +Property changes on: ../trunk-jpl/src/c/toolkits/codipack/CoDiPackGlobal.h +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property +Index: ../trunk-jpl/src/c/toolkits/codipack/ampi_interface.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/codipack/ampi_interface.cpp (nonexistent) ++++ ../trunk-jpl/src/c/toolkits/codipack/ampi_interface.cpp (revision 23241) +@@ -0,0 +1 @@ ++#include "externals/ampi_interface_realreverse.cpp" + +Property changes on: ../trunk-jpl/src/c/toolkits/codipack/ampi_interface.cpp +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property +Index: ../trunk-jpl/src/c/toolkits/toolkits.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/toolkits.h (revision 23240) ++++ ../trunk-jpl/src/c/toolkits/toolkits.h (revision 23241) +@@ -29,6 +29,10 @@ + #include "./adolc/adolcincludes.h" + #endif + ++#ifdef _HAVE_CODIPACK_ ++#include "./codipack/codipackincludes.h" ++#endif ++ + #ifdef _HAVE_TRIANGLE_ + #include "./triangle/triangleincludes.h" + #endif +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 23240) ++++ ../trunk-jpl/src/c/Makefile.am (revision 23241) +@@ -1,4 +1,4 @@ +-AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJ4INCL@ ++AM_CPPFLAGS = @NEOPZINCL@ @DAKOTAINCL@ @SHAPELIBINCL@ @PETSCINCL@ @SLEPCINCL@ @AMPIINCL@ @ADJOINTMPIINCL@ @MPIINCL@ @METISINCL@ @CHACOINCL@ @SCOTCHINCL@ @PLAPACKINCL@ @BLASLAPACKINCL@ @MKLINCL@ @MUMPSINCL@ @TRIANGLEINCL@ @SPAIINCL@ @HYPREINCL@ @PROMETHEUSINCL@ @SUPERLUINCL@ @SPOOLESINCL@ @PASTIXINCL@ @MLINCL@ @TAOINCL@ @ADIC2INCL@ @ADOLCINCL@ @CODIPACKINCL@ @GSLINCL@ @BOOSTINCL@ @ANDROID_NDKINCL@ @METEOIOINCL@ @SNOWPACKINCL@ @PROJ4INCL@ + + AUTOMAKE_OPTIONS = subdir-objects + +@@ -319,6 +319,11 @@ + ./classes/Inputs/PentaInput.cpp\ + ./classes/Inputs/TetraInput.cpp + #}}} ++# ADJOINTMPI sources {{{ ++if ADJOINTMPI ++issm_sources += ./toolkits/codipack/ampi_interface.cpp ++endif ++# }}} + #DAKOTA sources {{{ + if DAKOTA + issm_sources += ./classes/Dakota/IssmDirectApplicInterface.h\ +@@ -631,7 +636,7 @@ + + if !WINDOWS + if !STANDALONE_LIBRARIES +-libISSMCore_la_LIBADD = $(PETSCLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) ++libISSMCore_la_LIBADD = $(PETSCLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(ADOLCLIB) $(AMPILIB) $(ADJOINTMPILIB) $(METEOIOLIB) $(SNOWPACKLIB) + if FORTRAN + libISSMCore_la_LIBADD += $(FLIBS) $(FORTRANLIB) + endif +@@ -713,7 +718,7 @@ + endif + + #External packages +-LDADD += $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(PETSCLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(AMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJ4LIB) ++LDADD += $(NEOPZLIB) $(TAOLIB) $(M1QN3LIB) $(PLAPACKLIB) $(MUMPSLIB) $(SUPERLULIB) $(SPOOLESLIB) $(SCALAPACKLIB) $(BLACSLIB) $(PETSCLIB) $(HYPRELIB) $(SPAILIB) $(PROMETHEUSLIB) $(PASTIXLIB) $(MLLIB) $(DAKOTALIB) $(METISLIB) $(CHACOLIB) $(SCOTCHLIB) $(BLASLAPACKLIB) $(MKLLIB) $(MPILIB) $(MATHLIB) $(GRAPHICSLIB) $(MULTITHREADINGLIB) $(OSLIBS) $(GSLLIB) $(AMPILIB) $(ADJOINTMPILIB) $(ADOLCLIB) $(MPILIB) $(METEOIOLIB) $(SNOWPACKLIB) $(PROJ4LIB) + + if FORTRAN + LDADD += $(FLIBS) $(FORTRANLIB) Index: /issm/oecreview/Archive/23185-23389/ISSM-23241-23242.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23241-23242.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23241-23242.diff (revision 23390) @@ -0,0 +1,571 @@ +Index: ../trunk-jpl/src/c/classes/ExternalResults/GenericExternalResult.h +=================================================================== +--- ../trunk-jpl/src/c/classes/ExternalResults/GenericExternalResult.h (revision 23241) ++++ ../trunk-jpl/src/c/classes/ExternalResults/GenericExternalResult.h (revision 23242) +@@ -621,7 +621,7 @@ + } /*}}}*/ + + /*Specific instantiations for IssmDouble*: */ +-#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) //We hook off this specific specialization when not running ADOLC, otherwise we get a redeclaration with the next specialization. ++#if defined(_HAVE_AD_) && !defined(_WRAPPERS_) //We hook off this specific specialization when not running ADOLC, otherwise we get a redeclaration with the next specialization. + template <> inline GenericExternalResult::~GenericExternalResult(){ /*{{{*/ + xDelete(result_name); + xDelete(value); +@@ -708,7 +708,7 @@ + template <> inline Object* GenericExternalResult*>::copy(void){ /*{{{*/ + return new GenericExternalResult*>(this->id,StringToEnumx(this->result_name),this->value,this->step,this->time); + } /*}}}*/ +-#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) //We hook off this specific specialization when not running ADOLC, otherwise we get a redeclaration with the next specialization. ++#if defined(_HAVE_AD_) && !defined(_WRAPPERS_) //We hook off this specific specialization when not running ADOLC, otherwise we get a redeclaration with the next specialization. + template <> inline void GenericExternalResult*>::WriteData(FILE* fid,bool io_gather){ /*{{{*/ + + char *name = NULL; +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23241) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23242) +@@ -880,7 +880,7 @@ + results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentMemEnum, solution_memory)); + results->AddObject(new GenericExternalResult(results->Size()+1, ProfilingCurrentFlopsEnum, solution_flops)); + +- #ifdef _HAVE_ADOLC_ ++ #ifdef _HAVE_AD_ + solution_time = profiler->TotalTime(ADCORE); + solution_flops = profiler->TotalFlops(ADCORE); + solution_memory = profiler->Memory(ADCORE); +@@ -1844,7 +1844,7 @@ + parameters->FindParam(&isautodiff,AutodiffIsautodiffEnum); + + if(isautodiff){ +- #ifdef _HAVE_ADOLC_ ++ #ifdef _HAVE_AD_ + parameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); + parameters->FindParam(&dependent_objects,AutodiffDependentObjectsEnum); + if(num_dependents){ +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 23241) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 23242) +@@ -3132,7 +3132,10 @@ + fac += dz[i]*(rho_ice - fmin(d[i],rho_ice)); + } + +- #ifndef _HAVE_ADOLC_ //we want to avoid the round operation at all cost. Not differentiable. ++ #if defined(_HAVE_AD_) ++ /*we want to avoid the round operation at all cost. Not differentiable.*/ ++ _error_("not implemented yet"); ++ #else + dMass = sumMass + sumR + sumW - sumP - sumEC - initMass - sumMassAdd; + dMass = round(dMass * 100.0)/100.0; + +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 23241) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 23242) +@@ -52,6 +52,7 @@ + AutodiffNumDependentsEnum, + AutodiffNumIndependentsEnum, + AutodiffObufsizeEnum, ++ AutodiffTapeAllocEnum, + AutodiffTbufsizeEnum, + AutodiffXpEnum, + BalancethicknessStabilizationEnum, +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 23241) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 23242) +@@ -60,6 +60,7 @@ + case AutodiffNumDependentsEnum : return "AutodiffNumDependents"; + case AutodiffNumIndependentsEnum : return "AutodiffNumIndependents"; + case AutodiffObufsizeEnum : return "AutodiffObufsize"; ++ case AutodiffTapeAllocEnum : return "AutodiffTapeAlloc"; + case AutodiffTbufsizeEnum : return "AutodiffTbufsize"; + case AutodiffXpEnum : return "AutodiffXp"; + case BalancethicknessStabilizationEnum : return "BalancethicknessStabilization"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 23241) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 23242) +@@ -60,6 +60,7 @@ + else if (strcmp(name,"AutodiffNumDependents")==0) return AutodiffNumDependentsEnum; + else if (strcmp(name,"AutodiffNumIndependents")==0) return AutodiffNumIndependentsEnum; + else if (strcmp(name,"AutodiffObufsize")==0) return AutodiffObufsizeEnum; ++ else if (strcmp(name,"AutodiffTapeAlloc")==0) return AutodiffTapeAllocEnum; + else if (strcmp(name,"AutodiffTbufsize")==0) return AutodiffTbufsizeEnum; + else if (strcmp(name,"AutodiffXp")==0) return AutodiffXpEnum; + else if (strcmp(name,"BalancethicknessStabilization")==0) return BalancethicknessStabilizationEnum; +@@ -135,11 +136,11 @@ + else if (strcmp(name,"FrictionGamma")==0) return FrictionGammaEnum; + else if (strcmp(name,"FrictionLaw")==0) return FrictionLawEnum; + else if (strcmp(name,"FrictionPseudoplasticityExponent")==0) return FrictionPseudoplasticityExponentEnum; +- else if (strcmp(name,"FrictionThresholdSpeed")==0) return FrictionThresholdSpeedEnum; + else stage=2; + } + if(stage==2){ +- if (strcmp(name,"FrictionDelta")==0) return FrictionDeltaEnum; ++ if (strcmp(name,"FrictionThresholdSpeed")==0) return FrictionThresholdSpeedEnum; ++ else if (strcmp(name,"FrictionDelta")==0) return FrictionDeltaEnum; + else if (strcmp(name,"FrictionVoidRatio")==0) return FrictionVoidRatioEnum; + else if (strcmp(name,"GiaCrossSectionShape")==0) return GiaCrossSectionShapeEnum; + else if (strcmp(name,"GroundinglineMigration")==0) return GroundinglineMigrationEnum; +@@ -258,11 +259,11 @@ + else if (strcmp(name,"SealevelriseEquatorialMoi")==0) return SealevelriseEquatorialMoiEnum; + else if (strcmp(name,"SealevelriseFluidLove")==0) return SealevelriseFluidLoveEnum; + else if (strcmp(name,"SealevelriseGElastic")==0) return SealevelriseGElasticEnum; +- else if (strcmp(name,"SealevelriseGeodetic")==0) return SealevelriseGeodeticEnum; + else stage=3; + } + if(stage==3){ +- if (strcmp(name,"SealevelriseGeodeticRunFrequency")==0) return SealevelriseGeodeticRunFrequencyEnum; ++ if (strcmp(name,"SealevelriseGeodetic")==0) return SealevelriseGeodeticEnum; ++ else if (strcmp(name,"SealevelriseGeodeticRunFrequency")==0) return SealevelriseGeodeticRunFrequencyEnum; + else if (strcmp(name,"SealevelriseHElastic")==0) return SealevelriseHElasticEnum; + else if (strcmp(name,"SealevelriseHoriz")==0) return SealevelriseHorizEnum; + else if (strcmp(name,"SealevelriseLoopIncrement")==0) return SealevelriseLoopIncrementEnum; +@@ -381,11 +382,11 @@ + else if (strcmp(name,"TransientNumRequestedOutputs")==0) return TransientNumRequestedOutputsEnum; + else if (strcmp(name,"TransientRequestedOutputs")==0) return TransientRequestedOutputsEnum; + else if (strcmp(name,"Velocity")==0) return VelocityEnum; +- else if (strcmp(name,"WorldComm")==0) return WorldCommEnum; + else stage=4; + } + if(stage==4){ +- if (strcmp(name,"ParametersEND")==0) return ParametersENDEnum; ++ if (strcmp(name,"WorldComm")==0) return WorldCommEnum; ++ else if (strcmp(name,"ParametersEND")==0) return ParametersENDEnum; + else if (strcmp(name,"InputsSTART")==0) return InputsSTARTEnum; + else if (strcmp(name,"Adjoint")==0) return AdjointEnum; + else if (strcmp(name,"Adjointx")==0) return AdjointxEnum; +@@ -504,11 +505,11 @@ + else if (strcmp(name,"InversionVelObs")==0) return InversionVelObsEnum; + else if (strcmp(name,"InversionVxObs")==0) return InversionVxObsEnum; + else if (strcmp(name,"InversionVyObs")==0) return InversionVyObsEnum; +- else if (strcmp(name,"LevelsetfunctionSlopeX")==0) return LevelsetfunctionSlopeXEnum; + else stage=5; + } + if(stage==5){ +- if (strcmp(name,"LevelsetfunctionSlopeY")==0) return LevelsetfunctionSlopeYEnum; ++ if (strcmp(name,"LevelsetfunctionSlopeX")==0) return LevelsetfunctionSlopeXEnum; ++ else if (strcmp(name,"LevelsetfunctionSlopeY")==0) return LevelsetfunctionSlopeYEnum; + else if (strcmp(name,"LoadingforceX")==0) return LoadingforceXEnum; + else if (strcmp(name,"LoadingforceY")==0) return LoadingforceYEnum; + else if (strcmp(name,"LoadingforceZ")==0) return LoadingforceZEnum; +@@ -627,11 +628,11 @@ + else if (strcmp(name,"StrainRateperpendicular")==0) return StrainRateperpendicularEnum; + else if (strcmp(name,"StrainRatexx")==0) return StrainRatexxEnum; + else if (strcmp(name,"StrainRatexy")==0) return StrainRatexyEnum; +- else if (strcmp(name,"StrainRatexz")==0) return StrainRatexzEnum; + else stage=6; + } + if(stage==6){ +- if (strcmp(name,"StrainRateyy")==0) return StrainRateyyEnum; ++ if (strcmp(name,"StrainRatexz")==0) return StrainRatexzEnum; ++ else if (strcmp(name,"StrainRateyy")==0) return StrainRateyyEnum; + else if (strcmp(name,"StrainRateyz")==0) return StrainRateyzEnum; + else if (strcmp(name,"StrainRatezz")==0) return StrainRatezzEnum; + else if (strcmp(name,"StressMaxPrincipal")==0) return StressMaxPrincipalEnum; +@@ -750,11 +751,11 @@ + else if (strcmp(name,"DeviatoricStressErrorEstimator")==0) return DeviatoricStressErrorEstimatorEnum; + else if (strcmp(name,"Divergence")==0) return DivergenceEnum; + else if (strcmp(name,"Domain3Dsurface")==0) return Domain3DsurfaceEnum; +- else if (strcmp(name,"DoubleArrayInput")==0) return DoubleArrayInputEnum; + else stage=7; + } + if(stage==7){ +- if (strcmp(name,"DoubleExternalResult")==0) return DoubleExternalResultEnum; ++ if (strcmp(name,"DoubleArrayInput")==0) return DoubleArrayInputEnum; ++ else if (strcmp(name,"DoubleExternalResult")==0) return DoubleExternalResultEnum; + else if (strcmp(name,"DoubleInput")==0) return DoubleInputEnum; + else if (strcmp(name,"DoubleMatArrayParam")==0) return DoubleMatArrayParamEnum; + else if (strcmp(name,"DoubleMatExternalResult")==0) return DoubleMatExternalResultEnum; +@@ -873,11 +874,11 @@ + else if (strcmp(name,"LoveHi")==0) return LoveHiEnum; + else if (strcmp(name,"LoveHr")==0) return LoveHrEnum; + else if (strcmp(name,"LoveKernelsImag")==0) return LoveKernelsImagEnum; +- else if (strcmp(name,"LoveKernelsReal")==0) return LoveKernelsRealEnum; + else stage=8; + } + if(stage==8){ +- if (strcmp(name,"LoveKi")==0) return LoveKiEnum; ++ if (strcmp(name,"LoveKernelsReal")==0) return LoveKernelsRealEnum; ++ else if (strcmp(name,"LoveKi")==0) return LoveKiEnum; + else if (strcmp(name,"LoveKr")==0) return LoveKrEnum; + else if (strcmp(name,"LoveLi")==0) return LoveLiEnum; + else if (strcmp(name,"LoveLr")==0) return LoveLrEnum; +@@ -996,11 +997,11 @@ + else if (strcmp(name,"Outputdefinition45")==0) return Outputdefinition45Enum; + else if (strcmp(name,"Outputdefinition46")==0) return Outputdefinition46Enum; + else if (strcmp(name,"Outputdefinition47")==0) return Outputdefinition47Enum; +- else if (strcmp(name,"Outputdefinition48")==0) return Outputdefinition48Enum; + else stage=9; + } + if(stage==9){ +- if (strcmp(name,"Outputdefinition49")==0) return Outputdefinition49Enum; ++ if (strcmp(name,"Outputdefinition48")==0) return Outputdefinition48Enum; ++ else if (strcmp(name,"Outputdefinition49")==0) return Outputdefinition49Enum; + else if (strcmp(name,"Outputdefinition4")==0) return Outputdefinition4Enum; + else if (strcmp(name,"Outputdefinition50")==0) return Outputdefinition50Enum; + else if (strcmp(name,"Outputdefinition51")==0) return Outputdefinition51Enum; +@@ -1119,11 +1120,11 @@ + else if (strcmp(name,"SMBgradientsela")==0) return SMBgradientselaEnum; + else if (strcmp(name,"SMBgradients")==0) return SMBgradientsEnum; + else if (strcmp(name,"SMBhenning")==0) return SMBhenningEnum; +- else if (strcmp(name,"SmbMAdd")==0) return SmbMAddEnum; + else stage=10; + } + if(stage==10){ +- if (strcmp(name,"SMBmeltcomponents")==0) return SMBmeltcomponentsEnum; ++ if (strcmp(name,"SmbMAdd")==0) return SmbMAddEnum; ++ else if (strcmp(name,"SMBmeltcomponents")==0) return SMBmeltcomponentsEnum; + else if (strcmp(name,"SMBpdd")==0) return SMBpddEnum; + else if (strcmp(name,"SmbRlaps")==0) return SmbRlapsEnum; + else if (strcmp(name,"SmbRlapslgm")==0) return SmbRlapslgmEnum; +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 23241) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp (revision 23242) +@@ -373,7 +373,7 @@ + /*Now, deal with toolkits options, which need to be put into the parameters dataset: */ + ParseToolkitsOptionsx(parameters,toolkitsoptionsfid); + +- #ifdef _HAVE_ADOLC_ ++ #ifdef _HAVE_AD_ + if(VerboseMProcessor()) _printf0_(" starting autodiff parameters \n"); + CreateParametersAutodiff(parameters,iomodel); + if(VerboseMProcessor()) _printf0_(" ending autodiff parameters \n"); +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 23241) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 23242) +@@ -72,8 +72,36 @@ + /*Free ressources: */ + xDelete(options); + /*}}}*/ ++ #elif _HAVE_CODIPACK_ ++ //fprintf(stderr, "*** Codipack CreateParametersAutodiff()\n"); ++ /*initialize a placeholder to store solver pointers: {{{*/ ++ /*Solver pointers depend on what type of solver we are implementing: */ ++ options=OptionsFromAnalysis(parameters,DefaultAnalysisEnum); //options database is not filled in yet, use default. ++ ToolkitOptions::Init(options); + ++ switch(IssmSolverTypeFromToolkitOptions()){ ++ case MumpsEnum:{ ++ #ifndef _HAVE_MUMPS_ ++ _error_("CoDiPack: requesting mumps solver without MUMPS being compiled in!"); ++ #endif ++ break; ++ } ++ case GslEnum: { ++ #ifndef _HAVE_GSL_ ++ _error_("CoDiPack: requesting GSL solver without GSL being compiled in!"); ++ #endif ++ break; ++ } ++ default: ++ _error_("solver type not supported yet!"); ++ } ++ /*Free ressources: */ ++ xDelete(options); ++ #endif ++ #if defined(_HAVE_AD_) ++ + if(isautodiff){ ++#if _HAVE_ADOLC_ + /*Copy some parameters from IoModel to parameters dataset: {{{*/ + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.obufsize",AutodiffObufsizeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.cbufsize",AutodiffCbufsizeEnum)); +@@ -82,11 +110,16 @@ + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.gcTriggerRatio",AutodiffGcTriggerRatioEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.gcTriggerMaxSize",AutodiffGcTriggerMaxSizeEnum)); + /*}}}*/ ++#endif + /*retrieve driver: {{{*/ + iomodel->FindConstant(&autodiff_driver,"md.autodiff.driver"); + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.driver",AutodiffDriverEnum)); + + if(strcmp(autodiff_driver,"fos_forward")==0){ ++#if _HAVE_CODIPACK_ ++ // FIXME codi support Foward Mode (scalar) ++ _error_("Foward Mode (scalar) not supported yet!"); ++#endif + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.fos_forward_index",AutodiffFosForwardIndexEnum)); + } + else if(strcmp(autodiff_driver,"fos_reverse")==0){ +@@ -93,6 +126,10 @@ + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.fos_reverse_index",AutodiffFosReverseIndexEnum)); + } + else if(strcmp(autodiff_driver,"fov_forward")==0){ ++#if _HAVE_CODIPACK_ ++ // FIXME codi support Foward Mode (vector) ++ _error_("Foward Mode (vector) not supported yet!"); ++#endif + /*Retrieve list of indices: */ + iomodel->FetchData(&indices,&num_indices,&dummy,"md.autodiff.fov_forward_indices"); + parameters->AddObject(new IntMatParam(AutodiffFovForwardIndicesEnum,indices,num_indices,1)); +Index: ../trunk-jpl/src/c/modules/SurfaceMassBalancex/Gembx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/SurfaceMassBalancex/Gembx.cpp (revision 23241) ++++ ../trunk-jpl/src/c/modules/SurfaceMassBalancex/Gembx.cpp (revision 23242) +@@ -61,7 +61,7 @@ + //check to see if the top grid cell structure length (dzTop) goes evenly + //into specified top structure depth (zTop). Also make sure top grid cell + //structure length (dzTop) is greater than 5 cm +- #ifndef _HAVE_ADOLC_ //avoid the round operation check! ++ #ifndef _HAVE_AD_ //avoid the round operation check! + if (dgpTop != round(dgpTop)){ + _error_("top grid cell structure length does not go evenly into specified top structure depth, adjust dzTop or zTop"); + } +@@ -424,11 +424,11 @@ + + // spectral range: + // 0.3 - 0.8um +- IssmDouble a0 = fmin(0.98, 1 - 1.58 *pow(gsz,0.5)); ++ IssmDouble a0 = min(0.98, 1 - 1.58 *pow(gsz,0.5)); + // 0.8 - 1.5um +- IssmDouble a1 = fmax(0, 0.95 - 15.4 *pow(gsz,0.5)); ++ IssmDouble a1 = max(0, 0.95 - 15.4 *pow(gsz,0.5)); + // 1.5 - 2.8um +- IssmDouble a2 = fmax(0.127, 0.88 + 346.3*gsz - 32.31*pow(gsz,0.5)); ++ IssmDouble a2 = max(0.127, 0.88 + 346.3*gsz - 32.31*pow(gsz,0.5)); + + // broadband surface albedo + a[0] = sF[0]*a0 + sF[1]*a1 + sF[2]*a2; +@@ -666,7 +666,7 @@ + // determine minimum acceptable delta t (diffusion number > 1/2) [s] + // NS: 2.16.18 divided dt by scaling factor, default set to 1/11 for stability + dt=1e12; +- for(int i=0;i 1/2 + // must go evenly into one hour or the data frequency if it is smaller +@@ -751,7 +751,7 @@ + // calculated. The estimated enegy balance & melt are significanly + // less when Ts is taken as the mean of the x top grid cells. + Ts = (T[0] + T[1])/2.0; +- Ts = fmin(CtoK,Ts); // don't allow Ts to exceed 273.15 K (0 degC) ++ Ts = min(CtoK,Ts); // don't allow Ts to exceed 273.15 K (0 degC) + + //TURBULENT HEAT FLUX + +@@ -766,7 +766,7 @@ + // calculate Monin-Obukhov stability factors 'coefM' and 'coefH' + + // do not allow Ri to exceed 0.19 +- Ri = fmin(Ri, 0.19); ++ Ri = min(Ri, 0.19); + + // calculate momentum 'coefM' stability factor + if (Ri > 0.0+Ttol){ +@@ -946,11 +946,11 @@ + + // spectral albedos: + // 0.3 - 0.8um +- IssmDouble a0 = fmin(0.98, 1.0 - 1.58 *pow(gsz[0],0.5)); ++ IssmDouble a0 = min(0.98, 1.0 - 1.58 *pow(gsz[0],0.5)); + // 0.8 - 1.5um +- IssmDouble a1 = fmax(0.0, 0.95 - 15.4 *pow(gsz[0],0.5)); ++ IssmDouble a1 = max(0.0, 0.95 - 15.4 *pow(gsz[0],0.5)); + // 1.5 - 2.8um +- IssmDouble a2 = fmax(0.127, 0.88 + 346.3*gsz[0] - 32.31*pow(gsz[0],0.5)); ++ IssmDouble a2 = max(0.127, 0.88 + 346.3*gsz[0] - 32.31*pow(gsz[0],0.5)); + + // separate net shortwave radiative flux into spectral ranges + IssmDouble swfS[3]; +@@ -1203,7 +1203,7 @@ + + mass_diff = mass - massinit - P; + +- #ifndef _HAVE_ADOLC_ //avoid round operation. only check in forward mode. ++ #ifndef _HAVE_AD_ //avoid round operation. only check in forward mode. + mass_diff = round(mass_diff * 100.0)/100.0; + if (mass_diff > 0) _error_("mass not conserved in accumulation function"); + #endif +@@ -1322,11 +1322,11 @@ + + // calculate temperature excess above 0 deg C + exsT=xNewZeroInit(n); +- for(int i=0;i0.0+Wtol){ + if(VerboseSmb() && sid==0 && IssmComm::GetRank()==0)_printf0_(" pore water refreeze\n"); + // calculate maximum freeze amount, maxF [kg] +- for(int i=0;i(n); + for(int i=0;i(n); for(int i=0;i(n); for(int i=0;i 0.0 + Ttol ){ + // _printf_("T Surplus"); +@@ -1379,10 +1379,10 @@ + // use surplus energy to increase the temperature of lower cell + T[i+1] = surpE[i]/m[i+1]/CI + T[i+1]; + +- exsT[i+1] = fmax(0.0, T[i+1] - CtoK) + exsT[i+1]; +- T[i+1] = fmin(CtoK, T[i+1]); ++ exsT[i+1] = max(0.0, T[i+1] - CtoK) + exsT[i+1]; ++ T[i+1] = min(CtoK, T[i+1]); + +- surpT[i+1] = fmax(0.0, exsT[i+1] - LF/CI); ++ surpT[i+1] = max(0.0, exsT[i+1] - LF/CI); + surpE[i+1] = surpT[i+1] * CI * m[i+1]; + + // adjust current cell properties (again 159.1342 is the max T) +@@ -1393,11 +1393,11 @@ + } + + // convert temperature excess to melt [kg] +- for(int i=0;i(n); +@@ -1434,8 +1434,8 @@ + + m[i] = m[i] - M[i]; // mass after melt + Wi = (dIce-d[i]) * Swi * (m[i]/d[i]); // irreducible water +- dW[i] = fmax(fmin(inM, Wi - W[i]),-1*W[i]); // change in pore water +- R[i] = fmax(0.0, inM - dW[i]); // runoff ++ dW[i] = max(min(inM, Wi - W[i]),-1*W[i]); // change in pore water ++ R[i] = max(0.0, inM - dW[i]); // runoff + F[i] = 0.0; + } + // check if no energy to refreeze meltwater +@@ -1446,8 +1446,8 @@ + + m[i] = m[i] - M[i]; // mass after melt + Wi = (dIce-d[i]) * Swi * (m[i]/d[i]); // irreducible water +- dW[i] = fmax(fmin(inM, Wi - W[i]),-1*W[i]); // change in pore water +- flxDn[i+1] = fmax(0.0, inM - dW[i]); // meltwater out ++ dW[i] = max(min(inM, Wi - W[i]),-1*W[i]); // change in pore water ++ flxDn[i+1] = max(0.0, inM - dW[i]); // meltwater out + R[i] = 0.0; + F[i] = 0.0; // no freeze + } +@@ -1459,13 +1459,13 @@ + m[i] = m[i] - M[i]; + IssmDouble dz_0 = m[i]/d[i]; + IssmDouble dMax = (dIce - d[i])*dz_0; // d max = dIce +- IssmDouble F1 = fmin(fmin(inM,dMax),maxF[i]); // maximum refreeze ++ IssmDouble F1 = min(min(inM,dMax),maxF[i]); // maximum refreeze + m[i] = m[i] + F1; // mass after refreeze + d[i] = m[i]/dz_0; + + //-----------------------pore water----------------------------- + Wi = (dIce-d[i])* Swi * dz_0; // irreducible water +- dW[i] = fmin(inM - F1, Wi-W[i]); // change in pore water ++ dW[i] = min(inM - F1, Wi-W[i]); // change in pore water + if (dW[i] < 0.0-Wtol && -1*dW[i]>W[i]-Wtol ){ + dW[i]= -1*W[i]; + } +@@ -1473,8 +1473,8 @@ + + if (dW[i] < 0.0-Wtol){ // excess pore water + dMax = (dIce - d[i])*dz_0; // maximum refreeze +- IssmDouble maxF2 = fmin(dMax, maxF[i]-F1); // maximum refreeze +- F2 = fmin(-1*dW[i], maxF2); // pore water refreeze ++ IssmDouble maxF2 = min(dMax, maxF[i]-F1); // maximum refreeze ++ F2 = min(-1*dW[i], maxF2); // pore water refreeze + m[i] = m[i] + F2; // mass after refreeze + d[i] = m[i]/dz_0; + dW[i] = dW[i] - F2; +@@ -1752,7 +1752,7 @@ + for(int i=0;i 0.0+Ttol){ +Index: ../trunk-jpl/src/c/cores/controlvalidation_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controlvalidation_core.cpp (revision 23241) ++++ ../trunk-jpl/src/c/cores/controlvalidation_core.cpp (revision 23242) +@@ -87,7 +87,7 @@ + } + + /*output*/ +- #ifdef _HAVE_ADOLC_ ++ #ifdef _HAVE_AD_ + IssmPDouble* J_passive=xNew(2*num); + for(int i=0;i<2*num;i++) J_passive[i]=reCast(output[i]); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,JEnum,J_passive,num,2,0,0)); +Index: ../trunk-jpl/src/c/cores/control_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/control_core.cpp (revision 23241) ++++ ../trunk-jpl/src/c/cores/control_core.cpp (revision 23242) +@@ -96,7 +96,7 @@ + if(!dakota_analysis){ //do not save this if we are running the control core from a qmu run! + femmodel->OutputControlsx(&femmodel->results); + +- #ifdef _HAVE_ADOLC_ ++ #ifdef _HAVE_AD_ + IssmPDouble* J_passive=xNew(nsteps); + for(int i=0;i(J[i]); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,JEnum,J_passive,nsteps,1,0,0)); Index: /issm/oecreview/Archive/23185-23389/ISSM-23242-23243.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23242-23243.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23242-23243.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/modules/SurfaceMassBalancex/Gembx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/SurfaceMassBalancex/Gembx.cpp (revision 23242) ++++ ../trunk-jpl/src/c/modules/SurfaceMassBalancex/Gembx.cpp (revision 23243) +@@ -426,7 +426,7 @@ + // 0.3 - 0.8um + IssmDouble a0 = min(0.98, 1 - 1.58 *pow(gsz,0.5)); + // 0.8 - 1.5um +- IssmDouble a1 = max(0, 0.95 - 15.4 *pow(gsz,0.5)); ++ IssmDouble a1 = max(0., 0.95 - 15.4 *pow(gsz,0.5)); + // 1.5 - 2.8um + IssmDouble a2 = max(0.127, 0.88 + 346.3*gsz - 32.31*pow(gsz,0.5)); + Index: /issm/oecreview/Archive/23185-23389/ISSM-23243-23244.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23243-23244.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23243-23244.diff (revision 23390) @@ -0,0 +1,152 @@ +Index: ../trunk-jpl/src/c/shared/Numerics/isnan.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Numerics/isnan.h (revision 23243) ++++ ../trunk-jpl/src/c/shared/Numerics/isnan.h (revision 23244) +@@ -32,4 +32,10 @@ + template <> int xIsInf (const adouble& X); + #endif + ++#if defined(_HAVE_CODIPACK_) && !defined(_WRAPPERS_) ++#include "./types.h" ++template <> int xIsNan (const IssmDouble& X); ++template <> int xIsInf (const IssmDouble& X); + #endif ++ ++#endif +Index: ../trunk-jpl/src/c/shared/Numerics/recast.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Numerics/recast.h (revision 23243) ++++ ../trunk-jpl/src/c/shared/Numerics/recast.h (revision 23244) +@@ -14,7 +14,7 @@ + #error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" + #endif + +-#if !defined(_HAVE_ADOLC_) || defined(_WRAPPERS_) ++#if !defined(_HAVE_AD_) || defined(_WRAPPERS_) + + template To reCast(const From& from) { + return (To)from; +@@ -33,9 +33,16 @@ + /** + * partial specialization + */ ++#ifdef _HAVE_ADOLC_ + template struct ForPartialSpecialization { + static To reCast(const adouble& from ) { return (To) (from.getValue());} + }; ++#endif ++#ifdef _HAVE_CODIPACK_ ++template struct ForPartialSpecialization { ++ static To reCast(const IssmDouble& from ) { return (To) (from.getValue());} ++}; ++#endif + + #endif + +Index: ../trunk-jpl/src/c/shared/Numerics/numerics.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Numerics/numerics.h (revision 23243) ++++ ../trunk-jpl/src/c/shared/Numerics/numerics.h (revision 23244) +@@ -19,10 +19,13 @@ + #include "./constants.h" + #include "./OptPars.h" + ++#if !defined(_HAVE_CODIPACK_) ++// already defined in codipack headers + IssmDouble min(IssmDouble a,IssmDouble b); + IssmDouble max(IssmDouble a,IssmDouble b); ++#endif + +-#ifdef _HAVE_ADOLC_ ++#ifdef _HAVE_AD_ + IssmPDouble min(IssmPDouble a,IssmPDouble b); + IssmPDouble max(IssmPDouble a,IssmPDouble b); + #endif +Index: ../trunk-jpl/src/c/shared/Numerics/extrema.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Numerics/extrema.cpp (revision 23243) ++++ ../trunk-jpl/src/c/shared/Numerics/extrema.cpp (revision 23244) +@@ -10,24 +10,28 @@ + + #include "./types.h" + ++#ifndef _HAVE_CODIPACK_// already defined in codipack headers + IssmDouble min(IssmDouble a,IssmDouble b){ + if (ab)return a; + else return b; + } ++#endif + int max(int a,int b){ + if (a>b)return a; + else return b; + } + +-#ifdef _HAVE_ADOLC_ ++#ifdef _HAVE_AD_ + IssmPDouble min(IssmPDouble a,IssmPDouble b){ + if (a int xIsNan (const adouble& X){ + return std::isnan(X.getValue()); + } +-#endif +- +-#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) + template <> int xIsInf (const adouble& X){ + return std::isinf(X.getValue()); + } + #endif ++ ++#if defined(_HAVE_CODIPACK_) && !defined(_WRAPPERS_) ++template <> int xIsNan (const IssmDouble& X){ ++ return std::isnan(X.getValue()); ++} ++template <> int xIsInf (const IssmDouble& X){ ++ return std::isinf(X.getValue()); ++} ++#endif +Index: ../trunk-jpl/src/c/shared/Numerics/types.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Numerics/types.h (revision 23243) ++++ ../trunk-jpl/src/c/shared/Numerics/types.h (revision 23244) +@@ -21,15 +21,20 @@ + #endif + + #if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) ++/*ADOLC typedefs*/ + #include "adolc/adolc.h" +-// for active variables +-typedef adouble IssmDouble; +-// for passive variables ++typedef adouble IssmDouble; /*for active variables*/ ++typedef double IssmPDouble; /*for passive variables*/ ++ ++#elif defined(_HAVE_CODIPACK_) && !defined(_WRAPPERS_) ++/*CoDiPack typedefs*/ ++#include ++typedef codi::RealReverse IssmDouble; + typedef double IssmPDouble; ++ ++/*Non-AD typedefs*/ + #else +-// see above + typedef double IssmDouble; +-// see above + typedef IssmDouble IssmPDouble; + #endif + Index: /issm/oecreview/Archive/23185-23389/ISSM-23244-23245.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23244-23245.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23244-23245.diff (revision 23390) @@ -0,0 +1,142 @@ +Index: ../trunk-jpl/src/m/classes/autodiff.m +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.m (revision 23244) ++++ ../trunk-jpl/src/m/classes/autodiff.m (revision 23245) +@@ -16,6 +16,7 @@ + tbufsize = NaN; + gcTriggerRatio = NaN; + gcTriggerMaxSize = NaN; ++ tapeAlloc = NaN; + end + %}}} + methods +@@ -34,6 +35,7 @@ + self.tbufsize = 524288; + self.gcTriggerRatio=2.0; + self.gcTriggerMaxSize=65536; ++ self.tapeAlloc = 15000000; + end % }}} + function md = checkconsistency(self,md,solution,analyses) % {{{ + +@@ -50,6 +52,7 @@ + md = checkfield(md,'fieldname','autodiff.tbufsize','>=',16); + md = checkfield(md,'fieldname','autodiff.gcTriggerRatio','>=',0); + md = checkfield(md,'fieldname','autodiff.gcTriggerMaxSize','>=',65536); ++ md = checkfield(md,'fieldname','autodiff.tapeAlloc','>=',0); + + %go through our dependents and independents and check consistency: + for i=1:numel(self.dependents), +@@ -74,6 +77,7 @@ + fielddisplay(self,'tbufsize','Number of taylors per buffer (<=TBUFSIZE in usrparms.h)'); + fielddisplay(self,'gcTriggerRatio','free location block sorting/consolidation triggered if the ratio between allocated and used locations exceeds gcTriggerRatio'); + fielddisplay(self,'gcTriggerMaxSize','free location block sorting/consolidation triggered if the allocated locations exceed gcTriggerMaxSize'); ++ fielddisplay(self,'tapeAlloc','Iteration count of a priori memory allocation of the AD tape'); + end % }}} + function marshall(self,prefix,md,fid) % {{{ + +@@ -94,6 +98,7 @@ + WriteData(fid,prefix,'object',self,'fieldname','tbufsize','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','gcTriggerRatio','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','gcTriggerMaxSize','format','Double'); ++ WriteData(fid,prefix,'object',self,'fieldname','tapeAlloc','format','Integer'); + %}}} + %process dependent variables {{{ + num_dependent_objects=numel(self.dependents); +Index: ../trunk-jpl/src/m/classes/autodiff.py +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.py (revision 23244) ++++ ../trunk-jpl/src/m/classes/autodiff.py (revision 23245) +@@ -24,6 +24,7 @@ + self.tbufsize = float('NaN') + self.gcTriggerMaxSize = float('NaN') + self.gcTriggerRatio = float('NaN') ++ self.tapeAlloc = float('NaN') + if not len(args): + self.setdefaultparameters() + else: +@@ -42,6 +43,7 @@ + s+="%s\n" % fielddisplay(self,'tbufsize',"Number of taylors per buffer (<=TBUFSIZE in usrparms.h)") + s+="%s\n" % fielddisplay(self,'gcTriggerRatio',"free location block sorting/consolidation triggered if the ratio between allocated and used locations exceeds gcTriggerRatio") + s+="%s\n" % fielddisplay(self,'gcTriggerMaxSize',"free location block sorting/consolidation triggered if the allocated locations exceed gcTriggerMaxSize)") ++ s+="%s\n" % fielddisplay(self,'tapeAlloc','Iteration count of a priori memory allocation of the AD tape'); + + return s + # }}} +@@ -53,6 +55,7 @@ + self.tbufsize = 524288 + self.gcTriggerRatio=2.0 + self.gcTriggerMaxSize=65536 ++ self.tapeAlloc = 15000000; + return self + # }}} + def checkconsistency(self,md,solution,analyses): # {{{ +@@ -67,6 +70,7 @@ + md = checkfield(md,'fieldname','autodiff.tbufsize','>=',524288) + md = checkfield(md,'fieldname','autodiff.gcTriggerRatio','>=',2.0) + md = checkfield(md,'fieldname','autodiff.gcTriggerMaxSize','>=',65536) ++ md = checkfield(md,'fieldname','autodiff.tapeAlloc','>=',0); + + #Driver value: + md = checkfield(md,'fieldname','autodiff.driver','values',['fos_forward','fov_forward','fov_forward_all','fos_reverse','fov_reverse','fov_reverse_all']) +@@ -96,7 +100,8 @@ + WriteData(fid,prefix,'object',self,'fieldname','tbufsize','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','gcTriggerRatio','format','Double'); + WriteData(fid,prefix,'object',self,'fieldname','gcTriggerMaxSize','format','Double'); +- #}}} ++ WriteData(fid,prefix,'object',self,'fieldname','tapeAlloc','format','Integer'); ++ #}}} + #process dependent variables {{{ + num_dependent_objects=len(self.dependents) + WriteData(fid,prefix,'data',num_dependent_objects,'name','md.autodiff.num_dependent_objects','format','Integer') +Index: ../trunk-jpl/src/m/classes/autodiff.js +=================================================================== +--- ../trunk-jpl/src/m/classes/autodiff.js (revision 23244) ++++ ../trunk-jpl/src/m/classes/autodiff.js (revision 23245) +@@ -13,6 +13,7 @@ + this.tbufsize = 524288; + this.gcTriggerRatio=2.0; + this.gcTriggerMaxSize=65536; ++ this.tapeAlloc = 15000000; + + }// }}} + this.disp= function(){// {{{ +@@ -28,6 +29,7 @@ + fielddisplay(this,'tbufsize','Number of taylors per buffer (<=TBUFSIZE in usrparms.h)'); + fielddisplay(this,'gcTriggerRatio','free location block sorting/consolidation triggered if the ratio between allocated and used locations exceeds gcTriggerRatio'); + fielddisplay(this,'gcTriggerMaxSize','free location block sorting/consolidation triggered if the allocated locations exceed gcTriggerMaxSize'); ++ fielddisplay(this,'tapeAlloc','Iteration count of a priori memory allocation of the AD tape'); + + }// }}} + this.classname= function(){// {{{ +@@ -48,6 +50,7 @@ + checkfield(md,'fieldname','autodiff.tbufsize','>=',16); + checkfield(md,'fieldname','autodiff.gcTriggerRatio','>=',0); + checkfield(md,'fieldname','autodiff.gcTriggerMaxSize','>=',65536); ++ checkfield(md,'fieldname','autodiff.tapeAlloc','>=',0); + + //go through our dependents and independents and check consistency: + for (var i=0;iparameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); ++ femmodel->parameters->FindParam(&num_independents,AutodiffNumIndependentsEnum); ++ ++ /*if no dependents, no point in running a driver: */ ++ if(!(num_dependents*num_independents)) return; ++ ++ /*Branch according to AD driver: */ ++ femmodel->parameters->FindParam(&driver,AutodiffDriverEnum); ++ if(VerboseAutodiff())_printf0_(" driver: " << driver << "\n"); ++ ++ if (strcmp(driver,"fos_reverse")==0) { /*{{{*/ ++ if(VerboseAutodiff())_printf0_(" CoDiPack fos_reverse\n"); ++ int aDepIndex=0; ++ double *weightVectorTimesJac=NULL; ++ ++ /*retrieve direction index: */ ++ femmodel->parameters->FindParam(&aDepIndex,AutodiffFosReverseIndexEnum); ++ if (my_rank==0) { ++ if (aDepIndex<0 || aDepIndex>=num_dependents ++ || codi_global.output_indices.size() <= aDepIndex){ ++ _error_("index value for AutodiffFosReverseIndexEnum should be in [0,num_dependents-1]"); ++ } ++ tape_codi.setGradient(codi_global.output_indices[aDepIndex], 1.0); ++ } ++ ++ tape_codi.evaluate(); ++ ++ weightVectorTimesJac=xNew(num_independents); ++ /*call driver: */ ++ auto in_size = codi_global.input_indices.size(); ++ for(size_t i = 0; i < in_size; ++i) { ++ weightVectorTimesJac[i] = tape_codi.getGradient(codi_global.input_indices[i]); ++ } ++ ++ /*add to results*/ ++ femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,AutodiffJacobianEnum,weightVectorTimesJac,num_independents,1,0,0.0)); ++ ++ /*free resources :*/ ++ xDelete(weightVectorTimesJac); ++ } /*}}}*/ ++ else _error_("driver: " << driver << " not yet supported!"); ++ ++ if(VerboseAutodiff())_printf0_(" end CoDiPack ad core\n"); ++ xDelete(driver); + #else + _error_("Should not be requesting AD drivers when an AD library is not available!"); + #endif Index: /issm/oecreview/Archive/23185-23389/ISSM-23250-23251.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23250-23251.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23250-23251.diff (revision 23390) @@ -0,0 +1,763 @@ +Index: ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp (revision 23250) ++++ ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp (revision 23251) +@@ -17,6 +17,7 @@ + #include "../../classes/Params/Parameters.h" + #include "../mpi/issmmpi.h" + #include "../adolc/adolcincludes.h" ++#include "../codipack/codipackincludes.h" + #include "../issm/SparseRow.h" + #include "./mumpsincludes.h" + +@@ -97,7 +98,7 @@ + MumpsFinalize(theMumpsStruc); + } + +-#ifdef _HAVE_ADOLC_ ++#ifdef _HAVE_AD_ + // prototype for active variant + void MumpsSolve(int n, + int nnz, +@@ -353,8 +354,7 @@ + }/*}}}*/ + + #ifdef _HAVE_ADOLC_ +- +-int mumpsSolveEDF(int iArrLength, int* iArr, int /* ignored */, IssmPDouble* dp_x, int /* ignored */, IssmPDouble* dp_y) { ++int mumpsSolveEDF(int iArrLength, int* iArr, int /* ignored */, IssmPDouble* dp_x, int /* ignored */, IssmPDouble* dp_y){/*{{{*/ + // unpack parameters + int n=iArr[0]; + int nnz=iArr[1]; +@@ -380,9 +380,8 @@ + xDelete(local_jcn); + xDelete(local_irn); + return 0; +-} +- +-void MumpsSolve(int n,int nnz,int local_nnz,int* irn_loc,int* jcn_loc,IssmDouble *a_loc,IssmDouble *rhs,Parameters* parameters){ ++}/*}}}*/ ++void MumpsSolve(int n,int nnz,int local_nnz,int* irn_loc,int* jcn_loc,IssmDouble *a_loc,IssmDouble *rhs,Parameters* parameters){/*{{{*/ + int packedDimsSparseArrLength=1+1+1+local_nnz+local_nnz; + int *packedDimsSparseArr=xNew(packedDimsSparseArrLength); + packedDimsSparseArr[0]=n; +@@ -424,12 +423,8 @@ + xDelete(sol); + xDelete(pack_A_rhs); + xDelete(packedDimsSparseArr); +-} +- +-int fos_reverse_mumpsSolveEDF(int iArrLength, int* iArr, +- int m, IssmPDouble *dp_U, +- int nPlusNz, IssmPDouble *dp_Z, +- IssmPDouble *dp_x, IssmPDouble *dp_y) { ++}/*}}}*/ ++int fos_reverse_mumpsSolveEDF(int iArrLength, int* iArr, int m, IssmPDouble *dp_U, int nPlusNz, IssmPDouble *dp_Z, IssmPDouble *dp_x, IssmPDouble *dp_y) {/*{{{*/ + // unpack parameters + int n=iArr[0]; + int nnz=iArr[1]; +@@ -480,6 +475,153 @@ + xDelete(local_jcn); + xDelete(local_irn); + return 3; ++}/*}}}*/ ++#endif ++ ++#ifdef _HAVE_CODIPACK_ ++void MumpsSolve_codi_b(codi::DataStore* data) {/*{{{*/ ++ IssmDouble::TapeType& tape = IssmDouble::getGlobalTape(); ++ ++ IssmDouble::Real* valueATrans; ++ IssmDouble::GradientData* indexATrans; ++ int* irnATrans; ++ int* jcnATrans; ++ IssmDouble::GradientData* indexB; ++ IssmDouble::Real* valueX; ++ IssmDouble::GradientData* indexX; ++ int n; ++ int nnz; ++ int local_nnz; ++ Parameters* parameters; ++ ++ data->getData(valueATrans); ++ data->getData(indexATrans); ++ data->getData(irnATrans); ++ data->getData(jcnATrans); ++ data->getData(indexB); ++ data->getData(valueX); ++ data->getData(indexX); ++ data->getData(n); ++ data->getData(nnz); ++ data->getData(local_nnz); ++ data->getData(parameters); ++ ++ // create the adjoint vector for x and reset the adjoint values on the tape ++ IssmDouble::GradientValue* adjX = xNew(n); ++ getVectorAdjoint(tape, indexX, adjX, n); ++ ++ MumpsSolve(n, nnz, local_nnz, irnATrans, jcnATrans, valueATrans, adjX, parameters); ++ // adjX contains now the solution ++ ++ updateVectorAdjoint(tape, indexB, adjX, n); ++ for(int i=0; igetData(valueATrans); ++ data->getData(indexATrans); ++ data->getData(irnATrans); ++ data->getData(jcnATrans); ++ data->getData(indexB); ++ data->getData(valueX); ++ data->getData(indexX); ++ data->getData(n); ++ data->getData(nnz); ++ data->getData(local_nnz); ++ data->getData(parameters); ++ ++ xDelete(valueATrans); ++ xDelete(indexATrans); ++ xDelete(irnATrans); ++ xDelete(jcnATrans); ++ xDelete(indexB); ++ xDelete(valueX); ++ xDelete(indexX); ++} ++/*}}}*/ ++void MumpsSolve(int n,int nnz,int local_nnz,int* irn_loc,int* jcn_loc,IssmDouble *a_loc,IssmDouble *rhs,Parameters* parameters){/*{{{*/ ++ IssmDouble::TapeType& tape = IssmDouble::getGlobalTape(); ++ codi::DataStore* dataHandler = NULL; ++ ++ if(tape.isActive()) { ++ dataHandler = new codi::DataStore(); ++ ++ // create the index and double vector for the matrix ++ IssmDouble::Real* valueATrans = xNew(local_nnz); ++ IssmDouble::GradientData* indexATrans = xNew(local_nnz); ++ int* irnATrans = xNew(local_nnz); ++ int* jcnATrans = xNew(local_nnz); ++ ++ // read the data for the matrix A in a transposed fashion ++ for (int i=0; i(n); ++ getVectorGradData(rhs, indexB, n); ++ ++ dataHandler->addData(valueATrans); ++ dataHandler->addData(indexATrans); ++ dataHandler->addData(irnATrans); ++ dataHandler->addData(jcnATrans); ++ dataHandler->addData(indexB); ++ } ++ ++ // unpack the primal values from the matrix and the vector ++ IssmDouble::Real* valueA = xNew(local_nnz); ++ IssmDouble::Real* valueB = xNew(n); ++ // read the data from A and B ++ getVectorPrimal(a_loc, valueA, local_nnz); ++ getVectorPrimal(rhs, valueB, n); ++ ++ MumpsSolve(n, nnz, local_nnz, irn_loc, jcn_loc, valueA, valueB, parameters); ++ // valueB contains now the solution ++ ++ // pack the values into rhs ++ setVectorPrimal(rhs, valueB, n); ++ ++ if(tape.isActive()) { ++ // create the index vector X and register x as active variables ++ IssmDouble::GradientData* indexX = xNew(n); ++ registerVector(rhs, indexX, n); ++ ++ dataHandler->addData(valueB); // contains the values from x ++ dataHandler->addData(indexX); ++ ++ // store other arguments ++ dataHandler->addData(n); ++ dataHandler->addData(nnz); ++ dataHandler->addData(local_nnz); ++ dataHandler->addData(parameters); // we assume here that parameters is still intact when the reverse run is called ++ ++ tape.pushExternalFunction(&MumpsSolve_codi_b, dataHandler, &MumpsSolve_codi_delete); ++ } else { ++ // if the tape is active valueB is stored in the dataHandler and deleted in the reverse sweep ++ xDelete(valueB); ++ } ++ ++ xDelete(valueA); ++} ++/*}}}*/ + #endif +Index: ../trunk-jpl/src/c/toolkits/gsl/DenseGslSolve.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/gsl/DenseGslSolve.cpp (revision 23250) ++++ ../trunk-jpl/src/c/toolkits/gsl/DenseGslSolve.cpp (revision 23251) +@@ -13,6 +13,7 @@ + #include "../../classes/Params/GenericParam.h" + #include "../../classes/Params/Parameters.h" + #include "../adolc/adolcincludes.h" ++#include "../codipack/codipackincludes.h" + #include "./gslincludes.h" + + #ifdef _HAVE_GSL_ +@@ -250,3 +251,142 @@ + } + /*}}}*/ + #endif ++ ++#ifdef _HAVE_CODIPACK_ ++void SolverxSeq_codi_b(codi::DataStore* data) {/*{{{*/ ++ IssmDouble::TapeType& tape = IssmDouble::getGlobalTape(); ++ ++ IssmDouble::Real* valueATrans; ++ IssmDouble::GradientData* indexATrans; ++ IssmDouble::GradientData* indexB; ++ IssmDouble::Real* valueX; ++ IssmDouble::GradientData* indexX; ++ int n; ++ ++ data->getData(valueATrans); ++ data->getData(indexATrans); ++ data->getData(indexB); ++ data->getData(valueX); ++ data->getData(indexX); ++ data->getData(n); ++ ++ ++ // create the adjoint vector for x and reset the adjoint values on the tape ++ IssmDouble::GradientValue* adjX = xNew(n); ++ getVectorAdjoint(tape, indexX, adjX, n); ++ ++ IssmDouble::GradientValue* sol = xNew(n); ++ SolverxSeq(sol, valueATrans, adjX, n); ++ ++ updateVectorAdjoint(tape, indexB, sol, n); ++ for(int i=0; igetData(valueATrans); ++ data->getData(indexATrans); ++ data->getData(indexB); ++ data->getData(valueX); ++ data->getData(indexX); ++ data->getData(n); ++ ++ xDelete(valueATrans); ++ xDelete(indexATrans); ++ xDelete(indexB); ++ xDelete(valueX); ++ xDelete(indexX); ++} ++/*}}}*/ ++void SolverxSeq(IssmDouble *X,IssmDouble *A,IssmDouble *B,int n, Parameters* parameters){/*{{{*/ ++ IssmDouble::TapeType& tape = IssmDouble::getGlobalTape(); ++ codi::DataStore* dataHandler = NULL; ++ ++ if(tape.isActive()) { ++ dataHandler = new codi::DataStore(); ++ ++ // create the index vector and the double data for A and B ++ IssmDouble::Real* valueATrans = xNew(n*n); ++ IssmDouble::GradientData* indexATrans = xNew(n*n); ++ ++ // read the data for matrix in a transposed fashion ++ for (int i=0; i(n); ++ getVectorGradData(B, indexB, n); ++ ++ dataHandler->addData(valueATrans); ++ dataHandler->addData(indexATrans); ++ dataHandler->addData(indexB); ++ } ++ ++ // unpack the primal values from the matrix and the vector ++ IssmDouble::Real* valueA = xNew(n*n); ++ IssmDouble::Real* valueB = xNew(n); ++ // read the data from A and B ++ getVectorPrimal(A, valueA, n*n); ++ getVectorPrimal(B, valueB, n); ++ ++ // create the placeholder for X and solve the system ++ IssmDouble::Real* valueX = xNew(n); ++ SolverxSeq(valueX, valueA, valueB, n); ++ ++ // pack the values into x ++ setVectorPrimal(X, valueX, n); ++ ++ if(tape.isActive()) { ++ // create the index vector X and register x as active variables ++ IssmDouble::GradientData* indexX = xNew(n); ++ registerVector(X, indexX, n); ++ ++ dataHandler->addData(valueX); ++ dataHandler->addData(indexX); ++ ++ // store other arguments ++ dataHandler->addData(n); ++ ++ tape.pushExternalFunction(&SolverxSeq_codi_b, dataHandler, &SolverxSeq_codi_delete); ++ } else { ++ // if the tape is active valueX is stored in the dataHandler and deleted in the reverse sweep ++ xDelete(valueX); ++ } ++ ++ xDelete(valueB); ++ xDelete(valueA); ++} ++/*}}}*/ ++void DenseGslSolve(/*output*/ IssmDouble** px,/*stiffness matrix:*/ IssmDouble* Kff, int Kff_M, int Kff_N, /*right hand side load vector: */ IssmDouble* pf, int pf_M, Parameters* parameters){ /*{{{*/ ++ ++ /*Intermediary: */ ++ ++ if(Kff_N!=pf_M)_error_("Right hand side vector of size " << pf_M << ", when matrix is of size " << Kff_M << "-" << Kff_N << " !"); ++ if(Kff_M!=Kff_N)_error_("Stiffness matrix should be square!"); ++ ++ IssmDouble *x = xNew(Kff_N,"t"); ++ ++ SolverxSeq(x,Kff,pf,Kff_N,parameters); ++ ++ /*allocate output pointers: */ ++ *px=x; ++} ++/*}}}*/ ++#endif +Index: ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23250) ++++ ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23251) +@@ -18,7 +18,11 @@ + #ifdef _HAVE_MPI_ + /*Include header files: {{{*/ + #ifdef _HAVE_AMPI_ +- #include ++ #ifdef _HAVE_ADJOINTMPI_ ++ #include ++ #else ++ #include ++ #endif + #elif _HAVE_PETSC_MPI_ // Petsc now hides there MPI header. It can be reached through Petsc. + #include + #else +@@ -34,8 +38,10 @@ + + // data types + #define ISSM_MPI_CHAR MPI_CHAR +- #ifdef _HAVE_AMPI_ ++ #if defined(_HAVE_AMPI_) + #define ISSM_MPI_DOUBLE AMPI_ADOUBLE // corresponds to IssmDouble ++ #elif defined(_HAVE_ADJOINTMPI_) ++ #define ISSM_MPI_DOUBLE AMPI_DOUBLE // corresponds to IssmDouble + #else + #define ISSM_MPI_DOUBLE MPI_DOUBLE // corresponds to IssmDouble + #endif +Index: ../trunk-jpl/src/c/toolkits/mpi/issmmpi.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/issmmpi.cpp (revision 23250) ++++ ../trunk-jpl/src/c/toolkits/mpi/issmmpi.cpp (revision 23251) +@@ -59,7 +59,7 @@ + comm); + # endif + #else +-# ifdef _HAVE_ADOLC_ ++# ifdef _HAVE_AD_ + if (sendtype==ISSM_MPI_DOUBLE) { + IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; + IssmDouble* activeRecvBuf=(IssmDouble*)recvbuf; +@@ -96,7 +96,7 @@ + # endif + #else + assert(sendcount==recvcounts[0]); // we handle only identical representations +-# ifdef _HAVE_ADOLC_ ++# ifdef _HAVE_AD_ + if (sendtype==ISSM_MPI_DOUBLE) { + IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; + IssmDouble* activeRecvBuf=(IssmDouble*)(recvbuf)+displs[0]; +@@ -128,7 +128,7 @@ + comm); + # endif + #else +-# ifdef _HAVE_ADOLC_ ++#ifdef _HAVE_AD_ + if (datatype==ISSM_MPI_DOUBLE) { + IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; + IssmDouble* activeRecvBuf=(IssmDouble*)recvbuf; +@@ -214,14 +214,18 @@ + }/*}}}*/ + int ISSM_MPI_Finalize(void){ /*{{{*/ + +- int rc=0; +-#ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ +- rc=AMPI_Finalize_NT(); +-# else +- rc=MPI_Finalize(); +-# endif +-#endif ++ int rc=0; ++ #ifdef _HAVE_MPI_ ++ #ifdef _HAVE_AMPI_ ++ #ifdef _HAVE_ADJOINTMPI_ ++ rc=AMPI_Finalize(); ++ #else ++ rc=AMPI_Finalize_NT(); ++ #endif ++ #else ++ rc=MPI_Finalize(); ++ #endif ++ #endif + return rc; + }/*}}}*/ + int ISSM_MPI_Gather(void *sendbuf, int sendcnt, ISSM_MPI_Datatype sendtype, void *recvbuf, int recvcnt, ISSM_MPI_Datatype recvtype, int root, ISSM_MPI_Comm comm){ /*{{{*/ +@@ -249,7 +253,7 @@ + comm); + # endif + #else +-# ifdef _HAVE_ADOLC_ ++# ifdef _HAVE_AD_ + if (sendtype==ISSM_MPI_DOUBLE) { + IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; + IssmDouble* activeRecvBuf=(IssmDouble*)recvbuf; +@@ -289,7 +293,7 @@ + # endif + #else + assert(sendcnt==recvcnts[0]); // we handle only identical representations +-# ifdef _HAVE_ADOLC_ ++#ifdef _HAVE_AD_ + if (sendtype==ISSM_MPI_DOUBLE) { + IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; + IssmDouble* activeRecvBuf=(IssmDouble*)(recvbuf)+displs[0]; +@@ -303,14 +307,18 @@ + }/*}}}*/ + int ISSM_MPI_Init(int *argc, char ***argv){ /*{{{*/ + +- int rc=0; +-#ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ +- rc=AMPI_Init_NT(argc,argv); +-# else +- rc=MPI_Init(argc,argv); +-# endif +-#endif ++ int rc=0; ++ #ifdef _HAVE_MPI_ ++ #ifdef _HAVE_AMPI_ ++ #ifdef _HAVE_ADJOINTMPI_ ++ rc=AMPI_Init(argc,argv); ++ #else ++ rc=AMPI_Init_NT(argc,argv); ++ #endif ++ #else ++ rc=MPI_Init(argc,argv); ++ #endif ++ #endif + return rc; + }/*}}}*/ + int ISSM_MPI_Recv(void *buf, int count, ISSM_MPI_Datatype datatype, int source, int tag, ISSM_MPI_Comm comm, ISSM_MPI_Status *status){ /*{{{*/ +@@ -323,7 +331,9 @@ + datatype, + source, + tag, ++ #ifndef _HAVE_ADJOINTMPI_ + AMPI_FROM_SEND, // as long as there are no other variants ++ #endif + comm, + status); + # else +@@ -364,7 +374,7 @@ + comm); + # endif + #else +-# ifdef _HAVE_ADOLC_ ++# ifdef _HAVE_AD_ + if (datatype==ISSM_MPI_DOUBLE) { + IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; + IssmDouble* activeRecvBuf=(IssmDouble*)recvbuf; +@@ -401,7 +411,7 @@ + comm); + # endif + #else +-# ifdef _HAVE_ADOLC_ ++# ifdef _HAVE_AD_ + if (sendtype==ISSM_MPI_DOUBLE) { + IssmDouble* activeSendBuf=(IssmDouble*)sendbuf; + IssmDouble* activeRecvBuf=(IssmDouble*)recvbuf; +@@ -441,7 +451,7 @@ + # endif + #else + assert(sendcnts[0]==recvcnt); // we handle only identical representations +-# ifdef _HAVE_ADOLC_ ++# ifdef _HAVE_AD_ + if (sendtype==ISSM_MPI_DOUBLE) { + IssmDouble* activeSendBuf=(IssmDouble*)(sendbuf)+displs[0]; + IssmDouble* activeRecvBuf=(IssmDouble*)recvbuf; +@@ -463,7 +473,9 @@ + datatype, + dest, + tag, ++ #ifndef _HAVE_ADJOINTMPI_ + AMPI_TO_RECV, // as long as there are no other variants ++ #endif + comm); + # else + rc=MPI_Send(buf, +@@ -491,6 +503,8 @@ + + #ifdef _HAVE_ADOLC_ + ensureContiguousLocations(aSize); ++#else ++ fprintf(stderr, "*** Codipack ISSM_MPI_ContiguousInAdolc()\n"); + #endif + }/*}}}*/ + int ISSM_MPI_Comm_split(ISSM_MPI_Comm comm, int color, int key, ISSM_MPI_Comm *newcomm){ /*{{{*/ +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23250) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23251) +@@ -17,6 +17,11 @@ + #include "../shared/Enum/Enum.h" + #include "../analyses/analyses.h" + ++#if _HAVE_CODIPACK_ ++#include // for output of the CoDiPack tape ++extern CoDi_global codi_global; ++#endif ++ + /*module includes: {{{*/ + #include "../modules/ModelProcessorx/ModelProcessorx.h" + #include "../modules/VerticesDofx/VerticesDofx.h" +@@ -1850,12 +1855,22 @@ + if(num_dependents){ + dependents=xNew(num_dependents); + ++ #if defined(_HAVE_CODIPACK_) ++ auto& tape_codi = IssmDouble::getGlobalTape(); ++ #endif ++ + /*Go through our dependent variables, and compute the response:*/ + for(int i=0;iSize();i++){ + DependentObject* dep=(DependentObject*)dependent_objects->GetObjectByOffset(i); + dep->Responsex(&output_value,this); + if (my_rank==0) { +- output_value>>=dependents[i]; ++ #if defined(_HAVE_CODIPACK_) ++ tape_codi.registerOutput(output_value); ++ dependents[i] = output_value.getValue(); ++ codi_global.output_indices.push_back(output_value.getGradientData()); ++ #else ++ output_value>>=dependents[i]; ++ #endif + } + } + } +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 23250) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 23251) +@@ -27,6 +27,11 @@ + #include "../shared/io/io.h" + #include "../shared/shared.h" + ++#ifdef _HAVE_CODIPACK_ ++extern CoDi_global codi_global; ++#include // for output of the CoDiPack tape ++#endif ++ + /*IoConstant class and methods*/ + IoConstant::IoConstant(){/*{{{*/ + this->isindependent = false; +@@ -430,7 +435,8 @@ + + if(trace || (autodiff && !iscontrol)){ + +- #ifdef _HAVE_ADOLC_ ++ #ifdef _HAVE_AD_ ++ // FIXME codi here we should be able to execute codi version as normal + this->FetchData(&num_independent_objects,"md.autodiff.num_independent_objects"); + if(num_independent_objects){ + this->FetchData(&names,&temp,"md.autodiff.independent_object_names"); +@@ -459,7 +465,7 @@ + } + #else + /*if we asked for AD computations, we have a problem!: */ +- _error_("Cannot carry out AD mode computations without support of ADOLC compiled in!"); ++ _error_("Cannot carry out AD mode computations without support of ADOLC or CoDiPack compiled in!"); + #endif + } + } +@@ -1701,7 +1707,7 @@ + int Xcount = 0; + if(X) Xcount=*pXcount; + +- #ifdef _HAVE_ADOLC_ //cannot come here unless you are running AD mode, from DeclaredIndependents: ++ #ifdef _HAVE_AD_ //cannot come here unless you are running AD mode, from DeclaredIndependents: + + /*output: */ + IssmPDouble pscalar; +@@ -1718,12 +1724,24 @@ + + /*Now, before we even broadcast this to other nodes, declare the scalar as an independent variable!. If we + *have been supplied an X vector, use it instead of what we just read: */ +- if(X){ +- scalar<<=X[Xcount]; +- } +- else{ +- scalar<<=pscalar; +- } ++ #if defined(_HAVE_CODIPACK_) ++ // FIXME codi here we just assign instead of using "operator <<=" ++ if(X){ ++ scalar=X[Xcount]; ++ } else { ++ scalar=pscalar; ++ } ++ auto& tape_codi = IssmDouble::getGlobalTape(); ++ tape_codi.registerInput(scalar); ++ codi_global.input_indices.push_back(scalar.getGradientData()); ++ #else ++ if(X){ ++ scalar<<=X[Xcount]; ++ } ++ else{ ++ scalar<<=pscalar; ++ } ++ #endif + } + + ISSM_MPI_Bcast(&scalar,1,ISSM_MPI_DOUBLE,0,IssmComm::GetComm()); +@@ -1784,12 +1802,31 @@ + + /*Now, before we even broadcast this to other nodes, declare the whole matrix as a independent variable! + If we have been supplied an X vector, use it instead of what we just read: */ +- if(X){ +- for(int i=0;iAddDataIndependent(new IoData(matrix,code,layout,M,N,data_name)); + +@@ -2561,7 +2600,8 @@ + this->FetchData(&iscontrol,"md.inversion.iscontrol"); + + if(trace || (autodiff && !iscontrol)){ +- #ifdef _HAVE_ADOLC_ ++ ++ #if defined(_HAVE_ADOLC_) + /*Retrieve parameters: */ + this->FetchData(&keep,"md.autodiff.keep"); + int keepTaylors=keep?1:0; +@@ -2578,7 +2618,35 @@ + /*Start trace: */ + int skipFileDeletion=1; + trace_on(my_rank,keepTaylors,reCast(obufsize),reCast(lbufsize),reCast(cbufsize),reCast(tbufsize),skipFileDeletion); ++ ++ #elif defined(_HAVE_CODIPACK_) ++ //fprintf(stderr, "*** Codipack IoModel::StartTrace\n"); ++ /* ++ * FIXME codi ++ * - ADOL-C variant uses fine grained tracing with various arguments ++ * - ADOL-C variant sets a garbage collection parameter for its tape ++ * -> These parameters are not read for the CoDiPack ISSM version! ++ */ ++ auto& tape_codi = IssmDouble::getGlobalTape(); ++ tape_codi.setActive(); ++ #if _AD_TAPE_ALLOC_ ++ //alloc_profiler.Tag(StartInit, true); ++ IssmDouble x_t(1.0), y_t(1.0); ++ tape_codi.registerInput(y_t); ++ int codi_allocn = 0; ++ this->FetchData(&codi_allocn, AutodiffTapeAllocEnum); ++ for(int i = 0;i < codi_allocn;++i) { ++ x_t = y_t * y_t; ++ } ++ /* ++ std::stringstream out_s; ++ IssmDouble::getGlobalTape().printStatistics(out_s); ++ _printf0_("StartTrace::Tape Statistics : TapeAlloc count=[" << codi_allocn << "]\n" << out_s.str()); ++ */ ++ tape_codi.reset(); ++ //alloc_profiler.Tag(FinishInit, true); + #endif ++ #endif + } + + } Index: /issm/oecreview/Archive/23185-23389/ISSM-23251-23252.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23251-23252.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23251-23252.diff (revision 23390) @@ -0,0 +1,138 @@ +Index: ../trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp (revision 23251) ++++ ../trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp (revision 23252) +@@ -93,7 +93,7 @@ + }/*}}}*/ + + /*For autodiff, we sometimes need to cast our vectors to passive*/ +-#ifdef _HAVE_ADOLC_ ++#ifdef _HAVE_AD_ + void GetPassiveVectorFromControlInputsx(Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,const char* data){/*{{{*/ + + /*Get active vector first*/ +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 23251) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 23252) +@@ -76,8 +76,9 @@ + //fprintf(stderr, "*** Codipack CreateParametersAutodiff()\n"); + /*initialize a placeholder to store solver pointers: {{{*/ + /*Solver pointers depend on what type of solver we are implementing: */ +- options=OptionsFromAnalysis(parameters,DefaultAnalysisEnum); //options database is not filled in yet, use default. +- ToolkitOptions::Init(options); ++ options=OptionsFromAnalysis(&toolkit,parameters,DefaultAnalysisEnum); ++ ToolkitOptions::Init(toolkit,options); ++ xDelete(toolkit); + + switch(IssmSolverTypeFromToolkitOptions()){ + case MumpsEnum:{ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 23251) ++++ ../trunk-jpl/src/c/Makefile.am (revision 23252) +@@ -50,12 +50,15 @@ + ./modules/BamgConvertMeshx/BamgConvertMeshx.cpp\ + ./modules/BamgTriangulatex/BamgTriangulatex.cpp + +-#do not include AmrBamg with ADOLC ++#do not include AmrBamg with AD + if ADOLC + else ++if CODIPACK ++else + issm_sources += ./classes/AmrBamg.cpp + endif + endif ++endif + #}}} + #Core sources{{{ + issm_sources += ./datastructures/DataSet.cpp\ +Index: ../trunk-jpl/src/c/cores/transient_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/transient_core.cpp (revision 23251) ++++ ../trunk-jpl/src/c/cores/transient_core.cpp (revision 23252) +@@ -69,7 +69,7 @@ + femmodel->parameters->FindParam(&numoutputs,TransientNumRequestedOutputsEnum); + if(numoutputs) femmodel->parameters->FindParam(&requested_outputs,&numoutputs,TransientRequestedOutputsEnum); + +- #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) + if(amr_frequency){ + femmodel->parameters->FindParam(&amr_restart,AmrRestartEnum); + if(amr_restart) femmodel->ReMesh(); +@@ -77,7 +77,7 @@ + #endif + + if(isoceancoupling){ /*{{{*/ +- #ifndef _HAVE_ADOLC_ ++ #ifndef _HAVE_AD_ + if(VerboseSolution()) _printf0_(" ocean coupling: initialization \n"); + int my_rank; + ISSM_MPI_Comm tomitgcmcomm; +@@ -246,7 +246,7 @@ + + if(isoceancoupling){ /*{{{*/ + +- #ifndef _HAVE_ADOLC_ ++ #ifndef _HAVE_AD_ + if(VerboseSolution()) _printf0_(" ocean coupling: exchanging information\n"); + int my_rank; + ISSM_MPI_Comm tomitgcmcomm; +@@ -459,7 +459,7 @@ + /*Adaptive mesh refinement*/ + if(amr_frequency){ + +- #if !defined(_HAVE_ADOLC_) ++ #if !defined(_HAVE_AD_) + if(save_results) femmodel->WriteMeshInResults(); + if(step%amr_frequency==0 && timeFetchData(&codi_allocn, AutodiffTapeAllocEnum); ++ this->FetchData(&codi_allocn,"md.autodiff.tapeAlloc"); + for(int i = 0;i < codi_allocn;++i) { + x_t = y_t * y_t; + } Index: /issm/oecreview/Archive/23185-23389/ISSM-23252-23253.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23252-23253.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23252-23253.diff (revision 23390) @@ -0,0 +1,10 @@ +Index: ../trunk-jpl/externalpackages/codipack/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/codipack/install.sh (revision 23252) ++++ ../trunk-jpl/externalpackages/codipack/install.sh (revision 23253) +@@ -5,4 +5,4 @@ + rm -rf install + + #Download development version +-svn co https://github.com/SciCompKL/CoDiPack.git install ++svn co https://github.com/SciCompKL/CoDiPack.git/trunk install Index: /issm/oecreview/Archive/23185-23389/ISSM-23253-23254.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23253-23254.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23253-23254.diff (revision 23390) @@ -0,0 +1,208 @@ +Index: ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23253) ++++ ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23254) +@@ -39,9 +39,11 @@ + // data types + #define ISSM_MPI_CHAR MPI_CHAR + #if defined(_HAVE_AMPI_) ++ #ifdef _HAVE_ADJOINTMPI_ ++ #define ISSM_MPI_DOUBLE AMPI_DOUBLE // corresponds to IssmDouble ++ #else + #define ISSM_MPI_DOUBLE AMPI_ADOUBLE // corresponds to IssmDouble +- #elif defined(_HAVE_ADJOINTMPI_) +- #define ISSM_MPI_DOUBLE AMPI_DOUBLE // corresponds to IssmDouble ++ #endif + #else + #define ISSM_MPI_DOUBLE MPI_DOUBLE // corresponds to IssmDouble + #endif +Index: ../trunk-jpl/src/c/classes/Params/Parameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Params/Parameters.cpp (revision 23253) ++++ ../trunk-jpl/src/c/classes/Params/Parameters.cpp (revision 23254) +@@ -718,7 +718,7 @@ + /*}}}*/ + + /*Specific case with ADOL-C, we might need to get double params for m1qn3*/ +-#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) ++#if defined(_HAVE_AD_) && !defined(_WRAPPERS_) + void Parameters::FindParamAndMakePassive(double* pscalar,int param_enum){ _assert_(this);/*{{{*/ + _assert_(param_enum>ParametersSTARTEnum); + _assert_(param_enum inline void GenericOption::Get(IssmPDouble** pvalue){ /*{{{*/ + +Index: ../trunk-jpl/src/c/classes/FemModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23253) ++++ ../trunk-jpl/src/c/classes/FemModel.cpp (revision 23254) +@@ -88,13 +88,13 @@ + /*AMR stuff*/ + this->parameters->FindParam(&amr_frequency,TransientAmrFrequencyEnum); + this->parameters->FindParam(&amr_frequency,TransientAmrFrequencyEnum); +- #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) + this->amr = NULL; + #endif +- #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) + this->amrbamg = NULL; + #endif +- #if !defined(_HAVE_ADOLC_) ++ #if !defined(_HAVE_AD_) + if(amr_frequency && solution_type==TransientSolutionEnum){ + /*Verifications. AMR supports SSA, P1 and horizontal 2D domain*/ + bool isSSA; +@@ -151,10 +151,10 @@ + this->InitFromFiles(rootpath,inputfilename,outputfilename,toolkitsfilename,lockfilename,restartfilename, solution_type,traceon,X); + profiler->Stop(MPROCESSOR); + +- #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) + this->amr = NULL; + #endif +- #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) + this->amrbamg = NULL; + #endif + +@@ -188,11 +188,11 @@ + if(parameters)delete parameters; + if(results)delete results; + +- #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) + if(amr)delete amr; + #endif + +- #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) + if(amrbamg)delete amrbamg; + #endif + +@@ -327,10 +327,10 @@ + } + + /*AMR, no copy for now*/ +- #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) + this->amr = NULL; + #endif +- #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) + this->amrbamg = NULL; + #endif + +@@ -2563,11 +2563,11 @@ + /*Branch to specific amr depending on requested method*/ + this->parameters->FindParam(&amrtype,AmrTypeEnum); + switch(amrtype){ +- #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) + case AmrNeopzEnum: this->ReMeshNeopz(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; + #endif + +- #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) + case AmrBamgEnum: this->ReMeshBamg(&newnumberofvertices,&newnumberofelements,&newx,&newy,&newz,&newelementslist); break; + #endif + +@@ -4919,7 +4919,7 @@ + }/*}}}*/ + #endif + +-#if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++#if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) + void FemModel::ReMeshBamg(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist){/*{{{*/ + + /*Output*/ +@@ -5245,7 +5245,7 @@ + /*}}}*/ + #endif + +-#if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++#if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) + void FemModel::ReMeshNeopz(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist){/*{{{*/ + + /*pnewelementslist keep vertices in Matlab indexing*/ +Index: ../trunk-jpl/src/c/classes/FemModel.h +=================================================================== +--- ../trunk-jpl/src/c/classes/FemModel.h (revision 23253) ++++ ../trunk-jpl/src/c/classes/FemModel.h (revision 23254) +@@ -19,10 +19,10 @@ + class Materials; + class Profiler; + class Elements; +-#if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++#if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) + #include "./AdaptiveMeshRefinement.h" + #endif +-#if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++#if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) + #include "./AmrBamg.h" + #endif + /*}}}*/ +@@ -50,11 +50,11 @@ + Vertices *vertices; //one set of vertices + + //FIXME: do we want only one class and have virtual functions? or keep 2 classes, at least rename AdaptiveMeshRefinement -> AmrNeopz +- #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) + AdaptiveMeshRefinement *amr; //adaptive mesh refinement object. It keeps coarse mesh and execute refinement process + #endif + +- #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) + AmrBamg *amrbamg; //adaptive mesh refinement object. It keeps coarse mesh and execute refinement process + #endif + +@@ -163,7 +163,7 @@ + #endif + + /*AMR*/ +- #if !defined(_HAVE_ADOLC_) ++ #if !defined(_HAVE_AD_) + void ReMesh(void); + void BedrockFromMismipPlus(void); + void AdjustBaseThicknessAndMask(void); +@@ -190,7 +190,7 @@ + void GetZeroLevelSetPoints(IssmDouble** pzerolevelset_points,int &numberofpoints,int levelset_type); + #endif + +- #if defined(_HAVE_BAMG_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_BAMG_) && !defined(_HAVE_AD_) + void ReMeshBamg(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); + void InitializeAdaptiveRefinementBamg(void); + void GethmaxVerticesFromZeroLevelSetDistance(IssmDouble* hmaxvertices,int levelset_type); +@@ -198,7 +198,7 @@ + void GetVerticeDistanceToZeroLevelSet(IssmDouble** pverticedistance,int leveset_type); + #endif + +- #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_ADOLC_) ++ #if defined(_HAVE_NEOPZ_) && !defined(_HAVE_AD_) + void ReMeshNeopz(int* pnewnumberofvertices,int* pnewnumberofelements,IssmDouble** pnewx,IssmDouble** pnewy,IssmDouble** pnewz,int** pnewelementslist); + void InitializeAdaptiveRefinementNeopz(void); + void GetElementDistanceToZeroLevelSet(IssmDouble** pelementdistance,int levelset_type); Index: /issm/oecreview/Archive/23185-23389/ISSM-23254-23255.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23254-23255.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23254-23255.diff (revision 23390) @@ -0,0 +1,157 @@ +Index: ../trunk-jpl/src/c/shared/Elements/PrintArrays.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Elements/PrintArrays.cpp (revision 23254) ++++ ../trunk-jpl/src/c/shared/Elements/PrintArrays.cpp (revision 23255) +@@ -11,7 +11,7 @@ + } + _printf_("\n"); + } +-#ifdef _HAVE_ADOLC_ ++#ifdef _HAVE_AD_ + void printarray(IssmDouble* array,int lines,int cols){ + _printf_("\n"); + for(int i=0;ivector=NULL; +- #ifdef _HAVE_ADOLC_ ++ #ifdef _HAVE_AD_ + this->avector=NULL; + #endif + } +Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp (revision 23254) ++++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp (revision 23255) +@@ -20,7 +20,7 @@ + /*PetscMat constructors and destructor*/ + PetscMat::PetscMat(){/*{{{*/ + this->matrix=NULL; +- #ifdef _HAVE_ADOLC_ ++ #ifdef _HAVE_AD_ + this->amatrix=NULL; + #endif + +Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.h (revision 23254) ++++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.h (revision 23255) +@@ -24,7 +24,7 @@ + public: + Vec vector; + +- #ifdef _HAVE_ADOLC_ ++ #ifdef _HAVE_AD_ + IssmDouble* avector; + #endif + +Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.h (revision 23254) ++++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.h (revision 23255) +@@ -26,7 +26,7 @@ + public: + Mat matrix; + +- #ifdef _HAVE_ADOLC_ ++ #ifdef _HAVE_AD_ + IssmDouble* amatrix; + #endif + +Index: ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp (revision 23254) ++++ ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp (revision 23255) +@@ -615,7 +615,8 @@ + dataHandler->addData(local_nnz); + dataHandler->addData(parameters); // we assume here that parameters is still intact when the reverse run is called + +- tape.pushExternalFunction(&MumpsSolve_codi_b, dataHandler, &MumpsSolve_codi_delete); ++ tape.pushExternalFunction(&MumpsSolve_codi_b, dataHandler, &MumpsSolve_codi_delete); ++ //tape.pushExternalFunctionHandle(&MumpsSolve_codi_b, dataHandler, &MumpsSolve_codi_delete); + } else { + // if the tape is active valueB is stored in the dataHandler and deleted in the reverse sweep + xDelete(valueB); +Index: ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23254) ++++ ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23255) +@@ -97,7 +97,7 @@ + /*Dynamically return ISSM_MPI type from variable type */ + template ISSM_MPI_Datatype TypeToMPIType(){assert(false);}; + template <> inline ISSM_MPI_Datatype TypeToMPIType(){return ISSM_MPI_DOUBLE;}; +-#if defined(_HAVE_ADOLC_) && !defined(_WRAPPERS_) ++#if defined(_HAVE_AD_) && !defined(_WRAPPERS_) + template <> inline ISSM_MPI_Datatype TypeToMPIType(){return ISSM_MPI_PDOUBLE;}; + #endif + template <> inline ISSM_MPI_Datatype TypeToMPIType(){return ISSM_MPI_INT;}; +Index: ../trunk-jpl/src/c/cores/controlad_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controlad_core.cpp (revision 23254) ++++ ../trunk-jpl/src/c/cores/controlad_core.cpp (revision 23255) +@@ -10,6 +10,7 @@ + #include "../modules/modules.h" + #include "../solutionsequences/solutionsequences.h" + ++/*This file is probably never used!*/ + #if defined (_HAVE_M1QN3_) & defined (_HAVE_ADOLC_) + /*m1qn3 prototypes {{{*/ + extern "C" void *ctonbe_; // DIS mode : Conversion +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 23254) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 23255) +@@ -1761,7 +1761,7 @@ + int Xcount = 0; + if(X) Xcount=*pXcount; + +- #ifdef _HAVE_ADOLC_ //cannot come here unless you are running AD mode, from DeclaredIndependents: ++ #ifdef _HAVE_AD_ //cannot come here unless you are running AD mode, from DeclaredIndependents: + + /*Intermediaries*/ + int M,N; Index: /issm/oecreview/Archive/23185-23389/ISSM-23255-23256.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23255-23256.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23255-23256.diff (revision 23390) @@ -0,0 +1,36 @@ +Index: ../trunk-jpl/src/m/classes/geometry.py +=================================================================== +--- ../trunk-jpl/src/m/classes/geometry.py (revision 23255) ++++ ../trunk-jpl/src/m/classes/geometry.py (revision 23256) +@@ -12,11 +12,11 @@ + """ + + def __init__(self): # {{{ +- self.surface = float('NaN') +- self.thickness = float('NaN') ++ self.surface = float('NaN') ++ self.thickness = float('NaN') + self.base = float('NaN') +- self.bed = float('NaN') +- self.hydrostatic_ratio = float('NaN') ++ self.bed = float('NaN') ++ self.hydrostatic_ratio = float('NaN') + + #set defaults + self.setdefaultparameters() +Index: ../trunk-jpl/src/m/qmu/preqmu.py +=================================================================== +--- ../trunk-jpl/src/m/qmu/preqmu.py (revision 23255) ++++ ../trunk-jpl/src/m/qmu/preqmu.py (revision 23256) +@@ -44,8 +44,9 @@ + if os.path.isdir(qmudir): + raise RuntimeError('Existing '+str(options.qmudir)+' directory, cannot overwrite. Specify "overwrite","y" option in solve arguments.') + +- +- os.makedirs(qmudir) ++ # os.makedirs() raises error when dir exists, matlab's mkdir() does not ++ if not os.path.isdir(qmudir): ++ os.makedirs(qmudir) + os.chdir(qmudir) + + # when running in library mode, the in file needs to be called md.miscellaneous.name.qmu.in Index: /issm/oecreview/Archive/23185-23389/ISSM-23256-23257.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23256-23257.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23256-23257.diff (revision 23390) @@ -0,0 +1,76 @@ +Index: ../trunk-jpl/test/NightlyRun/test420.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test420.py (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test420.py (revision 23257) +@@ -0,0 +1,71 @@ ++#Test Name: SquareSheetShelfDakotaScaledResponse ++ ++import numpy as np ++from model import * ++from socket import gethostname ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++from partitioner import * ++ ++md = triangle(model(),'../Exp/Square.exp',200000.) ++md = setmask(md,'../Exp/SquareShelf.exp','') ++md = parameterize(md,'../Par/SquareSheetShelf.py') ++md = setflowequation(md,'SSA','all') ++md.cluster = generic('name',gethostname(),'np',3) ++ ++#partitioning ++md.qmu.numberofpartitions = 10 ++md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions) ++md.qmu.partition = md.qmu.partition-1 ++md.qmu.isdakota = 1 ++ ++#Dakota options ++ ++#dakota version ++version = IssmConfig('_DAKOTA_VERSION_') ++version = float(version[0]) ++ ++#variables ++md.qmu.variables.rho_ice = normal_uncertain.normal_uncertain('MaterialsRhoIce',md.materials.rho_ice,0.01) ++ ++#responses ++md.qmu.responses.MaxVel = response_function.response_function('scaled_Thickness',[],[0.0001,0.001,0.01,0.25,0.5,0.75,0.99,0.999,0.9999]) ++ ++#method ++md.qmu.method = dakota_method.dakota_method('nond_l') ++ ++#parameters ++md.qmu.params.direct = True ++md.qmu.params.interval_type = 'forward' ++ ++if version >= 6: ++ md.qmu.params.analysis_driver = 'matlab' ++ md.qmu.params.evaluation_scheduling = 'master' ++ md.qmu.params.processors_per_evaluation = 2 ++else: ++ md.qmu.params.analysis_driver = 'stressbalance' ++ md.qmu.params.evaluation_concurrency = 1 ++ ++#imperative! ++md.stressbalance.reltol = 10**-5 #tighten for qmu analysese ++ ++#solve ++md.verbose = verbose('000000000') # this line is recommended ++md = solve(md,'Stressbalance','overwrite','y') ++md.qmu.results = md.results.dakota ++ ++#test on thickness ++h = np.zeros((md.qmu.numberofpartitions,)) ++for i in range(md.qmu.numberofpartitions): ++ h[i] = md.qmu.results.dresp_out[i].mean ++ ++#project onto grid ++thickness = h[(md.qmu.partition).flatten()] ++ ++#Fields and tolerances to track changes ++field_names = ['Thickness'] ++field_tolerances = [1e-10] ++field_values = [thickness] Index: /issm/oecreview/Archive/23185-23389/ISSM-23257-23258.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23257-23258.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23257-23258.diff (revision 23390) @@ -0,0 +1,67 @@ +Index: ../trunk-jpl/test/NightlyRun/test417.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test417.py (revision 23257) ++++ ../trunk-jpl/test/NightlyRun/test417.py (revision 23258) +@@ -87,7 +87,7 @@ + md = solve(md,'Stressbalance','overwrite','y') + + #Fields and tolerances to track changes +-md.qmu.results = md.results.dakota; ++md.qmu.results = md.results.dakota + + #ok, mass flux of 3 profiles should be -3 Gt/yr -3 Gt/yr and the sum, which is -6 Gt/yr + #we recover those mass fluxes through the mean of the response. +@@ -103,4 +103,4 @@ + + field_names = ['moments'] + field_tolerances = [1e-11] +-field_values = [md.results.dakota.montecarlo] ++field_values = [md.results.dakota.montecarlo] +Index: ../trunk-jpl/test/NightlyRun/test418.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test418.py (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test418.py (revision 23258) +@@ -0,0 +1,43 @@ ++#Test Name: SquareSheetShelfDiadSSA3dDakotaAreaAverage ++ ++# this test may crash ++ ++import numpy as np ++from model import * ++from socket import gethostname ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++from partitioner import * ++from AreaAverageOntoPartition import * ++ ++#test partitioning, and partition averaging ++# python cannot handle resolutions greater than 30010 ++md = triangle(model(),'../Exp/Square.exp',30000.) ++#print md.mesh.numberofvertices ++md = setmask(md,'../Exp/SquareShelf.exp','') ++md = parameterize(md,'../Par/SquareSheetShelf.py') ++md = setflowequation(md,'SSA','all') ++md.cluster = generic('name',gethostname(),'np',3) ++ ++#partitioning ++md.qmu.numberofpartitions = 100 ++ ++#corrupted size vs. prev_size ++#Aborted (core dumped) ++md = partitioner(md,'package','chaco','npart',md.qmu.numberofpartitions) ++ ++ ++md.qmu.partition=md.qmu.partition-1 ++ ++vector = np.arange(1,1+md.mesh.numberofvertices,1).reshape(-1,1) ++# double check this before committing: ++#print 'before AreaAverageOntoPartition' ++vector_on_partition = AreaAverageOntoPartition(md,vector) ++vector_on_nodes = vector_on_partition[md.qmu.partition+1] ++ ++field_names = ['vector_on_nodes'] ++field_tolerances = [1e-11] ++field_values = [vector_on_nodes] Index: /issm/oecreview/Archive/23185-23389/ISSM-23258-23259.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23258-23259.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23258-23259.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/jenkins/linux64_ross_dakota +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_dakota (revision 23258) ++++ ../trunk-jpl/jenkins/linux64_ross_dakota (revision 23259) +@@ -31,7 +31,7 @@ + + #PYTHON and MATLAB testing + MATLAB_TEST=1 +-PYTHON_TEST=0 ++PYTHON_TEST=1 + + #-----------------------------------# + # 3: External packages installation # Index: /issm/oecreview/Archive/23185-23389/ISSM-23259-23260.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23259-23260.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23259-23260.diff (revision 23390) @@ -0,0 +1,29 @@ +Index: ../trunk-jpl/jenkins/linux64_ross_python +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_python (revision 23259) ++++ ../trunk-jpl/jenkins/linux64_ross_python (revision 23260) +@@ -13,7 +13,7 @@ + --with-python-numpy-dir=/home/jenkins/.local/lib/python2.7/site-packages/numpy \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ +- --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpifort" \ ++ --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi -lmpicxx -lmpifort" \ + --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \ +@@ -20,7 +20,7 @@ + --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ + --with-chaco-dir="$ISSM_DIR/externalpackages/chaco/install" \ +- --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \ ++ --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \ + --with-m1qn3-dir=$ISSM_DIR/externalpackages/m1qn3/install \ + --with-numthreads=4 \ + --enable-development \ +@@ -58,5 +58,5 @@ + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-PYTHON_NROPTIONS="--exclude_name 'Dakota'" ++PYTHON_NROPTIONS="benchmark 'nightly' --exclude_name 'Dakota'" + MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" Index: /issm/oecreview/Archive/23185-23389/ISSM-23260-23261.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23260-23261.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23260-23261.diff (revision 23390) @@ -0,0 +1,11 @@ +Index: ../trunk-jpl/jenkins/linux64_ross_python +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_python (revision 23260) ++++ ../trunk-jpl/jenkins/linux64_ross_python (revision 23261) +@@ -58,5 +58,5 @@ + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-PYTHON_NROPTIONS="benchmark 'nightly' --exclude_name 'Dakota'" ++PYTHON_NROPTIONS="--exclude_name 'Dakota' --numprocs 1" + MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" Index: /issm/oecreview/Archive/23185-23389/ISSM-23261-23262.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23261-23262.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23261-23262.diff (revision 23390) @@ -0,0 +1,22 @@ +Index: ../trunk-jpl/jenkins/linux64_ross_python +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_python (revision 23261) ++++ ../trunk-jpl/jenkins/linux64_ross_python (revision 23262) +@@ -49,14 +49,14 @@ + + #number of cpus used in ISSM installation and compilation (one is usually + #safer as some packages are very sensitive to parallel compilation) +-NUMCPUS_INSTALL=10 ++NUMCPUS_INSTALL=5 + + #number of cpus used in the nightly runs. +-NUMCPUS_RUN=5 ++NUMCPUS_RUN=3 + + #Nightly run options. The matlab routine runme.m will be called + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-PYTHON_NROPTIONS="--exclude_name 'Dakota' --numprocs 1" ++PYTHON_NROPTIONS="--exclude_name 'Dakota'" + MATLAB_NROPTIONS="'exclude',[IdFromString('Dakota')]" Index: /issm/oecreview/Archive/23185-23389/ISSM-23262-23263.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23262-23263.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23262-23263.diff (revision 23390) @@ -0,0 +1,21 @@ +Index: ../trunk-jpl/jenkins/linux64_ross_python +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_python (revision 23262) ++++ ../trunk-jpl/jenkins/linux64_ross_python (revision 23263) +@@ -9,6 +9,7 @@ + #ISSM CONFIGURATION + ISSM_CONFIG='--prefix=$ISSM_DIR \ + --disable-static \ ++ --with-matlab-dir=$MATLAB_PATH \ + --with-python-dir=/usr \ + --with-python-numpy-dir=/home/jenkins/.local/lib/python2.7/site-packages/numpy \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ +@@ -27,7 +28,7 @@ + --enable-debugging ' + + #PYTHON and MATLAB testing +-MATLAB_TEST=0 ++MATLAB_TEST=1 + PYTHON_TEST=1 + + #-----------------------------------# Index: /issm/oecreview/Archive/23185-23389/ISSM-23263-23264.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23263-23264.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23263-23264.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/jenkins/linux64_ross_python +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_python (revision 23263) ++++ ../trunk-jpl/jenkins/linux64_ross_python (revision 23264) +@@ -28,7 +28,7 @@ + --enable-debugging ' + + #PYTHON and MATLAB testing +-MATLAB_TEST=1 ++MATLAB_TEST=0 + PYTHON_TEST=1 + + #-----------------------------------# Index: /issm/oecreview/Archive/23185-23389/ISSM-23264-23265.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23264-23265.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23264-23265.diff (revision 23390) @@ -0,0 +1,228 @@ +Index: ../trunk-jpl/src/m/classes/clusters/tetralith.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/tetralith.m (nonexistent) ++++ ../trunk-jpl/src/m/classes/clusters/tetralith.m (revision 23265) +@@ -0,0 +1,216 @@ ++%teralith class definition ++% ++% Usage: ++% cluster=tetralith(); ++% cluster=tetralith('np',3); ++% cluster=tetralith('np',3,'login','username'); ++ ++classdef tetralith ++ properties (SetAccess=public) ++ % {{{ ++ name = 'tetralith'; ++ login = ''; ++ numnodes = 2; ++ cpuspernode = 32; ++ mem = 2000; %MB ++ queue = 'normal'; ++ time = 2*60; %[minutes] ++ codepath = ''; ++ executionpath = ''; ++ interactive = 0; ++ port = []; ++ accountname = ''; ++ % }}} ++ end ++ methods ++ function cluster=tetralith(varargin) % {{{ ++ ++ %initialize cluster using default settings if provided ++ if (exist('tetralith_settings')==2), tetralith_settings; end ++ ++ %use provided options to change fields ++ cluster=AssignObjectFields(pairoptions(varargin{:}),cluster); ++ end ++ %}}} ++ function disp(cluster) % {{{ ++ % display the object ++ disp(sprintf('class ''%s'' object ''%s'' = ',class(cluster),inputname(1))); ++ disp(sprintf(' name: %s',cluster.name)); ++ disp(sprintf(' login: %s',cluster.login)); ++ disp(sprintf(' accountname: %s',cluster.accountname)); ++ disp(sprintf(' numnodes: %i',cluster.numnodes)); ++ disp(sprintf(' cpuspernode: %i',cluster.cpuspernode)); ++ disp(sprintf(' np: %i', cluster.cpuspernode*cluster.numnodes)); ++ disp(sprintf(' queue: %s',cluster.queue)); ++ disp(sprintf(' codepath: %s',cluster.codepath)); ++ disp(sprintf(' executionpath: %s',cluster.executionpath)); ++ disp(sprintf(' interactive: %i',cluster.interactive)); ++ disp(sprintf(' time: %i',cluster.time)); ++ disp(sprintf(' memory: %i',cluster.mem)); ++ end ++ %}}} ++ function md = checkconsistency(cluster,md,solution,analyses) % {{{ ++ ++ available_queues={'normal','devel'}; ++ queue_requirements_time=[7*24*60 60]; ++ queue_requirements_np=[1024 2*32]; ++ ++ QueueRequirements(available_queues,queue_requirements_time,queue_requirements_np,cluster.queue,cluster.np,1) ++ ++ %Miscelaneous ++ if isempty(cluster.login), md = checkmessage(md,'login empty'); end ++ if isempty(cluster.accountname), md = checkmessage(md,'accountname empty'); end ++ if isempty(cluster.codepath), md = checkmessage(md,'codepath empty'); end ++ if isempty(cluster.executionpath), md = checkmessage(md,'executionpath empty'); end ++ ++ end ++ %}}} ++ function numprocs=np(self) % {{{ ++ %compute number of processors ++ numprocs=self.numnodes*self.cpuspernode; ++ end ++ %}}} ++ function BuildKrigingQueueScript(cluster,modelname,solution,io_gather,isvalgrind,isgprof) % {{{ ++ ++ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end ++ if(isgprof), disp('gprof not supported by cluster, ignoring...'); end ++ ++ %compute number of processors ++% cluster.np=cluster.numnodes*cluster.cpuspernode; ++ np(cluster);%=cluster.numnodes*cluster.cpuspernode; ++ ++ %write queuing script ++ fid=fopen([modelname '.queue'],'w'); ++ fprintf(fid,'#!/bin/bash\n'); ++ fprintf(fid,'#\n'); ++ fprintf(fid,'#SBATCH --job-name=%s\n',modelname); ++% fprintf(fid,'#SBATCH -p %s \n',cluster.partition); ++ fprintf(fid,'#SBATCH -A %s \n',cluster.accountname); ++% fprintf(fid,'#SBATCH --mail-type=ALL\n'); ++ fprintf(fid,'#SBATCH -N %i -n %i\n',cluster.numnodes,cluster.cpuspernode); ++ %calculate walltime in hh:mm:ss format ++ walltime=datestr(cluster.time/(60*24),'HH:MM:SS') ++ fprintf(fid,'#SBATCH -t %s\n',walltime); %walltime should be in hh:mm:ss ++ fprintf(fid,'#SBATCH --mem=%i\n',cluster.mem); ++ fprintf(fid,'#SBATCH -o %s.outlog \n',modelname); ++ fprintf(fid,'#SBATCH -e %s.errlog \n\n',modelname); ++% fprintf(fid,'module load intelcomp/17.0.0\n') %module load not recommended within job script at Tetralith ++% fprintf(fid,'module load mpt/2.14\n') ++% fprintf(fid,'module load petsc/3.7.4d\n') ++% fprintf(fid,'module load parmetis/4.0.3\n') ++% fprintf(fid,'module load mumps/5.0.2\n') ++% fprintf(fid,'export ISSM_DIR="%s"\n',cluster.codepath); %FIXME ++ fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME ++ fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME ++ fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname); ++% fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); ++% fprintf(fid,'mpiexec_mpt -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); ++ fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); ++% fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); ++ if ~io_gather, %concatenate the output files: ++ fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); ++ end ++ fclose(fid); ++ end ++ %}}} ++ function BuildQueueScript(cluster,dirname,modelname,solution,io_gather,isvalgrind,isgprof,isdakota,isoceancoupling) % {{{ ++ ++ if(isvalgrind), disp('valgrind not supported by cluster, ignoring...'); end ++ if(isgprof), disp('gprof not supported by cluster, ignoring...'); end ++ ++ executable='issm.exe'; ++ if isdakota, ++ version=IssmConfig('_DAKOTA_VERSION_'); version=str2num(version(1:3)); ++ if (version>=6), ++ executable='issm_dakota.exe'; ++ end ++ end ++ if isoceancoupling, ++ executable='issm_ocean.exe'; ++ end ++ ++ %compute number of processors ++% cluster.np=cluster.numnodes*cluster.cpuspernode; ++ np(cluster);%=cluster.numnodes*cluster.cpuspernode; ++% shortname = substring(modelname,1,min(12,length(modelname))); ++ ++ %write queuing script ++ fid=fopen([modelname '.queue'],'w'); ++ fprintf(fid,'#!/bin/bash\n'); ++ fprintf(fid,'#\n'); ++ fprintf(fid,'#SBATCH --job-name=%s\n',modelname); ++% fprintf(fid,'#SBATCH -p %s \n',cluster.partition); ++ fprintf(fid,'#SBATCH -A %s \n',cluster.accountname); ++% fprintf(fid,'#SBATCH --mail-type=ALL\n'); ++ fprintf(fid,'#SBATCH -N %i -n %i\n',cluster.numnodes,cluster.cpuspernode); ++ %calculate walltime in hh:mm:ss format ++ walltime=datestr(cluster.time/(60*24),'HH:MM:SS'); ++ fprintf(fid,'#SBATCH -t %s\n',walltime); %walltime should be in hh:mm:ss ++ fprintf(fid,'#SBATCH --mem=%i\n',cluster.mem); ++ fprintf(fid,'#SBATCH -o %s.outlog \n',modelname); ++ fprintf(fid,'#SBATCH -e %s.errlog \n\n',modelname); ++% fprintf(fid,'module load intelcomp/17.0.0\n') %module load not recommended within job script at Tetralith ++% fprintf(fid,'module load mpt/2.14\n') ++% fprintf(fid,'module load petsc/3.7.4d\n') ++% fprintf(fid,'module load parmetis/4.0.3\n') ++% fprintf(fid,'module load mumps/5.0.2\n') ++ fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath); %FIXME ++% fprintf(fid,'export ISSM_DIR="%s"\n',cluster.codepath); %FIXME ++ fprintf(fid,'source $ISSM_DIR/etc/environment.sh\n'); %FIXME ++ fprintf(fid,'cd %s/%s\n\n',cluster.executionpath,dirname); ++% fprintf(fid,'mpiexec -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); ++ fprintf(fid,'mpiexec -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); ++% fprintf(fid,'mpirun -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); ++% fprintf(fid,'mpiexec_mpt -np %i %s/%s %s %s %s\n',cluster.np,cluster.codepath,executable,solution,[cluster.executionpath '/' dirname],modelname); ++ ++ if ~io_gather, %concatenate the output files: ++ fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); ++ end ++ fclose(fid); ++ ++ %in interactive mode, create a run file, and errlog and outlog file ++ if cluster.interactive, ++ fid=fopen([modelname '.run'],'w'); ++ fprintf(fid,'mpiexec_mpt -np %i %s/issm.exe %s %s %s\n',cluster.np,cluster.codepath,solution,[cluster.executionpath '/' dirname],modelname); ++ if ~io_gather, %concatenate the output files: ++ fprintf(fid,'cat %s.outbin.* > %s.outbin',modelname,modelname); ++ end ++ fclose(fid); ++ fid=fopen([modelname '.errlog'],'w'); ++ fclose(fid); ++ fid=fopen([modelname '.outlog'],'w'); ++ fclose(fid); ++ end ++ end %}}} ++ function UploadQueueJob(cluster,modelname,dirname,filelist)% {{{ ++ ++ %compress the files into one zip. ++ compressstring=['tar -zcf ' dirname '.tar.gz ']; ++ for i=1:numel(filelist), ++ compressstring = [compressstring ' ' filelist{i}]; ++ end ++ system(compressstring); ++ disp('uploading input file and queueing script'); ++ directory=cluster.executionpath; ++% issmbbftpout(cluster.name,directory,cluster.login,cluster.port,cluster.numstreams,{[dirname '.tar.gz']}); ++ issmscpout(cluster.name,directory,cluster.login,cluster.port,{[dirname '.tar.gz']}); ++ ++ end ++ %}}} ++ function LaunchQueueJob(cluster,modelname,dirname,filelist,restart,batch)% {{{ ++ ++ disp('launching solution sequence on remote cluster'); ++ launchcommand=['cd ' cluster.executionpath ' && rm -rf ./' dirname ' && mkdir ' dirname ... ++ ' && cd ' dirname ' && mv ../' dirname '.tar.gz ./ && tar -zxf ' dirname '.tar.gz && hostname && sbatch ' modelname '.queue ']; ++ ++ issmssh(cluster.name,cluster.login,cluster.port,launchcommand); ++ end %}}} ++ function Download(cluster,dirname,filelist)% {{{ ++ ++ %copy files from cluster to current directory ++ directory=[cluster.executionpath '/' dirname '/']; ++ issmscpin(cluster.name,cluster.login,cluster.port,directory,filelist); ++ ++ end %}}} ++ end ++end + +Property changes on: ../trunk-jpl/src/m/classes/clusters/tetralith.m +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property Index: /issm/oecreview/Archive/23185-23389/ISSM-23265-23266.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23265-23266.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23265-23266.diff (revision 23390) @@ -0,0 +1,86 @@ +Index: ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp (revision 23265) ++++ ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp (revision 23266) +@@ -479,9 +479,14 @@ + #endif + + #ifdef _HAVE_CODIPACK_ +-void MumpsSolve_codi_b(codi::DataStore* data) {/*{{{*/ ++void MumpsSolve_codi_b(void* tape_in,void* data_in,void* ra) {/*{{{*/ ++ ++ /*recast data_in and tape*/ ++ codi::DataStore* data = (codi::DataStore*)data_in; ++ //IssmDouble::TapeType& tape = (IssmDouble::TapeType&)tape_in; + IssmDouble::TapeType& tape = IssmDouble::getGlobalTape(); + ++ + IssmDouble::Real* valueATrans; + IssmDouble::GradientData* indexATrans; + int* irnATrans; +@@ -523,7 +528,11 @@ + xDelete(adjX); + } + /*}}}*/ +-void MumpsSolve_codi_delete(codi::DataStore* data) {/*{{{*/ ++void MumpsSolve_codi_delete(void* tape_in,void* data_in) {/*{{{*/ ++ ++ /*recast data_in*/ ++ codi::DataStore* data = (codi::DataStore*)data_in; ++ + IssmDouble::Real* valueATrans; + IssmDouble::GradientData* indexATrans; + int* irnATrans; +@@ -615,8 +624,8 @@ + dataHandler->addData(local_nnz); + dataHandler->addData(parameters); // we assume here that parameters is still intact when the reverse run is called + +- tape.pushExternalFunction(&MumpsSolve_codi_b, dataHandler, &MumpsSolve_codi_delete); +- //tape.pushExternalFunctionHandle(&MumpsSolve_codi_b, dataHandler, &MumpsSolve_codi_delete); ++ //tape.pushExternalFunction(&MumpsSolve_codi_b, dataHandler, &MumpsSolve_codi_delete); ++ tape.pushExternalFunctionHandle(&MumpsSolve_codi_b,(void*)dataHandler, &MumpsSolve_codi_delete); + } else { + // if the tape is active valueB is stored in the dataHandler and deleted in the reverse sweep + xDelete(valueB); +Index: ../trunk-jpl/src/c/toolkits/gsl/DenseGslSolve.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/gsl/DenseGslSolve.cpp (revision 23265) ++++ ../trunk-jpl/src/c/toolkits/gsl/DenseGslSolve.cpp (revision 23266) +@@ -253,9 +253,13 @@ + #endif + + #ifdef _HAVE_CODIPACK_ +-void SolverxSeq_codi_b(codi::DataStore* data) {/*{{{*/ +- IssmDouble::TapeType& tape = IssmDouble::getGlobalTape(); ++void SolverxSeq_codi_b(void* tape_in,void* data_in,void* ra) {/*{{{*/ + ++ /*recast data_in and tape*/ ++ codi::DataStore* data = (codi::DataStore*)data_in; ++ //IssmDouble::TapeType& tape = (IssmDouble::TapeType&)tape_in; ++ IssmDouble::TapeType& tape = IssmDouble::getGlobalTape(); ++ + IssmDouble::Real* valueATrans; + IssmDouble::GradientData* indexATrans; + IssmDouble::GradientData* indexB; +@@ -290,7 +294,11 @@ + xDelete(adjX); + } + /*}}}*/ +-void SolverxSeq_codi_delete(codi::DataStore* data) {/*{{{*/ ++void SolverxSeq_codi_delete(void* tape_in,void* data_in) {/*{{{*/ ++ ++ /*recast data_in*/ ++ codi::DataStore* data = (codi::DataStore*)data_in; ++ + IssmDouble::Real* valueATrans; + IssmDouble::GradientData* indexATrans; + IssmDouble::GradientData* indexB; +@@ -364,7 +372,7 @@ + // store other arguments + dataHandler->addData(n); + +- tape.pushExternalFunction(&SolverxSeq_codi_b, dataHandler, &SolverxSeq_codi_delete); ++ tape.pushExternalFunctionHandle(&SolverxSeq_codi_b, dataHandler, &SolverxSeq_codi_delete); + } else { + // if the tape is active valueX is stored in the dataHandler and deleted in the reverse sweep + xDelete(valueX); Index: /issm/oecreview/Archive/23185-23389/ISSM-23266-23267.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23266-23267.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23266-23267.diff (revision 23390) @@ -0,0 +1,359 @@ +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 23266) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp (revision 23267) +@@ -102,8 +102,8 @@ + #if defined(_HAVE_AD_) + + if(isautodiff){ +-#if _HAVE_ADOLC_ +- /*Copy some parameters from IoModel to parameters dataset: {{{*/ ++ #if defined(_HAVE_ADOLC_) ++ /*Copy some parameters from IoModel to parameters dataset*/ + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.obufsize",AutodiffObufsizeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.cbufsize",AutodiffCbufsizeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.lbufsize",AutodiffLbufsizeEnum)); +@@ -110,8 +110,14 @@ + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.tbufsize",AutodiffTbufsizeEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.gcTriggerRatio",AutodiffGcTriggerRatioEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.gcTriggerMaxSize",AutodiffGcTriggerMaxSizeEnum)); +- /*}}}*/ +-#endif ++ ++ #elif defined(_HAVE_CODIPACK_) ++ parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.tapeAlloc",AutodiffTapeAllocEnum)); ++ ++ #else ++ _error_("not supported yet"); ++ #endif ++ + /*retrieve driver: {{{*/ + iomodel->FindConstant(&autodiff_driver,"md.autodiff.driver"); + parameters->AddObject(iomodel->CopyConstantObject("md.autodiff.driver",AutodiffDriverEnum)); +Index: ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp (revision 23266) ++++ ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp (revision 23267) +@@ -10,7 +10,12 @@ + #include "../modules/modules.h" + #include "../solutionsequences/solutionsequences.h" + +-#if defined (_HAVE_M1QN3_) && defined(_HAVE_ADOLC_) ++#ifdef _HAVE_CODIPACK_ ++extern CoDi_global codi_global; ++#include // for output of the CoDiPack tape ++#endif ++ ++#if defined (_HAVE_M1QN3_) && defined(_HAVE_AD_) + /*m1qn3 prototypes*/ + extern "C" void *ctonbe_; // DIS mode : Conversion + extern "C" void *ctcabe_; // DIS mode : Conversion +@@ -34,6 +39,7 @@ + /*m1qm3 functions*/ + void simul_starttrace(FemModel* femmodel){/*{{{*/ + ++ #if defined(_HAVE_ADOLC_) + /*Retrive ADOLC parameters*/ + IssmDouble gcTriggerRatio; + IssmDouble gcTriggerMaxSize; +@@ -56,7 +62,115 @@ + int keepTaylors=1; + int my_rank=IssmComm::GetRank(); + trace_on(my_rank,keepTaylors,reCast(obufsize),reCast(lbufsize),reCast(cbufsize),reCast(tbufsize),skipFileDeletion); ++ ++ #elif defined(_HAVE_CODIPACK_) ++ ++ //fprintf(stderr, "*** Codipack IoModel::StartTrace\n"); ++ /* ++ * FIXME codi ++ * - ADOL-C variant uses fine grained tracing with various arguments ++ * - ADOL-C variant sets a garbage collection parameter for its tape ++ * -> These parameters are not read for the CoDiPack ISSM version! ++ */ ++ auto& tape_codi = IssmDouble::getGlobalTape(); ++ tape_codi.setActive(); ++ #if _AD_TAPE_ALLOC_ ++ //alloc_profiler.Tag(StartInit, true); ++ IssmDouble x_t(1.0), y_t(1.0); ++ tape_codi.registerInput(y_t); ++ int codi_allocn = 0; ++ femmodel->parameters->FindParam(&codi_allocn,AutodiffTapeAllocEnum); ++ for(int i = 0;i < codi_allocn;++i) { ++ x_t = y_t * y_t; ++ } ++ /* ++ std::stringstream out_s; ++ IssmDouble::getGlobalTape().printStatistics(out_s); ++ _printf0_("StartTrace::Tape Statistics : TapeAlloc count=[" << codi_allocn << "]\n" << out_s.str()); ++ */ ++ tape_codi.reset(); ++ //alloc_profiler.Tag(FinishInit, true); ++ #endif ++ ++ #else ++ _error_("not implemented"); ++ #endif + }/*}}}*/ ++void simul_stoptrace(){/*{{{*/ ++ ++ #if defined(_HAVE_ADOLC_) ++ trace_off(); ++ if(VerboseAutodiff()){ /*{{{*/ ++ ++ #ifdef _HAVE_ADOLC_ ++ int my_rank=IssmComm::GetRank(); ++ size_t tape_stats[15]; ++ tapestats(my_rank,tape_stats); //reading of tape statistics ++ int commSize=IssmComm::GetSize(); ++ int *sstats=new int[7]; ++ sstats[0]=tape_stats[NUM_OPERATIONS]; ++ sstats[1]=tape_stats[OP_FILE_ACCESS]; ++ sstats[2]=tape_stats[NUM_LOCATIONS]; ++ sstats[3]=tape_stats[LOC_FILE_ACCESS]; ++ sstats[4]=tape_stats[NUM_VALUES]; ++ sstats[5]=tape_stats[VAL_FILE_ACCESS]; ++ sstats[6]=tape_stats[TAY_STACK_SIZE]; ++ int *rstats=NULL; ++ if (my_rank==0) rstats=new int[commSize*7]; ++ ISSM_MPI_Gather(sstats,7,ISSM_MPI_INT,rstats,7,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ if (my_rank==0) { ++ int offset=50; ++ int rOffset=(commSize/10)+1; ++ _printf_(" ADOLC statistics: \n"); ++ _printf_(" "<file":"") << "\n"); ++ _printf_(" locations: entry size " << sizeof(locint) << " Bytes\n"); ++ _printf_(" "<file":"") << "\n"); ++ _printf_(" constant values: entry size " << sizeof(double) << " Bytes\n"); ++ _printf_(" "<file":"") << "\n"); ++ _printf_(" Taylor stack: entry size " << sizeof(revreal) << " Bytes\n"); ++ _printf_(" "<tape_stats[TAY_BUFFER_SIZE]?" ->file":"") << "\n"); ++ delete []rstats; ++ } ++ delete [] sstats; ++ #endif ++ ++ #ifdef _HAVE_CODIPACK_ ++ #ifdef _AD_TAPE_ALLOC_ ++ //_printf_("Allocation time P(" << my_rank << "): " << alloc_profiler.DeltaTime(StartInit, FinishInit) << "\n"); ++ #endif ++ std::stringstream out_s; ++ IssmDouble::getGlobalTape().printStatistics(out_s); ++ _printf0_("CoDiPack Profiling::Tape Statistics :\n" << out_s.str()); ++ #endif ++ } /*}}}*/ ++ ++ #elif defined(_HAVE_CODIPACK_) ++ auto& tape_codi = IssmDouble::getGlobalTape(); ++ tape_codi.setPassive(); ++ if(VerboseAutodiff()){ ++ int my_rank=IssmComm::GetRank(); ++ if(my_rank == 0) { ++ // FIXME codi "just because" for now ++ tape_codi.printStatistics(std::cout); ++ codi_global.print(std::cout); ++ } ++ } ++ #else ++ _error_("not implemented"); ++ #endif ++}/*}}}*/ + void simul_ad(long* indic,long* n,double* X,double* pf,double* G,long izs[1],float rzs[1],void* dzs){/*{{{*/ + + /*Get rank*/ +@@ -72,9 +186,8 @@ + int N_add = 0; + int* control_enum = NULL; + +- if (solution_type == TransientSolutionEnum){ +- femmodel = input_struct->femmodel->copy(); +- } ++ /*In transient, we need to make sure we do not modify femmodel at each iteration, make a copy*/ ++ if(solution_type == TransientSolutionEnum) femmodel = input_struct->femmodel->copy(); + + IssmPDouble* Jlist = input_struct->Jlist; + int JlistM = input_struct->M; +@@ -116,11 +229,25 @@ + #else + IssmDouble* aX=xNew(intn); + #endif ++ ++ #if defined(_HAVE_ADOLC_) + if(my_rank==0){ + for(int i=0;iGetObjectByOffset(i); + if(solution_type==TransientSolutionEnum) output_value = dep->GetValue(); + if(solution_type!=TransientSolutionEnum) dep->Responsex(&output_value,femmodel); +- if (my_rank==0) { ++ if(my_rank==0) { ++ ++ #if defined(_HAVE_CODIPACK_) ++ tape_codi.registerOutput(output_value); ++ dependents[i] = output_value.getValue(); ++ codi_global.output_indices.push_back(output_value.getGradientData()); ++ ++ #elif defined(_HAVE_ADOLC_) + output_value>>=dependents[i]; ++ ++ #else ++ _error_("not suppoted"); ++ #endif + J+=output_value; + } + } + + /*Turning off trace tape*/ +- trace_off(); ++ simul_stoptrace(); + //time_t now = time(NULL); + //if(my_rank==0) _printf_("\nTIME: "<file":"") << "\n"); +- _printf_(" locations: entry size " << sizeof(locint) << " Bytes\n"); +- _printf_(" "<file":"") << "\n"); +- _printf_(" constant values: entry size " << sizeof(double) << " Bytes\n"); +- _printf_(" "<file":"") << "\n"); +- _printf_(" Taylor stack: entry size " << sizeof(revreal) << " Bytes\n"); +- _printf_(" "<tape_stats[TAY_BUFFER_SIZE]?" ->file":"") << "\n"); +- delete []rstats; +- } +- delete [] sstats; +- #endif +- +- #ifdef _HAVE_CODIPACK_ +- #ifdef _AD_TAPE_ALLOC_ +- //_printf_("Allocation time P(" << my_rank << "): " << alloc_profiler.DeltaTime(StartInit, FinishInit) << "\n"); +- #endif +- std::stringstream out_s; +- IssmDouble::getGlobalTape().printStatistics(out_s); +- _printf0_("CoDiPack Profiling::Tape Statistics :\n" << out_s.str()); +- #endif +- } /*}}}*/ +- + /*diverse: */ + int dummy; + int num_independents=0; +@@ -246,6 +328,9 @@ + num_independents = 0; + } + ++ #if defined(_HAVE_ADOLC_) ++ /*Get gradient for ADOLC {{{*/ ++ + /*get the EDF pointer:*/ + ext_diff_fct *anEDF_for_solverx_p=xDynamicCast * >(femmodel->parameters->FindParamObject(AdolcParamEnum))->GetParameterValue().myEDF_for_solverx_p; + +@@ -289,7 +374,42 @@ + xDelete(weightVectorTimesJac); + xDelete(aWeightVector); + } ++ /*}}}*/ ++ #elif defined(_HAVE_CODIPACK_) ++ /*Get gradient for CoDiPack{{{*/ ++ if(VerboseAutodiff())_printf0_(" CoDiPack fos_reverse\n"); ++ int aDepIndex=0; /*FIXME: do we really need this?*/ + ++ /*retrieve direction index: */ ++ femmodel->parameters->FindParam(&aDepIndex,AutodiffFosReverseIndexEnum); ++ if (my_rank==0) { ++ if (aDepIndex<0 || aDepIndex>=num_dependents || codi_global.output_indices.size() <= aDepIndex){ ++ _error_("index value for AutodiffFosReverseIndexEnum should be in [0,num_dependents-1]"); ++ } ++ tape_codi.setGradient(codi_global.output_indices[aDepIndex], 1.0); ++ } ++ tape_codi.evaluate(); ++ ++ weightVectorTimesJac=xNew(num_independents); ++ /*call driver: */ ++ auto in_size = codi_global.input_indices.size(); ++ for(size_t i = 0; i < in_size; ++i) { ++ weightVectorTimesJac[i] = tape_codi.getGradient(codi_global.input_indices[i]); ++ } ++ ++ /*Add to totalgradient: */ ++ totalgradient=xNewZeroInit(num_independents_old); ++ if(my_rank==0) for(int i=0;i(scaling_factors); + xDelete(mystruct.Jlist); + xDelete(mystruct.i); +-} ++}/*}}}*/ ++void simul(long* indic,long* n,double* X,double* pf,double* G,long izs[1],float rzs[1],void* dzs){/*{{{*/ + +-/*Cost function definition*/ +-void simul(long* indic,long* n,double* X,double* pf,double* G,long izs[1],float rzs[1],void* dzs){ +- + /*Recover Arguments*/ + m1qn3_struct *input_struct = (m1qn3_struct*)dzs; + FemModel *femmodel = input_struct->femmodel; +@@ -277,10 +276,8 @@ + xDelete(XU); + xDelete(XL); + xDelete(scaling_factors); +-} ++}/*}}}*/ + + #else +-void controlm1qn3_core(FemModel* femmodel){ +- _error_("M1QN3 not installed"); +-} ++void controlm1qn3_core(FemModel* femmodel){_error_("M1QN3 not installed");} + #endif //_HAVE_M1QN3_ +Index: ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp (revision 23267) ++++ ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp (revision 23268) +@@ -16,7 +16,7 @@ + #endif + + #if defined (_HAVE_M1QN3_) && defined(_HAVE_AD_) +-/*m1qn3 prototypes*/ ++/*m1qn3 prototypes {{{*/ + extern "C" void *ctonbe_; // DIS mode : Conversion + extern "C" void *ctcabe_; // DIS mode : Conversion + extern "C" void *euclid_; // Scalar product +@@ -35,6 +35,7 @@ + int N; + int* i; + } m1qn3_struct; ++/*}}}*/ + + /*m1qm3 functions*/ + void simul_starttrace(FemModel* femmodel){/*{{{*/ +@@ -90,6 +91,8 @@ + */ + tape_codi.reset(); + //alloc_profiler.Tag(FinishInit, true); ++ #else ++ tape_codi.reset(); + #endif + + #else +@@ -180,11 +183,8 @@ + m1qn3_struct *input_struct = (m1qn3_struct*)dzs; + + FemModel* femmodel = input_struct->femmodel; +- int num_responses,num_controls,numberofvertices,solution_type; ++ int num_responses,num_controls,solution_type; + femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); +- int* N = NULL; +- int N_add = 0; +- int* control_enum = NULL; + + /*In transient, we need to make sure we do not modify femmodel at each iteration, make a copy*/ + if(solution_type == TransientSolutionEnum) femmodel = input_struct->femmodel->copy(); +@@ -196,13 +196,15 @@ + int intn = (int)*n; + + /*Recover some parameters*/ +- IssmDouble* scaling_factors = NULL; ++ IssmDouble *scaling_factors = NULL; ++ int *N = NULL; ++ int *control_enum = NULL; + femmodel->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); + femmodel->parameters->FindParam(&num_controls,InversionNumControlParametersEnum); + femmodel->parameters->FindParam(&scaling_factors,NULL,InversionControlScalingFactorsEnum); + femmodel->parameters->FindParam(&N,NULL,ControlInputSizeNEnum); + femmodel->parameters->FindParam(&control_enum,NULL,InversionControlParametersEnum); +- numberofvertices=femmodel->vertices->NumberOfVertices(); ++ int numberofvertices=femmodel->vertices->NumberOfVertices(); + + /*Constrain input vector and update controls*/ + double *XL = NULL; +@@ -210,7 +212,7 @@ + GetPassiveVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); + GetPassiveVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + +- N_add = 0; ++ int N_add = 0; + for (int c=0;c(num_independents); + +- /*output: */ +- IssmPDouble *totalgradient=NULL; +- +- /*retrieve parameters: */ +- num_independents = intn; +- + /*if no dependents, no point in running a driver: */ + if(!(num_dependents*num_independents)) _error_("this is not allowed"); + +@@ -340,8 +334,6 @@ + + /* Ok, now we are going to call the fos_reverse in a loop on the index, from 0 to num_dependents, so + * as to generate num_dependents gradients: */ +- totalgradient=xNewZeroInit(num_independents_old); +- + for(int aDepIndex=0;aDepIndexparameters->FindParam(&aDepIndex,AutodiffFosReverseIndexEnum); +- if (my_rank==0) { +- if (aDepIndex<0 || aDepIndex>=num_dependents || codi_global.output_indices.size() <= aDepIndex){ +- _error_("index value for AutodiffFosReverseIndexEnum should be in [0,num_dependents-1]"); +- } +- tape_codi.setGradient(codi_global.output_indices[aDepIndex], 1.0); +- } +- tape_codi.evaluate(); ++ /* call the fos_reverse in a loop on the index, from 0 to num_dependents, so ++ * as to generate num_dependents gradients: */ ++ for(int aDepIndex=0;aDepIndex(num_independents); +- /*call driver: */ +- auto in_size = codi_global.input_indices.size(); +- for(size_t i = 0; i < in_size; ++i) { +- weightVectorTimesJac[i] = tape_codi.getGradient(codi_global.input_indices[i]); +- } ++ /*initialize direction index in the weights vector: */ ++ aWeightVector=xNewZeroInit(num_dependents); ++ if(my_rank==0) tape_codi.setGradient(codi_global.output_indices[aDepIndex],1.0); ++ tape_codi.evaluate(); + +- /*Add to totalgradient: */ +- totalgradient=xNewZeroInit(num_independents_old); +- if(my_rank==0) for(int i=0;i(num_independents); ++ auto in_size = codi_global.input_indices.size(); ++ for(size_t i = 0; i < in_size; ++i) { ++ weightVectorTimesJac[i] = tape_codi.getGradient(codi_global.input_indices[i]); ++ } ++ if(my_rank==0) for(int i=0;i(dependents[i]); + Jlist[(*Jlisti)*JlistN+num_responses] = reCast(J); + +-/* +- IssmDouble* test = xNew(intn); +- femmodel->parameters->FindParam(&test,NULL,InversionXBestEnum); +- for(int i=0;i<10;i++)_printf_("X "<(intn); +-*/ + if(*indic==0){ + /*dry run, no gradient required*/ + Index: /issm/oecreview/Archive/23185-23389/ISSM-23268-23269.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23268-23269.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23268-23269.diff (revision 23390) @@ -0,0 +1,43 @@ +Index: ../trunk-jpl/test/NightlyRun/runme.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/runme.py (revision 23268) ++++ ../trunk-jpl/test/NightlyRun/runme.py (revision 23269) +@@ -81,26 +81,21 @@ + #GET ids {{{ + flist=glob('test*.py') #File name must start with 'test' and must end by '.py' and must be different than 'test.py' + list_ids=[int(file[4:-3]) for file in flist if not file == 'test.py'] #Keep test id only (skip 'test' and '.py') +- #print 'list_ids =',list_ids + + i1,i2=parallelrange(rank,numprocs,len(list_ids)) #Get tests for this cpu only + list_ids=list_ids[i1:i2+1] +- #print 'list_ids after parallelrange =',list_ids + +- if id: ++ if np.size(id) > 0: + test_ids = set(GetIds(id)).intersection(set(list_ids)) + else: + # if no tests are specifically provided, do them all + test_ids = set(list_ids) + +- #print 'test_ids after list =',test_ids + # }}} + #GET exclude {{{ + exclude_ids = GetIds(exclude) + + test_ids=test_ids.difference(exclude_ids) +- #print 'test_ids after exclude =',sorted(test_ids) +- #return + # }}} + #Process Ids according to benchmarks {{{ + if benchmark=='nightly': +@@ -123,10 +118,8 @@ + test_ids=test_ids.intersection(set(range(2001,2500))) + elif benchmark=='adolc': + test_ids=test_ids.intersection(set(range(3001,3200))) +- #print 'test_ids after benchmark =',test_ids + test_ids=list(test_ids) + test_ids.sort() +- #print 'test_ids after sort =',test_ids + # }}} + + #Loop over tests and launch sequence Index: /issm/oecreview/Archive/23185-23389/ISSM-23269-23270.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23269-23270.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23269-23270.diff (revision 23390) @@ -0,0 +1,64 @@ +Index: ../trunk-jpl/src/m/partition/AreaAverageOntoPartition.py +=================================================================== +--- ../trunk-jpl/src/m/partition/AreaAverageOntoPartition.py (nonexistent) ++++ ../trunk-jpl/src/m/partition/AreaAverageOntoPartition.py (revision 23270) +@@ -0,0 +1,59 @@ ++import numpy as np ++ ++def AreaAverageOntoPartition(md,vector,layer=None): ++ '''AREAAVERAGEONTOPARTITION ++ compute partition values for a certain vector expressed on the vertices of the mesh. ++ Use area weighted average. ++ ++ Usage: ++ average=AreaAverageOntoPartition(md,vector) ++ average=AreaAverageOntoPartition(md,vector,layer) #if in 3D, chose which layer is partitioned ++''' ++ #some checks ++ if len(np.shape(md.mesh)) == 3: ++ if layer == None: ++ raise RuntimeError('AreaAverageOntoPartition: layer should be provided onto which Area Averaging occurs') ++ ++ #save 3D model ++ md3d = md ++ ++ md.mesh.elements = md.mesh.elements2d ++ md.mesh.x = md.mesh.x2d ++ md.mesh.y = md.mesh.y2d ++ md.mesh.numberofvertices = md.mesh.numberofvertices2d ++ md.mesh.numberofelements = md.mesh.numberofelements2d ++ md.qmu.vertex_weight = [] ++ md.mesh.vertexconnectivity = [] ++ ++ #run connectivity routine ++ md = adjacency(md) ++ ++ #finally, project vector: ++ vector = project2d(md3d,vector,layer) ++ md.qmu.partition = project2d(md3d,md3d.qmu.partition,layer) ++ ++ ++ #ok, first check that part is Matlab indexed ++ #part = md.qmu.partition ++ ++ #some check: ++ if md.qmu.numberofpartitions != max(md.qmu.partition): ++ raise RuntimeError('AreaAverageOntoPartition error message: ''npart'' should be equal to max(md.qmu.partition)') ++ ++ ++ #initialize output ++ partvector = np.zeros((max(md.qmu.partition),)) ++ ++ #start weight average ++ weightedvector = vector*md.qmu.vertex_weight ++ for i in range(max(md.qmu.partition)): ++ pos=np.where(md.qmu.partition==i) ++ partvector[i]=sum(weightedvector[pos])/sum(md.qmu.vertex_weight[pos]) ++ ++ ++ #in 3D, restore 3D model: ++ if len(np.shape(md.mesh)) == 3: ++ md = md3d ++ ++ return partvector ++ Index: /issm/oecreview/Archive/23185-23389/ISSM-23270-23271.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23270-23271.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23270-23271.diff (revision 23390) @@ -0,0 +1,35 @@ +Index: ../trunk-jpl/test/NightlyRun/test2084.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test2084.m (revision 23270) ++++ ../trunk-jpl/test/NightlyRun/test2084.m (revision 23271) +@@ -113,7 +113,7 @@ + %md=solve(md,'lv'); + % + %field_names ={field_names{:},'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'}; +-%field_tolerances={field_tolerances{:},6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7}; ++%field_tolerances={field_tolerances{:},2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6}; + %field_values={field_values{:},... + % (md.results.LoveSolution.LoveHr(:,1)),... + % (md.results.LoveSolution.LoveKr(:,1)),... +@@ -145,7 +145,7 @@ + md.love.nfreq=length(md.love.frequencies); + + field_names ={field_names{:},'LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'}; +-field_tolerances={field_tolerances{:},6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7}; ++field_tolerances={field_tolerances{:},2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6}; + field_values={field_values{:},... + (md.results.LoveSolution.LoveHr(:,1)),... + (md.results.LoveSolution.LoveKr(:,1)),... +Index: ../trunk-jpl/test/NightlyRun/test2084.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test2084.py (revision 23270) ++++ ../trunk-jpl/test/NightlyRun/test2084.py (revision 23271) +@@ -187,7 +187,7 @@ + md.love.nfreq=len(md.love.frequencies) + + field_names+=['LoveH_loadingVSS96_elastic','LoveK_loadingVSS96_elastic','LoveL_loadingVSS96_elastic','LoveH_loadingVSS96_realpart','LoveK_loadingVSS96_realpart','LoveL_loadingVSS96_realpart','LoveH_loadingVSS96_imagpart','LoveK_loadingVSS96_imagpart','LoveL_loadingVSS96_imagpart'] +-field_tolerances+=[6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7,6e-7] ++field_tolerances+=[2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6,2e-6] + field_values+=[ + np.array(md.results.LoveSolution.LoveHr)[:,0], + np.array(md.results.LoveSolution.LoveKr)[:,0], Index: /issm/oecreview/Archive/23185-23389/ISSM-23271-23272.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23271-23272.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23271-23272.diff (revision 23390) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/NightlyRun/test2084.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test2084.py (revision 23271) ++++ ../trunk-jpl/test/NightlyRun/test2084.py (revision 23272) +@@ -88,7 +88,7 @@ + + #tidal love numbers, check + field_names+=['LoveH_tidal_elastic','LoveK_tidal_elastic','LoveL_tidal_elastic','LoveH_tidal_realpart','LoveK_tidal_realpart','LoveL_tidal_realpart','LoveH_tidal_imagpart','LoveK_tidal_imagpart','LoveL_tidal_imagpart'] +-field_tolerances+=[3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6] ++field_tolerances+=[8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6] + field_values+=[ + np.array(md.results.LoveSolution.LoveHr)[:,0], + np.array(md.results.LoveSolution.LoveKr)[:,0], +Index: ../trunk-jpl/test/NightlyRun/test2084.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test2084.m (revision 23271) ++++ ../trunk-jpl/test/NightlyRun/test2084.m (revision 23272) +@@ -73,7 +73,7 @@ + + %tidal love numbers + field_names ={field_names{:},'LoveH_tidal_elastic','LoveK_tidal_elastic','LoveL_tidal_elastic','LoveH_tidal_realpart','LoveK_tidal_realpart','LoveL_tidal_realpart','LoveH_tidal_imagpart','LoveK_tidal_imagpart','LoveL_tidal_imagpart'}; +-field_tolerances={field_tolerances{:},3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6,3e-6}; ++field_tolerances={field_tolerances{:},8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6,8e-6}; + field_values={field_values{:},... + (md.results.LoveSolution.LoveHr(:,1)),... + (md.results.LoveSolution.LoveKr(:,1)),... Index: /issm/oecreview/Archive/23185-23389/ISSM-23272-23273.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23272-23273.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23272-23273.diff (revision 23390) @@ -0,0 +1,31 @@ +Index: ../trunk-jpl/jenkins/macosx_pine-island_dakota +=================================================================== +--- ../trunk-jpl/jenkins/macosx_pine-island_dakota (revision 23272) ++++ ../trunk-jpl/jenkins/macosx_pine-island_dakota (revision 23273) +@@ -6,7 +6,7 @@ + #MATLAB path + MATLAB_PATH="/Applications/MATLAB_R2015b.app/" + +-#ISSM CONFIGURATION ++#ISSM CONFIGURATION + ISSM_CONFIG='--prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_PATH \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ +@@ -26,7 +26,7 @@ + + #PYTHON and MATLAB testing + MATLAB_TEST=1 +-PYTHON_TEST=0 ++PYTHON_TEST=1 + + #-----------------------------------# + # 3: External packages installation # +@@ -58,6 +58,6 @@ + #Nightly run options. The matlab routine runme.m will be called + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m +-#ex: "'id',[101 102 103]" ERRORS ARE LARGE FOR: 418 420 +-PYTHON_NROPTIONS="" ++#ex: "'id',[101 102 103]" ERRORS ARE LARGE FOR: 418 420 ++PYTHON_NROPTIONS="--exclude 119 243 514 701 702 703 234 235 418 420 --include_name 'Dakota'" + MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,234,235,418,420]" Index: /issm/oecreview/Archive/23185-23389/ISSM-23273-23274.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23273-23274.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23273-23274.diff (revision 23390) @@ -0,0 +1,20 @@ +Index: ../trunk-jpl/jenkins/macosx_pine-island_dakota +=================================================================== +--- ../trunk-jpl/jenkins/macosx_pine-island_dakota (revision 23273) ++++ ../trunk-jpl/jenkins/macosx_pine-island_dakota (revision 23274) +@@ -26,7 +26,7 @@ + + #PYTHON and MATLAB testing + MATLAB_TEST=1 +-PYTHON_TEST=1 ++PYTHON_TEST=0 + + #-----------------------------------# + # 3: External packages installation # +@@ -59,5 +59,5 @@ + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" ERRORS ARE LARGE FOR: 418 420 +-PYTHON_NROPTIONS="--exclude 119 243 514 701 702 703 234 235 418 420 --include_name 'Dakota'" ++PYTHON_NROPTIONS="" + MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,234,235,418,420]" Index: /issm/oecreview/Archive/23185-23389/ISSM-23274-23275.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23274-23275.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23274-23275.diff (revision 23390) @@ -0,0 +1,133 @@ +Index: ../trunk-jpl/jenkins/macosx_pine-island_dakota_static +=================================================================== +--- ../trunk-jpl/jenkins/macosx_pine-island_dakota_static (revision 23274) ++++ ../trunk-jpl/jenkins/macosx_pine-island_dakota_static (revision 23275) +@@ -3,9 +3,9 @@ + #-------------------------------# + + #MATLAB path +-MATLAB_PATH="/Applications/MATLAB_R2015b.app/" ++MATLAB_PATH="/Applications/MATLAB_R2015b.app" + +-#ISSM CONFIGURATION ++#ISSM CONFIGURATION + ISSM_CONFIG='--prefix=$ISSM_DIR \ + --disable-static \ + --enable-standalone-executables \ +@@ -55,12 +55,12 @@ + NUMCPUS_INSTALL=4 + + #number of cpus used in the nightly runs. +-NUMCPUS_RUN=2 ++NUMCPUS_RUN=4 + + #Nightly run options. The matlab routine runme.m will be called + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-## bamg mesh FS ++## bamg mesh FS + #PYTHON_NROPTIONS="--exclude_name 'Dakota'" + #MATLAB_NROPTIONS="'exclude',[243,701,702,703,435,IdFromString('Dakota')]" +Index: ../trunk-jpl/jenkins/macosx_pine-island_examples +=================================================================== +--- ../trunk-jpl/jenkins/macosx_pine-island_examples (revision 23274) ++++ ../trunk-jpl/jenkins/macosx_pine-island_examples (revision 23275) +@@ -4,9 +4,9 @@ + #-------------------------------# + + #MATLAB path +-MATLAB_PATH="/Applications/MATLAB_R2015b.app/" ++MATLAB_PATH="/Applications/MATLAB_R2015b.app" + +-#ISSM CONFIGURATION ++#ISSM CONFIGURATION + ISSM_CONFIG='--prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_PATH \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ +Index: ../trunk-jpl/jenkins/macosx_pine-island +=================================================================== +--- ../trunk-jpl/jenkins/macosx_pine-island (revision 23274) ++++ ../trunk-jpl/jenkins/macosx_pine-island (revision 23275) +@@ -4,7 +4,7 @@ + #-------------------------------# + + #MATLAB path +-MATLAB_PATH="/Applications/MATLAB_R2015b.app/" ++MATLAB_PATH="/Applications/MATLAB_R2015b.app" + + #ISSM CONFIGURATION + ISSM_CONFIG='--prefix=$ISSM_DIR \ +@@ -47,7 +47,7 @@ + NUMCPUS_INSTALL=4 + + #number of cpus used in the nightly runs. +-NUMCPUS_RUN=2 ++NUMCPUS_RUN=4 + + #Nightly run options. The matlab routine runme.m will be called + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable +Index: ../trunk-jpl/jenkins/macosx_pine-island_static +=================================================================== +--- ../trunk-jpl/jenkins/macosx_pine-island_static (revision 23274) ++++ ../trunk-jpl/jenkins/macosx_pine-island_static (revision 23275) +@@ -4,7 +4,7 @@ + #-------------------------------# + + #MATLAB path +-MATLAB_PATH="/Applications/MATLAB_R2015b.app/" ++MATLAB_PATH="/Applications/MATLAB_R2015b.app" + + #ISSM CONFIGURATION + ISSM_CONFIG='--prefix=$ISSM_DIR \ +@@ -54,7 +54,7 @@ + NUMCPUS_INSTALL=4 + + #number of cpus used in the nightly runs. +-NUMCPUS_RUN=2 ++NUMCPUS_RUN=4 + + #Nightly run options. The matlab routine runme.m will be called + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable +Index: ../trunk-jpl/jenkins/macosx_pine-island_dakota +=================================================================== +--- ../trunk-jpl/jenkins/macosx_pine-island_dakota (revision 23274) ++++ ../trunk-jpl/jenkins/macosx_pine-island_dakota (revision 23275) +@@ -4,11 +4,13 @@ + #-------------------------------# + + #MATLAB path +-MATLAB_PATH="/Applications/MATLAB_R2015b.app/" ++MATLAB_PATH="/Applications/MATLAB_R2015b.app" + + #ISSM CONFIGURATION + ISSM_CONFIG='--prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_PATH \ ++ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 \ ++ --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ + --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpi" \ +@@ -26,7 +28,7 @@ + + #PYTHON and MATLAB testing + MATLAB_TEST=1 +-PYTHON_TEST=0 ++PYTHON_TEST=1 + + #-----------------------------------# + # 3: External packages installation # +@@ -53,11 +55,11 @@ + NUMCPUS_INSTALL=4 + + #number of cpus used in the nightly runs. +-NUMCPUS_RUN=2 ++NUMCPUS_RUN=4 + + #Nightly run options. The matlab routine runme.m will be called + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" ERRORS ARE LARGE FOR: 418 420 +-PYTHON_NROPTIONS="" ++PYTHON_NROPTIONS="--exclude 119 243 514 701 702 703 234 235 418 420 --include_name 'Dakota'" + MATLAB_NROPTIONS="'exclude',[119,243,514,701,702,703,234,235,418,420]" Index: /issm/oecreview/Archive/23185-23389/ISSM-23275-23276.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23275-23276.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23275-23276.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/jenkins/macosx_pine-island_dakota +=================================================================== +--- ../trunk-jpl/jenkins/macosx_pine-island_dakota (revision 23275) ++++ ../trunk-jpl/jenkins/macosx_pine-island_dakota (revision 23276) +@@ -9,7 +9,7 @@ + #ISSM CONFIGURATION + ISSM_CONFIG='--prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_PATH \ +- --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 \ ++ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/bin \ + --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ Index: /issm/oecreview/Archive/23185-23389/ISSM-23276-23277.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23276-23277.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23276-23277.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/jenkins/macosx_pine-island_dakota +=================================================================== +--- ../trunk-jpl/jenkins/macosx_pine-island_dakota (revision 23276) ++++ ../trunk-jpl/jenkins/macosx_pine-island_dakota (revision 23277) +@@ -9,7 +9,7 @@ + #ISSM CONFIGURATION + ISSM_CONFIG='--prefix=$ISSM_DIR \ + --with-matlab-dir=$MATLAB_PATH \ +- --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/bin \ ++ --with-python-dir=/System/Library/Frameworks/Python.framework/Versions/2.7 \ + --with-python-numpy-dir=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python \ + --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ + --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ Index: /issm/oecreview/Archive/23185-23389/ISSM-23277-23278.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23277-23278.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23277-23278.diff (revision 23390) @@ -0,0 +1,48 @@ +Index: ../trunk-jpl/test/NightlyRun/test211.js +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test211.js (revision 23277) ++++ ../trunk-jpl/test/NightlyRun/test211.js (revision 23278) +@@ -11,12 +11,12 @@ + + //Fields and tolerances to track changes + field_names=[ +- 'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsGroundediceMeltingRate1', +- 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', ++ 'Vx1','Vy1','Vz1','Vel1','Pressure1','Bed1','Surface1','Thickness1','Temperature1','BasalforcingsGroundediceMeltingRate1', ++ 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3']; + field_tolerances=[ + 2e-08,2e-08,5e-05,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08, +- 5e-06,5e-06,8e-05,5e-06,1e-07,5e-07,5e-07,5e-07,3e-06,5e-05, ++ 5e-06,5e-06,8e-05,5e-06,3e-07,5e-07,5e-07,5e-07,3e-06,5e-05, + 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05]; + field_values=[ + (md.results.TransientSolution[0](1).Vx), +Index: ../trunk-jpl/test/NightlyRun/test211.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test211.py (revision 23277) ++++ ../trunk-jpl/test/NightlyRun/test211.py (revision 23278) +@@ -25,8 +25,8 @@ + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'] + field_tolerances=[2e-08,2e-08,5e-05,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08, +- 5e-06,5e-06,8e-05,5e-06,1e-07,5e-07,5e-07,5e-07,3e-06,5e-05, +- 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05] ++ 5e-06,5e-06,8e-05,5e-06,3e-07,5e-07,5e-07,5e-07,3e-06,5e-05, ++ 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05] + field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vz, +Index: ../trunk-jpl/test/NightlyRun/test211.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test211.m (revision 23277) ++++ ../trunk-jpl/test/NightlyRun/test211.m (revision 23278) +@@ -15,7 +15,7 @@ + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'}; + field_tolerances={... + 2e-08,2e-08,5e-05,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,... +- 5e-06,5e-06,8e-05,5e-06,1e-07,5e-07,5e-07,5e-07,3e-06,5e-05,... ++ 5e-06,5e-06,8e-05,5e-06,3e-07,5e-07,5e-07,5e-07,3e-06,5e-05,... + 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05}; + field_values={... + (md.results.TransientSolution(1).Vx),... Index: /issm/oecreview/Archive/23185-23389/ISSM-23278-23279.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23278-23279.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23278-23279.diff (revision 23390) @@ -0,0 +1,18 @@ +Index: ../trunk-jpl/externalpackages/adjointmpi/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/adjointmpi/install.sh (revision 23278) ++++ ../trunk-jpl/externalpackages/adjointmpi/install.sh (revision 23279) +@@ -2,10 +2,10 @@ + set -eu + + #Some cleanup +-rm -rf install ++rm -rf install src + +-#Almost the same as adjoinable mpi but some adaptations to CoDiPack https://github.com/michel2323/AdjointMPI +-svn co https://github.com/michel2323/AdjointMPI.git/trunk src ++#Almost the same as adjoinable mpi but some adaptations to CoDiPack ++svn co https://github.com/michel2323/AdjointMPI.git/branches/doubleFixMaster src + mkdir install + + cd src Index: /issm/oecreview/Archive/23185-23389/ISSM-23279-23280.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23279-23280.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23279-23280.diff (revision 23390) @@ -0,0 +1,32 @@ +Index: ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp (revision 23279) ++++ ../trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp (revision 23280) +@@ -25,6 +25,11 @@ + #include + + void MumpsInit(DMUMPS_STRUC_C &theMumpsStruc){ ++ theMumpsStruc.n = 0; ++ theMumpsStruc.nz = 0; ++ theMumpsStruc.a = NULL; ++ theMumpsStruc.jcn = NULL; ++ theMumpsStruc.irn = NULL; + theMumpsStruc.par = 1; + theMumpsStruc.sym = 0; + #ifdef _HAVE_MPI_ +Index: ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23279) ++++ ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23280) +@@ -39,11 +39,7 @@ + // data types + #define ISSM_MPI_CHAR MPI_CHAR + #if defined(_HAVE_AMPI_) +- #ifdef _HAVE_ADJOINTMPI_ +- #define ISSM_MPI_DOUBLE AMPI_DOUBLE // corresponds to IssmDouble +- #else + #define ISSM_MPI_DOUBLE AMPI_ADOUBLE // corresponds to IssmDouble +- #endif + #else + #define ISSM_MPI_DOUBLE MPI_DOUBLE // corresponds to IssmDouble + #endif Index: /issm/oecreview/Archive/23185-23389/ISSM-23280-23281.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23280-23281.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23280-23281.diff (revision 23390) @@ -0,0 +1,30 @@ +Index: ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp (revision 23280) ++++ ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp (revision 23281) +@@ -240,6 +240,7 @@ + } + #elif defined(_HAVE_CODIPACK_) + auto& tape_codi = IssmDouble::getGlobalTape(); ++ codi_global.input_indices.clear(); + if(my_rank==0){ + for (int i=0;i(num_dependents); ++ #if defined(_HAVE_CODIPACK_) ++ codi_global.output_indices.clear(); ++ #endif + for(int i=0;iSize();i++){ + DependentObject* dep=(DependentObject*)dependent_objects->GetObjectByOffset(i); + if(solution_type==TransientSolutionEnum) output_value = dep->GetValue(); +@@ -384,6 +388,7 @@ + weightVectorTimesJac=xNew(num_independents); + auto in_size = codi_global.input_indices.size(); + for(size_t i = 0; i < in_size; ++i) { ++ _assert_(i + +-void CoordinateSystemTransformx(IssmDouble** px_dest,IssmDouble** py_dest,IssmDouble* x_src,IssmDouble* y_src,int size,const char* str_src,const char* str_dst){ ++void CoordinateSystemTransformx(double** px_dest,double** py_dest,double* x_src,double* y_src,int size,const char* str_src,const char* str_dst){ + + #if !defined(_HAVE_PROJ4_) + _error_("proj.4 has not been installed"); +@@ -16,8 +16,8 @@ + + /*Allocate output and initialize values as src*/ + _assert_(size>0); +- IssmDouble* x_dest = xNew(size); +- IssmDouble* y_dest = xNew(size); ++ double* x_dest = xNew(size); ++ double* y_dest = xNew(size); + for(int i=0;inumberofelements;i++){ + for(j=0;j<3;j++){ + if(my_nodes[3*i+j]){ +- nodes->AddObject(new Node(id0+3*i+j+1,id0+3*i+j,lid++,iomodel->elements[+3*i+j]-1,iomodel,analysis,approximation)); ++ nodes->AddObject(new Node(id0+3*i+j+1,id0+3*i+j,lid++,iomodel->elements[3*i+j]-1,iomodel,analysis,approximation)); + + } + } Index: /issm/oecreview/Archive/23185-23389/ISSM-23285-23286.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23285-23286.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23285-23286.diff (revision 23390) @@ -0,0 +1,11 @@ +Index: ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp (revision 23285) ++++ ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp (revision 23286) +@@ -279,5 +279,5 @@ + }/*}}}*/ + + #else +-void controlm1qn3_core(FemModel* femmodel){_error_("M1QN3 not installed");} ++void controlm1qn3_core(FemModel* femmodel){_error_("M1QN3 not installed (or you might have turned AD on)");} + #endif //_HAVE_M1QN3_ Index: /issm/oecreview/Archive/23185-23389/ISSM-23286-23287.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23286-23287.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23286-23287.diff (revision 23390) @@ -0,0 +1,34 @@ +Index: ../trunk-jpl/src/wrappers/IssmConfig/IssmConfig.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/IssmConfig/IssmConfig.cpp (revision 23286) ++++ ../trunk-jpl/src/wrappers/IssmConfig/IssmConfig.cpp (revision 23287) +@@ -68,6 +68,16 @@ + value = 1.; + #endif + } ++ else if(strcmp(name,"_HAVE_ADOLC_")==0){ ++ #ifdef _HAVE_ADOLC_ ++ value = 1.; ++ #endif ++ } ++ else if(strcmp(name,"_HAVE_CODIPACK_")==0){ ++ #ifdef _HAVE_CODIPACK_ ++ value = 1.; ++ #endif ++ } + else if(strcmp(name,"_HAVE_PETSC_")==0){ + #ifdef _HAVE_PETSC_ + value = 1.; +Index: ../trunk-jpl/src/wrappers/DistanceToMaskBoundary/DistanceToMaskBoundary.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/DistanceToMaskBoundary/DistanceToMaskBoundary.cpp (revision 23286) ++++ ../trunk-jpl/src/wrappers/DistanceToMaskBoundary/DistanceToMaskBoundary.cpp (revision 23287) +@@ -42,7 +42,7 @@ + FetchData(&mask,NULL,NULL,MASK); + + /*Call core of computation: */ +- DistanceToMaskBoundaryx(&distance,x,y,mask,nods); ++ //DistanceToMaskBoundaryx(&distance,x,y,mask,nods); + + /*Write results: */ + WriteData(DISTANCE,distance,nods); Index: /issm/oecreview/Archive/23185-23389/ISSM-23287-23288.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23287-23288.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23287-23288.diff (revision 23390) @@ -0,0 +1,12 @@ +Index: ../trunk-jpl/src/wrappers/DistanceToMaskBoundary/DistanceToMaskBoundary.cpp +=================================================================== +--- ../trunk-jpl/src/wrappers/DistanceToMaskBoundary/DistanceToMaskBoundary.cpp (revision 23287) ++++ ../trunk-jpl/src/wrappers/DistanceToMaskBoundary/DistanceToMaskBoundary.cpp (revision 23288) +@@ -42,6 +42,7 @@ + FetchData(&mask,NULL,NULL,MASK); + + /*Call core of computation: */ ++ _error_("messing up with AD, is this fonction really used??"); + //DistanceToMaskBoundaryx(&distance,x,y,mask,nods); + + /*Write results: */ Index: /issm/oecreview/Archive/23185-23389/ISSM-23288-23289.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23288-23289.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23288-23289.diff (revision 23390) @@ -0,0 +1,82 @@ +Index: ../trunk-jpl/jenkins/linux64_ross_codi +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_codi (nonexistent) ++++ ../trunk-jpl/jenkins/linux64_ross_codi (revision 23289) +@@ -0,0 +1,70 @@ ++# ++#-------------------------------# ++# 1: ISSM general configuration # ++#-------------------------------# ++ ++#MATLAB path ++MATLAB_PATH="/usr/local/MATLAB/R2015a" ++ ++#ISSM CONFIGURATION ++ISSM_CONFIG='--prefix=$ISSM_DIR\ ++ --without-kriging \ ++ --without-kml \ ++ --without-GiaIvins \ ++ --without-Love \ ++ --with-gsl-dir=$ISSM_DIR/externalpackages/gsl/install \ ++ --with-matlab-dir=$MATLAB_PATH \ ++ --with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include \ ++ --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpifort -lmpi" \ ++ --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \ ++ --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/ \ ++ --with-numthreads=4 \ ++ --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \ ++ --with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9/ -lgfortran" \ ++ --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \ ++ --with-codipack-dir="$ISSM_DIR/externalpackages/codipack/install" \ ++ --enable-tape-alloc \ ++ --with-cxxoptflags="-DAD_TYPE=codi::RealReverse" \ ++ --with-adjointmpi-dir="$ISSM_DIR/externalpackages/adjointmpi/install" \ ++ --enable-development \ ++ --enable-debugging ' ++ ++#PYTHON and MATLAB testing ++MATLAB_TEST=1 ++PYTHON_TEST=0 ++ ++#-----------------------------------# ++# 3: External packages installation # ++#-----------------------------------# ++ ++#List of external pakages to be installed and their installation scripts ++EXTERNALPACKAGES="autotools install.sh ++ cmake install.sh ++ mpich install-3.2-linux64.sh ++ petsc install-3.7-linux64.sh ++ metis install-5.0.1-linux64.sh ++ triangle install-linux64.sh ++ gsl install-linux64.sh ++ adjointmpi install.sh ++ codipack install.sh ++ shell2junit install.sh" ++ ++#-----------------# ++# 4: test options # ++#-----------------# ++ ++#number of cpus used in ISSM installation and compilation (one is usually ++#safer as some packages are very sensitive to parallel compilation) ++NUMCPUS_INSTALL=5 ++ ++#number of cpus used in the nightly runs. ++NUMCPUS_RUN=1 ++ ++#Nightly run options. The matlab routine runme.m will be called ++#as follows: runme($MATLAB_NROPTIONS). The options must be understandable ++#by Matlab and runme.m ++#ex: "'id',[101 102 103]" ++MATLAB_NROPTIONS="'benchmark','all','id',[3105]" ++PYTHON_NROPTIONS="--benchmark='all' -i 3105" + +Property changes on: ../trunk-jpl/jenkins/linux64_ross_codi +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property Index: /issm/oecreview/Archive/23185-23389/ISSM-23289-23290.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23289-23290.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23289-23290.diff (revision 23390) @@ -0,0 +1,53 @@ +Index: ../trunk-jpl/test/NightlyRun/test3015.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3015.m (revision 23289) ++++ ../trunk-jpl/test/NightlyRun/test3015.m (revision 23290) +@@ -14,15 +14,26 @@ + + %setup autodiff parameters + index=1; %this is the scalar component we are checking against +-md.autodiff.independents={... +- independent('name','md.geometry.thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',index) +- }; + +-md.autodiff.dependents={... +- dependent('name','IceVolume','type','scalar')... ++if IssmConfig('_HAVE_CODIPACK_') ++ md.autodiff.independents={... ++ independent('name','md.geometry.thickness','type','vertex','nods',md.mesh.numberofvertices) + }; +-md.autodiff.driver='fos_forward'; ++ md.autodiff.dependents={... ++ dependent('name','IceVolume','type','scalar','fos_reverse_index',index)... ++ }; ++ md.autodiff.driver='fos_reverse'; ++else ++ md.autodiff.independents={... ++ independent('name','md.geometry.thickness','type','vertex','nods',md.mesh.numberofvertices,'fos_forward_index',index) ++ }; + ++ md.autodiff.dependents={... ++ dependent('name','IceVolume','type','scalar')... ++ }; ++ md.autodiff.driver='fos_forward'; ++end ++ + %parameters for the step-wise derivative + delta=0.001; + h1=md.geometry.thickness(index); +@@ -69,9 +80,13 @@ + + md=solve(md,'Masstransport'); + %retrieve directly +-dVdh_ad=md.results.MasstransportSolution.AutodiffJacobian; ++if IssmConfig('_HAVE_CODIPACK_') ++ dVdh_ad=md.results.MasstransportSolution.AutodiffJacobian(index); ++else ++ dVdh_ad=md.results.MasstransportSolution.AutodiffJacobian; ++end + +-disp(sprintf('dV/dh: analytical: %16.16g\n using adolc: %16.16g\n',dVdh_an,dVdh_ad)); ++disp(sprintf('dV/dh: analytical: %16.16g\n using ad: %16.16g\n',dVdh_an,dVdh_ad)); + + %Fields and tolerances to track changes + field_names ={'dV/dh'}; Index: /issm/oecreview/Archive/23185-23389/ISSM-23290-23291.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23290-23291.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23290-23291.diff (revision 23390) @@ -0,0 +1,32 @@ +Index: ../trunk-jpl/jenkins/linux64_ross_codi +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_codi (revision 23290) ++++ ../trunk-jpl/jenkins/linux64_ross_codi (revision 23291) +@@ -40,16 +40,17 @@ + #-----------------------------------# + + #List of external pakages to be installed and their installation scripts +-EXTERNALPACKAGES="autotools install.sh +- cmake install.sh +- mpich install-3.2-linux64.sh +- petsc install-3.7-linux64.sh +- metis install-5.0.1-linux64.sh +- triangle install-linux64.sh +- gsl install-linux64.sh +- adjointmpi install.sh +- codipack install.sh +- shell2junit install.sh" ++EXTERNALPACKAGES="autotools install.sh ++ cmake install.sh ++ mpich install-3.2-linux64.sh ++ petsc install-3.7-linux64.sh ++ metis install-5.0.1-linux64.sh ++ triangle install-linux64.sh ++ gsl install-linux64.sh ++ m1qn3 install.sh ++ adjointmpi install.sh ++ codipack install.sh ++ shell2junit install.sh" + + #-----------------# + # 4: test options # Index: /issm/oecreview/Archive/23185-23389/ISSM-23291-23292.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23291-23292.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23291-23292.diff (revision 23390) @@ -0,0 +1,56 @@ +Index: ../trunk-jpl/test/NightlyRun/test3480.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3480.m (revision 23291) ++++ ../trunk-jpl/test/NightlyRun/test3480.m (revision 23292) +@@ -17,6 +17,7 @@ + md.inversion=adm1qn3inversion(md.inversion); + md.inversion.iscontrol=1; + md.autodiff.isautodiff=1; ++md.autodiff.driver='fos_reverse'; + + md.friction.coefficient(1:md.mesh.numberofvertices,1)=50; + md.autodiff.independents = {independent('name','FrictionCoefficient',... +@@ -54,6 +55,9 @@ + md.autodiff.dependents{1} = dependent('name','Outputdefinition1','type','scalar','fos_reverse_index',1); + md.inversion.maxiter = 2; + md.cluster=generic('name',oshostname(),'np',3); ++if IssmConfig('_HAVE_CODIPACK_') ++ md.cluster.np=1; ++end + md=solve(md,'transient'); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test3481.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3481.m (revision 23291) ++++ ../trunk-jpl/test/NightlyRun/test3481.m (revision 23292) +@@ -17,6 +17,7 @@ + md.inversion=adm1qn3inversion(md.inversion); + md.inversion.iscontrol=1; + md.autodiff.isautodiff=1; ++md.autodiff.driver='fos_reverse'; + + md.friction.coefficient(1:md.mesh.numberofvertices,1)=50; + md.friction.coefficient(1:md.mesh.numberofvertices,2)=25; +@@ -60,6 +61,9 @@ + md.autodiff.dependents{1} = dependent('name','Outputdefinition1','type','scalar','fos_reverse_index',1); + md.inversion.maxiter = 2; + md.cluster=generic('name',oshostname(),'np',3); ++if IssmConfig('_HAVE_CODIPACK_') ++ md.cluster.np=1; ++end + md=solve(md,'transient'); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/jenkins/linux64_ross_codi +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_codi (revision 23291) ++++ ../trunk-jpl/jenkins/linux64_ross_codi (revision 23292) +@@ -67,5 +67,5 @@ + #as follows: runme($MATLAB_NROPTIONS). The options must be understandable + #by Matlab and runme.m + #ex: "'id',[101 102 103]" +-MATLAB_NROPTIONS="'benchmark','all','id',[3105]" +-PYTHON_NROPTIONS="--benchmark='all' -i 3105" ++MATLAB_NROPTIONS="'benchmark','all','id',[3015,3119,3480]" ++PYTHON_NROPTIONS="--benchmark='all' -i 3015 3119 3480" Index: /issm/oecreview/Archive/23185-23389/ISSM-23292-23293.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23292-23293.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23292-23293.diff (revision 23390) @@ -0,0 +1,70 @@ +Index: ../trunk-jpl/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp (revision 23292) ++++ ../trunk-jpl/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp (revision 23293) +@@ -228,6 +228,7 @@ + xDelete(independents_fullmin); + xDelete(independents_fullmax); + xDelete(start_point); ++ xDelete(control_sizes); + /*Step2: create cost functions (dependents)*/ + + return; +Index: ../trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp (revision 23292) ++++ ../trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp (revision 23293) +@@ -32,6 +32,8 @@ + } + + xDelete(control_type); ++ xDelete(M); ++ xDelete(N); + } + else{ + +Index: ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp (revision 23292) ++++ ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp (revision 23293) +@@ -321,14 +321,14 @@ + /*for adolc to run in parallel, we 0 out on rank~=0. But we still keep track of num_dependents:*/ + int num_dependents_old = num_dependents; + int num_independents_old = num_independents; ++ ++ #if defined(_HAVE_ADOLC_) ++ /*Get gradient for ADOLC {{{*/ + if(my_rank!=0){ + num_dependents = 0; + num_independents = 0; + } + +- #if defined(_HAVE_ADOLC_) +- /*Get gradient for ADOLC {{{*/ +- + /*get the EDF pointer:*/ + ext_diff_fct *anEDF_for_solverx_p=xDynamicCast * >(femmodel->parameters->FindParamObject(AdolcParamEnum))->GetParameterValue().myEDF_for_solverx_p; + +@@ -381,7 +381,12 @@ + + /*initialize direction index in the weights vector: */ + aWeightVector=xNewZeroInit(num_dependents); +- if(my_rank==0) tape_codi.setGradient(codi_global.output_indices[aDepIndex],1.0); ++ if(my_rank==0){ ++ if(aDepIndex<0 || aDepIndex>=num_dependents || codi_global.output_indices.size() <= aDepIndex){ ++ _error_("index value for AutodiffFosReverseIndexEnum should be in [0,num_dependents-1]"); ++ } ++ tape_codi.setGradient(codi_global.output_indices[aDepIndex],1.0); ++ } + tape_codi.evaluate(); + + /*Get gradient for this dependent */ +@@ -460,6 +465,8 @@ + *Jlisti = (*Jlisti) +1; + xDelete(XU); + xDelete(XL); ++ xDelete(control_enum); ++ xDelete(N); + xDelete(scaling_factors); + xDelete(totalgradient); + Index: /issm/oecreview/Archive/23185-23389/ISSM-23293-23294.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23293-23294.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23293-23294.diff (revision 23390) @@ -0,0 +1,19 @@ +Index: ../trunk-jpl/src/c/toolkits/issm/IssmMpiSparseMat.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/issm/IssmMpiSparseMat.h (revision 23293) ++++ ../trunk-jpl/src/c/toolkits/issm/IssmMpiSparseMat.h (revision 23294) +@@ -263,10 +263,10 @@ + } + + for(i=0;iparameters->FindParam(&solution_type,SolutionTypeEnum); +@@ -52,8 +52,8 @@ + femmodel->parameters->FindParam(&num_cost_functions,InversionNumCostFunctionsEnum); + femmodel->parameters->FindParam(&maxsteps,InversionMaxstepsEnum); + femmodel->parameters->FindParam(&maxiter,InversionMaxiterEnum); +- femmodel->parameters->FindParam(&dxmin,InversionDxminEnum); +- femmodel->parameters->FindParam(>tol,InversionGttolEnum); ++ femmodel->parameters->FindParamAndMakePassive(&dxmin,InversionDxminEnum); ++ femmodel->parameters->FindParamAndMakePassive(>tol,InversionGttolEnum); + femmodel->parameters->FindParam(&scaling_factors,NULL,InversionControlScalingFactorsEnum); + femmodel->parameters->SetParam(false,SaveResultsEnum); + numberofvertices=femmodel->vertices->NumberOfVertices(); +@@ -77,8 +77,8 @@ + long nsim = long(maxiter);/*Maximum number of function calls*/ + + /*Get initial guess*/ +- Vector *Xpetsc = NULL; +- GetVectorFromControlInputsx(&Xpetsc,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); ++ Vector *Xpetsc = NULL; ++ GetPassiveVectorFromControlInputsx(&Xpetsc,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); + X = Xpetsc->ToMPISerial(); + Xpetsc->GetSize(&intn); + delete Xpetsc; +@@ -92,7 +92,7 @@ + for(int c=0;c(scaling_factors[c]); + } + } + +@@ -111,7 +111,7 @@ + mystruct.femmodel = femmodel; + mystruct.M = maxiter; + mystruct.N = num_cost_functions+1; +- mystruct.Jlist = xNewZeroInit(mystruct.M*mystruct.N); ++ mystruct.Jlist = xNewZeroInit(mystruct.M*mystruct.N); + mystruct.i = xNewZeroInit(1); + + /*Initialize Gradient and cost function of M1QN3*/ +@@ -140,20 +140,36 @@ + } + + /*Constrain solution vector*/ +- IssmDouble *XL = NULL; +- IssmDouble *XU = NULL; +- GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); +- GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); ++ double *XL = NULL; ++ double *XU = NULL; ++ GetPassiveVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); ++ GetPassiveVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + for(int c=0;c(scaling_factors[c]); + if(X[index]>XU[index]) X[index]=XU[index]; + if(X[index](intn); ++ IssmDouble* aG=xNew(intn); ++ for(int i=0;i(X[i]); ++ aG[i] = reCast(G[i]); ++ } ++ ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,aG); ++ SetControlInputsFromVectorx(femmodel,aX); ++ xDelete(aX); ++ xDelete(aG); ++ #else + SetControlInputsFromVectorx(femmodel,X); + ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,G); ++ #endif ++ + femmodel->OutputControlsx(&femmodel->results); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,JEnum,mystruct.Jlist,(*mystruct.i),mystruct.N,0,0)); + +@@ -170,7 +186,7 @@ + xDelete(dz); + xDelete(XU); + xDelete(XL); +- xDelete(scaling_factors); ++ xDelete(scaling_factors); + xDelete(mystruct.Jlist); + xDelete(mystruct.i); + }/*}}}*/ +@@ -179,7 +195,7 @@ + /*Recover Arguments*/ + m1qn3_struct *input_struct = (m1qn3_struct*)dzs; + FemModel *femmodel = input_struct->femmodel; +- IssmDouble *Jlist = input_struct->Jlist; ++ IssmPDouble *Jlist = input_struct->Jlist; + int JlistM = input_struct->M; + int JlistN = input_struct->N; + int *Jlisti = input_struct->i; +@@ -194,19 +210,31 @@ + numberofvertices=femmodel->vertices->NumberOfVertices(); + + /*Constrain input vector and update controls*/ +- IssmDouble *XL = NULL; +- IssmDouble *XU = NULL; ++ double *XL = NULL; ++ double *XU = NULL; ++ #ifdef _HAVE_AD_ ++ GetPassiveVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); ++ GetPassiveVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); ++ #else + GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); + GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); ++ #endif + for(int c=0;c(scaling_factors[c]); + if(X[index]>XU[index]) X[index]=XU[index]; + if(X[index](*n); ++ for(int i=0;i<*n;i++) aX[i] = reCast(X[i]); ++ SetControlInputsFromVectorx(femmodel,aX); ++ xDelete(aX); ++ #else + SetControlInputsFromVectorx(femmodel,X); ++ #endif + + /*Compute solution and adjoint*/ + void (*solutioncore)(FemModel*)=NULL; +@@ -220,11 +248,13 @@ + + /*Compute objective function*/ + IssmDouble* Jtemp = NULL; +- femmodel->CostFunctionx(pf,&Jtemp,NULL); ++ IssmDouble J; ++ femmodel->CostFunctionx(&J,&Jtemp,NULL); ++ *pf = reCast(J); + _printf0_("f(x) = "<(Jtemp[i]); + Jlist[(*Jlisti)*JlistN+num_responses] = *pf; + xDelete(Jtemp); + +@@ -237,8 +267,8 @@ + _printf0_("\n"); + + *Jlisti = (*Jlisti) +1; +- xDelete(XU); +- xDelete(XL); ++ xDelete(XU); ++ xDelete(XL); + return; + } + +@@ -249,7 +279,7 @@ + /*Compute gradient*/ + IssmDouble* G2 = NULL; + Gradjx(&G2,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); +- for(long i=0;i<*n;i++) G[i] = -G2[i]; ++ for(long i=0;i<*n;i++) G[i] = -reCast(G2[i]); + xDelete(G2); + + /*Constrain Gradient*/ +@@ -259,8 +289,8 @@ + int index = numberofvertices*c+i; + if(X[index]>=XU[index]) G[index]=0.; + if(X[index]<=XL[index]) G[index]=0.; +- G[index] = G[index]*scaling_factors[c]; +- X[index] = X[index]/scaling_factors[c]; ++ G[index] = G[index]*reCast(scaling_factors[c]); ++ X[index] = X[index]/reCast(scaling_factors[c]); + Gnorm += G[index]*G[index]; + } + } +@@ -273,11 +303,11 @@ + + /*Clean-up and return*/ + *Jlisti = (*Jlisti) +1; +- xDelete(XU); +- xDelete(XL); ++ xDelete(XU); ++ xDelete(XL); + xDelete(scaling_factors); + }/*}}}*/ + + #else +-void controlm1qn3_core(FemModel* femmodel){_error_("M1QN3 not installed (or you might have turned AD on)");} ++void controlm1qn3_core(FemModel* femmodel){_error_("M1QN3 not installed");} + #endif //_HAVE_M1QN3_ Index: /issm/oecreview/Archive/23185-23389/ISSM-23306-23307.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23306-23307.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23306-23307.diff (revision 23390) @@ -0,0 +1,94 @@ +Index: ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp (revision 23306) ++++ ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp (revision 23307) +@@ -38,13 +38,13 @@ + void controlm1qn3_core(FemModel* femmodel){/*{{{*/ + + /*Intermediaries*/ +- long omode; +- double f,dxmin,gttol; +- int maxsteps,maxiter; +- int intn,numberofvertices,num_controls,num_cost_functions,solution_type; +- IssmDouble *scaling_factors = NULL; +- double *X = NULL; +- double *G = NULL; ++ long omode; ++ double f,dxmin,gttol; ++ int maxsteps,maxiter; ++ int intn,numberofvertices,num_controls,num_cost_functions,solution_type; ++ double *scaling_factors = NULL; ++ double *X = NULL; ++ double *G = NULL; + + /*Recover some parameters*/ + femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); +@@ -92,7 +92,7 @@ + for(int c=0;c(scaling_factors[c]); ++ X[index] = X[index]/scaling_factors[c]; + } + } + +@@ -147,7 +147,7 @@ + for(int c=0;c(scaling_factors[c]); ++ X[index] = X[index]*scaling_factors[c]; + if(X[index]>XU[index]) X[index]=XU[index]; + if(X[index](dz); + xDelete(XU); + xDelete(XL); +- xDelete(scaling_factors); ++ xDelete(scaling_factors); + xDelete(mystruct.Jlist); + xDelete(mystruct.i); + }/*}}}*/ +@@ -202,10 +202,10 @@ + + /*Recover some parameters*/ + int num_responses,num_controls,numberofvertices,solution_type; +- IssmDouble* scaling_factors = NULL; ++ double* scaling_factors = NULL; + femmodel->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); + femmodel->parameters->FindParam(&num_controls,InversionNumControlParametersEnum); +- femmodel->parameters->FindParam(&scaling_factors,NULL,InversionControlScalingFactorsEnum); ++ femmodel->parameters->FindParamAndMakePassive(&scaling_factors,NULL,InversionControlScalingFactorsEnum); + femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); + numberofvertices=femmodel->vertices->NumberOfVertices(); + +@@ -222,7 +222,7 @@ + for(int c=0;c(scaling_factors[c]); ++ X[index] = X[index]*scaling_factors[c]; + if(X[index]>XU[index]) X[index]=XU[index]; + if(X[index]=XU[index]) G[index]=0.; + if(X[index]<=XL[index]) G[index]=0.; +- G[index] = G[index]*reCast(scaling_factors[c]); +- X[index] = X[index]/reCast(scaling_factors[c]); ++ G[index] = G[index]*scaling_factors[c]; ++ X[index] = X[index]/scaling_factors[c]; + Gnorm += G[index]*G[index]; + } + } +@@ -305,7 +305,7 @@ + *Jlisti = (*Jlisti) +1; + xDelete(XU); + xDelete(XL); +- xDelete(scaling_factors); ++ xDelete(scaling_factors); + }/*}}}*/ + + #else Index: /issm/oecreview/Archive/23185-23389/ISSM-23307-23308.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23307-23308.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23307-23308.diff (revision 23390) @@ -0,0 +1,20 @@ +Index: ../trunk-jpl/src/c/toolkits/petsc/objects/PetscSolver.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/petsc/objects/PetscSolver.cpp (revision 23307) ++++ ../trunk-jpl/src/c/toolkits/petsc/objects/PetscSolver.cpp (revision 23308) +@@ -14,6 +14,7 @@ + #include "../../../shared/Exceptions/exceptions.h" + #include "../../../shared/io/Comm/IssmComm.h" + #include "../../../shared/Enum/Enum.h" ++#include "../../../shared/io/Print/Print.h" + + void PetscSolve(PetscVec** puf, PetscMat* Kff, PetscVec* pf, PetscVec* uf0,PetscVec* df, Parameters* parameters){ /*{{{*/ + +@@ -155,6 +156,7 @@ + /*Check convergence*/ + KSPGetIterationNumber(ksp,&iteration_number); + if (iteration_number<0) _error_("Solver diverged at iteration number: " << -iteration_number); ++ if (VerboseSolver()) _printf0_("Petsc: "<< iteration_number << " KSP iterations\n"); + + /*Free resources:*/ + KSPFree(&ksp); Index: /issm/oecreview/Archive/23185-23389/ISSM-23308-23309.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23308-23309.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23308-23309.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp (revision 23308) ++++ ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp (revision 23309) +@@ -54,7 +54,7 @@ + femmodel->parameters->FindParam(&maxiter,InversionMaxiterEnum); + femmodel->parameters->FindParamAndMakePassive(&dxmin,InversionDxminEnum); + femmodel->parameters->FindParamAndMakePassive(>tol,InversionGttolEnum); +- femmodel->parameters->FindParam(&scaling_factors,NULL,InversionControlScalingFactorsEnum); ++ femmodel->parameters->FindParamAndMakePassive(&scaling_factors,NULL,InversionControlScalingFactorsEnum); + femmodel->parameters->SetParam(false,SaveResultsEnum); + numberofvertices=femmodel->vertices->NumberOfVertices(); + Index: /issm/oecreview/Archive/23185-23389/ISSM-23309-23310.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23309-23310.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23309-23310.diff (revision 23390) @@ -0,0 +1,45 @@ +Index: ../trunk-jpl/src/c/classes/Params/Parameters.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Params/Parameters.h (revision 23309) ++++ ../trunk-jpl/src/c/classes/Params/Parameters.h (revision 23310) +@@ -52,6 +52,7 @@ + void FindParam(FILE** pfid,int enum_type); + void FindParam(DataSet** pdataset, int enum_type); + void FindParamAndMakePassive(IssmPDouble* pscalar, int enum_type); ++ void FindParamAndMakePassive(IssmPDouble** pvec,int* pM,int enum_type); + void FindParamInDataset(IssmDouble** pIssmDoublearray,int* pM,int* pN,int dataset_type,int enum_type); + + void SetParam(bool boolean,int enum_type); +Index: ../trunk-jpl/src/c/classes/Params/Parameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Params/Parameters.cpp (revision 23309) ++++ ../trunk-jpl/src/c/classes/Params/Parameters.cpp (revision 23310) +@@ -439,6 +439,28 @@ + *pscalar=reCast(intermediary); + } + /*}}}*/ ++void Parameters::FindParamAndMakePassive(IssmPDouble** pvec,int* pM, int param_enum){ _assert_(this);/*{{{*/ ++ ++ _assert_(param_enum>ParametersSTARTEnum); ++ _assert_(param_enumparams[index]) _error_("Parameter " << EnumToStringx(param_enum) <<" not set"); ++ this->params[index]->GetParameterValue(&vector,&n); ++ ++ /*Make output passive*/ ++ IssmPDouble* output = xNew(n); ++ for(int i=0;i(vector[i]); ++ ++ /*assign output pointers*/ ++ if(pvec) *pvec = output; ++ if(pM) *pM = n; ++}/*}}}*/ + void Parameters::FindParamInDataset(IssmDouble** pIssmDoublearray,int* pM,int* pN,int dataset_type,int enum_type){/*{{{*/ + _assert_(this); + Index: /issm/oecreview/Archive/23185-23389/ISSM-23310-23311.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23310-23311.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23310-23311.diff (revision 23390) @@ -0,0 +1,184 @@ +Index: ../trunk-jpl/src/c/cores/control_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/control_core.cpp (revision 23310) ++++ ../trunk-jpl/src/c/cores/control_core.cpp (revision 23311) +@@ -80,8 +80,8 @@ + if(VerboseControl()) _printf0_(" preparing final solution\n"); + IssmDouble *XL = NULL; + IssmDouble *XU = NULL; +- GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); +- GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); ++ GetVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); ++ GetVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + for(long i=0;iXU[i]) X0[i]=XU[i]; + if(X0[i]elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); +- GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); ++ GetVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); ++ GetVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + for(long i=0;iXU[i]) X[i]=XU[i]; + if(X[i]elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); +- GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); ++ GetVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); ++ GetVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + for(long i=0;iXU[i]) X[i]=XU[i]; + if(X[i] *Xpetsc = NULL; +- GetPassiveVectorFromControlInputsx(&Xpetsc,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); +- X = Xpetsc->ToMPISerial(); +- Xpetsc->GetSize(&intn); +- delete Xpetsc; ++ GetPassiveVectorFromControlInputsx(&X,&intn,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); + _assert_(intn==numberofvertices*num_controls); + + /*Get problem dimension and initialize gradient and initial guess*/ +@@ -142,8 +138,8 @@ + /*Constrain solution vector*/ + double *XL = NULL; + double *XU = NULL; +- GetPassiveVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); +- GetPassiveVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); ++ GetPassiveVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); ++ GetPassiveVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + for(int c=0;celements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); +- GetPassiveVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); +- #else +- GetVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); +- GetVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); +- #endif ++ GetPassiveVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); ++ GetPassiveVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + for(int c=0;c** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); +-void GetVectorFromControlInputsx( IssmDouble** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); ++void GetVectorFromControlInputsx( IssmDouble** pvector,int* pN, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); + +-void GetPassiveVectorFromControlInputsx(Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); +-void GetPassiveVectorFromControlInputsx(double** pvector, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); ++void GetPassiveVectorFromControlInputsx(double** pvector,int* pN, Elements* elements,Nodes* nodes, Vertices* vertices,Loads* loads, Materials* materials, Parameters* parameters,const char* data="value"); + + #endif /* _GETVECTORFROMCONTROLINPUTSXX_H */ +Index: ../trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp (revision 23310) ++++ ../trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp (revision 23311) +@@ -77,54 +77,31 @@ + } + + }/*}}}*/ +-void GetVectorFromControlInputsx( IssmDouble** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, const char* data){/*{{{*/ ++void GetVectorFromControlInputsx( IssmDouble** pvector,int *pN, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, const char* data){/*{{{*/ + + /*intermediary: */ ++ int N; + Vector* vec_vector=NULL; + ++ /*Get PETSc vector*/ + GetVectorFromControlInputsx( &vec_vector, elements,nodes, vertices, loads, materials, parameters,data); ++ ++ /*Serialize*/ ++ vec_vector->GetSize(&N); + IssmDouble* vector=vec_vector->ToMPISerial(); +- +- /*Free ressources:*/ + delete vec_vector; + + /*Assign output pointers:*/ + *pvector=vector; ++ if(pN) *pN=N; + }/*}}}*/ + + /*For autodiff, we sometimes need to cast our vectors to passive*/ + #ifdef _HAVE_AD_ +-void GetPassiveVectorFromControlInputsx(Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,const char* data){/*{{{*/ ++void GetPassiveVectorFromControlInputsx(IssmPDouble** pvector,int* pN, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, const char* data){/*{{{*/ + + /*Get active vector first*/ + Vector* activevector=NULL; +- Vector* vector=NULL; +- int size; +- +- /*Retrieve some parameters*/ +- GetVectorFromControlInputsx(&activevector, elements,nodes, vertices, loads, materials, parameters,data); +- +- /*Serialize vector*/ +- activevector->GetSize(&size); +- IssmDouble* dactivevector=activevector->ToMPISerial(); +- +- /*Cast to passive*/ +- vector=new Vector(size); +- for(int i=0;iSetValue(i,reCast(dactivevector[i]),INS_VAL); +- } +- vector->Assemble(); +- +- /*Assign output pointers:*/ +- delete activevector; +- xDelete(dactivevector); +- *pvector=vector; +- +-}/*}}}*/ +-void GetPassiveVectorFromControlInputsx(IssmPDouble** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, const char* data){/*{{{*/ +- +- /*Get active vector first*/ +- Vector* activevector=NULL; + IssmPDouble* vector=NULL; + int size; + +@@ -143,16 +120,12 @@ + delete activevector; + xDelete(dactivevector); + *pvector=vector; ++ if(pN) *pN=size; + + }/*}}}*/ + #else +-void GetPassiveVectorFromControlInputsx(Vector** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters,const char* data){/*{{{*/ ++void GetPassiveVectorFromControlInputsx(IssmPDouble** pvector,int* pN, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, const char* data){/*{{{*/ + +- GetVectorFromControlInputsx(pvector, elements,nodes, vertices, loads, materials, parameters,data); +- ++ GetVectorFromControlInputsx(pvector,pN,elements,nodes, vertices, loads, materials, parameters,data); + }/*}}}*/ +-void GetPassiveVectorFromControlInputsx(IssmPDouble** pvector, Elements* elements,Nodes* nodes, Vertices* vertices, Loads* loads, Materials* materials, Parameters* parameters, const char* data){/*{{{*/ +- +- GetVectorFromControlInputsx(pvector, elements,nodes, vertices, loads, materials, parameters,data); +-}/*}}}*/ + #endif Index: /issm/oecreview/Archive/23185-23389/ISSM-23315-23316.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23315-23316.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23315-23316.diff (revision 23390) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp (revision 23315) ++++ ../trunk-jpl/src/c/cores/controladm1qn3_core.cpp (revision 23316) +@@ -579,8 +579,8 @@ + /*Constrain solution vector*/ + double *XL = NULL; + double *XU = NULL; +- GetPassiveVectorFromControlInputsx(&XL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); +- GetPassiveVectorFromControlInputsx(&XU,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); ++ GetPassiveVectorFromControlInputsx(&XL,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"lowerbound"); ++ GetPassiveVectorFromControlInputsx(&XU,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"upperbound"); + + N_add = 0; + for (int c=0;csolution_enum==TransientSolutionEnum){ + int smb_model; + iomodel->FindConstant(&smb_model,"md.smb.model"); +- if(smb_model==SMBpddEnum) isdynamic=true; +- if(smb_model==SMBd18opddEnum) isdynamic=true; ++ if(smb_model==SMBpddEnum) isdynamic=true; ++ if(smb_model==SMBd18opddEnum) isdynamic=true; ++ if(smb_model==SMBpddSicopolisEnum) isdynamic=true; + } + + /*Convert spcs from temperatures to enthalpy*/ +@@ -1199,6 +1200,8 @@ + } + _assert_((Hc+Ht)>0.); + lambda = Hc/(Hc+Ht); ++ _assert_(lambda>=0.); ++ _assert_(lambda<=1.); + kappa = kappa_c*kappa_t/(lambda*kappa_t+(1.-lambda)*kappa_c); // ==(lambda/kappa_c + (1.-lambda)/kappa_t)^-1 + } + +Index: ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 23316) ++++ ../trunk-jpl/src/c/analyses/ThermalAnalysis.cpp (revision 23317) +@@ -32,8 +32,9 @@ + else if (iomodel->solution_enum==TransientSolutionEnum){ + int smb_model; + iomodel->FindConstant(&smb_model,"md.smb.model"); +- if(smb_model==SMBpddEnum) isdynamic=true; +- if(smb_model==SMBd18opddEnum) isdynamic=true; ++ if(smb_model==SMBpddEnum) isdynamic=true; ++ if(smb_model==SMBd18opddEnum) isdynamic=true; ++ if(smb_model==SMBpddSicopolisEnum) isdynamic=true; + } + else{ + _error_("Solution "<solution_enum)<<" not supported yet"); +Index: ../trunk-jpl/src/c/analyses/SmbAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/SmbAnalysis.cpp (revision 23316) ++++ ../trunk-jpl/src/c/analyses/SmbAnalysis.cpp (revision 23317) +@@ -4,6 +4,9 @@ + #include "../shared/shared.h" + #include "../modules/modules.h" + ++// FIX ++#include "./shared/io/Print/Print.h" ++ + /*Model processing*/ + void SmbAnalysis::CreateConstraints(Constraints* constraints,IoModel* iomodel){/*{{{*/ + /*No constraints*/ +@@ -20,7 +23,7 @@ + void SmbAnalysis::UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ + + int smb_model; +- bool isdelta18o,ismungsm,isd18opd,issetpddfac,isprecipscaled,istemperaturescaled; ++ bool isdelta18o,ismungsm,isd18opd,issetpddfac,isprecipscaled,istemperaturescaled,isfirnwarming; + + /*Update elements: */ + int counter=0; +@@ -87,6 +90,16 @@ + iomodel->FetchDataToInput(elements,"md.smb.monthlytemperatures",SmbMonthlytemperaturesEnum); + } + break; ++ case SMBpddSicopolisEnum: ++ iomodel->FetchDataToInput(elements,"md.smb.s0p",SmbS0pEnum); ++ iomodel->FetchDataToInput(elements,"md.smb.s0t",SmbS0tEnum); ++ iomodel->FindConstant(&isfirnwarming,"md.smb.isfirnwarming"); ++ iomodel->FetchDataToInput(elements,"md.smb.smb_corr",SmbSmbCorrEnum); ++ iomodel->FetchDataToInput(elements,"md.smb.precipitation",SmbPrecipitationEnum); ++ iomodel->FetchDataToInput(elements,"md.smb.monthlytemperatures",SmbMonthlytemperaturesEnum); ++ iomodel->FetchDataToInput(elements,"md.smb.precipitation_anomaly",SmbPrecipitationsAnomalyEnum); ++ iomodel->FetchDataToInput(elements,"md.smb.temperature_anomaly",SmbTemperaturesAnomalyEnum); ++ break; + case SMBd18opddEnum: + iomodel->FindConstant(&istemperaturescaled,"md.smb.istemperaturescaled"); + iomodel->FindConstant(&isprecipscaled,"md.smb.isprecipscaled"); +@@ -147,7 +160,7 @@ + + int numoutputs; + char** requestedoutputs = NULL; +- bool isdelta18o,ismungsm,isd18opd,issetpddfac,interp; ++ bool isdelta18o,ismungsm,isd18opd,issetpddfac,interp,isfirnwarming; + int smb_model; + IssmDouble *temp = NULL; + int N,M; +@@ -214,6 +227,9 @@ + iomodel->DeleteData(temp,"md.smb.delta18o_surface"); + } + break; ++ case SMBpddSicopolisEnum: ++ parameters->AddObject(iomodel->CopyConstantObject("md.smb.isfirnwarming",SmbIssetpddfacEnum)); ++ break; + case SMBd18opddEnum: + parameters->AddObject(iomodel->CopyConstantObject("md.smb.ismungsm",SmbIsmungsmEnum)); + parameters->AddObject(iomodel->CopyConstantObject("md.smb.isd18opd",SmbIsd18opdEnum)); +@@ -287,6 +303,10 @@ + if(VerboseSolution()) _printf0_(" call positive degree day module\n"); + PositiveDegreeDayx(femmodel); + break; ++ case SMBpddSicopolisEnum: ++ if(VerboseSolution()) _printf0_(" call SICOPOLIS positive degree day module\n"); ++ PositiveDegreeDaySicopolisx(femmodel); ++ break; + case SMBd18opddEnum: + bool isd18opd; + femmodel->parameters->FindParam(&isd18opd,SmbIsd18opdEnum); +@@ -295,7 +315,7 @@ + Delta18opdParameterizationx(femmodel); + if(VerboseSolution()) _printf0_(" call positive degree day module\n"); + PositiveDegreeDayx(femmodel); +- } ++ } + break; + case SMBgradientsEnum: + if(VerboseSolution())_printf0_(" call smb gradients module\n"); +Index: ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 23316) ++++ ../trunk-jpl/src/c/shared/Enum/EnumDefinitions.h (revision 23317) +@@ -1156,6 +1156,11 @@ + XTaylorHoodEnum, + XYEnum, + XYZEnum, ++ SMBpddSicopolisEnum, ++ SmbIsfirnwarmingEnum, ++ SmbSmbCorrEnum, ++ SmbTemperaturesAnomalyEnum, ++ SmbPrecipitationsAnomalyEnum, + /*}}}*/ + /*Unused?{{{*/ + BalancethicknessD0Enum, +Index: ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 23316) ++++ ../trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp (revision 23317) +@@ -172,6 +172,7 @@ + case 7: return SMBhenningEnum; + case 8: return SMBgembEnum; + case 9: return SMBgradientselaEnum; ++ case 10: return SMBpddSicopolisEnum; + default: _error_("Marshalled SMB code \""< (m IE)/(a*deg C) ++ beta2=beta2*(0.001*365)*sconv; // (mm WE)/(d*deg C) --> (m IE)/(a*deg C) ++ ++ /* initalize fields */ ++ precip=0.0; ++ tstar=0.0; ++ snowfall=0.0; ++ pdd=0.0; ++ /* seasonal loop */ ++ for(imonth=0;imonth<12;imonth++){ ++ ++ /********* Surface temperature correction *******/ ++ st=(s-s0t)/1000.; ++ ++ // FIXME rlaps ?? ++ rlaps=-6.309e-03+(-5.426e-03-(-6.309e-03))*sin((imonth+1-4)*PI/6.0)*1000.0; ++ monthlytemperatures[imonth]=monthlytemperatures[imonth]-rlaps*st;//*max(st,1e-3); ++ tstar=monthlytemperatures[imonth]+t_ampl[0]; ++ ++ /********* Precipitation correction *************/ ++ /* Ref: Vizcaino et al 2010; DOI 10.1007/s00382-009-0591-y */ ++ if(s0p<2000.0) ++ q=exp(desfac*(max(s,2000.0)-2000.0)); ++ else ++ q=exp(desfac*(max(s,2000.0)-s0p)); ++ ++ precip_star=q*monthlyprec[imonth]*sconv*p_ampl[0]*yts; // convert precip from m/s -> m/a ++ precip=precip+precip_star*inv_twelve; ++ ++ /********* compute PDD **************************/ ++ /* Ref: Calov & Greve 2005 Journal of Glaciology, Vol. 51, No. 172, 2005, Correspondence */ ++ IssmDouble s_stat=5.0; ++ IssmDouble inv_sqrt2pi =1.0/sqrt(2.0*PI); ++ IssmDouble inv_s_stat =1.0/s_stat; ++ IssmDouble inv_sqrt2 =1.0/sqrt(2.0); ++ pdd=pdd+(s_stat*inv_sqrt2pi*exp(-0.5*pow(tstar*inv_s_stat,2)) ++ +0.5*tstar*erfc(-tstar*inv_s_stat*inv_sqrt2))*inv_twelve; ++ ++ /*Partition of precip in solid and liquid parts, Bales et al. (2009) */ ++ IssmDouble temp_rain=7.2; // Threshold monthly mean temperature for ++ // precipitation = 101% rain, in deg C ++ IssmDouble temp_snow=-11.6; // Threshold monthly mean temperature for ++ // precipitation = 100% snow, in deg C ++ ++ IssmDouble coeff1=5.4714e-01; // Coefficients ++ IssmDouble coeff2=-9.1603e-02; // of ++ IssmDouble coeff3=-3.314e-03; // the ++ IssmDouble coeff4= 4.66e-04; // fifth-order ++ IssmDouble coeff5=3.8e-05; // polynomial ++ IssmDouble coeff6=6.0e-07; // fit ++ ++ if(tstar>=temp_rain) ++ frac_solid = 0.0; ++ else if(tstar<=temp_snow) ++ frac_solid = 1.0; ++ else{ ++ frac_solid=coeff1+tstar*(coeff2 ++ +tstar*(coeff3+tstar*(coeff4+tstar*(coeff5+tstar*coeff6)))); ++ } ++ ++ snowfall=snowfall+precip_star*frac_solid*inv_twelve; ++ } ++ /* end of seasonal loop */ ++ ++ rainfall=precip-snowfall; ++ if(snowfall<0.0) snowfall=0.0; // correction of ++ if(rainfall<0.0) rainfall=0.0; // negative values ++ ++ if(rainfall<=(Pmax*snowfall)){ ++ if((rainfall+beta1*pdd)<=(Pmax*snowfall)) { ++ smelt_star = rainfall+beta1*pdd; ++ smelt = 0.0; ++ runoff = smelt; ++ } ++ else{ ++ smelt_star = Pmax*snowfall; ++ smelt = beta2*(pdd-(smelt_star-rainfall)/beta1); ++ runoff = smelt; ++ } ++ } ++ else{ ++ smelt_star = Pmax*snowfall; ++ smelt = beta2*pdd; ++ runoff = smelt+rainfall-Pmax*snowfall; ++ } ++ ++ saccu = precip; ++ ++ /* asign output*/ ++ melt[0]=runoff/yts; ++ accu[0]=saccu/yts; ++ melt_star[0]=smelt_star/yts; ++ B=(saccu-runoff)/yts; ++ ++ return B; ++} +Index: ../trunk-jpl/src/c/shared/Elements/elements.h +=================================================================== +--- ../trunk-jpl/src/c/shared/Elements/elements.h (revision 23316) ++++ ../trunk-jpl/src/c/shared/Elements/elements.h (revision 23317) +@@ -23,6 +23,10 @@ + IssmDouble s0p, IssmDouble rlaps, IssmDouble rlapslgm, + IssmDouble TdiffTime,IssmDouble sealevTime,IssmDouble pddsnowfac,IssmDouble pddicefac, + IssmDouble rho_water, IssmDouble rho_ice); ++IssmDouble PddSurfaceMassBalanceSicopolis(IssmDouble* monthlytemperatures, IssmDouble* monthlyprec, ++ IssmDouble* melt, IssmDouble* accu, IssmDouble* melt_star, IssmDouble* t_ampl, IssmDouble* p_ampl, ++ IssmDouble yts, IssmDouble s, IssmDouble desfac,IssmDouble s0t, ++ IssmDouble s0p, IssmDouble rlaps, IssmDouble rho_water, IssmDouble rho_ice); + void ComputeDelta18oTemperaturePrecipitation(IssmDouble Delta18oSurfacePresent, IssmDouble Delta18oSurfaceLgm, IssmDouble Delta18oSurfaceTime, + IssmDouble Delta18oPresent, IssmDouble Delta18oLgm, IssmDouble Delta18oTime, + IssmDouble* PrecipitationsPresentday, +Index: ../trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h +=================================================================== +--- ../trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h (revision 23316) ++++ ../trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h (revision 23317) +@@ -15,6 +15,7 @@ + void MungsmtpParameterizationx(FemModel* femmodel); + void Delta18opdParameterizationx(FemModel* femmodel); + void PositiveDegreeDayx(FemModel* femmodel); ++void PositiveDegreeDaySicopolisx(FemModel* femmodel); + void SmbHenningx(FemModel* femmodel); + void SmbComponentsx(FemModel* femmodel); + void SmbMeltComponentsx(FemModel* femmodel); +Index: ../trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp +=================================================================== +--- ../trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp (revision 23316) ++++ ../trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp (revision 23317) +@@ -261,6 +261,17 @@ + xDelete(pdds); + xDelete(pds); + }/*}}}*/ ++void PositiveDegreeDaySicopolisx(FemModel* femmodel){/*{{{*/ ++ ++ bool isfirnwarming; ++ femmodel->parameters->FindParam(&isfirnwarming,SmbIssetpddfacEnum); ++ ++ for(int i=0;ielements->Size();i++){ ++ Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); ++ element->PositiveDegreeDaySicopolis(isfirnwarming); ++ } ++ ++}/*}}}*/ + void SmbHenningx(FemModel* femmodel){/*{{{*/ + + /*Intermediaries*/ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 23316) ++++ ../trunk-jpl/src/c/Makefile.am (revision 23317) +@@ -174,6 +174,7 @@ + ./shared/Elements/LliboutryDuval.cpp \ + ./shared/Elements/PrintArrays.cpp\ + ./shared/Elements/PddSurfaceMassBalance.cpp\ ++ ./shared/Elements/PddSurfaceMassBalanceSicopolis.cpp\ + ./shared/Elements/ComputeDelta18oTemperaturePrecipitation.cpp\ + ./shared/Elements/ComputeMungsmTemperaturePrecipitation.cpp\ + ./shared/Elements/ComputeD18OTemperaturePrecipitationFromPD.cpp\ +Index: ../trunk-jpl/src/c/cores/transient_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/transient_core.cpp (revision 23316) ++++ ../trunk-jpl/src/c/cores/transient_core.cpp (revision 23317) +@@ -370,12 +370,14 @@ + femmodel->parameters->FindParam(&isenthalpy,ThermalIsenthalpyEnum); + femmodel->parameters->FindParam(&smb_model,SmbEnum); + if(isenthalpy){ +- if(smb_model==SMBpddEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); +- if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); ++ if(smb_model==SMBpddEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); ++ if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); ++ if(smb_model==SMBpddSicopolisEnum) ResetBoundaryConditions(femmodel,EnthalpyAnalysisEnum); + } + else{ +- if(smb_model==SMBpddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); +- if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); ++ if(smb_model==SMBpddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); ++ if(smb_model==SMBd18opddEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); ++ if(smb_model==SMBpddSicopolisEnum) ResetBoundaryConditions(femmodel,ThermalAnalysisEnum); + } + } + thermal_core(femmodel); +Index: ../trunk-jpl/src/c/classes/Elements/Element.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.h (revision 23316) ++++ ../trunk-jpl/src/c/classes/Elements/Element.h (revision 23317) +@@ -144,6 +144,7 @@ + ElementMatrix* NewElementMatrixCoupling(int number_nodes,int approximation_enum=NoneApproximationEnum); + ElementVector* NewElementVector(int approximation_enum=NoneApproximationEnum); + void PositiveDegreeDay(IssmDouble* pdds,IssmDouble* pds,IssmDouble signorm,bool ismungsm,bool issetpddfac); ++ void PositiveDegreeDaySicopolis(bool isfirnwarming); + IssmDouble PureIceEnthalpy(IssmDouble pressure); + void ResultInterpolation(int* pinterpolation,int*nodesperelement,int* parray_size, int output_enum); + void ResultToPatch(IssmDouble* values,int nodesperelement,int output_enum); +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 23316) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 23317) +@@ -2560,6 +2560,171 @@ + + } + /*}}}*/ ++void Element::PositiveDegreeDaySicopolis(bool isfirnwarming){/*{{{*/ ++ ++ /* General FIXMEs: get Tmelting point, pddicefactor, pddsnowfactor, sigma from parameters/user input */ ++ ++ int numvertices = this->GetNumberOfVertices(); ++ ++ int i; ++ IssmDouble* smb=xNew(numvertices); // surface mass balance ++ IssmDouble* melt=xNew(numvertices); // melting comp. of surface mass balance ++ IssmDouble* accu=xNew(numvertices); // accuumulation comp. of surface mass balance ++ IssmDouble* melt_star=xNew(numvertices); ++ IssmDouble* monthlytemperatures=xNew(12*numvertices); ++ IssmDouble* monthlyprec=xNew(12*numvertices); ++ IssmDouble* yearlytemperatures=xNew(numvertices); memset(yearlytemperatures, 0., numvertices*sizeof(IssmDouble)); ++ IssmDouble* s=xNew(numvertices); // actual surface height ++ IssmDouble* s0p=xNew(numvertices); // reference elevation for precip. ++ IssmDouble* s0t=xNew(numvertices); // reference elevation for temperature ++ IssmDouble* smbcorr=xNew(numvertices); // surface mass balance correction; will be added after pdd call ++ IssmDouble* p_ampl=xNew(numvertices); // precip anomaly ++ IssmDouble* t_ampl=xNew(numvertices); // remperature anomaly ++ IssmDouble rho_water,rho_ice,desfac,rlaps; ++ IssmDouble inv_twelve=1./12.; //factor for monthly average ++ IssmDouble time,yts,time_yr; ++ ++ /*Get material parameters :*/ ++ rho_water=this->matpar->GetMaterialParameter(MaterialsRhoSeawaterEnum); ++ rho_ice=this->matpar->GetMaterialParameter(MaterialsRhoIceEnum); ++ ++ /*Get parameters for height corrections*/ ++ desfac=this->matpar->GetMaterialParameter(SmbDesfacEnum); ++ rlaps=this->matpar->GetMaterialParameter(SmbRlapsEnum); ++ ++ /*Recover monthly temperatures and precipitation*/ ++ Input* input=this->inputs->GetInput(SmbMonthlytemperaturesEnum); _assert_(input); ++ Input* input2=this->inputs->GetInput(SmbPrecipitationEnum); _assert_(input2); ++ /*Recover smb correction term */ ++ Input* input3=this->inputs->GetInput(SmbSmbCorrEnum); _assert_(input3); ++ ++ /* Get time */ ++ this->parameters->FindParam(&time,TimeEnum); ++ this->parameters->FindParam(&yts,ConstantsYtsEnum); ++ time_yr=floor(time/yts)*yts; ++ ++ /* Set parameters for finrnwarming */ ++ IssmDouble MU_0 = 9.7155; //Firn-warming correction, in (d*deg C)/(mm WE) ++ IssmDouble mu = MU_0*(1000.0*86400.0)*(rho_ice/rho_water); // (d*deg C)/(mm WE) --> (s*deg C)/(m IE) ++ ++ /*loop over vertices: */ ++ Gauss* gauss=this->NewGauss(); ++ for(int month=0;month<12;month++){ ++ for(int iv=0;ivGaussVertex(iv); ++ input->GetInputValue(&monthlytemperatures[iv*12+month],gauss,(month+1)/12.*yts); ++ monthlytemperatures[iv*12+month]=monthlytemperatures[iv*12+month]-273.15; // conversion from Kelvin to celcius for PDD module ++ input2->GetInputValue(&monthlyprec[iv*12+month],gauss,(month+1)/12.*yts); ++ monthlyprec[iv*12+month]=monthlyprec[iv*12+month]*yts; ++ } ++ } ++ ++ /*Recover info at the vertices: */ ++ GetInputListOnVertices(&s[0],SurfaceEnum); ++ GetInputListOnVertices(&s0p[0],SmbS0pEnum); ++ GetInputListOnVertices(&s0t[0],SmbS0tEnum); ++ GetInputListOnVertices(&smbcorr[0],SmbSmbCorrEnum); ++ GetInputListOnVertices(&t_ampl[0],SmbTemperaturesAnomalyEnum); ++ GetInputListOnVertices(&p_ampl[0],SmbPrecipitationsAnomalyEnum); ++ ++ /*measure the surface mass balance*/ ++ for (int iv = 0; iv=melt[iv]){ ++ yearlytemperatures[iv]= yearlytemperatures[iv]+mu*(melt_star[iv]-melt[iv]); ++ } ++ else{ ++ yearlytemperatures[iv]= yearlytemperatures[iv]; ++ } ++ } ++ if (yearlytemperatures[iv]>273.15) yearlytemperatures[iv]=273.15; ++ } ++ ++ switch(this->ObjectEnum()){ ++ case TriaEnum: ++ // this->inputs->AddInput(new TriaInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); ++ this->inputs->AddInput(new TriaInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); ++ this->inputs->AddInput(new TriaInput(SmbMassBalanceEnum,&smb[0],P1Enum)); ++ this->inputs->AddInput(new TriaInput(SmbAccumulationEnum,&accu[0],P1Enum)); ++ this->inputs->AddInput(new TriaInput(SmbMeltEnum,&melt[0],P1Enum)); ++ break; ++ case PentaEnum: ++ bool isthermal; ++ this->parameters->FindParam(&isthermal,TransientIsthermalEnum); ++ if(isthermal){ ++ bool isenthalpy; ++ this->parameters->FindParam(&isenthalpy,ThermalIsenthalpyEnum); ++ if(IsOnSurface()){ ++ /*Here, we want to change the BC of the thermal model, keep ++ * the temperatures as they are for the base of the penta and ++ * use yearlytemperatures for the top*/ ++ GetInputListOnVertices(&s[0],TemperatureEnum); ++ yearlytemperatures[0] = s[0]; ++ yearlytemperatures[1] = s[1]; ++ yearlytemperatures[2] = s[2]; ++ this->inputs->AddInput(new PentaInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); ++ if(isenthalpy){ ++ /*Convert that to enthalpy for the enthalpy model*/ ++ IssmDouble enthalpy[6]; ++ GetInputListOnVertices(&enthalpy[0],EnthalpyEnum); ++ ThermalToEnthalpy(&enthalpy[3],yearlytemperatures[3],0.,0.); ++ ThermalToEnthalpy(&enthalpy[4],yearlytemperatures[4],0.,0.); ++ ThermalToEnthalpy(&enthalpy[5],yearlytemperatures[5],0.,0.); ++ this->inputs->AddInput(new PentaInput(EnthalpyEnum,&enthalpy[0],P1Enum)); ++ } ++ } ++ } ++ this->inputs->AddInput(new PentaInput(SmbMassBalanceEnum,&smb[0],P1Enum)); ++ this->inputs->AddInput(new PentaInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); ++ this->inputs->AddInput(new PentaInput(SmbAccumulationEnum,&accu[0],P1Enum)); ++ this->inputs->AddInput(new PentaInput(SmbMeltEnum,&melt[0],P1Enum)); ++ this->InputExtrude(TemperaturePDDEnum,-1); ++ this->InputExtrude(SmbMassBalanceEnum,-1); ++ this->InputExtrude(SmbAccumulationEnum,-1); ++ this->InputExtrude(SmbMeltEnum,-1); ++ break; ++ case TetraEnum: ++ if(IsOnSurface()){ ++ GetInputListOnVertices(&s[0],TemperatureEnum); ++ yearlytemperatures[0] = s[0]; ++ yearlytemperatures[1] = s[1]; ++ yearlytemperatures[2] = s[2]; ++ this->inputs->AddInput(new TetraInput(TemperatureEnum,&yearlytemperatures[0],P1Enum)); ++ } ++ this->inputs->AddInput(new TetraInput(SmbMassBalanceEnum,&smb[0],P1Enum)); ++ this->inputs->AddInput(new TetraInput(TemperaturePDDEnum,&yearlytemperatures[0],P1Enum)); ++ this->InputExtrude(TemperaturePDDEnum,-1); ++ this->InputExtrude(SmbMassBalanceEnum,-1); ++ break; ++ default: _error_("Not implemented yet"); ++ } ++ ++ /*clean-up*/ ++ delete gauss; ++ xDelete(monthlytemperatures); ++ xDelete(monthlyprec); ++ xDelete(smb); ++ xDelete(melt); ++ xDelete(accu); ++ xDelete(yearlytemperatures); ++ xDelete(s); ++ xDelete(s0t); ++ xDelete(s0p); ++ xDelete(t_ampl); ++ xDelete(p_ampl); ++ xDelete(smbcorr); ++ xDelete(melt_star); ++} ++/*}}}*/ + IssmDouble Element::PureIceEnthalpy(IssmDouble pressure){/*{{{*/ + return this->matpar->PureIceEnthalpy(pressure); + }/*}}}*/ +Index: ../trunk-jpl/src/c/classes/Materials/Matpar.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Materials/Matpar.cpp (revision 23316) ++++ ../trunk-jpl/src/c/classes/Materials/Matpar.cpp (revision 23317) +@@ -106,6 +106,10 @@ + iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); + iomodel->FindConstant(&this->rlapslgm,"md.smb.rlapslgm"); + break; ++ case SMBpddSicopolisEnum: ++ iomodel->FindConstant(&this->desfac,"md.smb.desfac"); ++ iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); ++ break; + case SMBd18opddEnum: + iomodel->FindConstant(&this->desfac,"md.smb.desfac"); + iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); +@@ -210,6 +214,10 @@ + iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); + iomodel->FindConstant(&this->rlapslgm,"md.smb.rlapslgm"); + break; ++ case SMBpddSicopolisEnum: ++ iomodel->FindConstant(&this->desfac,"md.smb.desfac"); ++ iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); ++ break; + case SMBd18opddEnum: + iomodel->FindConstant(&this->desfac,"md.smb.desfac"); + iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); +Index: ../trunk-jpl/src/m/classes/SMBpddSicopolis.m +=================================================================== +--- ../trunk-jpl/src/m/classes/SMBpddSicopolis.m (nonexistent) ++++ ../trunk-jpl/src/m/classes/SMBpddSicopolis.m (revision 23317) +@@ -0,0 +1,133 @@ ++%SMBpddSicopolis Class definition ++% ++% Usage: ++% SMBpddSicopolis=SMBpddSicopolis(); ++ ++classdef SMBpddSicopolis ++ properties (SetAccess=public) ++ precipitation = NaN; ++ monthlytemperatures = NaN; ++ temperature_anomaly = NaN; ++ precipitation_anomaly = NaN; ++ smb_corr = NaN; ++ desfac = 0; ++ s0p = NaN; ++ s0t = NaN; ++ rlaps = 0; ++ isfirnwarming = 0; ++ requested_outputs = {}; ++ end ++ methods ++ function self = SMBpddSicopolis(varargin) % {{{ ++ switch nargin ++ case 0 ++ self=setdefaultparameters(self); ++ otherwise ++ error('constructor not supported'); ++ end ++ end % }}} ++ function self = extrude(self,md) % {{{ ++ self.precipitation=project3d(md,'vector',self.precipitation,'type','node'); ++ self.monthlytemperatures=project3d(md,'vector',self.monthlytemperatures,'type','node'); ++ self.temperature_anomaly=project3d(md,'vector',self.temperature_anomaly,'type','node'); ++ self.precipitation_anomaly=project3d(md,'vector',self.precipitation_anomaly,'type','node'); ++ self.smb_corr=project3d(md,'vector',self.smb_corr,'type','node'); ++ self.s0p=project3d(md,'vector',self.s0p,'type','node'); ++ self.s0t=project3d(md,'vector',self.s0t,'type','node'); ++ ++ end % }}} ++ function list = defaultoutputs(self,md) % {{{ ++ list = {''}; ++ end % }}} ++ function self = initialize(self,md) % {{{ ++ ++ if isnan(self.s0p), ++ self.s0p=zeros(md.mesh.numberofvertices,1); ++ disp(' no SMBpddSicopolis.s0p specified: values set as zero'); ++ end ++ if isnan(self.s0t), ++ self.s0t=zeros(md.mesh.numberofvertices,1); ++ disp(' no SMBpddSicopolis.s0t specified: values set as zero'); ++ end ++ if isnan(self.temperature_anomaly), ++ self.temperature_anomaly=zeros(md.mesh.numberofvertices,1); ++ disp(' no SMBpddSicopolis.temperature_anomaly specified: values set as zero'); ++ end ++ if isnan(self.precipitation_anomaly), ++ self.precipitation_anomaly=ones(md.mesh.numberofvertices,1); ++ disp(' no SMBpddSicopolis.precipitation_anomaly specified: values set as ones'); ++ end ++ if isnan(self.smb_corr), ++ self.smb_corr=zeros(md.mesh.numberofvertices,1); ++ disp(' no SMBpddSicopolis.smb_corr specified: values set as zero'); ++ end ++ ++ end % }}} ++ function self = setdefaultparameters(self) % {{{ ++ ++ self.isfirnwarming = 1; ++ self.desfac = -log(2.0)/1000; ++ self.rlaps = 7.4; ++ ++ end % }}} ++ function md = checkconsistency(self,md,solution,analyses) % {{{ ++ ++ if (strcmp(solution,'TransientSolution') & md.transient.issmb == 0), return; end ++ ++ if ismember('MasstransportAnalysis',analyses), ++ md = checkfield(md,'fieldname','smb.desfac','<=',1,'numel',1); ++ md = checkfield(md,'fieldname','smb.s0p','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1]); ++ md = checkfield(md,'fieldname','smb.s0t','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices 1]); ++ md = checkfield(md,'fieldname','smb.rlaps','>=',0,'numel',1); ++ md = checkfield(md,'fieldname','smb.monthlytemperatures','timeseries',1,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices+1 12]); ++ md = checkfield(md,'fieldname','smb.precipitation','timeseries',1,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices+1 12]); ++ end ++ md = checkfield(md,'fieldname','smb.requested_outputs','stringrow',1); ++ ++ end % }}} ++ function disp(self) % {{{ ++ disp(sprintf(' surface forcings parameters:')); ++ ++ disp(sprintf('\n SICOPOLIS PDD scheme (Calov & Greve, 2005) :')); ++ fielddisplay(self,'monthlytemperatures','monthly surface temperatures [K]'); ++ fielddisplay(self,'precipitation','monthly surface precipitation [m/yr water eq]'); ++ fielddisplay(self,'temperature_anomaly','anomaly to monthly reference temperature (additive; [K])'); ++ fielddisplay(self,'precipitation_anomaly','anomaly to monthly precipitation (multiplicative, e.g. q=q0*exp(0.070458*DeltaT) after Huybrechts (2002)); [no unit])'); ++ fielddisplay(self,'smb_corr','correction of smb after PDD call [m/a]'); ++ fielddisplay(self,'s0p','should be set to elevation from precip source (between 0 and a few 1000s m, default is 0) [m]'); ++ fielddisplay(self,'s0t','should be set to elevation from temperature source (between 0 and a few 1000s m, default is 0) [m]'); ++ fielddisplay(self,'rlaps','present day lapse rate (default is 7.4 degree/km)'); ++ fielddisplay(self,'desfac','desertification elevation factor (default is -log(2.0)/1000)'); ++ fielddisplay(self,'isfirnwarming','is firnwarming (Reeh 1991) activated (0 or 1, default is 1)'); ++ fielddisplay(self,'requested_outputs','additional outputs requested (TemperaturePDD, SmbAccumulation, SmbMelt)'); ++ end % }}} ++ function marshall(self,prefix,md,fid) % {{{ ++ ++ yts=md.constants.yts; ++ ++ WriteData(fid,prefix,'name','md.smb.model','data',10,'format','Integer'); ++ ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','isfirnwarming','format','Boolean'); ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','desfac','format','Double'); ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0p','format','DoubleMat','mattype',1); ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0t','format','DoubleMat','mattype',1); ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','rlaps','format','Double'); ++ ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','monthlytemperatures','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','temperature_anomaly','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitation_anomaly','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','smb_corr','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ ++ %process requested outputs ++ outputs = self.requested_outputs; ++ pos = find(ismember(outputs,'default')); ++ if ~isempty(pos), ++ outputs(pos) = []; %remove 'default' from outputs ++ outputs = [outputs defaultoutputs(self,md)]; %add defaults ++ end ++ WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray'); ++ ++ end % }}} ++ end ++end Index: /issm/oecreview/Archive/23185-23389/ISSM-23317-23318.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23317-23318.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23317-23318.diff (revision 23390) @@ -0,0 +1,334 @@ +Index: ../trunk-jpl/src/c/cores/controlvalidation_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controlvalidation_core.cpp (revision 23317) ++++ ../trunk-jpl/src/c/cores/controlvalidation_core.cpp (revision 23318) +@@ -8,41 +8,252 @@ + #include "../shared/shared.h" + #include "../modules/modules.h" + ++#ifdef _HAVE_CODIPACK_ ++extern CoDi_global codi_global; ++#include // for output of the CoDiPack tape ++#endif ++ ++#ifdef _HAVE_AD_ ++void simul_starttrace2(FemModel* femmodel){/*{{{*/ ++ ++ #if defined(_HAVE_ADOLC_) ++ /*Retrive ADOLC parameters*/ ++ IssmDouble gcTriggerRatio; ++ IssmDouble gcTriggerMaxSize; ++ IssmDouble obufsize; ++ IssmDouble lbufsize; ++ IssmDouble cbufsize; ++ IssmDouble tbufsize; ++ femmodel->parameters->FindParam(&gcTriggerRatio,AutodiffGcTriggerRatioEnum); ++ femmodel->parameters->FindParam(&gcTriggerMaxSize,AutodiffGcTriggerMaxSizeEnum); ++ femmodel->parameters->FindParam(&obufsize,AutodiffObufsizeEnum); ++ femmodel->parameters->FindParam(&lbufsize,AutodiffLbufsizeEnum); ++ femmodel->parameters->FindParam(&cbufsize,AutodiffCbufsizeEnum); ++ femmodel->parameters->FindParam(&tbufsize,AutodiffTbufsizeEnum); ++ ++ /*Set garbage collection parameters: */ ++ setStoreManagerControl(reCast(gcTriggerRatio),reCast(gcTriggerMaxSize)); ++ ++ /*Start trace: */ ++ int skipFileDeletion=1; ++ int keepTaylors=1; ++ int my_rank=IssmComm::GetRank(); ++ trace_on(my_rank,keepTaylors,reCast(obufsize),reCast(lbufsize),reCast(cbufsize),reCast(tbufsize),skipFileDeletion); ++ ++ #elif defined(_HAVE_CODIPACK_) ++ ++ //fprintf(stderr, "*** Codipack IoModel::StartTrace\n"); ++ /* ++ * FIXME codi ++ * - ADOL-C variant uses fine grained tracing with various arguments ++ * - ADOL-C variant sets a garbage collection parameter for its tape ++ * -> These parameters are not read for the CoDiPack ISSM version! ++ */ ++ auto& tape_codi = IssmDouble::getGlobalTape(); ++ tape_codi.setActive(); ++ #if _AD_TAPE_ALLOC_ ++ //alloc_profiler.Tag(StartInit, true); ++ IssmDouble x_t(1.0), y_t(1.0); ++ tape_codi.registerInput(y_t); ++ int codi_allocn = 0; ++ femmodel->parameters->FindParam(&codi_allocn,AutodiffTapeAllocEnum); ++ for(int i = 0;i < codi_allocn;++i) { ++ x_t = y_t * y_t; ++ } ++ /* ++ std::stringstream out_s; ++ IssmDouble::getGlobalTape().printStatistics(out_s); ++ _printf0_("StartTrace::Tape Statistics : TapeAlloc count=[" << codi_allocn << "]\n" << out_s.str()); ++ */ ++ tape_codi.reset(); ++ //alloc_profiler.Tag(FinishInit, true); ++ #else ++ tape_codi.reset(); ++ #endif ++ ++ #else ++ _error_("not implemented"); ++ #endif ++}/*}}}*/ ++void simul_stoptrace2(){/*{{{*/ ++ ++ #if defined(_HAVE_ADOLC_) ++ trace_off(); ++ if(VerboseAutodiff()){ /*{{{*/ ++ ++ #ifdef _HAVE_ADOLC_ ++ int my_rank=IssmComm::GetRank(); ++ size_t tape_stats[15]; ++ tapestats(my_rank,tape_stats); //reading of tape statistics ++ int commSize=IssmComm::GetSize(); ++ int *sstats=new int[7]; ++ sstats[0]=tape_stats[NUM_OPERATIONS]; ++ sstats[1]=tape_stats[OP_FILE_ACCESS]; ++ sstats[2]=tape_stats[NUM_LOCATIONS]; ++ sstats[3]=tape_stats[LOC_FILE_ACCESS]; ++ sstats[4]=tape_stats[NUM_VALUES]; ++ sstats[5]=tape_stats[VAL_FILE_ACCESS]; ++ sstats[6]=tape_stats[TAY_STACK_SIZE]; ++ int *rstats=NULL; ++ if (my_rank==0) rstats=new int[commSize*7]; ++ ISSM_MPI_Gather(sstats,7,ISSM_MPI_INT,rstats,7,ISSM_MPI_INT,0,IssmComm::GetComm()); ++ if (my_rank==0) { ++ int offset=50; ++ int rOffset=(commSize/10)+1; ++ _printf_(" ADOLC statistics: \n"); ++ _printf_(" "<file":"") << "\n"); ++ _printf_(" locations: entry size " << sizeof(locint) << " Bytes\n"); ++ _printf_(" "<file":"") << "\n"); ++ _printf_(" constant values: entry size " << sizeof(double) << " Bytes\n"); ++ _printf_(" "<file":"") << "\n"); ++ _printf_(" Taylor stack: entry size " << sizeof(revreal) << " Bytes\n"); ++ _printf_(" "<tape_stats[TAY_BUFFER_SIZE]?" ->file":"") << "\n"); ++ delete []rstats; ++ } ++ delete [] sstats; ++ #endif ++ ++ #ifdef _HAVE_CODIPACK_ ++ #ifdef _AD_TAPE_ALLOC_ ++ //_printf_("Allocation time P(" << my_rank << "): " << alloc_profiler.DeltaTime(StartInit, FinishInit) << "\n"); ++ #endif ++ std::stringstream out_s; ++ IssmDouble::getGlobalTape().printStatistics(out_s); ++ _printf0_("CoDiPack Profiling::Tape Statistics :\n" << out_s.str()); ++ #endif ++ } /*}}}*/ ++ ++ #elif defined(_HAVE_CODIPACK_) ++ auto& tape_codi = IssmDouble::getGlobalTape(); ++ tape_codi.setPassive(); ++ if(VerboseAutodiff()){ ++ int my_rank=IssmComm::GetRank(); ++ if(my_rank == 0) { ++ // FIXME codi "just because" for now ++ tape_codi.printStatistics(std::cout); ++ codi_global.print(std::cout); ++ } ++ } ++ #else ++ _error_("not implemented"); ++ #endif ++}/*}}}*/ ++#endif ++ + void controlvalidation_core(FemModel* femmodel){ + + int solution_type,n; + int num_responses; +- IssmDouble j0,j,yts; ++ IssmDouble j0,j; + IssmDouble Ialpha,exponent,alpha; + IssmDouble* scaling_factors = NULL; + IssmDouble* jlist = NULL; +- IssmDouble *G = NULL; +- IssmDouble *X = NULL; +- IssmDouble *X0= NULL; ++ int my_rank=IssmComm::GetRank(); + +- /*Solution and Adjoint core pointer*/ +- void (*solutioncore)(FemModel*) = NULL; +- void (*adjointcore)(FemModel*) = NULL; +- + /*Recover parameters used throughout the solution*/ + femmodel->parameters->FindParam(&solution_type,SolutionTypeEnum); + femmodel->parameters->SetParam(false,SaveResultsEnum); + femmodel->parameters->FindParam(&num_responses,InversionNumCostFunctionsEnum); +- femmodel->parameters->FindParam(&yts,ConstantsYtsEnum); + femmodel->parameters->FindParam(&scaling_factors,NULL,InversionControlScalingFactorsEnum); + + /*Get initial guess*/ +- Vector *Xpetsc = NULL; +- GetVectorFromControlInputsx(&Xpetsc,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); +- Xpetsc->GetSize(&n); +- X0 = Xpetsc->ToMPISerial(); +- delete Xpetsc; ++ IssmPDouble* X0 = NULL; ++ GetPassiveVectorFromControlInputsx(&X0,&n,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,"value"); + +- /*Allocate current vector*/ +- X = xNew(n); ++ /*Allocate vectors*/ ++ IssmDouble* X = xNew(n); ++ IssmPDouble* G = xNew(n); + + /*out of solution_type, figure out solution core and adjoint function pointer*/ ++ void (*solutioncore)(FemModel*)=NULL; + CorePointerFromSolutionEnum(&solutioncore,femmodel->parameters,solution_type); ++ ++ #if defined(_HAVE_ADOLC_) ++ /*{{{*/ ++ IssmDouble* aX=xNew(n); ++ if(my_rank==0){ ++ for(int i=0;i(n); ++ auto& tape_codi = IssmDouble::getGlobalTape(); ++ codi_global.input_indices.clear(); ++ if(my_rank==0){ ++ for (int i=0;iparameters->FindParam(&num_dependents,AutodiffNumDependentsEnum); ++ femmodel->parameters->FindParam(&dependent_objects,AutodiffDependentObjectsEnum); ++ ++ /*Go through our dependent variables, and compute the response:*/ ++ dependents=xNew(num_dependents); ++ codi_global.output_indices.clear(); ++ for(int i=0;iSize();i++){ ++ DependentObject* dep=(DependentObject*)dependent_objects->GetObjectByOffset(i); ++ if(solution_type==TransientSolutionEnum){ ++ output_value = dep->GetValue(); ++ } ++ else{ ++ dep->Responsex(&output_value,femmodel); ++ } ++ _printf0_("=== output ="<0.); ++ simul_stoptrace2(); ++ /*initialize direction index in the weights vector: */ ++ if(my_rank==0){ ++ tape_codi.setGradient(codi_global.output_indices[0],1.0); ++ } ++ tape_codi.evaluate(); ++ ++ /*Get gradient for this dependent */ ++ auto in_size = codi_global.input_indices.size(); ++ for(size_t i = 0; i < in_size; ++i) { ++ G[i] = tape_codi.getGradient(codi_global.input_indices[i]); ++ } ++ #else ++ /*{{{*/ ++ void (*adjointcore)(FemModel*) = NULL; + AdjointCorePointerFromSolutionEnum(&adjointcore,solution_type); + + if(VerboseControl()) _printf0_(" Compute Initial solution\n"); +@@ -58,6 +269,8 @@ + if(VerboseControl()) _printf0_(" Compute Gradient\n"); + Gradjx(&G,NULL,femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + for(int i=0;iSize();i++){ ++ DependentObject* dep=(DependentObject*)dependent_objects->GetObjectByOffset(i); ++ if(solution_type==TransientSolutionEnum){ ++ output_value = dep->GetValue(); ++ } ++ else{ ++ dep->Responsex(&output_value,femmodel); ++ } ++ j+=output_value; ++ } ++ #else + femmodel->CostFunctionx(&j,NULL,NULL); ++ #endif + + IssmDouble Den = 0.; + for(int i=0;i0.); + + _printf0_(" " << setw(11) << setprecision (5)<(output[i]); + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,JEnum,J_passive,num,2,0,0)); + xDelete(J_passive); ++ IssmDouble* aG=xNew(n); ++ for(int i=0;ielements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,aG); ++ xDelete(aG); + #else + femmodel->results->AddObject(new GenericExternalResult(femmodel->results->Size()+1,JEnum,output,num,2,0,0)); ++ ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,G); + #endif +- ControlInputSetGradientx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters,G); + femmodel->OutputControlsx(&femmodel->results); + + /*Clean up and return*/ + xDelete(output); +- xDelete(G); ++ xDelete(G); + xDelete(X); +- xDelete(X0); ++ xDelete(X0); + xDelete(scaling_factors); + } Index: /issm/oecreview/Archive/23185-23389/ISSM-23318-23319.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23318-23319.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23318-23319.diff (revision 23390) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/src/c/classes/IoModel.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/IoModel.cpp (revision 23318) ++++ ../trunk-jpl/src/c/classes/IoModel.cpp (revision 23319) +@@ -2510,7 +2510,9 @@ + + /*recover my_rank:*/ + my_rank=IssmComm::GetRank(); +- _assert_(strncmp(data_name,mddot,3)==0); ++ if(strncmp(data_name,mddot,3)!=0){ ++ _error_("Cannot fetch \""<(n); + if(my_rank==0){ +- for(int i=0;iparameters->FindParam(&isfirnwarming,SmbIssetpddfacEnum); ++ femmodel->parameters->FindParam(&isfirnwarming,SmbIsfirnwarmingEnum); + + for(int i=0;ielements->Size();i++){ + Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); +Index: ../trunk-jpl/src/c/analyses/SmbAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/SmbAnalysis.cpp (revision 23327) ++++ ../trunk-jpl/src/c/analyses/SmbAnalysis.cpp (revision 23328) +@@ -228,7 +228,7 @@ + } + break; + case SMBpddSicopolisEnum: +- parameters->AddObject(iomodel->CopyConstantObject("md.smb.isfirnwarming",SmbIssetpddfacEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.smb.isfirnwarming",SmbIsfirnwarmingEnum)); + break; + case SMBd18opddEnum: + parameters->AddObject(iomodel->CopyConstantObject("md.smb.ismungsm",SmbIsmungsmEnum)); Index: /issm/oecreview/Archive/23185-23389/ISSM-23328-23329.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23328-23329.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23328-23329.diff (revision 23390) @@ -0,0 +1,199 @@ +Index: ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 23328) ++++ ../trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp (revision 23329) +@@ -298,6 +298,7 @@ + case SmbIsdelta18oEnum : return "SmbIsdelta18o"; + case SmbIsdensificationEnum : return "SmbIsdensification"; + case SmbIsgraingrowthEnum : return "SmbIsgraingrowth"; ++ case SmbIsfirnwarmingEnum : return "SmbIsfirnwarming"; + case SmbIsmeltEnum : return "SmbIsmelt"; + case SmbIsmungsmEnum : return "SmbIsmungsm"; + case SmbIssetpddfacEnum : return "SmbIssetpddfac"; +@@ -583,6 +584,7 @@ + case SmbPddfacSnowEnum : return "SmbPddfacSnow"; + case SmbPEnum : return "SmbP"; + case SmbPrecipitationEnum : return "SmbPrecipitation"; ++ case SmbPrecipitationsAnomalyEnum : return "SmbPrecipitationsAnomaly"; + case SmbPrecipitationsLgmEnum : return "SmbPrecipitationsLgm"; + case SmbPrecipitationsPresentdayEnum : return "SmbPrecipitationsPresentday"; + case SmbPrecipitationsReconstructedEnum : return "SmbPrecipitationsReconstructed"; +@@ -594,7 +596,9 @@ + case SmbS0tEnum : return "SmbS0t"; + case SmbSizeiniEnum : return "SmbSizeini"; + case SmbSmbrefEnum : return "SmbSmbref"; ++ case SmbSmbCorrEnum : return "SmbSmbCorr"; + case SmbTaEnum : return "SmbTa"; ++ case SmbTemperaturesAnomalyEnum : return "SmbTemperaturesAnomaly"; + case SmbTemperaturesLgmEnum : return "SmbTemperaturesLgm"; + case SmbTemperaturesPresentdayEnum : return "SmbTemperaturesPresentday"; + case SmbTemperaturesReconstructedEnum : return "SmbTemperaturesReconstructed"; +@@ -1099,6 +1103,7 @@ + case SmbMAddEnum : return "SmbMAdd"; + case SMBmeltcomponentsEnum : return "SMBmeltcomponents"; + case SMBpddEnum : return "SMBpdd"; ++ case SMBpddSicopolisEnum : return "SMBpddSicopolis"; + case SmbRlapsEnum : return "SmbRlaps"; + case SmbRlapslgmEnum : return "SmbRlapslgm"; + case SmbSolutionEnum : return "SmbSolution"; +Index: ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp +=================================================================== +--- ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 23328) ++++ ../trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp (revision 23329) +@@ -304,6 +304,7 @@ + else if (strcmp(name,"SmbIsdelta18o")==0) return SmbIsdelta18oEnum; + else if (strcmp(name,"SmbIsdensification")==0) return SmbIsdensificationEnum; + else if (strcmp(name,"SmbIsgraingrowth")==0) return SmbIsgraingrowthEnum; ++ else if (strcmp(name,"SmbIsfirnwarming")==0) return SmbIsfirnwarmingEnum; + else if (strcmp(name,"SmbIsmelt")==0) return SmbIsmeltEnum; + else if (strcmp(name,"SmbIsmungsm")==0) return SmbIsmungsmEnum; + else if (strcmp(name,"SmbIssetpddfac")==0) return SmbIssetpddfacEnum; +@@ -381,11 +382,11 @@ + else if (strcmp(name,"TransientIsthermal")==0) return TransientIsthermalEnum; + else if (strcmp(name,"TransientNumRequestedOutputs")==0) return TransientNumRequestedOutputsEnum; + else if (strcmp(name,"TransientRequestedOutputs")==0) return TransientRequestedOutputsEnum; +- else if (strcmp(name,"Velocity")==0) return VelocityEnum; + else stage=4; + } + if(stage==4){ +- if (strcmp(name,"WorldComm")==0) return WorldCommEnum; ++ if (strcmp(name,"Velocity")==0) return VelocityEnum; ++ else if (strcmp(name,"WorldComm")==0) return WorldCommEnum; + else if (strcmp(name,"ParametersEND")==0) return ParametersENDEnum; + else if (strcmp(name,"InputsSTART")==0) return InputsSTARTEnum; + else if (strcmp(name,"Adjoint")==0) return AdjointEnum; +@@ -504,11 +505,11 @@ + else if (strcmp(name,"InversionThicknessObs")==0) return InversionThicknessObsEnum; + else if (strcmp(name,"InversionVelObs")==0) return InversionVelObsEnum; + else if (strcmp(name,"InversionVxObs")==0) return InversionVxObsEnum; +- else if (strcmp(name,"InversionVyObs")==0) return InversionVyObsEnum; + else stage=5; + } + if(stage==5){ +- if (strcmp(name,"LevelsetfunctionSlopeX")==0) return LevelsetfunctionSlopeXEnum; ++ if (strcmp(name,"InversionVyObs")==0) return InversionVyObsEnum; ++ else if (strcmp(name,"LevelsetfunctionSlopeX")==0) return LevelsetfunctionSlopeXEnum; + else if (strcmp(name,"LevelsetfunctionSlopeY")==0) return LevelsetfunctionSlopeYEnum; + else if (strcmp(name,"LoadingforceX")==0) return LoadingforceXEnum; + else if (strcmp(name,"LoadingforceY")==0) return LoadingforceYEnum; +@@ -595,6 +596,7 @@ + else if (strcmp(name,"SmbPddfacSnow")==0) return SmbPddfacSnowEnum; + else if (strcmp(name,"SmbP")==0) return SmbPEnum; + else if (strcmp(name,"SmbPrecipitation")==0) return SmbPrecipitationEnum; ++ else if (strcmp(name,"SmbPrecipitationsAnomaly")==0) return SmbPrecipitationsAnomalyEnum; + else if (strcmp(name,"SmbPrecipitationsLgm")==0) return SmbPrecipitationsLgmEnum; + else if (strcmp(name,"SmbPrecipitationsPresentday")==0) return SmbPrecipitationsPresentdayEnum; + else if (strcmp(name,"SmbPrecipitationsReconstructed")==0) return SmbPrecipitationsReconstructedEnum; +@@ -606,7 +608,9 @@ + else if (strcmp(name,"SmbS0t")==0) return SmbS0tEnum; + else if (strcmp(name,"SmbSizeini")==0) return SmbSizeiniEnum; + else if (strcmp(name,"SmbSmbref")==0) return SmbSmbrefEnum; ++ else if (strcmp(name,"SmbSmbCorr")==0) return SmbSmbCorrEnum; + else if (strcmp(name,"SmbTa")==0) return SmbTaEnum; ++ else if (strcmp(name,"SmbTemperaturesAnomaly")==0) return SmbTemperaturesAnomalyEnum; + else if (strcmp(name,"SmbTemperaturesLgm")==0) return SmbTemperaturesLgmEnum; + else if (strcmp(name,"SmbTemperaturesPresentday")==0) return SmbTemperaturesPresentdayEnum; + else if (strcmp(name,"SmbTemperaturesReconstructed")==0) return SmbTemperaturesReconstructedEnum; +@@ -624,14 +628,14 @@ + else if (strcmp(name,"SmbZTop")==0) return SmbZTopEnum; + else if (strcmp(name,"SmbZY")==0) return SmbZYEnum; + else if (strcmp(name,"StrainRateeffective")==0) return StrainRateeffectiveEnum; +- else if (strcmp(name,"StrainRateparallel")==0) return StrainRateparallelEnum; ++ else stage=6; ++ } ++ if(stage==6){ ++ if (strcmp(name,"StrainRateparallel")==0) return StrainRateparallelEnum; + else if (strcmp(name,"StrainRateperpendicular")==0) return StrainRateperpendicularEnum; + else if (strcmp(name,"StrainRatexx")==0) return StrainRatexxEnum; + else if (strcmp(name,"StrainRatexy")==0) return StrainRatexyEnum; +- else stage=6; +- } +- if(stage==6){ +- if (strcmp(name,"StrainRatexz")==0) return StrainRatexzEnum; ++ else if (strcmp(name,"StrainRatexz")==0) return StrainRatexzEnum; + else if (strcmp(name,"StrainRateyy")==0) return StrainRateyyEnum; + else if (strcmp(name,"StrainRateyz")==0) return StrainRateyzEnum; + else if (strcmp(name,"StrainRatezz")==0) return StrainRatezzEnum; +@@ -747,14 +751,14 @@ + else if (strcmp(name,"Dense")==0) return DenseEnum; + else if (strcmp(name,"DependentObject")==0) return DependentObjectEnum; + else if (strcmp(name,"DepthAverageAnalysis")==0) return DepthAverageAnalysisEnum; +- else if (strcmp(name,"DeviatoricStresseffective")==0) return DeviatoricStresseffectiveEnum; ++ else stage=7; ++ } ++ if(stage==7){ ++ if (strcmp(name,"DeviatoricStresseffective")==0) return DeviatoricStresseffectiveEnum; + else if (strcmp(name,"DeviatoricStressErrorEstimator")==0) return DeviatoricStressErrorEstimatorEnum; + else if (strcmp(name,"Divergence")==0) return DivergenceEnum; + else if (strcmp(name,"Domain3Dsurface")==0) return Domain3DsurfaceEnum; +- else stage=7; +- } +- if(stage==7){ +- if (strcmp(name,"DoubleArrayInput")==0) return DoubleArrayInputEnum; ++ else if (strcmp(name,"DoubleArrayInput")==0) return DoubleArrayInputEnum; + else if (strcmp(name,"DoubleExternalResult")==0) return DoubleExternalResultEnum; + else if (strcmp(name,"DoubleInput")==0) return DoubleInputEnum; + else if (strcmp(name,"DoubleMatArrayParam")==0) return DoubleMatArrayParamEnum; +@@ -870,14 +874,14 @@ + else if (strcmp(name,"SpatialLinearFloatingMeltRate")==0) return SpatialLinearFloatingMeltRateEnum; + else if (strcmp(name,"LliboutryDuval")==0) return LliboutryDuvalEnum; + else if (strcmp(name,"Loads")==0) return LoadsEnum; +- else if (strcmp(name,"LoveAnalysis")==0) return LoveAnalysisEnum; ++ else stage=8; ++ } ++ if(stage==8){ ++ if (strcmp(name,"LoveAnalysis")==0) return LoveAnalysisEnum; + else if (strcmp(name,"LoveHi")==0) return LoveHiEnum; + else if (strcmp(name,"LoveHr")==0) return LoveHrEnum; + else if (strcmp(name,"LoveKernelsImag")==0) return LoveKernelsImagEnum; +- else stage=8; +- } +- if(stage==8){ +- if (strcmp(name,"LoveKernelsReal")==0) return LoveKernelsRealEnum; ++ else if (strcmp(name,"LoveKernelsReal")==0) return LoveKernelsRealEnum; + else if (strcmp(name,"LoveKi")==0) return LoveKiEnum; + else if (strcmp(name,"LoveKr")==0) return LoveKrEnum; + else if (strcmp(name,"LoveLi")==0) return LoveLiEnum; +@@ -993,14 +997,14 @@ + else if (strcmp(name,"Outputdefinition41")==0) return Outputdefinition41Enum; + else if (strcmp(name,"Outputdefinition42")==0) return Outputdefinition42Enum; + else if (strcmp(name,"Outputdefinition43")==0) return Outputdefinition43Enum; +- else if (strcmp(name,"Outputdefinition44")==0) return Outputdefinition44Enum; ++ else stage=9; ++ } ++ if(stage==9){ ++ if (strcmp(name,"Outputdefinition44")==0) return Outputdefinition44Enum; + else if (strcmp(name,"Outputdefinition45")==0) return Outputdefinition45Enum; + else if (strcmp(name,"Outputdefinition46")==0) return Outputdefinition46Enum; + else if (strcmp(name,"Outputdefinition47")==0) return Outputdefinition47Enum; +- else stage=9; +- } +- if(stage==9){ +- if (strcmp(name,"Outputdefinition48")==0) return Outputdefinition48Enum; ++ else if (strcmp(name,"Outputdefinition48")==0) return Outputdefinition48Enum; + else if (strcmp(name,"Outputdefinition49")==0) return Outputdefinition49Enum; + else if (strcmp(name,"Outputdefinition4")==0) return Outputdefinition4Enum; + else if (strcmp(name,"Outputdefinition50")==0) return Outputdefinition50Enum; +@@ -1116,16 +1120,17 @@ + else if (strcmp(name,"SmbFAC")==0) return SmbFACEnum; + else if (strcmp(name,"SMBforcing")==0) return SMBforcingEnum; + else if (strcmp(name,"SMBgcm")==0) return SMBgcmEnum; +- else if (strcmp(name,"SMBgemb")==0) return SMBgembEnum; ++ else stage=10; ++ } ++ if(stage==10){ ++ if (strcmp(name,"SMBgemb")==0) return SMBgembEnum; + else if (strcmp(name,"SMBgradientsela")==0) return SMBgradientselaEnum; + else if (strcmp(name,"SMBgradients")==0) return SMBgradientsEnum; + else if (strcmp(name,"SMBhenning")==0) return SMBhenningEnum; +- else stage=10; +- } +- if(stage==10){ +- if (strcmp(name,"SmbMAdd")==0) return SmbMAddEnum; ++ else if (strcmp(name,"SmbMAdd")==0) return SmbMAddEnum; + else if (strcmp(name,"SMBmeltcomponents")==0) return SMBmeltcomponentsEnum; + else if (strcmp(name,"SMBpdd")==0) return SMBpddEnum; ++ else if (strcmp(name,"SMBpddSicopolis")==0) return SMBpddSicopolisEnum; + else if (strcmp(name,"SmbRlaps")==0) return SmbRlapsEnum; + else if (strcmp(name,"SmbRlapslgm")==0) return SmbRlapslgmEnum; + else if (strcmp(name,"SmbSolution")==0) return SmbSolutionEnum; Index: /issm/oecreview/Archive/23185-23389/ISSM-23329-23330.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23329-23330.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23329-23330.diff (revision 23390) @@ -0,0 +1,60 @@ +Index: ../trunk-jpl/jenkins/linux64_caladan_ad +=================================================================== +--- ../trunk-jpl/jenkins/linux64_caladan_ad (revision 23329) ++++ ../trunk-jpl/jenkins/linux64_caladan_ad (revision 23330) +@@ -31,7 +31,6 @@ + cmake install.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh +- metis install-5.0.1-linux64.sh + triangle install-linux64.sh + gsl install-linux64.sh + adolc install.sh +Index: ../trunk-jpl/jenkins/linux64_caladan_ampi +=================================================================== +--- ../trunk-jpl/jenkins/linux64_caladan_ampi (revision 23329) ++++ ../trunk-jpl/jenkins/linux64_caladan_ampi (revision 23330) +@@ -40,7 +40,6 @@ + cmake install.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh +- metis install-5.0.1-linux64.sh + triangle install-linux64.sh + gsl install-linux64.sh + adjoinablempi install.sh +Index: ../trunk-jpl/jenkins/linux64_ross_ad +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_ad (revision 23329) ++++ ../trunk-jpl/jenkins/linux64_ross_ad (revision 23330) +@@ -36,7 +36,6 @@ + cmake install.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh +- metis install-5.0.1-linux64.sh + triangle install-linux64.sh + gsl install-linux64.sh + adolc install.sh +Index: ../trunk-jpl/jenkins/linux64_ross_ampi +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_ampi (revision 23329) ++++ ../trunk-jpl/jenkins/linux64_ross_ampi (revision 23330) +@@ -43,7 +43,6 @@ + cmake install.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh +- metis install-5.0.1-linux64.sh + triangle install-linux64.sh + gsl install-linux64.sh + adjoinablempi install.sh +Index: ../trunk-jpl/jenkins/linux64_ross_codi +=================================================================== +--- ../trunk-jpl/jenkins/linux64_ross_codi (revision 23329) ++++ ../trunk-jpl/jenkins/linux64_ross_codi (revision 23330) +@@ -44,7 +44,6 @@ + cmake install.sh + mpich install-3.2-linux64.sh + petsc install-3.7-linux64.sh +- metis install-5.0.1-linux64.sh + triangle install-linux64.sh + gsl install-linux64.sh + m1qn3 install.sh Index: /issm/oecreview/Archive/23185-23389/ISSM-23330-23331.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23330-23331.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23330-23331.diff (revision 23390) @@ -0,0 +1,83 @@ +Index: ../trunk-jpl/src/m/classes/cfdragcoeffabsgrad.m +=================================================================== +--- ../trunk-jpl/src/m/classes/cfdragcoeffabsgrad.m (nonexistent) ++++ ../trunk-jpl/src/m/classes/cfdragcoeffabsgrad.m (revision 23331) +@@ -0,0 +1,78 @@ ++%CFDRAGCOEFFABSGRAD class definition ++% ++% Usage: ++% cfdragcoeffabsgrad=cfdragcoeffabsgrad(); ++% cfdragcoeffabsgrad=cfdragcoeffabsgrad('name','SurfaceAltimetry',... ++% 'definitionstring','Outputdefinition1',... ++% 'model_string','Surface',... ++% 'weights',ones(md.mesh.numberofvertices,1),... ++% 'weights_string','WeightsSurfaceObservations'); ++% ++% ++ ++classdef cfdragcoeffabsgrad ++ properties (SetAccess=public) ++ %cfdragcoeffabsgrad ++ name = ''; ++ definitionstring = ''; %string that identifies this output definition uniquely, from 'Outputdefinition[1-100]' ++ weights = NaN; %weight coefficients for every vertex ++ weights_string = ''; %string to identify this particular set of weights ++ cumulated = NaN; %do we cumulate cfdragcoeffabsgrad through time? ++ end ++ ++ methods ++ function self = extrude(self,md) % {{{ ++ if ~isnan(self.weights) ++ self.weights=project3d(md,'vector',self.weights,'type','node'); ++ end ++ end % }}} ++ function self = cfdragcoeffabsgrad(varargin) % {{{ ++ if nargin==0, ++ self=setdefaultparameters(self); ++ else ++ %use provided options to change fields ++ options=pairoptions(varargin{:}); ++ ++ %get name ++ self.name=getfieldvalue(options,'name',''); ++ self.definitionstring=getfieldvalue(options,'definitionstring'); ++ self.weights=getfieldvalue(options,'weights',NaN); ++ self.weights_string=getfieldvalue(options,'weights_string',''); ++ ++ end ++ end % }}} ++ function self = setdefaultparameters(self) % {{{ ++ end % }}} ++ function md = checkconsistency(self,md,solution,analyses) % {{{ ++ ++ if ~ischar(self.name), ++ error('cfdragcoeffabsgrad error message: ''name'' field should be a string!'); ++ end ++ OutputdefinitionStringArray={}; ++ for i=1:100 ++ OutputdefinitionStringArray{i}=strcat('Outputdefinition',num2str(i)); ++ end ++ md = checkfield(md,'fieldname','self.definitionstring','field',self.definitionstring,'values',OutputdefinitionStringArray); ++ ++ md = checkfield(md,'fieldname','self.weights','field',self.weights,'timeseries',1,'NaN',1,'Inf',1); ++ ++ end % }}} ++ function md = disp(self) % {{{ ++ ++ disp(sprintf(' TimeMisfit:\n')); ++ ++ fielddisplay(self,'name','identifier for this cfdragcoeffabsgrad response'); ++ fielddisplay(self,'definitionstring','string that identifies this output definition uniquely, from ''Outputdefinition[1-10]'''); ++ fielddisplay(self,'weights','weights (at vertices) to apply to the cfdragcoeffabsgrad'); ++ fielddisplay(self,'weights_string','string for weights for identification purposes'); ++ ++ end % }}} ++ function md = marshall(self,prefix,md,fid) % {{{ ++ ++ WriteData(fid,prefix,'data',self.name,'name','md.cfdragcoeffabsgrad.name','format','String'); ++ WriteData(fid,prefix,'data',self.definitionstring,'name','md.cfdragcoeffabsgrad.definitionstring','format','String'); ++ WriteData(fid,prefix,'data',self.weights,'name','md.cfdragcoeffabsgrad.weights','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts); ++ WriteData(fid,prefix,'data',self.weights_string,'name','md.cfdragcoeffabsgrad.weights_string','format','String'); ++ end % }}} ++ end ++end Index: /issm/oecreview/Archive/23185-23389/ISSM-23331-23332.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23331-23332.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23331-23332.diff (revision 23390) @@ -0,0 +1,50 @@ +Index: ../trunk-jpl/src/m/plot/googlemaps.m +=================================================================== +--- ../trunk-jpl/src/m/plot/googlemaps.m (revision 23331) ++++ ../trunk-jpl/src/m/plot/googlemaps.m (revision 23332) +@@ -122,7 +122,22 @@ + '&sensor=false'... + '&scale=' num2str(scale)]; + url = ['http://maps.google.com/maps/api/staticmap?' params]; +- [X, map]=imread(url,'png'); ++ count = 0; ++ countmax = 10; ++ while(true) ++ try, ++ [X, map]=imread(url,'png'); ++ break; ++ catch me, ++ count = count+1; ++ disp('Failed, trying again... (' num2str(countmax-count) ' more attempts)'); ++ pause(.3); ++ if count>countmax, ++ disp('Giving up...'); ++ rethrow(me); ++ end ++ end ++ end + X=ind2rgb(X,map); + indx1 = floor(x*width)+1; + indx2 = min(floor(dx),floor(x*width)+size(X,2)); +Index: ../trunk-jpl/src/m/plot/applyoptions.m +=================================================================== +--- ../trunk-jpl/src/m/plot/applyoptions.m (revision 23331) ++++ ../trunk-jpl/src/m/plot/applyoptions.m (revision 23332) +@@ -141,6 +141,8 @@ + if getfieldvalue(options,'colorbar',1)==1, + if exist(options,'colorbarcornerposition'), + c=colorbar(getfieldvalue(options,'colorbarcornerposition'),'peer',gca); ++ elseif exist(options,'colorbarpos') & ischar(getfieldvalue(options,'colorbarpos')), ++ c=colorbar(getfieldvalue(options,'colorbarpos')); + else + c=colorbar('peer',gca); + end +@@ -150,7 +152,7 @@ + lim=[lim(1) lim(1)+(lim(2)-lim(1))/getfieldvalue(options,'wrapping')]; + set(c,'Ylim',lim); + end +- if exist(options,'colorbarpos'), ++ if exist(options,'colorbarpos') & isnumeric(getfieldvalue(options,'colorbarpos')), + set(c,'Position',getfieldvalue(options,'colorbarpos')); + end + if exist(options,'log'), Index: /issm/oecreview/Archive/23185-23389/ISSM-23332-23333.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23332-23333.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23332-23333.diff (revision 23390) @@ -0,0 +1,235 @@ +Index: ../trunk-jpl/test/NightlyRun/test245.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test245.py (nonexistent) ++++ ../trunk-jpl/test/NightlyRun/test245.py (revision 23333) +@@ -0,0 +1,59 @@ ++#Test Name: SquareShelfTranIspddSicopolisSSA2d ++import numpy as np ++from model import * ++from socket import gethostname ++from triangle import * ++from setmask import * ++from parameterize import * ++from setflowequation import * ++from solve import * ++ ++from SMBpddSicopolis import * ++ ++md = triangle(model(),'../Exp/Square.exp',150000.) ++md = setmask(md,'all','') ++md = parameterize(md,'../Par/SquareShelf.py') ++ ++# Use of SMBpddSicopolis ++md.smb = SMBpddSicopolis() ++# initalize pdd fields ++md.smb.initialize(md) ++md.smb.s0p = md.geometry.surface ++md.smb.s0t = md.geometry.surface ++ ++# ++md.smb.monthlytemperatures = np.empty((md.mesh.numberofvertices+1,12)) ++md.smb.precipitation = np.empty((md.mesh.numberofvertices+1,12)) ++temp_ma_present = -10. * np.ones((md.mesh.numberofvertices,)) - md.smb.rlaps * md.geometry.surface / 1000. ++temp_mj_present = 10. * np.ones((md.mesh.numberofvertices,)) - md.smb.rlaps * md.geometry.surface / 1000. ++precipitation = 5. * np.ones((md.mesh.numberofvertices,)) ++for imonth in range(12): ++ md.smb.monthlytemperatures[0:md.mesh.numberofvertices,imonth] = md.materials.meltingpoint + temp_ma_present + (temp_mj_present - temp_ma_present) * np.sin((imonth + 1. - 4.) * np.pi / 6.0) ++ md.smb.monthlytemperatures[md.mesh.numberofvertices,imonth] = ((imonth+1)/12.) ++ md.smb.precipitation[0:md.mesh.numberofvertices,imonth] = precipitation ++ md.smb.precipitation[md.mesh.numberofvertices,imonth] = ((imonth+1)/12.) ++ ++# time steps and resolution ++md.timestepping.time_step = 1 ++md.settings.output_frequency = 1 ++md.timestepping.final_time = 2 ++ ++md.transient.issmb = 1 ++md.transient.ismasstransport = 1 ++md.transient.isstressbalance = 0 ++md.transient.isthermal = 0 ++ ++md.transient.requested_outputs = ['default','TemperaturePDD'] ++md.cluster = generic('name',gethostname(),'np',1) # 3 for the cluster ++md = solve(md,'Transient') ++ ++#Fields and tolerances to track changes ++field_names = ['TemperaturePDD1','SmbMassBalance1','TemperaturePDD2','SmbMassBalance2'] ++field_tolerances = [1e-13,1e-13,1e-13,1e-13] ++field_values = [ ++ md.results.TransientSolution[0].TemperaturePDD, ++ md.results.TransientSolution[0].SmbMassBalance, ++ md.results.TransientSolution[1].TemperaturePDD, ++ md.results.TransientSolution[1].SmbMassBalance, ++ ] ++ +Index: ../trunk-jpl/src/m/classes/SMBpddSicopolis.py +=================================================================== +--- ../trunk-jpl/src/m/classes/SMBpddSicopolis.py (nonexistent) ++++ ../trunk-jpl/src/m/classes/SMBpddSicopolis.py (revision 23333) +@@ -0,0 +1,153 @@ ++import numpy as np ++from fielddisplay import fielddisplay ++from checkfield import checkfield ++from WriteData import WriteData ++from project3d import project3d ++from MatlabFuncs import * ++from helpers import * ++ ++class SMBpddSicopolis(object): ++ """ ++ SMBpddSicopolis Class definition ++ ++ Usage: ++ SMBpddSicopolis=SMBpddSicopolis() ++""" ++ ++ def __init__(self): # {{{ ++ self.precipitation = float('NaN') ++ self.monthlytemperatures = float('NaN') ++ self.temperature_anomaly = float('NaN') ++ self.precipitation_anomaly = float('NaN') ++ self.smb_corr = float('NaN') ++ self.desfac = 0 ++ self.s0p = float('NaN') ++ self.s0t = float('NaN') ++ self.rlaps = 0 ++ self.isfirnwarming = 0 ++ self.requested_outputs = [] ++ ++ self.setdefaultparameters() ++ # }}} ++ ++ @staticmethod ++ def SMBpddSicopolis(*args): # {{{ ++ nargin = len(args) ++ ++ if nargin == 0: ++ return SMBpddSicopolis() ++ else: ++ raise RuntimeError('SMBpddSicopolis: constructor not supported') ++ # }}} ++ ++ def extrude(self,md): # {{{ ++ self.precipitation = project3d(md,'vector',self.precipitation,'type','node') ++ self.monthlytemperatures = project3d(md,'vector',self.monthlytemperatures,'type','node') ++ self.temperature_anomaly = project3d(md,'vector',self.temperature_anomaly,'type','node') ++ self.precipitation_anomaly = project3d(md,'vector',self.precipitation_anomaly,'type','node') ++ self.smb_corr = project3d(md,'vector',self.smb_corr,'type','node') ++ self.s0p = project3d(md,'vector',self.s0p,'type','node') ++ self.s0t = project3d(md,'vector',self.s0t,'type','node') ++ # }}} ++ ++ def defaultoutputs(self,md): # {{{ ++ l = [''] ++ return l ++ # }}} ++ ++ def initialize(self,md): # {{{ ++ ++ if np.isnan(self.s0p): ++ self.s0p = np.zeros((md.mesh.numberofvertices,)) ++ print ' no SMBpddSicopolis.s0p specified: values set as zero' ++ ++ if np.isnan(self.s0t): ++ self.s0t = np.zeros((md.mesh.numberofvertices,)) ++ print ' no SMBpddSicopolis.s0t specified: values set as zero' ++ ++ if np.isnan(self.temperature_anomaly): ++ self.temperature_anomaly = np.zeros((md.mesh.numberofvertices,)) ++ print ' no SMBpddSicopolis.temperature_anomaly specified: values set as zero' ++ ++ if np.isnan(self.precipitation_anomaly): ++ self.precipitation_anomaly = np.ones((md.mesh.numberofvertices,)) ++ print ' no SMBpddSicopolis.precipitation_anomaly specified: values set as ones' ++ ++ if np.isnan(self.smb_corr): ++ self.smb_corr = np.zeros((md.mesh.numberofvertices,)) ++ print ' no SMBpddSicopolis.smb_corr specified: values set as zero' ++ # }}} ++ ++ def setdefaultparameters(self): # {{{ ++ ++ self.isfirnwarming = 1 ++ self.desfac = -np.log(2.0)/1000 ++ self.rlaps = 7.4 ++ ++ # }}} ++ ++ def checkconsistency(self,md,solution,analyses): # {{{ ++ ++ if (strcmp(solution,'TransientSolution') and md.transient.issmb == 0): ++ return ++ ++ if 'MasstransportAnalysis' in analyses: ++ md = checkfield(md,'fieldname','smb.desfac','<=',1,'numel',1) ++ md = checkfield(md,'fieldname','smb.s0p','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1]) ++ md = checkfield(md,'fieldname','smb.s0t','>=',0,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices,1]) ++ md = checkfield(md,'fieldname','smb.rlaps','>=',0,'numel',1) ++ md = checkfield(md,'fieldname','smb.monthlytemperatures','timeseries',1,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices+1,12]) ++ md = checkfield(md,'fieldname','smb.precipitation','timeseries',1,'NaN',1,'Inf',1,'size',[md.mesh.numberofvertices+1,12]) ++ ++ md = checkfield(md,'fieldname','smb.requested_outputs','stringrow',1) ++ ++ return md ++ # }}} ++ ++ def __repr__(self): # {{{ ++ string = ' surface forcings parameters:' ++ string += '\n SICOPOLIS PDD scheme (Calov & Greve, 2005) :' ++ ++ string = "%s\n%s"%(string,fielddisplay(self,'monthlytemperatures','monthly surface temperatures [K]')) ++ string = "%s\n%s"%(string,fielddisplay(self,'precipitation','monthly surface precipitation [m/yr water eq]')) ++ string = "%s\n%s"%(string,fielddisplay(self,'temperature_anomaly','anomaly to monthly reference temperature (additive [K])')) ++ string = "%s\n%s"%(string,fielddisplay(self,'precipitation_anomaly','anomaly to monthly precipitation (multiplicative, e.g. q=q0*exp(0.070458*DeltaT) after Huybrechts (2002)) [no unit])')) ++ string = "%s\n%s"%(string,fielddisplay(self,'smb_corr','correction of smb after PDD call [m/a]')) ++ string = "%s\n%s"%(string,fielddisplay(self,'s0p','should be set to elevation from precip source (between 0 and a few 1000s m, default is 0) [m]')) ++ string = "%s\n%s"%(string,fielddisplay(self,'s0t','should be set to elevation from temperature source (between 0 and a few 1000s m, default is 0) [m]')) ++ string = "%s\n%s"%(string,fielddisplay(self,'rlaps','present day lapse rate (default is 7.4 degree/km)')) ++ string = "%s\n%s"%(string,fielddisplay(self,'desfac','desertification elevation factor (default is -log(2.0)/1000)')) ++ string = "%s\n%s"%(string,fielddisplay(self,'isfirnwarming','is firnwarming (Reeh 1991) activated (0 or 1, default is 1)')) ++ string = "%s\n%s"%(string,fielddisplay(self,'requested_outputs','additional outputs requested (TemperaturePDD, SmbAccumulation, SmbMelt)')) ++ # }}} ++ ++ def marshall(self,prefix,md,fid): # {{{ ++ ++ yts=md.constants.yts ++ ++ WriteData(fid,prefix,'name','md.smb.model','data',10,'format','Integer') ++ ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','isfirnwarming','format','Boolean') ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','desfac','format','Double') ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0p','format','DoubleMat','mattype',1) ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','s0t','format','DoubleMat','mattype',1) ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','rlaps','format','Double') ++ ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','monthlytemperatures','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitation','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','temperature_anomaly','format','DoubleMat','mattype',1,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','precipitation_anomaly','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) ++ WriteData(fid,prefix,'object',self,'class','smb','fieldname','smb_corr','format','DoubleMat','mattype',1,'scale',1./yts,'timeserieslength',md.mesh.numberofvertices+1,'yts',md.constants.yts) ++ ++ #process requested outputs ++ outputs = self.requested_outputs ++ pos = np.where('default' in outputs) ++ if not isempty(pos): ++ outputs[pos] = [] #remove 'default' from outputs ++ outputs = [outputs,defaultoutputs(self,md)] #add defaults ++ ++ WriteData(fid,prefix,'data',outputs,'name','md.smb.requested_outputs','format','StringArray') ++ ++ # }}} ++ ++ +Index: ../trunk-jpl/src/m/qmu/helpers.py +=================================================================== +--- ../trunk-jpl/src/m/qmu/helpers.py (revision 23332) ++++ ../trunk-jpl/src/m/qmu/helpers.py (revision 23333) +@@ -249,7 +249,7 @@ + except (TypeError): + pass + +- # if all of that fails, then if is not empty ++ # if all of that fails, then it is not empty + return False + + def fieldnames(x,ignore_internals = True): Index: /issm/oecreview/Archive/23185-23389/ISSM-23333-23334.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23333-23334.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23333-23334.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/m/plot/googlemaps.m +=================================================================== +--- ../trunk-jpl/src/m/plot/googlemaps.m (revision 23333) ++++ ../trunk-jpl/src/m/plot/googlemaps.m (revision 23334) +@@ -130,7 +130,7 @@ + break; + catch me, + count = count+1; +- disp('Failed, trying again... (' num2str(countmax-count) ' more attempts)'); ++ disp(['Failed, trying again... (' num2str(countmax-count) ' more attempts)']); + pause(.3); + if count>countmax, + disp('Giving up...'); Index: /issm/oecreview/Archive/23185-23389/ISSM-23334-23335.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23334-23335.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23334-23335.diff (revision 23390) @@ -0,0 +1,44 @@ +Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 23334) ++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 23335) +@@ -123,7 +123,6 @@ + bool ismovingfront; + bool isoceancoupling; + bool issmb; +- int basalforcingsmodel; + + /*Fetch data needed: */ + iomodel->FindConstant(&stabilization,"md.masstransport.stabilization"); +@@ -132,7 +131,6 @@ + iomodel->FindConstant(&ismovingfront,"md.transient.ismovingfront"); + iomodel->FindConstant(&isoceancoupling,"md.transient.isoceancoupling"); + iomodel->FindConstant(&issmb,"md.transient.issmb"); +- iomodel->FindConstant(&basalforcingsmodel,"md.basalforcings.model"); + + /*Finite element type*/ + finiteelement = P1Enum; +@@ -157,11 +155,6 @@ + iomodel->FetchDataToInput(elements,"md.mask.ice_levelset",MaskIceLevelsetEnum); + iomodel->FetchDataToInput(elements,"md.mask.groundedice_levelset",MaskGroundediceLevelsetEnum); + iomodel->FetchDataToInput(elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum); +- if (basalforcingsmodel==SpatialLinearFloatingMeltRateEnum){ +- iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); +- iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); +- iomodel->FetchDataToInput(elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); +- } + iomodel->FetchDataToInput(elements,"md.initialization.vx",VxEnum); + iomodel->FetchDataToInput(elements,"md.initialization.vy",VyEnum); + +@@ -181,6 +174,11 @@ + break; + case MantlePlumeGeothermalFluxEnum: + break; ++ case SpatialLinearFloatingMeltRateEnum: ++ iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); ++ iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); ++ iomodel->FetchDataToInput(elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); ++ break; + case BasalforcingsPicoEnum: + iomodel->FetchDataToInput(elements,"md.basalforcings.basin_id",BasalforcingsPicoBasinIdEnum); + break; Index: /issm/oecreview/Archive/23185-23389/ISSM-23335-23336.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23335-23336.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23335-23336.diff (revision 23390) @@ -0,0 +1,81 @@ +Index: ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp (revision 23335) ++++ ../trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp (revision 23336) +@@ -765,7 +765,31 @@ + } + if(isFS){ + iomodel->FetchDataToInput(elements,"md.initialization.pressure",PressureEnum,0.); +- iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum,0.); ++ ++ /*Add basal forcings to compute melt rate*/ ++ int basalforcing_model; ++ iomodel->FindConstant(&basalforcing_model,"md.basalforcings.model"); ++ switch(basalforcing_model){ ++ case FloatingMeltRateEnum: ++ iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum); ++ break; ++ case LinearFloatingMeltRateEnum: ++ break; ++ case MismipFloatingMeltRateEnum: ++ break; ++ case MantlePlumeGeothermalFluxEnum: ++ break; ++ case SpatialLinearFloatingMeltRateEnum: ++ iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); ++ iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); ++ iomodel->FetchDataToInput(elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); ++ break; ++ case BasalforcingsPicoEnum: ++ iomodel->FetchDataToInput(elements,"md.basalforcings.basin_id",BasalforcingsPicoBasinIdEnum); ++ break; ++ default: ++ _error_("Basal forcing model "<FindConstant(&fe_FS,"md.flowequation.fe_FS"); +Index: ../trunk-jpl/src/c/analyses/FreeSurfaceBaseAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/FreeSurfaceBaseAnalysis.cpp (revision 23335) ++++ ../trunk-jpl/src/c/analyses/FreeSurfaceBaseAnalysis.cpp (revision 23336) +@@ -79,7 +79,6 @@ + iomodel->FetchDataToInput(elements,"md.slr.sealevel",SealevelEnum,0); + iomodel->FetchDataToInput(elements,"md.mask.ice_levelset",MaskIceLevelsetEnum); + iomodel->FetchDataToInput(elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum,0.); +- iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum); + iomodel->FetchDataToInput(elements,"md.initialization.vx",VxEnum); + iomodel->FetchDataToInput(elements,"md.initialization.vy",VyEnum); + if(iomodel->domaindim==3){ +@@ -89,6 +88,31 @@ + iomodel->FetchDataToInput(elements,"md.mesh.vertexonbase",MeshVertexonbaseEnum); + iomodel->FetchDataToInput(elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum); + } ++ ++ /*Get what we need for ocean-induced basal melting*/ ++ int basalforcing_model; ++ iomodel->FindConstant(&basalforcing_model,"md.basalforcings.model"); ++ switch(basalforcing_model){ ++ case FloatingMeltRateEnum: ++ iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum); ++ break; ++ case LinearFloatingMeltRateEnum: ++ break; ++ case MismipFloatingMeltRateEnum: ++ break; ++ case MantlePlumeGeothermalFluxEnum: ++ break; ++ case SpatialLinearFloatingMeltRateEnum: ++ iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); ++ iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); ++ iomodel->FetchDataToInput(elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); ++ break; ++ case BasalforcingsPicoEnum: ++ iomodel->FetchDataToInput(elements,"md.basalforcings.basin_id",BasalforcingsPicoBasinIdEnum); ++ break; ++ default: ++ _error_("Basal forcing model "<Core(femmodel); + delete analysis; Index: /issm/oecreview/Archive/23185-23389/ISSM-23337-23338.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23337-23338.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23337-23338.diff (revision 23390) @@ -0,0 +1,15 @@ +Index: ../trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 23337) ++++ ../trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 23338) +@@ -109,8 +109,8 @@ + iomodel->FetchDataToInput(elements,"md.mesh.vertexonbase",MeshVertexonbaseEnum); + iomodel->FetchDataToInput(elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum); + } +- iomodel->FetchDataToInput(elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum); +- iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum,0.); ++ //iomodel->FetchDataToInput(elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum); ++ //iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum,0.); + //iomodel->FetchDataToInput(elements,"md.smb.mass_balance",SmbMassBalanceEnum); + iomodel->FetchDataToInput(elements,"md.initialization.vx",VxEnum,0.); + iomodel->FetchDataToInput(elements,"md.initialization.vy",VyEnum,0.); Index: /issm/oecreview/Archive/23185-23389/ISSM-23338-23339.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23338-23339.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23338-23339.diff (revision 23390) @@ -0,0 +1,48 @@ +Index: ../trunk-jpl/test/NightlyRun/test701.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test701.py (revision 23338) ++++ ../trunk-jpl/test/NightlyRun/test701.py (revision 23339) +@@ -41,6 +41,7 @@ + md.stressbalance.spcvz = np.nan * np.ones((md.mesh.numberofvertices,)) + md.stressbalance.spcvx[np.where(md.mesh.vertexflags(4))] = 0. + md.stressbalance.spcvy[np.where(md.mesh.vertexflags(4))] = 0. ++md.basalforcings.floatingice_melting_rate=np.zeros((md.mesh.numberofvertices,)) + + #Misc + md = setflowequation(md,'FS','all') +Index: ../trunk-jpl/test/NightlyRun/test702.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test702.py (revision 23338) ++++ ../trunk-jpl/test/NightlyRun/test702.py (revision 23339) +@@ -52,6 +52,7 @@ + md.stressbalance.loadingforce = np.zeros((md.mesh.numberofvertices,3)) + md.stressbalance.spcvx[np.where(md.mesh.vertexflags(4))] = 800. + md.stressbalance.spcvy[np.where(md.mesh.vertexflags(4))] = 0. ++md.basalforcings.floatingice_melting_rate=np.zeros((md.mesh.numberofvertices,)) + + #misc + md = setflowequation(md,'FS','all') +Index: ../trunk-jpl/test/NightlyRun/test701.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test701.m (revision 23338) ++++ ../trunk-jpl/test/NightlyRun/test701.m (revision 23339) +@@ -34,6 +34,7 @@ + md.stressbalance.spcvz = NaN*ones(md.mesh.numberofvertices,1); + md.stressbalance.spcvx(find(vertexflags(md.mesh,4)))=0; + md.stressbalance.spcvy(find(vertexflags(md.mesh,4)))=0; ++md.basalforcings.floatingice_melting_rate=zeros(md.mesh.numberofvertices,1); + + %Misc + md=setflowequation(md,'FS','all'); +Index: ../trunk-jpl/test/NightlyRun/test702.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test702.m (revision 23338) ++++ ../trunk-jpl/test/NightlyRun/test702.m (revision 23339) +@@ -33,6 +33,7 @@ + md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3); + md.stressbalance.spcvx(find(vertexflags(md.mesh,4)))=800; + md.stressbalance.spcvy(find(vertexflags(md.mesh,4)))=0; ++md.basalforcings.floatingice_melting_rate=zeros(md.mesh.numberofvertices,1); + + %Misc + md=setflowequation(md,'FS','all'); Index: /issm/oecreview/Archive/23185-23389/ISSM-23339-23340.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23339-23340.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23339-23340.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 23339) ++++ ../trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 23340) +@@ -109,7 +109,7 @@ + iomodel->FetchDataToInput(elements,"md.mesh.vertexonbase",MeshVertexonbaseEnum); + iomodel->FetchDataToInput(elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum); + } +- //iomodel->FetchDataToInput(elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum); ++ iomodel->FetchDataToInput(elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum); + //iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum,0.); + //iomodel->FetchDataToInput(elements,"md.smb.mass_balance",SmbMassBalanceEnum); + iomodel->FetchDataToInput(elements,"md.initialization.vx",VxEnum,0.); Index: /issm/oecreview/Archive/23185-23389/ISSM-23340-23341.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23340-23341.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23340-23341.diff (revision 23390) @@ -0,0 +1,39 @@ +Index: ../trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 23340) ++++ ../trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp (revision 23341) +@@ -110,8 +110,33 @@ + iomodel->FetchDataToInput(elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum); + } + iomodel->FetchDataToInput(elements,"md.basalforcings.groundedice_melting_rate",BasalforcingsGroundediceMeltingRateEnum); +- //iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum,0.); + //iomodel->FetchDataToInput(elements,"md.smb.mass_balance",SmbMassBalanceEnum); ++ ++ ++ /*Add basal forcings to compute melt rate*/ ++ int basalforcing_model; ++ iomodel->FindConstant(&basalforcing_model,"md.basalforcings.model"); ++ switch(basalforcing_model){ ++ case FloatingMeltRateEnum: ++ iomodel->FetchDataToInput(elements,"md.basalforcings.floatingice_melting_rate",BasalforcingsFloatingiceMeltingRateEnum); ++ break; ++ case LinearFloatingMeltRateEnum: ++ break; ++ case MismipFloatingMeltRateEnum: ++ break; ++ case MantlePlumeGeothermalFluxEnum: ++ break; ++ case SpatialLinearFloatingMeltRateEnum: ++ iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_melting_rate",BasalforcingsDeepwaterMeltingRateEnum); ++ iomodel->FetchDataToInput(elements,"md.basalforcings.deepwater_elevation",BasalforcingsDeepwaterElevationEnum); ++ iomodel->FetchDataToInput(elements,"md.basalforcings.upperwater_elevation",BasalforcingsUpperwaterElevationEnum); ++ break; ++ case BasalforcingsPicoEnum: ++ iomodel->FetchDataToInput(elements,"md.basalforcings.basin_id",BasalforcingsPicoBasinIdEnum); ++ break; ++ default: ++ _error_("Basal forcing model "<FetchDataToInput(elements,"md.initialization.vx",VxEnum,0.); + iomodel->FetchDataToInput(elements,"md.initialization.vy",VyEnum,0.); + }/*}}}*/ Index: /issm/oecreview/Archive/23185-23389/ISSM-23341-23342.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23341-23342.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23341-23342.diff (revision 23390) @@ -0,0 +1,39 @@ +Index: ../trunk-jpl/m4/issm_options.m4 +=================================================================== +--- ../trunk-jpl/m4/issm_options.m4 (revision 23341) ++++ ../trunk-jpl/m4/issm_options.m4 (revision 23342) +@@ -591,7 +591,7 @@ + dnl python specifics + if test "x$HAVE_PYTHON" = "xyes"; then + AC_MSG_CHECKING([for python version]) +- dnl Query Python for its version number.  Getting [:3] seems to be the ++ dnl Query Python for its version number. Getting [:3] seems to be the + dnl best way to do this; it's what "site.py" does in the standard library. + PYTHON_VERSION=$($PYTHON_ROOT/bin/python -c "import sys; print sys.version[[:3]]") + AC_MSG_RESULT($PYTHON_VERSION) +@@ -644,6 +644,11 @@ + AS_HELP_STRING([--with-python-numpy-dir=DIR], [python-numpy root directory.]), + [PYTHON_NUMPY_ROOT=$withval],[PYTHON_NUMPY_ROOT="no"]) + ++ dnl you can find numpy by typing ++ dnl >>> import numpy ++ dnl >>> numpy.__file__ ++ dnl '/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/__init__.pyc' ++ + dnl Check whether numpy is enabled + AC_MSG_CHECKING(for python-numpy) + if test "x$PYTHON_NUMPY_ROOT" = "xno" ; then +@@ -2165,6 +2170,13 @@ + esac + AC_DEFINE([_MULTITHREADING_],[1],[with numthreads enabled]) + fi ++ dnl check that it is an integer ++ if [[ "$NUMTHREADS_VALUE" -eq "$NUMTHREADS_VALUE" 2> /dev/null ]] ; then ++ dnl cool we have an integer ++ : ++ else ++ AC_MSG_ERROR([Number of threads provided ($NUMTHREADS_VALUE) is not an integer]); ++ fi + AC_DEFINE_UNQUOTED([_NUMTHREADS_],[$NUMTHREADS_VALUE],[number of threads]) + AC_SUBST([MULTITHREADINGLIB]) + AC_MSG_RESULT($NUMTHREADS_VALUE) Index: /issm/oecreview/Archive/23185-23389/ISSM-23348-23349.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23348-23349.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23348-23349.diff (revision 23390) @@ -0,0 +1,169 @@ +Index: ../trunk-jpl/src/c/toolkits/mpi/issmmpi.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/issmmpi.cpp (revision 23348) ++++ ../trunk-jpl/src/c/toolkits/mpi/issmmpi.cpp (revision 23349) +@@ -41,7 +41,7 @@ + int rc=0; + assert(sendcount==recvcount || sendtype==recvtype); // we handle only identical representations + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Allgather(sendbuf, + sendcount, + sendtype, +@@ -75,7 +75,7 @@ + int rc=0; + assert(sendtype==recvtype); // we handle only identical representations + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Allgatherv(sendbuf, + sendcount, + sendtype, +@@ -112,7 +112,7 @@ + + int rc=0; + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Allreduce(sendbuf, + recvbuf, + count, +@@ -144,7 +144,7 @@ + + int rc=0; + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Barrier(comm); + # else + rc=MPI_Barrier(comm); +@@ -158,7 +158,7 @@ + + int rc=0; + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Bcast(buffer, + count, + datatype, +@@ -180,7 +180,7 @@ + + int rc=0; + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + assert(0); // to be implemented + # else + rc=MPI_Comm_free(comm); +@@ -216,9 +216,12 @@ + + int rc=0; + #ifdef _HAVE_MPI_ +- #ifdef _HAVE_AMPI_ +- #ifdef _HAVE_ADJOINTMPI_ ++ #if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) ++ #if defined(_HAVE_ADJOINTMPI_) + rc=AMPI_Finalize(); ++ #elif defined(_HAVE_MEDIPACK_) ++ TOOL::finalize(); ++ rc=AMPI_Finalize(); + #else + rc=AMPI_Finalize_NT(); + #endif +@@ -233,7 +236,7 @@ + int rc=0; + assert(sendtype==recvtype && sendcnt==recvcnt); // we handle only identical representations + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Gather(sendbuf, + sendcnt, + sendtype, +@@ -270,7 +273,7 @@ + int rc=0; + assert(sendtype==recvtype); // we handle only identical representations + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Gatherv(sendbuf, + sendcnt, + sendtype, +@@ -309,9 +312,12 @@ + + int rc=0; + #ifdef _HAVE_MPI_ +- #ifdef _HAVE_AMPI_ +- #ifdef _HAVE_ADJOINTMPI_ ++ #if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) ++ #if defined(_HAVE_ADJOINTMPI_) + rc=AMPI_Init(argc,argv); ++ #elif defined(_HAVE_MEDIPACK_) ++ rc=AMPI_Init(argc,argv); ++ TOOL::init(); + #else + rc=AMPI_Init_NT(argc,argv); + #endif +@@ -325,7 +331,7 @@ + + int rc=0; + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Recv(buf, + count, + datatype, +@@ -356,7 +362,7 @@ + + int rc=0; + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Reduce(sendbuf, + recvbuf, + count, +@@ -391,7 +397,7 @@ + int rc=0; + assert(sendtype==recvtype && sendcnt==recvcnt); // we handle only identical representations + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Scatter(sendbuf, + sendcnt, + sendtype, +@@ -428,7 +434,7 @@ + int rc=0; + assert(sendtype==recvtype); // we handle only identical representations + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Scatterv(sendbuf, + sendcnts, + displs, +@@ -467,7 +473,7 @@ + + int rc=0; + #ifdef _HAVE_MPI_ +-# ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=AMPI_Send(buf, + count, + datatype, +@@ -511,7 +517,7 @@ + + int rc=0; + #ifdef _HAVE_MPI_ +-#ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=MPI_Comm_split(comm, color, key, newcomm); + #else + rc=MPI_Comm_split(comm, color, key, newcomm); +@@ -525,7 +531,7 @@ + + int rc=0; + #ifdef _HAVE_MPI_ +-#ifdef _HAVE_AMPI_ ++#if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) + rc=MPI_Intercomm_create(comm,local_leader,peer_comm,remote_leader,tag,newintercomm); + #else + rc=MPI_Intercomm_create(comm,local_leader,peer_comm,remote_leader,tag,newintercomm); Index: /issm/oecreview/Archive/23185-23389/ISSM-23349-23350.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23349-23350.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23349-23350.diff (revision 23390) @@ -0,0 +1,103 @@ +Index: ../trunk-jpl/m4/issm_options.m4 +=================================================================== +--- ../trunk-jpl/m4/issm_options.m4 (revision 23349) ++++ ../trunk-jpl/m4/issm_options.m4 (revision 23350) +@@ -988,6 +988,38 @@ + fi + AM_CONDITIONAL([ADJOINTMPI], [test x$HAVE_ADJOINTMPI = xyes]) + dnl }}} ++ dnl medipack (CoDiPack, ADOLC dev){{{ ++ AC_ARG_WITH([medipack-dir], ++ AS_HELP_STRING([--with-medipack-dir=DIR], [MeDiPack root directory.]), ++ [MEDIPACK_ROOT=$withval],[MEDIPACK_ROOT="no"]) ++ ++ dnl Check whether medipack is enabled ++ AC_MSG_CHECKING([for medipack]) ++ if test "x$MEDIPACK_ROOT" = "xno" ; then ++ HAVE_MEDIPACK=no ++ else ++ HAVE_MEDIPACK=yes ++ if ! test -d "$MEDIPACK_ROOT"; then ++ AC_MSG_ERROR([medipack directory provided ($MEDIPACK_ROOT) does not exist]); ++ fi ++ fi ++ AC_MSG_RESULT($HAVE_MEDIPACK) ++ ++ dnl medipack headers and libraries ++ if test "x$HAVE_MEDIPACK" == "xyes"; then ++ if test "x$CODIPACK_ROOT" == "xno"; then ++ AC_MSG_ERROR([cannot run MeDiPack without CoDiPack]); ++ fi ++ MEDIPACKINCL="-I$MEDIPACK_ROOT/include -I$MEDIPACK_ROOT/src" ++ dnl Also set _HAVE_AMPI_, because the interface is (almost) the ++ dnl same as for adjoinable mpi... ++ AC_DEFINE([_HAVE_AMPI_],[1],[with adjoint mpi in ISSM src]) ++ AC_DEFINE([_HAVE_MEDIPACK_],[1],[with MeDiPack in ISSM src]) ++ AC_SUBST([MEDIPACKINCL]) ++ fi ++ AM_CONDITIONAL([MEDIPACK], [test x$HAVE_MEDIPACK = xyes]) ++ ++ dnl }}} + dnl rose{{{ + AC_ARG_WITH([rose-dir], + AS_HELP_STRING([--with-rose-dir=DIR], [rose root directory.]), +@@ -2234,6 +2266,9 @@ + if test "$HAVE_ADOLC" = "yes" && test "$HAVE_PETSC" = "yes" ; then + AC_MSG_ERROR([cannot compile ISSM with both PETSc and adolc]); + fi ++ if test "$HAVE_ADOLC" = "yes" && test "$HAVE_CODIPACK" = "yes" ; then ++ AC_MSG_ERROR([cannot compile ISSM with both ADOLC and CoDiPack]); ++ fi + dnl check that if we run meteoio, we have snowpack also + if test "$HAVE_METEOIO" = "yes" && test "$HAVE_SNOWPACK" = "no" ; then + AC_MSG_ERROR([cannot compile MeteoIO package without Snowpack!]); +Index: ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp (revision 23349) ++++ ../trunk-jpl/src/c/cores/controlm1qn3_core.cpp (revision 23350) +@@ -123,6 +123,7 @@ + >tol,normtype,&impres,&io,imode,&omode,&niter,&nsim,iz,dz,&ndz, + &reverse,&indic,izs,rzs,(void*)&mystruct); + ++ /*Print exit flag*/ + switch(int(omode)){ + case 0: _printf0_(" Stop requested (indic = 0)\n"); break; + case 1: _printf0_(" Convergence reached (gradient satisfies stopping criterion)\n"); break; +Index: ../trunk-jpl/src/c/toolkits/codipack/ampi_interface.cpp +=================================================================== +--- ../trunk-jpl/src/c/toolkits/codipack/ampi_interface.cpp (revision 23349) ++++ ../trunk-jpl/src/c/toolkits/codipack/ampi_interface.cpp (revision 23350) +@@ -1 +1,14 @@ ++#ifdef HAVE_CONFIG_H ++#include ++#else ++#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" ++#endif ++ ++#if defined(_HAVE_ADJOINTMPI_) + #include "externals/ampi_interface_realreverse.cpp" ++#elif defined(_HAVE_MEDIPACK_) ++#include "medi/medi.cpp" ++#else ++#error "Cannot compile without MeDiPack and AdjointMpi" ++#endif ++ +Index: ../trunk-jpl/src/c/Makefile.am +=================================================================== +--- ../trunk-jpl/src/c/Makefile.am (revision 23349) ++++ ../trunk-jpl/src/c/Makefile.am (revision 23350) +@@ -323,10 +323,13 @@ + ./classes/Inputs/PentaInput.cpp\ + ./classes/Inputs/TetraInput.cpp + #}}} +-# ADJOINTMPI sources {{{ ++#ADJOINTMPI/MeDiPack sources {{{ + if ADJOINTMPI + issm_sources += ./toolkits/codipack/ampi_interface.cpp + endif ++if MEDIPACK ++issm_sources += ./toolkits/codipack/ampi_interface.cpp ++endif + # }}} + #DAKOTA sources {{{ + if DAKOTA Index: /issm/oecreview/Archive/23185-23389/ISSM-23350-23351.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23350-23351.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23350-23351.diff (revision 23390) @@ -0,0 +1,41 @@ +Index: ../trunk-jpl/test/NightlyRun/test211.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test211.m (revision 23350) ++++ ../trunk-jpl/test/NightlyRun/test211.m (revision 23351) +@@ -15,7 +15,7 @@ + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'}; + field_tolerances={... + 2e-08,2e-08,5e-05,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08,... +- 5e-06,5e-06,8e-05,5e-06,3e-07,5e-07,5e-07,5e-07,3e-06,5e-05,... ++ 5e-06,5e-06,8e-05,5e-06,5e-07,5e-07,5e-07,5e-07,3e-06,5e-05,... + 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05}; + field_values={... + (md.results.TransientSolution(1).Vx),... +Index: ../trunk-jpl/test/NightlyRun/test211.js +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test211.js (revision 23350) ++++ ../trunk-jpl/test/NightlyRun/test211.js (revision 23351) +@@ -16,7 +16,7 @@ + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3']; + field_tolerances=[ + 2e-08,2e-08,5e-05,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08, +- 5e-06,5e-06,8e-05,5e-06,3e-07,5e-07,5e-07,5e-07,3e-06,5e-05, ++ 5e-06,5e-06,8e-05,5e-06,5e-07,5e-07,5e-07,5e-07,3e-06,5e-05, + 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05]; + field_values=[ + (md.results.TransientSolution[0](1).Vx), +Index: ../trunk-jpl/test/NightlyRun/test211.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test211.py (revision 23350) ++++ ../trunk-jpl/test/NightlyRun/test211.py (revision 23351) +@@ -25,8 +25,8 @@ + 'Vx2','Vy2','Vz2','Vel2','Pressure2','Bed2','Surface2','Thickness2','Temperature2','BasalforcingsGroundediceMeltingRate2', + 'Vx3','Vy3','Vz3','Vel3','Pressure3','Bed3','Surface3','Thickness3','Temperature3','BasalforcingsGroundediceMeltingRate3'] + field_tolerances=[2e-08,2e-08,5e-05,2e-08,1e-08,1e-08,1e-08,1e-08,1e-08,1e-08, +- 5e-06,5e-06,8e-05,5e-06,3e-07,5e-07,5e-07,5e-07,3e-06,5e-05, +- 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05] ++ 5e-06,5e-06,8e-05,5e-06,5e-07,5e-07,5e-07,5e-07,3e-06,5e-05, ++ 8e-06,8e-06,8e-05,8e-06,5e-07,8e-07,8e-07,8e-07,5e-06,8e-05] + field_values=[md.results.TransientSolution[0].Vx, + md.results.TransientSolution[0].Vy, + md.results.TransientSolution[0].Vz, Index: /issm/oecreview/Archive/23185-23389/ISSM-23351-23352.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23351-23352.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23351-23352.diff (revision 23390) @@ -0,0 +1,111 @@ +Index: ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23351) ++++ ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23352) +@@ -17,9 +17,24 @@ + + #ifdef _HAVE_MPI_ + /*Include header files: {{{*/ +- #ifdef _HAVE_AMPI_ +- #ifdef _HAVE_ADJOINTMPI_ ++ #if defined(_HAVE_AMPI_) ++ #if defined(_HAVE_ADJOINTMPI_) + #include ++ ++ #elif defined(_HAVE_MEDIPACK_) ++ #include "medi/medi.hpp" ++ using namespace medi; ++ #include "medi/codiMediPackTypes.hpp" ++ #if defined(_HAVE_CODIPACK_) ++ #define TOOL CoDiPackTool ++ #define AMPI_ADOUBLE TOOL::MPI_TYPE ++ #elif defined(_HAVE_ADOLC_) ++ #include "adolc/medipacksupport.h" ++ #define TOOL AdolcTool ++ #else ++ #error "don't know about AD tool" ++ #endif ++ + #else + #include + #endif +@@ -30,34 +45,61 @@ + #endif + /*}}}*/ + /*MPI defines: *{{{*/ ++ + // types ++ #if defined(_HAVE_MEDIPACK_) ++ typedef AMPI_Comm ISSM_MPI_Comm; ++ typedef AMPI_Datatype ISSM_MPI_Datatype; ++ typedef AMPI_Op ISSM_MPI_Op; ++ typedef AMPI_Status ISSM_MPI_Status; ++ #else + typedef MPI_Comm ISSM_MPI_Comm; + typedef MPI_Datatype ISSM_MPI_Datatype; + typedef MPI_Op ISSM_MPI_Op; + typedef MPI_Status ISSM_MPI_Status; +- +- // data types +- #define ISSM_MPI_CHAR MPI_CHAR +- #if defined(_HAVE_AMPI_) +- #define ISSM_MPI_DOUBLE AMPI_ADOUBLE // corresponds to IssmDouble +- #else +- #define ISSM_MPI_DOUBLE MPI_DOUBLE // corresponds to IssmDouble + #endif +- #define ISSM_MPI_PDOUBLE MPI_DOUBLE // corresponds to IssmPDouble +- #define ISSM_MPI_INT MPI_INT + ++ #if defined(_HAVE_MEDIPACK_) ++ #define ISSM_MPI_CHAR AMPI_CHAR ++ #define ISSM_MPI_DOUBLE AMPI_ADOUBLE // corresponds to IssmDouble ++ #define ISSM_MPI_PDOUBLE AMPI_DOUBLE // corresponds to IssmPDouble ++ #define ISSM_MPI_INT AMPI_INT ++ + // operations +- #define ISSM_MPI_MAX MPI_MAX +- #define ISSM_MPI_MIN MPI_MIN +- #define ISSM_MPI_PROD MPI_PROD +- #define ISSM_MPI_SUM MPI_SUM +- ++ #define ISSM_MPI_MAX AMPI_MAX ++ #define ISSM_MPI_MIN AMPI_MIN ++ #define ISSM_MPI_PROD AMPI_PROD ++ #define ISSM_MPI_SUM AMPI_SUM ++ + // others +- #define ISSM_MPI_COMM_WORLD MPI_COMM_WORLD +- #define ISSM_MPI_STATUS_IGNORE MPI_STATUS_IGNORE +- #define ISSM_MPI_ANY_TAG MPI_ANY_TAG +- #define ISSM_MPI_ANY_SOURCE MPI_ANY_SOURCE ++ #define ISSM_MPI_COMM_WORLD AMPI_COMM_WORLD ++ #define ISSM_MPI_STATUS_IGNORE AMPI_STATUS_IGNORE ++ #define ISSM_MPI_ANY_TAG AMPI_ANY_TAG ++ #define ISSM_MPI_ANY_SOURCE AMPI_ANY_SOURCE + ++ #else ++ #if defined(_HAVE_AMPI_) ++ #define ISSM_MPI_DOUBLE AMPI_ADOUBLE // corresponds to IssmDouble ++ #else ++ #define ISSM_MPI_DOUBLE MPI_DOUBLE // corresponds to IssmDouble ++ #endif ++ #define ISSM_MPI_PDOUBLE MPI_DOUBLE // corresponds to IssmPDouble ++ #define ISSM_MPI_INT MPI_INT ++ #define ISSM_MPI_CHAR MPI_CHAR ++ ++ // operations ++ #define ISSM_MPI_MAX MPI_MAX ++ #define ISSM_MPI_MIN MPI_MIN ++ #define ISSM_MPI_PROD MPI_PROD ++ #define ISSM_MPI_SUM MPI_SUM ++ ++ // others ++ #define ISSM_MPI_COMM_WORLD MPI_COMM_WORLD ++ #define ISSM_MPI_STATUS_IGNORE MPI_STATUS_IGNORE ++ #define ISSM_MPI_ANY_TAG MPI_ANY_TAG ++ #define ISSM_MPI_ANY_SOURCE MPI_ANY_SOURCE ++ #endif ++ + /*other include files: */ + #include "./commops/commops.h" + /*}}}*/ Index: /issm/oecreview/Archive/23185-23389/ISSM-23352-23353.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23352-23353.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23352-23353.diff (revision 23390) @@ -0,0 +1,20 @@ +Index: ../trunk-jpl/externalpackages/medipack/install.sh +=================================================================== +--- ../trunk-jpl/externalpackages/medipack/install.sh (nonexistent) ++++ ../trunk-jpl/externalpackages/medipack/install.sh (revision 23353) +@@ -0,0 +1,8 @@ ++#!/bin/bash ++set -eu ++ ++#Some cleanup ++rm -rf install ++ ++#Download development version ++svn co https://github.com/SciCompKL/MeDiPack/trunk install + +Property changes on: ../trunk-jpl/externalpackages/medipack/install.sh +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property Index: /issm/oecreview/Archive/23185-23389/ISSM-23353-23354.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23353-23354.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23353-23354.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/m/classes/groundingline.m +=================================================================== +--- ../trunk-jpl/src/m/classes/groundingline.m (revision 23353) ++++ ../trunk-jpl/src/m/classes/groundingline.m (revision 23354) +@@ -32,7 +32,7 @@ + md = checkfield(md,'fieldname','groundingline.friction_interpolation','values',{'NoFrictionOnPartiallyFloating' 'SubelementFriction1' 'SubelementFriction2'}); + md = checkfield(md,'fieldname','groundingline.melt_interpolation','values',{'NoMeltOnPartiallyFloating' 'SubelementMelt1' 'SubelementMelt2' 'FullMeltOnPartiallyFloating'}); + +- if ~strcmp(self.migration,'None'), ++ if ~strcmp(self.migration,'None') & strcmp(solution,'TransientSolution') & md.transient.isgroundingline==1, + if isnan(md.geometry.bed), + md = checkmessage(md,['requesting grounding line migration, but bathymetry is absent!']); + end Index: /issm/oecreview/Archive/23185-23389/ISSM-23354-23355.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23354-23355.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23354-23355.diff (revision 23390) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/src/m/classes/groundingline.py +=================================================================== +--- ../trunk-jpl/src/m/classes/groundingline.py (revision 23354) ++++ ../trunk-jpl/src/m/classes/groundingline.py (revision 23355) +@@ -44,7 +44,7 @@ + md = checkfield(md,'fieldname','groundingline.friction_interpolation','values',['SubelementFriction1','SubelementFriction2','NoFrictionOnPartiallyFloating']) + md = checkfield(md,'fieldname','groundingline.melt_interpolation','values',['SubelementMelt1','SubelementMelt2','NoMeltOnPartiallyFloating','FullMeltOnPartiallyFloating']) + +- if not m.strcmp(self.migration,'None'): ++ if(not m.strcmp(self.migration,'None') and md.transient.isgroundingline and solution=='TransientSolution'): + if np.any(np.isnan(md.geometry.bed)): + md.checkmessage("requesting grounding line migration, but bathymetry is absent!") + pos=np.nonzero(md.mask.groundedice_levelset>0.)[0] +Index: ../trunk-jpl/src/m/classes/groundingline.js +=================================================================== +--- ../trunk-jpl/src/m/classes/groundingline.js (revision 23354) ++++ ../trunk-jpl/src/m/classes/groundingline.js (revision 23355) +@@ -28,7 +28,7 @@ + checkfield(md,'fieldname','groundingline.friction_interpolation','values',['NoFrictionOnPartiallyFloating', 'SubelementFriction1', 'SubelementFriction2']); + checkfield(md,'fieldname','groundingline.melt_interpolation','values',['NoMeltOnPartiallyFloating', 'SubelementMelt1', 'SubelementMelt2', 'FullMeltOnPartiallyFloating']); + +- if (this.migration !='None'){ ++ if(this.migration !='None' & md.trans.isgroundingline==1 & solution == 'TransientSolution'){ + if (isNaN(md.geometry.bed)){ + md.checkmessage('requesting grounding line migration, but bathymetry is absent!'); + } Index: /issm/oecreview/Archive/23185-23389/ISSM-23357-23358.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23357-23358.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23357-23358.diff (revision 23390) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/m4/issm_options.m4 +=================================================================== +--- ../trunk-jpl/m4/issm_options.m4 (revision 23357) ++++ ../trunk-jpl/m4/issm_options.m4 (revision 23358) +@@ -2269,6 +2269,9 @@ + if test "$HAVE_ADOLC" = "yes" && test "$HAVE_CODIPACK" = "yes" ; then + AC_MSG_ERROR([cannot compile ISSM with both ADOLC and CoDiPack]); + fi ++ if test "$HAVE_ADJOINTMPI" = "yes" && test "$HAVE_MEDIPACK" = "yes" ; then ++ AC_MSG_ERROR([cannot compile ISSM with both MeDiPack and AdjointMPI]); ++ fi + dnl check that if we run meteoio, we have snowpack also + if test "$HAVE_METEOIO" = "yes" && test "$HAVE_SNOWPACK" = "no" ; then + AC_MSG_ERROR([cannot compile MeteoIO package without Snowpack!]); Index: /issm/oecreview/Archive/23185-23389/ISSM-23358-23359.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23358-23359.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23358-23359.diff (revision 23390) @@ -0,0 +1,28 @@ +Index: ../trunk-jpl/test/NightlyRun/test3480.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3480.m (revision 23358) ++++ ../trunk-jpl/test/NightlyRun/test3480.m (revision 23359) +@@ -55,9 +55,6 @@ + md.autodiff.dependents{1} = dependent('name','Outputdefinition1','type','scalar','fos_reverse_index',1); + md.inversion.maxiter = 2; + md.cluster=generic('name',oshostname(),'np',3); +-if IssmConfig('_HAVE_CODIPACK_') +- md.cluster.np=1; +-end + md=solve(md,'transient'); + + %Fields and tolerances to track changes +Index: ../trunk-jpl/test/NightlyRun/test3481.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test3481.m (revision 23358) ++++ ../trunk-jpl/test/NightlyRun/test3481.m (revision 23359) +@@ -61,9 +61,6 @@ + md.autodiff.dependents{1} = dependent('name','Outputdefinition1','type','scalar','fos_reverse_index',1); + md.inversion.maxiter = 2; + md.cluster=generic('name',oshostname(),'np',3); +-if IssmConfig('_HAVE_CODIPACK_') +- md.cluster.np=1; +-end + md=solve(md,'transient'); + + %Fields and tolerances to track changes Index: /issm/oecreview/Archive/23185-23389/ISSM-23365-23366.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23365-23366.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23365-23366.diff (revision 23390) @@ -0,0 +1,1114 @@ +Index: ../trunk-jpl/src/c/analyses/SmbAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/SmbAnalysis.cpp (revision 23365) ++++ ../trunk-jpl/src/c/analyses/SmbAnalysis.cpp (revision 23366) +@@ -37,7 +37,6 @@ + + /*Figure out smb model: */ + iomodel->FindConstant(&smb_model,"md.smb.model"); +- + switch(smb_model){ + case SMBforcingEnum: + iomodel->FetchDataToInput(elements,"md.smb.mass_balance",SmbMassBalanceEnum,0.); +@@ -151,6 +150,12 @@ + iomodel->FetchDataToInput(elements,"md.smb.melt",SmbMeltEnum,0.); + iomodel->FetchDataToInput(elements,"md.smb.refreeze",SmbRefreezeEnum,0.); + break; ++ case SMBgradientscomponentsEnum: ++ iomodel->FetchDataToInput(elements,"md.smb.accualti",SmbAccualtiEnum); ++ iomodel->FetchDataToInput(elements,"md.smb.accugrad",SmbAccugradEnum); ++ iomodel->FetchDataToInput(elements,"md.smb.runoffalti",SmbRunoffaltiEnum); ++ iomodel->FetchDataToInput(elements,"md.smb.runoffgrad",SmbRunoffgradEnum); ++ break; + default: + _error_("Surface mass balance model "<AddObject(iomodel->CopyConstantObject("md.smb.accualti",SmbAccualtiEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.smb.accugrad",SmbAccugradEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.smb.runoffalti",SmbRunoffaltiEnum)); ++ parameters->AddObject(iomodel->CopyConstantObject("md.smb.runoffgrad",SmbRunoffgradEnum)); ++ ++ iomodel->FetchData(&temp,&N,&M,"md.smb.accuref"); _assert_(N==2); ++ parameters->AddObject(new TransientParam(SmbAccurefEnum,&temp[0],&temp[M],interp,M)); ++ iomodel->DeleteData(temp,"md.smb.accuref"); ++ ++ iomodel->FetchData(&temp,&N,&M,"md.smb.runoffref"); _assert_(N==2); ++ parameters->AddObject(new TransientParam(SmbRunoffrefEnum,&temp[0],&temp[M],interp,M)); ++ iomodel->DeleteData(temp,"md.smb.runoffref"); ++ break; + default: + _error_("Surface mass balance model "<ela[v]){ ++ if(s[v]>ela[v]){ + smb[v]=b_pos[v]*(s[v]-ela[v]); + } + // if surface is below or equal to the ELA +@@ -166,7 +166,7 @@ + // INPUT parameters: ni: working size of arrays + // INPUT: surface elevation (m): hd(NA) + // monthly mean surface sealevel temperature (degrees C): vTempsea(NA +- // ,NTIME) ++ // ,NTIME) + // monthly mean precip rate (m/yr water equivalent): vPrec(NA,NTIME) + // OUTPUT: mass-balance (m/yr ice): agd(NA) + // mean annual surface temperature (degrees C): Tsurf(NA) +@@ -173,13 +173,13 @@ + + int i, it, jj, itm; + IssmDouble DT = 0.02, sigfac, snormfac; +- IssmDouble signorm = 5.5; // signorm : sigma of the temperature distribution for a normal day ++ IssmDouble signorm = 5.5; // signorm : sigma of the temperature distribution for a normal day + IssmDouble siglim; // sigma limit for the integration which is equal to 2.5 sigmanorm + IssmDouble signormc = signorm - 0.5; // sigma of the temperature distribution for cloudy day + IssmDouble siglimc, siglim0, siglim0c; + IssmDouble tstep, tsint, tint, tstepc; + int NPDMAX = 1504, NPDCMAX = 1454; +- //IssmDouble pdds[NPDMAX]={0}; ++ //IssmDouble pdds[NPDMAX]={0}; + //IssmDouble pds[NPDCMAX]={0}; + IssmDouble pddt, pd ; // pd : snow/precip fraction, precipitation falling as snow + IssmDouble PDup, PDCUT = 2.0; // PDcut: rain/snow cutoff temperature (C) +@@ -192,8 +192,8 @@ + IssmDouble *pds = NULL; + Element *element = NULL; + +- pdds=xNew(NPDMAX+1); +- pds=xNew(NPDCMAX+1); ++ pdds=xNew(NPDMAX+1); ++ pds=xNew(NPDCMAX+1); + + // Get ismungsm parameter + femmodel->parameters->FindParam(&ismungsm,SmbIsmungsmEnum); +@@ -215,7 +215,7 @@ + itm = reCast((2*siglim/DT + 1.5)); + + if(itm >= NPDMAX) _error_("increase NPDMAX in massBalance.cpp"); +- for(it = 0; it < itm; it++){ ++ for(it = 0; it < itm; it++){ + // tstar = REAL(it)*DT-siglim; + tstar = it*DT-siglim; + tint = tsint; +@@ -262,10 +262,10 @@ + xDelete(pds); + }/*}}}*/ + void PositiveDegreeDaySicopolisx(FemModel* femmodel){/*{{{*/ +- ++ + bool isfirnwarming; + femmodel->parameters->FindParam(&isfirnwarming,SmbIsfirnwarmingEnum); +- ++ + for(int i=0;ielements->Size();i++){ + Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); + element->PositiveDegreeDaySicopolis(isfirnwarming); +@@ -356,9 +356,9 @@ + + /*Allocate all arrays*/ + int numvertices = element->GetNumberOfVertices(); +- IssmDouble* acc = xNew(numvertices); ++ IssmDouble* acc = xNew(numvertices); + IssmDouble* evap = xNew(numvertices); +- IssmDouble* runoff = xNew(numvertices); ++ IssmDouble* runoff = xNew(numvertices); + IssmDouble* smb = xNew(numvertices); + + /*Recover Smb Components*/ +@@ -398,7 +398,7 @@ + /*Allocate all arrays*/ + int numvertices = element->GetNumberOfVertices(); + IssmDouble* acc = xNew(numvertices); +- IssmDouble* evap = xNew(numvertices); ++ IssmDouble* evap = xNew(numvertices); + IssmDouble* melt = xNew(numvertices); + IssmDouble* refreeze = xNew(numvertices); + IssmDouble* smb = xNew(numvertices); +@@ -424,3 +424,16 @@ + } + + }/*}}}*/ ++void SmbGradientsComponentsx(FemModel* femmodel){/*{{{*/ ++ ++ // void SurfaceMassBalancex(hd,agd,ni){ ++ // INPUT parameters: ni: working size of arrays ++ // INPUT: surface elevation (m): hd(NA) ++ // OUTPUT: mass-balance (m/yr ice): agd(NA) ++ ++ for(int i=0;ielements->Size();i++){ ++ Element* element=xDynamicCast(femmodel->elements->GetObjectByOffset(i)); ++ element->SmbGradCompParameterization(); ++ } ++ ++}/*}}}*/ +Index: ../trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h +=================================================================== +--- ../trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h (revision 23365) ++++ ../trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h (revision 23366) +@@ -1,6 +1,6 @@ + /*!\file: SurfaceMassBalancex.h + * \brief header file for SMB +- */ ++ */ + + #ifndef _SurfaceMassBalancex_H + #define _SurfaceMassBalancex_H +@@ -18,17 +18,17 @@ + void PositiveDegreeDaySicopolisx(FemModel* femmodel); + void SmbHenningx(FemModel* femmodel); + void SmbComponentsx(FemModel* femmodel); +-void SmbMeltComponentsx(FemModel* femmodel); +- ++void SmbMeltComponentsx(FemModel* femmodel); ++void SmbGradientsComponentsx(FemModel* femmodel); + /*GEMB: */ + void Gembx(FemModel* femmodel); +-void GembgridInitialize(IssmDouble** pdz, int* psize, IssmDouble zTop, IssmDouble dzTop, IssmDouble zMax, IssmDouble zY); ++void GembgridInitialize(IssmDouble** pdz, int* psize, IssmDouble zTop, IssmDouble dzTop, IssmDouble zMax, IssmDouble zY); + IssmDouble Marbouty(IssmDouble T, IssmDouble d, IssmDouble dT); + void grainGrowth(IssmDouble** pre, IssmDouble** pgdn, IssmDouble** pgsp, IssmDouble* T,IssmDouble* dz,IssmDouble* d, IssmDouble* W,IssmDouble smb_dt,int m,int aIdx, int sid); + void albedo(IssmDouble** a,int aIdx, IssmDouble* re, IssmDouble* d, IssmDouble cldFrac, IssmDouble aIce, IssmDouble aSnow, IssmDouble aValue, IssmDouble adThresh, IssmDouble* T, IssmDouble* W, IssmDouble P, IssmDouble EC, IssmDouble t0wet, IssmDouble t0dry, IssmDouble K, IssmDouble dt, IssmDouble dIce, int m, int sid); + void shortwave(IssmDouble** pswf, int swIdx, int aIdx, IssmDouble dsw, IssmDouble as, IssmDouble* d, IssmDouble* dz, IssmDouble* re, IssmDouble dIce, int m, int sid); + void thermo(IssmDouble* pEC, IssmDouble** T, IssmDouble* dz, IssmDouble* d, IssmDouble* swf, IssmDouble dlw, IssmDouble Ta, IssmDouble V, IssmDouble eAir, IssmDouble pAir, IssmDouble teValue, IssmDouble Ws, IssmDouble dt0, int m, IssmDouble Vz, IssmDouble Tz, IssmDouble thermo_scaling, IssmDouble dIce, int sid); +-void accumulation(IssmDouble** pT, IssmDouble** pdz, IssmDouble** pd, IssmDouble** pW, IssmDouble** pa, IssmDouble** pre, IssmDouble** pgdn, IssmDouble** pgsp, int* pm, int aIdx,IssmDouble Ta, IssmDouble P, IssmDouble dzMin, IssmDouble aSnow, IssmDouble dIce, int sid); ++void accumulation(IssmDouble** pT, IssmDouble** pdz, IssmDouble** pd, IssmDouble** pW, IssmDouble** pa, IssmDouble** pre, IssmDouble** pgdn, IssmDouble** pgsp, int* pm, int aIdx,IssmDouble Ta, IssmDouble P, IssmDouble dzMin, IssmDouble aSnow, IssmDouble dIce, int sid); + void melt(IssmDouble* pM, IssmDouble* pR, IssmDouble* pmAdd, IssmDouble* pdz_add, IssmDouble** pT, IssmDouble** pd, IssmDouble** pdz, IssmDouble** pW, IssmDouble** pa, IssmDouble** pre, IssmDouble** pgdn, IssmDouble** pgsp, int* pn, IssmDouble dzMin, IssmDouble zMax, IssmDouble zMin, IssmDouble zTop, IssmDouble dIce, int sid); + void densification(IssmDouble** pd,IssmDouble** pdz, IssmDouble* T, IssmDouble* re, int denIdx, IssmDouble C, IssmDouble dt, IssmDouble Tmean, IssmDouble dIce, int m, int sid); + void turbulentFlux(IssmDouble* pshf, IssmDouble* plhf, IssmDouble* pEC, IssmDouble Ta, IssmDouble Ts, IssmDouble V, IssmDouble eAir, IssmDouble pAir, IssmDouble ds, IssmDouble Ws, IssmDouble Vz, IssmDouble Tz, IssmDouble dIce, int sid); +Index: ../trunk-jpl/src/c/classes/Materials/Matpar.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Materials/Matpar.cpp (revision 23365) ++++ ../trunk-jpl/src/c/classes/Materials/Matpar.cpp (revision 23366) +@@ -114,7 +114,7 @@ + iomodel->FindConstant(&this->desfac,"md.smb.desfac"); + iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); + iomodel->FindConstant(&this->rlapslgm,"md.smb.rlapslgm"); +- iomodel->FindConstant(&this->dpermil,"md.smb.dpermil"); ++ iomodel->FindConstant(&this->dpermil,"md.smb.dpermil"); + case SMBgradientsEnum: + /*Nothing to add*/ + break; +@@ -130,6 +130,9 @@ + case SMBmeltcomponentsEnum: + /*Nothing to add*/ + break; ++ case SMBgradientscomponentsEnum: ++ /*Nothing to add*/ ++ break; + default: + _error_("Surface mass balance model "<FetchData(&nature,&nnat,&dummy,"md.materials.nature"); + +- //go through list of materials, and create constant parameters accordingly: +- for(int i=0;iFindConstant(&this->desfac,"md.smb.desfac"); + iomodel->FindConstant(&this->rlaps,"md.smb.rlaps"); + iomodel->FindConstant(&this->rlapslgm,"md.smb.rlapslgm"); +- iomodel->FindConstant(&this->dpermil,"md.smb.dpermil"); ++ iomodel->FindConstant(&this->dpermil,"md.smb.dpermil"); + case SMBgradientsEnum: + /*Nothing to add*/ + break; +@@ -240,7 +243,7 @@ + break; + default: + _error_("Surface mass balance model "<FindConstant(&this->sediment_compressibility,"md.hydrology.sediment_compressibility"); + iomodel->FindConstant(&this->sediment_porosity,"md.hydrology.sediment_porosity"); +@@ -357,7 +360,7 @@ + void Matpar::DeepEcho(void){/*{{{*/ + + this->Echo(); +-} ++} + /*}}}*/ + void Matpar::Echo(void){/*{{{*/ + +@@ -388,18 +391,18 @@ + _printf_(" sediment_compressibility: " << sediment_compressibility << "\n"); + _printf_(" sediment_porosity: " << sediment_porosity << "\n"); + _printf_(" sediment_thickness: " << sediment_thickness << "\n"); +- _printf_(" water_compressibility: " << water_compressibility << "\n"); +- _printf_(" epl_compressibility: " << epl_compressibility << "\n"); +- _printf_(" epl_porosity: " << epl_porosity << "\n"); +- _printf_(" epl_init_thickness: " << epl_init_thickness << "\n"); +- _printf_(" epl_colapse_thickness: " << epl_colapse_thickness << "\n"); +- _printf_(" epl_max_thickness: " << epl_max_thickness << "\n"); +- _printf_(" epl_conductivity: " << epl_conductivity << "\n"); +- _printf_(" lithosphere_shear_modulus: " << lithosphere_shear_modulus << "\n"); +- _printf_(" lithosphere_density: " << lithosphere_density << "\n"); +- _printf_(" mantle_shear_modulus: " << mantle_shear_modulus << "\n"); +- _printf_(" mantle_density: " << mantle_density << "\n"); +- _printf_(" earth_density: " << earth_density << "\n"); ++ _printf_(" water_compressibility: " << water_compressibility << "\n"); ++ _printf_(" epl_compressibility: " << epl_compressibility << "\n"); ++ _printf_(" epl_porosity: " << epl_porosity << "\n"); ++ _printf_(" epl_init_thickness: " << epl_init_thickness << "\n"); ++ _printf_(" epl_colapse_thickness: " << epl_colapse_thickness << "\n"); ++ _printf_(" epl_max_thickness: " << epl_max_thickness << "\n"); ++ _printf_(" epl_conductivity: " << epl_conductivity << "\n"); ++ _printf_(" lithosphere_shear_modulus: " << lithosphere_shear_modulus << "\n"); ++ _printf_(" lithosphere_density: " << lithosphere_density << "\n"); ++ _printf_(" mantle_shear_modulus: " << mantle_shear_modulus << "\n"); ++ _printf_(" mantle_density: " << mantle_density << "\n"); ++ _printf_(" earth_density: " << earth_density << "\n"); + return; + } + /*}}}*/ +@@ -519,7 +522,7 @@ + case SmbDpermilEnum: + this->dpermil=constant; + break; +- default: ++ default: + break; + } + +Index: ../trunk-jpl/src/c/classes/Elements/Element.h +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.h (revision 23365) ++++ ../trunk-jpl/src/c/classes/Elements/Element.h (revision 23366) +@@ -1,8 +1,8 @@ + /*!\file: Element.h + * \brief abstract class for Element object +- * This class is a place holder for the Tria and the Penta elements. ++ * This class is a place holder for the Tria and the Penta elements. + * It is derived from Element, so DataSets can contain them. +- */ ++ */ + + #ifndef _ELEMENT_H_ + #define _ELEMENT_H_ +@@ -49,7 +49,7 @@ + int* element_type_list; + int element_type; + +- public: ++ public: + /*Constructors/Destructores*/ + Element(); + ~Element(); +@@ -67,6 +67,7 @@ + void DeleteMaterials(void); + void Delta18oParameterization(void); + void Delta18opdParameterization(void); ++ void SmbGradCompParameterization(void); + IssmDouble Divergence(void); + void dViscositydBFS(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input,Input* vz_input); + void dViscositydBHO(IssmDouble* pdmudB,int dim,IssmDouble* xyz_list,Gauss* gauss,Input* vx_input,Input* vy_input); +@@ -129,16 +130,16 @@ + void InputUpdateFromConstant(IssmDouble constant, int name); + void InputUpdateFromConstant(int constant, int name); + void InputUpdateFromConstant(bool constant, int name); +- bool IsFloating(); ++ bool IsFloating(); + bool IsIceInElement(); + bool IsLandInElement(); + bool IsWaterInElement(); +- void LinearFloatingiceMeltingRate(); +- void SpatialLinearFloatingiceMeltingRate(); +- void MantlePlumeGeothermalFlux(); ++ void LinearFloatingiceMeltingRate(); ++ void SpatialLinearFloatingiceMeltingRate(); ++ void MantlePlumeGeothermalFlux(); + void MarshallElement(char** pmarshalled_data,int* pmarshalled_data_size, int marshall_direction,int numanalyses); + void MigrateGroundingLine(IssmDouble* sheet_ungrounding); +- void MismipFloatingiceMeltingRate(); ++ void MismipFloatingiceMeltingRate(); + void MungsmtpParameterization(void); + ElementMatrix* NewElementMatrix(int approximation_enum=NoneApproximationEnum); + ElementMatrix* NewElementMatrixCoupling(int number_nodes,int approximation_enum=NoneApproximationEnum); +@@ -240,7 +241,7 @@ + virtual void InputUpdateFromSolutionOneDof(IssmDouble* solution,int inputenum)=0; + virtual bool IsFaceOnBoundary(void)=0; + virtual bool IsIcefront(void)=0; +- virtual bool IsNodeOnShelfFromFlags(IssmDouble* flags)=0; ++ virtual bool IsNodeOnShelfFromFlags(IssmDouble* flags)=0; + virtual bool IsOnBase()=0; + virtual bool IsOnSurface()=0; + virtual bool IsZeroLevelset(int levelset_enum)=0; +@@ -330,7 +331,7 @@ + virtual IssmDouble GetAreaSpherical(void)=0; + virtual IssmDouble OceanAverage(IssmDouble* Sg)=0; + virtual IssmDouble OceanArea(void)=0; +- virtual void SealevelriseMomentOfInertia(IssmDouble* dI_list,IssmDouble* Sg_old,IssmDouble eartharea)=0; ++ virtual void SealevelriseMomentOfInertia(IssmDouble* dI_list,IssmDouble* Sg_old,IssmDouble eartharea)=0; + virtual void SealevelriseEustatic(Vector* pSgi,IssmDouble* peustatic,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble oceanarea,IssmDouble eartharea)=0; + virtual void SealevelriseNonEustatic(Vector* pSgo,IssmDouble* Sg_old,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble eartharea)=0; + virtual void SealevelriseGeodetic(Vector* pUp,Vector* pNorth,Vector* pEast,IssmDouble* Sg,IssmDouble* latitude,IssmDouble* longitude,IssmDouble* radius,IssmDouble* xx,IssmDouble* yy,IssmDouble* zz,IssmDouble eartharea,int horiz)=0; +Index: ../trunk-jpl/src/c/classes/Elements/Element.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 23365) ++++ ../trunk-jpl/src/c/classes/Elements/Element.cpp (revision 23366) +@@ -654,6 +654,76 @@ + + } + /*}}}*/ ++void Element::SmbGradCompParameterization(void){/*{{{*/ ++ ++ /*Are we on the base? If not, return*/ ++ if(!IsOnBase()) return; ++ int numvertices = this->GetNumberOfVertices(); ++ ++ int i; ++ IssmDouble accuref, runoffref; //reference values at given altitude ++ IssmDouble accualti, runoffalti; //reference altitudes ++ IssmDouble accugrad, runoffgrad; //gradients from reference altitude ++ IssmDouble rho_water, rho_ice; ++ IssmDouble time; ++ ++ IssmDouble* smb = xNew(numvertices); ++ IssmDouble* surf = xNew(numvertices); ++ IssmDouble* accu = xNew(numvertices); ++ IssmDouble* runoff = xNew(numvertices); ++ ++ /*Get material parameters :*/ ++ rho_water=this->matpar->GetMaterialParameter(MaterialsRhoSeawaterEnum); ++ rho_ice=this->matpar->GetMaterialParameter(MaterialsRhoIceEnum); ++ ++ /*Recover parameters*/ ++ parameters->FindParam(&time,TimeEnum); ++ parameters->FindParam(&accualti,SmbAccualtiEnum); ++ parameters->FindParam(&accugrad,SmbAccugradEnum); ++ parameters->FindParam(&runoffalti,SmbRunoffaltiEnum); ++ parameters->FindParam(&runoffgrad,SmbRunoffgradEnum); ++ ++ /*Recover reference values at current time*/ ++ parameters->FindParam(&accuref,SmbAccurefEnum,time); ++ parameters->FindParam(&runoffref,SmbRunoffrefEnum,time); ++ ++ /*Recover surface elevation*/ ++ GetInputListOnVertices(&surf[0],SurfaceEnum); ++ ++ /*Compute the temperature and precipitation*/ ++ for(int iv=0;ivObjectEnum()){ ++ case TriaEnum: ++ this->inputs->AddInput(new TriaInput(SmbMassBalanceEnum,&smb[0],P1Enum)); ++ this->inputs->AddInput(new TriaInput(SmbRunoffEnum,&runoff[0],P1Enum)); ++ break; ++ case PentaEnum: ++ this->inputs->AddInput(new PentaInput(SmbMassBalanceEnum,&smb[0],P1Enum)); ++ this->inputs->AddInput(new PentaInput(SmbRunoffEnum,&runoff[0],P1Enum)); ++ this->InputExtrude(SmbMassBalanceEnum,-1); ++ this->InputExtrude(SmbRunoffEnum,-1); ++ break; ++ case TetraEnum: ++ this->inputs->AddInput(new TetraInput(SmbMassBalanceEnum,&smb[0],P1Enum)); ++ this->inputs->AddInput(new TetraInput(SmbRunoffEnum,&runoff[0],P1Enum)); ++ this->InputExtrude(SmbMassBalanceEnum,-1); ++ this->InputExtrude(SmbRunoffEnum,-1); ++ break; ++ default: _error_("Not implemented yet"); ++ } ++ /* this->AddInput(SmbMassBalanceEnum,smb,P1Enum); */ ++ /* this->AddInput(SmbRunoffEnum,runoff,P1Enum); */ ++ /*clean-up*/ ++ xDelete(surf); ++ xDelete(accu); ++ xDelete(runoff); ++ xDelete(smb); ++} ++/*}}}*/ + IssmDouble Element::Divergence(void){/*{{{*/ + /*Compute element divergence*/ + +@@ -2587,17 +2657,17 @@ + /*Get material parameters :*/ + rho_water=this->matpar->GetMaterialParameter(MaterialsRhoSeawaterEnum); + rho_ice=this->matpar->GetMaterialParameter(MaterialsRhoIceEnum); +- ++ + /*Get parameters for height corrections*/ + desfac=this->matpar->GetMaterialParameter(SmbDesfacEnum); + rlaps=this->matpar->GetMaterialParameter(SmbRlapsEnum); +- ++ + /*Recover monthly temperatures and precipitation*/ + Input* input=this->inputs->GetInput(SmbMonthlytemperaturesEnum); _assert_(input); + Input* input2=this->inputs->GetInput(SmbPrecipitationEnum); _assert_(input2); + /*Recover smb correction term */ + Input* input3=this->inputs->GetInput(SmbSmbCorrEnum); _assert_(input3); +- ++ + /* Get time */ + this->parameters->FindParam(&time,TimeEnum); + this->parameters->FindParam(&yts,ConstantsYtsEnum); +@@ -2606,7 +2676,7 @@ + /* Set parameters for finrnwarming */ + IssmDouble MU_0 = 9.7155; //Firn-warming correction, in (d*deg C)/(mm WE) + IssmDouble mu = MU_0*(1000.0*86400.0)*(rho_ice/rho_water); // (d*deg C)/(mm WE) --> (s*deg C)/(m IE) +- ++ + /*loop over vertices: */ + Gauss* gauss=this->NewGauss(); + for(int month=0;month<12;month++){ +@@ -2637,8 +2707,8 @@ + smb[iv] = smb[iv]+smbcorr[iv]; + /*Get yearlytemperatures */ + for(int month=0;month<12;month++) yearlytemperatures[iv]=yearlytemperatures[iv]+((monthlytemperatures[iv*12+month]+273.15)+t_ampl[iv])*inv_twelve; // Has to be in Kelvin +- +- if(isfirnwarming){ ++ ++ if(isfirnwarming){ + if(melt_star[iv]>=melt[iv]){ + yearlytemperatures[iv]= yearlytemperatures[iv]+mu*(melt_star[iv]-melt[iv]); + } +@@ -2719,8 +2789,8 @@ + xDelete(s); + xDelete(s0t); + xDelete(s0p); +- xDelete(t_ampl); +- xDelete(p_ampl); ++ xDelete(t_ampl); ++ xDelete(p_ampl); + xDelete(smbcorr); + xDelete(melt_star); + } +@@ -2732,8 +2802,8 @@ + + /*Some intputs need to be computed, even if they are already in inputs, they might not be up to date!*/ + switch(output_enum){ +- case ViscousHeatingEnum: this->ViscousHeatingCreateInput(); break; +- case StressMaxPrincipalEnum: this->StressMaxPrincipalCreateInput(); break; ++ case ViscousHeatingEnum: this->ViscousHeatingCreateInput(); break; ++ case StressMaxPrincipalEnum: this->StressMaxPrincipalCreateInput(); break; + case StressTensorxxEnum: + case StressTensorxyEnum: + case StressTensorxzEnum: +@@ -2746,7 +2816,7 @@ + case StrainRateyyEnum: + case StrainRateyzEnum: + case StrainRatezzEnum: +- case StrainRateeffectiveEnum: this->ComputeStrainRate(); break; ++ case StrainRateeffectiveEnum: this->ComputeStrainRate(); break; + case DeviatoricStressxxEnum: + case DeviatoricStressxyEnum: + case DeviatoricStressxzEnum: +Index: ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23365) ++++ ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23366) +@@ -104,7 +104,6 @@ + iomodel->FetchDataToInput(elements,"md.mesh.vertexonbase",MeshVertexonbaseEnum); + iomodel->FetchDataToInput(elements,"md.mesh.vertexonsurface",MeshVertexonsurfaceEnum); + } +- + if(isefficientlayer){ + iomodel->FetchDataToInput(elements,"md.hydrology.mask_eplactive_node",HydrologydcMaskEplactiveNodeEnum); + iomodel->FetchDataToInput(elements,"md.initialization.epl_head",EplHeadHydrostepEnum); +@@ -341,14 +340,16 @@ + + /*Intermediaries */ + bool active_element,isefficientlayer; ++ int smb_model; + IssmDouble dt,scalar,sediment_storing; + IssmDouble water_head,sediment_transmitivity; +- IssmDouble water_load,transfer; ++ IssmDouble water_load,runoff_value,transfer; + IssmDouble Jdet; + + IssmDouble *xyz_list = NULL; + Input* active_element_input = NULL; +- Input* old_wh_input = NULL; ++ Input* old_wh_input = NULL; ++ Input* surface_runoff_input = NULL; + + /*Fetch number of nodes and dof for this finite element*/ + int numnodes = basalelement->GetNumberOfNodes(); +@@ -360,18 +361,23 @@ + /*Retrieve all inputs and parameters*/ + basalelement->GetVerticesCoordinates(&xyz_list); + //basalelement->FindParam(&dt,TimesteppingTimeStepEnum); +- basalelement ->FindParam(&dt,HydrologydtEnum); ++ basalelement->FindParam(&dt,HydrologydtEnum); + basalelement->FindParam(&isefficientlayer,HydrologydcIsefficientlayerEnum); ++ basalelement->FindParam(&smb_model,SmbEnum); + +- Input* sed_head_input = basalelement->GetInput(SedimentHeadHydrostepEnum); +- Input* epl_head_input = basalelement->GetInput(EplHeadHydrostepEnum); +- Input* base_input = basalelement->GetInput(BaseEnum); +- Input* water_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(water_input); +- Input* SedTrans_input = basalelement->GetInput(HydrologydcSedimentTransmitivityEnum); _assert_(SedTrans_input); ++ Input* sed_head_input = basalelement->GetInput(SedimentHeadHydrostepEnum); ++ Input* epl_head_input = basalelement->GetInput(EplHeadHydrostepEnum); ++ Input* base_input = basalelement->GetInput(BaseEnum); ++ Input* basal_melt_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(basal_melt_input); ++ Input* SedTrans_input = basalelement->GetInput(HydrologydcSedimentTransmitivityEnum); _assert_(SedTrans_input); + + if(dt!= 0.){ + old_wh_input = basalelement->GetInput(SedimentHeadOldEnum); _assert_(old_wh_input); + } ++ if(smb_model==SMBgradientscomponentsEnum){ ++ surface_runoff_input = basalelement->GetInput(SmbRunoffEnum); ++ } ++ + /*Transfer related Inputs*/ + if(isefficientlayer){ + active_element_input = basalelement->GetInput(HydrologydcMaskEplactiveEltEnum); _assert_(active_element_input); +@@ -387,8 +393,9 @@ + + /*Loading term*/ + if(!isefficientlayer){ +- water_input->GetInputValue(&water_load,gauss); +- scalar = Jdet*gauss->weight*(water_load); ++ basal_melt_input->GetInputValue(&water_load,gauss); ++ surface_runoff_input->GetInputValue(&runoff_value,gauss); ++ scalar = Jdet*gauss->weight*(water_load+runoff_value); + //scalar = Jdet*gauss->weight*(water_load)/sediment_transmitivity; + if(dt!=0.) scalar = scalar*dt; + for(int i=0;iGetInputValue(&active_element); + if(!active_element){ +- water_input->GetInputValue(&water_load,gauss); +- scalar = Jdet*gauss->weight*(water_load); ++ basal_melt_input->GetInputValue(&water_load,gauss); ++ surface_runoff_input->GetInputValue(&runoff_value,gauss); ++ scalar = Jdet*gauss->weight*(water_load+runoff_value); + //scalar = Jdet*gauss->weight*(water_load)/sediment_transmitivity; + if(dt!=0.) scalar = scalar*dt; + for(int i=0;iGetNumberOfNodes(); +@@ -333,17 +335,22 @@ + basalelement->GetVerticesCoordinates(&xyz_list); + //basalelement->FindParam(&dt,TimesteppingTimeStepEnum); + basalelement ->FindParam(&dt,HydrologydtEnum); ++ basalelement ->FindParam(&smb_model,SmbEnum); + +- Input* epl_thick_input = basalelement->GetInput(HydrologydcEplThicknessHydrostepEnum); _assert_(epl_thick_input); +- Input* sed_head_input = basalelement->GetInput(SedimentHeadHydrostepEnum); _assert_(sed_head_input); +- Input* epl_head_input = basalelement->GetInput(EplHeadHydrostepEnum); _assert_(epl_head_input); +- Input* water_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(water_input); +- Input* residual_input = basalelement->GetInput(SedimentHeadResidualEnum); _assert_(residual_input); +- Input* base_input = basalelement->GetInput(BaseEnum); _assert_(base_input); ++ Input* epl_thick_input = basalelement->GetInput(HydrologydcEplThicknessHydrostepEnum); _assert_(epl_thick_input); ++ Input* sed_head_input = basalelement->GetInput(SedimentHeadHydrostepEnum); _assert_(sed_head_input); ++ Input* epl_head_input = basalelement->GetInput(EplHeadHydrostepEnum); _assert_(epl_head_input); ++ Input* basal_melt_input = basalelement->GetInput(BasalforcingsGroundediceMeltingRateEnum); _assert_(basal_melt_input); ++ Input* residual_input = basalelement->GetInput(SedimentHeadResidualEnum); _assert_(residual_input); ++ Input* base_input = basalelement->GetInput(BaseEnum); _assert_(base_input); + + if(dt!= 0.){ + old_wh_input = basalelement->GetInput(EplHeadOldEnum); _assert_(old_wh_input); + } ++ if(smb_model==SMBgradientscomponentsEnum){ ++ surface_runoff_input = basalelement->GetInput(SmbRunoffEnum); ++ } ++ + /* Start looping on the number of gaussian points: */ + Gauss* gauss = basalelement->NewGauss(2); + for(int ig=gauss->begin();igend();ig++){ +@@ -354,8 +361,9 @@ + epl_transmitivity = EplTransmitivity(basalelement,gauss,epl_thick_input,epl_head_input,base_input); + + /*Loading term*/ +- water_input->GetInputValue(&water_load,gauss); +- scalar = Jdet*gauss->weight*(water_load); ++ basal_melt_input->GetInputValue(&water_load,gauss); ++ surface_runoff_input->GetInputValue(&runoff_value,gauss); ++ scalar = Jdet*gauss->weight*(water_load+runoff_value); + //scalar = Jdet*gauss->weight*(water_load)/epl_transmitivity; + if(dt!=0.) scalar = scalar*dt; + for(int i=0;ivalues[i]+=scalar*basis[i]; +@@ -523,6 +531,7 @@ + IssmDouble dt,A; + IssmDouble EPLgrad2; + IssmDouble EPL_N; ++ IssmDouble opening,closing; + + femmodel->parameters->FindParam(&domaintype,DomainTypeEnum); + femmodel->parameters->FindParam(&iseplthickcomp,HydrologydcEplThickCompEnum); +@@ -588,9 +597,22 @@ + /*Get then the square of the gradient of EPL heads*/ + EPLgrad2 = (epl_slopeX[i]*epl_slopeX[i])+(epl_slopeY[i]*epl_slopeY[i]); + /*And proceed to the real thing*/ +- thickness[i] = old_thickness[i]/(1.0 +- -((rho_water*gravity*epl_conductivity*EPLgrad2*dt)/(rho_ice*latentheat)) +- +((2.0*A*dt*pow(EPL_N,n))/(pow(n,n)))); ++ opening=(rho_water*gravity*epl_conductivity*EPLgrad2*dt)/(rho_ice*latentheat); ++ closing=(2.0*A*dt*pow(EPL_N,n))/(pow(n,n)); ++ /*implicit*/ ++ thickness[i] = old_thickness[i]/(1.0-opening+closing); ++ /*explicit*/ ++ //thickness[i] = old_thickness[i]*(1.0+opening-closing); ++ /*centered*/ ++ //thickness[i] = old_thickness[i]*(1.0+opening-closing)/(1.0-opening+closing); ++ ++ if(element->nodes[i]->Sid()==2299){ ++ printf("for node %i \n",element->nodes[i]->Sid()); ++ printf(" old thickness is %g \n",old_thickness[i]); ++ printf(" new thickness is %g \n",thickness[i]); ++ printf(" closing is %g \n",((2.0*A*dt*pow(EPL_N,n))/(pow(n,n)))); ++ printf(" opening is %g \n",((rho_water*gravity*epl_conductivity*EPLgrad2*dt)/(rho_ice*latentheat))); ++ } + /*Take care of otherthikening*/ + if(thickness[i]>max_thick){ + thickness[i] = max_thick; +@@ -688,7 +710,11 @@ + if(old_active[i]>0.){ + vec_mask->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + /* If epl thickness gets under colapse thickness, close the layer */ ++ if(element->nodes[i]->Sid()==2299){ ++ printf("thickness for maksing for node %i is %g \n",element->nodes[i]->Sid(),epl_thickness[i]);} + if(epl_thickness[i]nodes[i]->Sid()==2299){ ++ printf("maksing node %i\n",element->nodes[i]->Sid());} + vec_mask->SetValue(basalelement->nodes[i]->Sid(),0.,INS_VAL); + recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + } +Index: ../trunk-jpl/src/c/cores/transient_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/transient_core.cpp (revision 23365) ++++ ../trunk-jpl/src/c/cores/transient_core.cpp (revision 23366) +@@ -179,7 +179,7 @@ + /*Put +9999 for places where there is no ice!*/ + for(int i=0;i0.) icebase_oceangrid[i]=+9999.; + xDelete(icemask_oceangrid); +- ++ + if(my_rank==0){ + ISSM_MPI_Send(icebase_oceangrid,ngrids_ocean,ISSM_MPI_DOUBLE,0,10001008,tomitgcmcomm); + } +@@ -383,6 +383,9 @@ + thermal_core(femmodel); + } + ++ /*duplicating smb position to have runoff value*/ ++ if(issmb) smb_core(femmodel); ++ + if(ishydrology) hydrology_core(femmodel); + + if(isstressbalance) stressbalance_core(femmodel); +@@ -392,7 +395,6 @@ + if(ismovingfront) movingfront_core(femmodel); + + /* from here on, prepare geometry for next time step*/ +- + if(issmb) smb_core(femmodel); + + if(ismasstransport){ +@@ -402,10 +404,10 @@ + } + + if(isgroundingline){ +- ++ + /*Start profiler*/ + femmodel->profiler->Start(GROUNDINGLINECORE); +- ++ + if(VerboseSolution()) _printf0_(" computing new grounding line position\n"); + GroundinglineMigrationx(femmodel->elements,femmodel->nodes,femmodel->vertices,femmodel->loads,femmodel->materials,femmodel->parameters); + +@@ -415,7 +417,7 @@ + extrudefrombase_core(femmodel); + femmodel->parameters->SetParam(SurfaceEnum,InputToExtrudeEnum); + extrudefrombase_core(femmodel); +- ++ + /*Stop profiler*/ + femmodel->profiler->Stop(GROUNDINGLINECORE); + Index: /issm/oecreview/Archive/23185-23389/ISSM-23366-23367.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23366-23367.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23366-23367.diff (revision 23390) @@ -0,0 +1,25 @@ +Index: ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 23366) ++++ ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 23367) +@@ -606,13 +606,13 @@ + /*centered*/ + //thickness[i] = old_thickness[i]*(1.0+opening-closing)/(1.0-opening+closing); + +- if(element->nodes[i]->Sid()==2299){ +- printf("for node %i \n",element->nodes[i]->Sid()); +- printf(" old thickness is %g \n",old_thickness[i]); +- printf(" new thickness is %g \n",thickness[i]); +- printf(" closing is %g \n",((2.0*A*dt*pow(EPL_N,n))/(pow(n,n)))); +- printf(" opening is %g \n",((rho_water*gravity*epl_conductivity*EPLgrad2*dt)/(rho_ice*latentheat))); +- } ++ /* if(element->nodes[i]->Sid()==2299){ */ ++ /* printf("for node %i \n",element->nodes[i]->Sid()); */ ++ /* printf(" old thickness is %g \n",old_thickness[i]); */ ++ /* printf(" new thickness is %g \n",thickness[i]); */ ++ /* printf(" closing is %g \n",((2.0*A*dt*pow(EPL_N,n))/(pow(n,n)))); */ ++ /* printf(" opening is %g \n",((rho_water*gravity*epl_conductivity*EPLgrad2*dt)/(rho_ice*latentheat))); */ ++ /* } */ + /*Take care of otherthikening*/ + if(thickness[i]>max_thick){ + thickness[i] = max_thick; Index: /issm/oecreview/Archive/23185-23389/ISSM-23367-23368.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23367-23368.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23367-23368.diff (revision 23390) @@ -0,0 +1,20 @@ +Index: ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 23367) ++++ ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 23368) +@@ -710,11 +710,11 @@ + if(old_active[i]>0.){ + vec_mask->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + /* If epl thickness gets under colapse thickness, close the layer */ +- if(element->nodes[i]->Sid()==2299){ +- printf("thickness for maksing for node %i is %g \n",element->nodes[i]->Sid(),epl_thickness[i]);} ++ /* if(element->nodes[i]->Sid()==2299){ */ ++ /* printf("thickness for maksing for node %i is %g \n",element->nodes[i]->Sid(),epl_thickness[i]);} */ + if(epl_thickness[i]nodes[i]->Sid()==2299){ +- printf("maksing node %i\n",element->nodes[i]->Sid());} ++ /* if(element->nodes[i]->Sid()==2299){ */ ++ /* printf("maksing node %i\n",element->nodes[i]->Sid());} */ + vec_mask->SetValue(basalelement->nodes[i]->Sid(),0.,INS_VAL); + recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + } Index: /issm/oecreview/Archive/23185-23389/ISSM-23368-23369.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23368-23369.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23368-23369.diff (revision 23390) @@ -0,0 +1,83 @@ +Index: ../trunk-jpl/test/NightlyRun/runme.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/runme.py (revision 23368) ++++ ../trunk-jpl/test/NightlyRun/runme.py (revision 23369) +@@ -10,7 +10,7 @@ + def runme(id=None,exclude=None,benchmark='nightly',procedure='check',output='none',rank=1,numprocs=1): + """ + RUNME - test deck for ISSM nightly runs +- ++ + In a test deck directory (tests/Vertification/NightlyRun for example) + The following command will launch all the existing tests: + >> runme() +@@ -17,7 +17,7 @@ + To run the tests 101 and 102: + >> runme(id=[101,102]) + etc... +- ++ + Available options: + 'id' followed by the list of ids or (parts of) test names requested + Note: runs all tests by default +@@ -36,10 +36,10 @@ + + 'procedure' 'check' : run the test (default) + 'update': update the archive +- ++ + Usage: + runme(varargin) +- ++ + Examples: + runme() + runme(101) +@@ -48,7 +48,6 @@ + runme(exclude='Dakota',benchmark='all') + runme(id=[[101,102],['Dakota','Slr']]) + """ +- + from parallelrange import parallelrange + from IdToName import IdToName + from arch import archread +@@ -84,13 +83,13 @@ + + i1,i2=parallelrange(rank,numprocs,len(list_ids)) #Get tests for this cpu only + list_ids=list_ids[i1:i2+1] +- +- if np.size(id) > 0: ++ ++ if np.size(id) > 0 and not id==None: + test_ids = set(GetIds(id)).intersection(set(list_ids)) + else: + # if no tests are specifically provided, do them all + test_ids = set(list_ids) +- ++ + # }}} + #GET exclude {{{ + exclude_ids = GetIds(exclude) +@@ -182,7 +181,7 @@ + field = field.T + if np.shape(field) != np.shape(archive): + raise RuntimeError("Field '"+archive_name+"' from test is malformed; shape is "+str(np.shape(field.T))+", should be "+str(np.shape(archive))+" (or "+str(np.shape(archive.T))+").") +- ++ + error_diff=np.amax(np.abs(archive-field),axis=0)/(np.amax(np.abs(archive),axis=0)+float_info.epsilon) + + if not np.isscalar(error_diff): error_diff=error_diff[0] +Index: ../trunk-jpl/test/NightlyRun/test101.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test101.m (revision 23368) ++++ ../trunk-jpl/test/NightlyRun/test101.m (revision 23369) +@@ -3,7 +3,8 @@ + md=setmask(md,'all',''); + md=parameterize(md,'../Par/SquareShelfConstrained.par'); + md=setflowequation(md,'SSA','all'); +-md.cluster=generic('name',oshostname(),'np',2); ++md.cluster=stallo('numnodes',1,'cpuspernode',16,'time',60,'queue','devel') ++%md.cluster=generic('name',oshostname(),'np',2); + + %output + md.stressbalance.requested_outputs={'default','DeviatoricStressxx','DeviatoricStressyy','DeviatoricStressxy','MassFlux1','MassFlux2','MassFlux3','MassFlux4','MassFlux5','MassFlux6'}; Index: /issm/oecreview/Archive/23185-23389/ISSM-23369-23370.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23369-23370.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23369-23370.diff (revision 23390) @@ -0,0 +1,287 @@ +Index: ../trunk-jpl/src/c/cores/transient_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/transient_core.cpp (revision 23369) ++++ ../trunk-jpl/src/c/cores/transient_core.cpp (revision 23370) +@@ -383,7 +383,7 @@ + thermal_core(femmodel); + } + +- /*duplicating smb position to have runoff value*/ ++ /*shifting smb position to have runoff value*/ + if(issmb) smb_core(femmodel); + + if(ishydrology) hydrology_core(femmodel); +@@ -395,7 +395,7 @@ + if(ismovingfront) movingfront_core(femmodel); + + /* from here on, prepare geometry for next time step*/ +- if(issmb) smb_core(femmodel); ++ //if(issmb) smb_core(femmodel); + + if(ismasstransport){ + bmb_core(femmodel); +Index: ../trunk-jpl/src/c/cores/hydrology_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/hydrology_core.cpp (revision 23369) ++++ ../trunk-jpl/src/c/cores/hydrology_core.cpp (revision 23370) +@@ -13,7 +13,7 @@ + + /*Start profiler*/ + femmodel->profiler->Start(HYDROLOGYCORE); +- ++ + /*intermediary*/ + int hydrology_model; + int solution_type; +@@ -49,7 +49,6 @@ + else if (hydrology_model==HydrologydcEnum){ + /*intermediary: */ + bool isefficientlayer; +- bool isthermal; + int step,hydroslices; + IssmDouble time,init_time,hydrotime,yts; + IssmDouble dt,hydrodt; +@@ -61,7 +60,6 @@ + femmodel->parameters->FindParam(&hydroslices,HydrologyStepsPerStepEnum); + femmodel->parameters->FindParam(&yts,ConstantsYtsEnum); + +- femmodel->parameters->FindParam(&isthermal,TransientIsthermalEnum); + /*first we exclude frozen nodes of the solved nodes*/ + femmodel->SetCurrentConfiguration(HydrologyDCInefficientAnalysisEnum); + femmodel->HydrologyIDSupdateDomainx(&ThawedNodes); +@@ -152,7 +150,7 @@ + } + xDelete(requested_outputs); + } +- ++ + /*End profiler*/ + femmodel->profiler->Stop(HYDROLOGYCORE); + } +Index: ../trunk-jpl/src/c/classes/Params/Parameters.cpp +=================================================================== +--- ../trunk-jpl/src/c/classes/Params/Parameters.cpp (revision 23369) ++++ ../trunk-jpl/src/c/classes/Params/Parameters.cpp (revision 23370) +@@ -91,7 +91,7 @@ + return output; + } + /*}}}*/ +-void Parameters::DeepEcho(void){/*{{{*/ ++void Parameters::DeepEcho(void){/*{{{*/ + for(int i=0;iparams[i]) this->params[i]->DeepEcho(); + } +@@ -98,7 +98,7 @@ + return; + } + /*}}}*/ +-void Parameters::Echo(void){/*{{{*/ ++void Parameters::Echo(void){/*{{{*/ + for(int i=0;iparams[i]) this->params[i]->Echo(); + } +@@ -138,7 +138,7 @@ + for(int i=0;iMarshall(pmarshalled_data,pmarshalled_data_size,marshall_direction); + delete fileparam; +- /* No need to add this object, the pointer is not valid ++ /* No need to add this object, the pointer is not valid + The FemModel should reset all FileParams in the restart function */ + } + else if(obj_enum==StringParamEnum){ +@@ -648,7 +648,7 @@ + /*Methods relating to parameters: */ + char* OptionsFromAnalysis(char** pouttoolkit,Parameters* parameters,int analysis_type){ /*{{{*/ + +- /* figure out ISSM options for current analysis, return a string. */ ++ /* figure out ISSM options for current analysis, return a string. */ + + /*output: */ + char *outstring = NULL; +@@ -666,8 +666,8 @@ + int i; + + parameters->FindParam(&strings,&numanalyses,ToolkitsOptionsStringsEnum); +- parameters->FindParam(&toolkits,&dummy,ToolkitsTypesEnum); _assert_(dummy==numanalyses); +- parameters->FindParam(&analyses,&dummy,ToolkitsOptionsAnalysesEnum); _assert_(dummy==numanalyses); ++ parameters->FindParam(&toolkits,&dummy,ToolkitsTypesEnum); _assert_(dummy==numanalyses); ++ parameters->FindParam(&analyses,&dummy,ToolkitsOptionsAnalysesEnum); _assert_(dummy==numanalyses); + + if(numanalyses==0)return NULL; //we did not find petsc options, don't bother. + +@@ -709,16 +709,16 @@ + xDelete(strings); + xDelete(analyses); + return outstring; +-} ++} + /*}}}*/ + void ToolkitsOptionsFromAnalysis(Parameters* parameters,int analysis_type){ /*{{{*/ + + /*!\file: ToolkitsOptionsFromAnalysis.cpp +- * \brief: for each analysis, setup the issmoptions string. +- * This is mainly for the case where we run our toolkits using petsc. In this case, we need to +- * plug our toolkits options directly into the petsc options database. This is the case for each analysis type ++ * \brief: for each analysis, setup the issmoptions string. ++ * This is mainly for the case where we run our toolkits using petsc. In this case, we need to ++ * plug our toolkits options directly into the petsc options database. This is the case for each analysis type + * and parameters +- */ ++ */ + + char* options = NULL; + char* toolkit = NULL; +@@ -730,7 +730,7 @@ + ToolkitOptions::Init(toolkit,options); + + #ifdef _HAVE_PETSC_ +- /*In case we are using PETSC, we do not rely on issmoptions. Instead, we dump issmoptions into the Petsc ++ /*In case we are using PETSC, we do not rely on issmoptions. Instead, we dump issmoptions into the Petsc + * options database: */ + #if (_PETSC_MINOR_>=7) + PetscOptionsSetFromOptions(NULL); +Index: ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 23369) ++++ ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 23370) +@@ -606,13 +606,11 @@ + /*centered*/ + //thickness[i] = old_thickness[i]*(1.0+opening-closing)/(1.0-opening+closing); + +- /* if(element->nodes[i]->Sid()==2299){ */ +- /* printf("for node %i \n",element->nodes[i]->Sid()); */ +- /* printf(" old thickness is %g \n",old_thickness[i]); */ +- /* printf(" new thickness is %g \n",thickness[i]); */ +- /* printf(" closing is %g \n",((2.0*A*dt*pow(EPL_N,n))/(pow(n,n)))); */ +- /* printf(" opening is %g \n",((rho_water*gravity*epl_conductivity*EPLgrad2*dt)/(rho_ice*latentheat))); */ +- /* } */ ++ if(element->nodes[i]->Sid()==2299){ ++ printf("for node %i \n",element->nodes[i]->Sid()); ++ printf(" old thickness is %g \n",old_thickness[i]); ++ printf(" new thickness is %g \n",thickness[i]); ++ } + /*Take care of otherthikening*/ + if(thickness[i]>max_thick){ + thickness[i] = max_thick; +@@ -710,19 +708,12 @@ + if(old_active[i]>0.){ + vec_mask->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + /* If epl thickness gets under colapse thickness, close the layer */ +- /* if(element->nodes[i]->Sid()==2299){ */ +- /* printf("thickness for maksing for node %i is %g \n",element->nodes[i]->Sid(),epl_thickness[i]);} */ + if(epl_thickness[i]nodes[i]->Sid()==2299){ */ +- /* printf("maksing node %i\n",element->nodes[i]->Sid());} */ ++ if(element->nodes[i]->Sid()==2299){ ++ printf("masking node %i with thickness %f\n",element->nodes[i]->Sid(),epl_thickness[i]);} + vec_mask->SetValue(basalelement->nodes[i]->Sid(),0.,INS_VAL); + recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + } +- /* //If epl head gets under base elevation, close the layer */ +- /* else if(eplhead[i]<(base[i]-1.0e-8)){ */ +- /* vec_mask->SetValue(basalelement->nodes[i]->Sid(),0.,INS_VAL); */ +- /* recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); */ +- /* } */ + } + /*If node is now closed bring its thickness back to initial*/ + if (old_active[i]==0.){ +Index: ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23369) ++++ ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23370) +@@ -28,6 +28,8 @@ + char** requestedoutputs = NULL; + + /*retrieve some parameters: */ ++ /* bool issmb; */ ++ /* iomodel->FindConstant(&issmb,"md.transient.issmb"); */ + iomodel->FindConstant(&hydrology_model,"md.hydrology.model"); + + /*Now, do we really want DC?*/ +@@ -62,6 +64,10 @@ + iomodel->FetchData(&sedimentlimit,"md.hydrology.sedimentlimit"); + parameters->AddObject(new DoubleParam(HydrologydcSedimentlimitEnum,sedimentlimit)); + } ++ /* if(!issmb){ */ ++ /* parameters->AddObject(iomodel->CopyConstantObject("md.smb.model",SmbEnum)); */ ++ /* } */ ++ + /*Requested outputs*/ + iomodel->FindConstant(&requestedoutputs,&numoutputs,"md.hydrology.requested_outputs"); + parameters->AddObject(new IntParam(HydrologyNumRequestedOutputsEnum,numoutputs)); +@@ -76,6 +82,8 @@ + + /*Fetch data needed: */ + iomodel->FindConstant(&hydrology_model,"md.hydrology.model"); ++ bool issmb; ++ iomodel->FindConstant(&issmb,"md.transient.issmb"); + + /*Now, do we really want DC?*/ + if(hydrology_model!=HydrologydcEnum) return; +@@ -108,6 +116,10 @@ + iomodel->FetchDataToInput(elements,"md.hydrology.mask_eplactive_node",HydrologydcMaskEplactiveNodeEnum); + iomodel->FetchDataToInput(elements,"md.initialization.epl_head",EplHeadHydrostepEnum); + } ++ if(!issmb){ ++ iomodel->FetchDataToInput(elements,"md.smb.model",SmbEnum); ++} ++ + }/*}}}*/ + + void HydrologyDCInefficientAnalysis::CreateNodes(Nodes* nodes,IoModel* iomodel){/*{{{*/ +@@ -637,9 +649,7 @@ + IssmDouble groundedice; + IssmDouble base_elev,prestep_head,water_sheet; + IssmDouble sediment_thickness = element->GetMaterialParameter(HydrologydcSedimentThicknessEnum); +- bool isthermal; + +- element->FindParam(&isthermal,TransientIsthermalEnum); + element->FindParam(&unconf_scheme,HydrologydcUnconfinedFlagEnum); + SedTrans_input->GetInputValue(&FullLayer_transmitivity,gauss); + +Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 23369) ++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 23370) +@@ -187,7 +187,7 @@ + } + + if(!issmb){ +- iomodel->FetchDataToInput(elements,"md.smb.mass_balance",SmbMassBalanceEnum); ++ iomodel->FetchDataToInput(elements,"md.smb.model",SmbEnum); + } + if(stabilization==3){ + iomodel->FetchDataToInput(elements,"md.masstransport.spcthickness",MasstransportSpcthicknessEnum); //for DG, we need the spc in the element +@@ -628,9 +628,9 @@ + return pe; + }/*}}}*/ + void MasstransportAnalysis::GetB(IssmDouble* B,Element* element,int dim,IssmDouble* xyz_list,Gauss* gauss){/*{{{*/ +- /*Compute B matrix. B=[B1 B2 B3] where Bi is of size 3*NDOF2. ++ /*Compute B matrix. B=[B1 B2 B3] where Bi is of size 3*NDOF2. + * For node i, Bi can be expressed in the actual coordinate system +- * by: ++ * by: + * Bi=[ N ] + * [ N ] + * where N is the finiteelement function for node i. +@@ -656,9 +656,9 @@ + xDelete(basis); + }/*}}}*/ + void MasstransportAnalysis::GetBprime(IssmDouble* Bprime,Element* element,int dim,IssmDouble* xyz_list,Gauss* gauss){/*{{{*/ +- /*Compute B' matrix. B'=[B1' B2' B3'] where Bi' is of size 3*NDOF2. ++ /*Compute B' matrix. B'=[B1' B2' B3'] where Bi' is of size 3*NDOF2. + * For node i, Bi' can be expressed in the actual coordinate system +- * by: ++ * by: + * Bi_prime=[ dN/dx ] + * [ dN/dy ] + * where N is the finiteelement function for node i. Index: /issm/oecreview/Archive/23185-23389/ISSM-23370-23371.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23370-23371.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23370-23371.diff (revision 23390) @@ -0,0 +1,14 @@ +Index: ../trunk-jpl/test/NightlyRun/test101.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test101.m (revision 23370) ++++ ../trunk-jpl/test/NightlyRun/test101.m (revision 23371) +@@ -3,8 +3,7 @@ + md=setmask(md,'all',''); + md=parameterize(md,'../Par/SquareShelfConstrained.par'); + md=setflowequation(md,'SSA','all'); +-md.cluster=stallo('numnodes',1,'cpuspernode',16,'time',60,'queue','devel') +-%md.cluster=generic('name',oshostname(),'np',2); ++md.cluster=generic('name',oshostname(),'np',2); + + %output + md.stressbalance.requested_outputs={'default','DeviatoricStressxx','DeviatoricStressyy','DeviatoricStressxy','MassFlux1','MassFlux2','MassFlux3','MassFlux4','MassFlux5','MassFlux6'}; Index: /issm/oecreview/Archive/23185-23389/ISSM-23371-23372.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23371-23372.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23371-23372.diff (revision 23390) @@ -0,0 +1,13 @@ +Index: ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 23371) ++++ ../trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp (revision 23372) +@@ -187,7 +187,7 @@ + } + + if(!issmb){ +- iomodel->FetchDataToInput(elements,"md.smb.model",SmbEnum); ++ iomodel->FetchDataToInput(elements,"md.smb.mass_balance",SmbMassBalanceEnum); + } + if(stabilization==3){ + iomodel->FetchDataToInput(elements,"md.masstransport.spcthickness",MasstransportSpcthicknessEnum); //for DG, we need the spc in the element Index: /issm/oecreview/Archive/23185-23389/ISSM-23372-23373.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23372-23373.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23372-23373.diff (revision 23390) @@ -0,0 +1,243 @@ +Index: ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 23372) ++++ ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 23373) +@@ -606,11 +606,11 @@ + /*centered*/ + //thickness[i] = old_thickness[i]*(1.0+opening-closing)/(1.0-opening+closing); + +- if(element->nodes[i]->Sid()==2299){ +- printf("for node %i \n",element->nodes[i]->Sid()); +- printf(" old thickness is %g \n",old_thickness[i]); +- printf(" new thickness is %g \n",thickness[i]); +- } ++ //if(element->nodes[i]->Sid()==2299){ ++ // printf("for node %i \n",element->nodes[i]->Sid()); ++ // printf(" old thickness is %g \n",old_thickness[i]); ++ // printf(" new thickness is %g \n",thickness[i]); ++ //} + /*Take care of otherthikening*/ + if(thickness[i]>max_thick){ + thickness[i] = max_thick; +@@ -709,8 +709,8 @@ + vec_mask->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + /* If epl thickness gets under colapse thickness, close the layer */ + if(epl_thickness[i]nodes[i]->Sid()==2299){ +- printf("masking node %i with thickness %f\n",element->nodes[i]->Sid(),epl_thickness[i]);} ++ //if(element->nodes[i]->Sid()==2299){ ++ //printf("masking node %i with thickness %f\n",element->nodes[i]->Sid(),epl_thickness[i]);} + vec_mask->SetValue(basalelement->nodes[i]->Sid(),0.,INS_VAL); + recurence->SetValue(basalelement->nodes[i]->Sid(),1.,INS_VAL); + } +Index: ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23372) ++++ ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23373) +@@ -9,7 +9,6 @@ + int HydrologyDCInefficientAnalysis::DofsPerNode(int** doflist,int domaintype,int approximation){/*{{{*/ + return 1; + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::UpdateParameters(Parameters* parameters,IoModel* iomodel,int solution_enum,int analysis_enum){/*{{{*/ + + int hydrology_model; +@@ -28,8 +27,8 @@ + char** requestedoutputs = NULL; + + /*retrieve some parameters: */ +- /* bool issmb; */ +- /* iomodel->FindConstant(&issmb,"md.transient.issmb"); */ ++ bool issmb; ++ iomodel->FindConstant(&issmb,"md.transient.issmb"); + iomodel->FindConstant(&hydrology_model,"md.hydrology.model"); + + /*Now, do we really want DC?*/ +@@ -64,9 +63,9 @@ + iomodel->FetchData(&sedimentlimit,"md.hydrology.sedimentlimit"); + parameters->AddObject(new DoubleParam(HydrologydcSedimentlimitEnum,sedimentlimit)); + } +- /* if(!issmb){ */ +- /* parameters->AddObject(iomodel->CopyConstantObject("md.smb.model",SmbEnum)); */ +- /* } */ ++ if(!issmb){ ++ parameters->AddObject(iomodel->CopyConstantObject("md.smb.model",SmbEnum)); ++ } + + /*Requested outputs*/ + iomodel->FindConstant(&requestedoutputs,&numoutputs,"md.hydrology.requested_outputs"); +@@ -74,7 +73,6 @@ + if(numoutputs)parameters->AddObject(new StringArrayParam(HydrologyRequestedOutputsEnum,requestedoutputs,numoutputs)); + iomodel->DeleteData(&requestedoutputs,numoutputs,"md.hydrology.requested_outputs"); + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::UpdateElements(Elements* elements,IoModel* iomodel,int analysis_counter,int analysis_type){/*{{{*/ + + bool isefficientlayer; +@@ -82,8 +80,6 @@ + + /*Fetch data needed: */ + iomodel->FindConstant(&hydrology_model,"md.hydrology.model"); +- bool issmb; +- iomodel->FindConstant(&issmb,"md.transient.issmb"); + + /*Now, do we really want DC?*/ + if(hydrology_model!=HydrologydcEnum) return; +@@ -116,12 +112,8 @@ + iomodel->FetchDataToInput(elements,"md.hydrology.mask_eplactive_node",HydrologydcMaskEplactiveNodeEnum); + iomodel->FetchDataToInput(elements,"md.initialization.epl_head",EplHeadHydrostepEnum); + } +- if(!issmb){ +- iomodel->FetchDataToInput(elements,"md.smb.model",SmbEnum); +-} + + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::CreateNodes(Nodes* nodes,IoModel* iomodel){/*{{{*/ + + /*Fetch parameters: */ +@@ -137,7 +129,6 @@ + ::CreateNodes(nodes,iomodel,HydrologyDCInefficientAnalysisEnum,P1Enum); + iomodel->DeleteData(2,"md.mesh.vertexonbase","md.mesh.vertexonsurface"); + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::CreateConstraints(Constraints* constraints,IoModel* iomodel){/*{{{*/ + + /*retrieve some parameters: */ +@@ -147,7 +138,6 @@ + + IoModelToConstraintsx(constraints,iomodel,"md.hydrology.spcsediment_head",HydrologyDCInefficientAnalysisEnum,P1Enum); + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::CreateLoads(Loads* loads, IoModel* iomodel){/*{{{*/ + + /*Fetch parameters: */ +@@ -182,16 +172,13 @@ + void HydrologyDCInefficientAnalysis::Core(FemModel* femmodel){/*{{{*/ + _error_("not implemented"); + }/*}}}*/ +- + ElementVector* HydrologyDCInefficientAnalysis::CreateDVector(Element* element){/*{{{*/ + /*Default, return NULL*/ + return NULL; + }/*}}}*/ +- + ElementMatrix* HydrologyDCInefficientAnalysis::CreateJacobianMatrix(Element* element){/*{{{*/ + _error_("Not implemented"); + }/*}}}*/ +- + ElementMatrix* HydrologyDCInefficientAnalysis::CreateKMatrix(Element* element){/*{{{*/ + + /*Intermediaries*/ +@@ -317,7 +304,6 @@ + } + return Ke; + }/*}}}*/ +- + ElementVector* HydrologyDCInefficientAnalysis::CreatePVector(Element* element){/*{{{*/ + + /*Intermediaries*/ +@@ -463,7 +449,6 @@ + } + return pe; + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::GetB(IssmDouble* B,Element* element,IssmDouble* xyz_list,Gauss* gauss){/*{{{*/ + /*Compute B matrix. B=[B1 B2 B3] where Bi is of size 3*NDOF2. + * For node i, Bi can be expressed in the actual coordinate system +@@ -491,15 +476,12 @@ + /*Clean-up*/ + xDelete(dbasis); + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::GetSolutionFromInputs(Vector* solution,Element* element){/*{{{*/ + element->GetSolutionFromInputsOneDof(solution,SedimentHeadHydrostepEnum); + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::GradientJ(Vector* gradient,Element* element,int control_type,int control_index){/*{{{*/ + _error_("Not implemented yet"); + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::InputUpdateFromSolution(IssmDouble* solution,Element* element){/*{{{*/ + + /*Intermediaries*/ +@@ -594,12 +576,10 @@ + delete basalelement; + } + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::UpdateConstraints(FemModel* femmodel){/*{{{*/ + /*Default, do nothing*/ + return; + }/*}}}*/ +- + IssmDouble HydrologyDCInefficientAnalysis::SedimentStoring(Element* element,Gauss* gauss,Input* sed_head_input, Input* base_input){/*{{{*/ + int unconf_scheme; + IssmDouble expfac; +@@ -639,7 +619,6 @@ + } + return sediment_storing; + }/*}}}*/ +- + IssmDouble HydrologyDCInefficientAnalysis::SedimentTransmitivity(Element* element,Gauss* gauss,Input* sed_head_input, Input* base_input,Input* SedTrans_input){/*{{{*/ + int unconf_scheme; + IssmDouble ratio,expfac; +@@ -674,7 +653,6 @@ + } + return sediment_transmitivity; + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::GetHydrologyDCInefficientHmax(IssmDouble* ph_max,Element* element, Node* innode){/*{{{*/ + + int hmax_flag; +@@ -710,7 +688,6 @@ + *ph_max=h_max; + } + /*}}}*/ +- + IssmDouble HydrologyDCInefficientAnalysis::GetHydrologyKMatrixTransfer(Element* element){/*{{{*/ + + int transfermethod; +@@ -732,7 +709,6 @@ + } + return transfer; + }/*}}}*/ +- + IssmDouble HydrologyDCInefficientAnalysis::GetHydrologyPVectorTransfer(Element* element, Gauss* gauss, Input* epl_head_input){/*{{{*/ + + int transfermethod; +@@ -757,7 +733,6 @@ + } + return transfer; + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::ElementizeEplMask(FemModel* femmodel){/*{{{*/ + + bool element_active; +@@ -776,8 +751,7 @@ + element->AddInput(new BoolInput(HydrologydcMaskEplactiveEltEnum,element_active)); + } + }/*}}}*/ +- +-void HydrologyDCInefficientAnalysis::HydrologyIDSGetMask(Vector* vec_mask, Element* element){ ++void HydrologyDCInefficientAnalysis::HydrologyIDSGetMask(Vector* vec_mask, Element* element){/*{{{*/ + bool active_element; + int domaintype; + Element* basalelement=NULL; +@@ -818,7 +792,7 @@ + } + xDelete(meltingrate); + xDelete(groundedice); +-} ++}/*}}}*/ + void HydrologyDCInefficientAnalysis::ElementizeIdsMask(FemModel* femmodel){/*{{{*/ + + bool element_active; +@@ -837,7 +811,6 @@ + element->AddInput(new BoolInput(HydrologydcMaskThawedEltEnum,element_active)); + } + }/*}}}*/ +- + void HydrologyDCInefficientAnalysis::HydrologyIdsGetActive(Vector* active_vec, Element* element){/*{{{*/ + /*Constants*/ + int domaintype; Index: /issm/oecreview/Archive/23185-23389/ISSM-23373-23374.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23373-23374.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23373-23374.diff (revision 23390) @@ -0,0 +1,21 @@ +Index: ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h +=================================================================== +--- ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23373) ++++ ../trunk-jpl/src/c/toolkits/mpi/issmmpi.h (revision 23374) +@@ -78,12 +78,12 @@ + #define ISSM_MPI_ANY_SOURCE AMPI_ANY_SOURCE + + #else +- #if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) +- #define ISSM_MPI_DOUBLE AMPI_ADOUBLE // corresponds to IssmDouble ++ #if defined(_HAVE_AMPI_) && !defined(_WRAPPERS_) ++ #define ISSM_MPI_DOUBLE AMPI_ADOUBLE + #else +- #define ISSM_MPI_DOUBLE MPI_DOUBLE // corresponds to IssmDouble ++ #define ISSM_MPI_DOUBLE MPI_DOUBLE + #endif +- #define ISSM_MPI_PDOUBLE MPI_DOUBLE // corresponds to IssmPDouble ++ #define ISSM_MPI_PDOUBLE MPI_DOUBLE + #define ISSM_MPI_INT MPI_INT + #define ISSM_MPI_CHAR MPI_CHAR + Index: /issm/oecreview/Archive/23185-23389/ISSM-23374-23375.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23374-23375.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23374-23375.diff (revision 23390) @@ -0,0 +1,19 @@ +Index: ../trunk-jpl/jenkins/jenkins.sh +=================================================================== +--- ../trunk-jpl/jenkins/jenkins.sh (revision 23374) ++++ ../trunk-jpl/jenkins/jenkins.sh (revision 23375) +@@ -323,10 +323,10 @@ + + #concatenate reports + cd $ISSM_DIR/nightlylog/ +-echo 'CHECKING NIGHTLYLOG DIRECTORY' +-echo '-----------------------------' +-ls -la +-echo '-----------------------------' ++#echo 'CHECKING NIGHTLYLOG DIRECTORY' ++#echo '-----------------------------' ++#ls -la ++#echo '-----------------------------' + + if [ -f matlab_log.log ]; then + rm matlab_log.log Index: /issm/oecreview/Archive/23185-23389/ISSM-23375-23376.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23375-23376.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23375-23376.diff (revision 23390) @@ -0,0 +1,23 @@ +Index: ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23375) ++++ ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23376) +@@ -373,7 +373,7 @@ + old_wh_input = basalelement->GetInput(SedimentHeadOldEnum); _assert_(old_wh_input); + } + if(smb_model==SMBgradientscomponentsEnum){ +- surface_runoff_input = basalelement->GetInput(SmbRunoffEnum); ++ surface_runoff_input = basalelement->GetInput(SmbRunoffEnum); _assert_(surface_runoff_input); + } + + /*Transfer related Inputs*/ +@@ -392,7 +392,8 @@ + /*Loading term*/ + if(!isefficientlayer){ + basal_melt_input->GetInputValue(&water_load,gauss); +- surface_runoff_input->GetInputValue(&runoff_value,gauss); ++ if(surface_runoff_input) surface_runoff_input->GetInputValue(&runoff_value,gauss); ++ else runoff_value = 0.; + scalar = Jdet*gauss->weight*(water_load+runoff_value); + //scalar = Jdet*gauss->weight*(water_load)/sediment_transmitivity; + if(dt!=0.) scalar = scalar*dt; Index: /issm/oecreview/Archive/23185-23389/ISSM-23376-23377.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23376-23377.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23376-23377.diff (revision 23390) @@ -0,0 +1,37 @@ +Index: ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 23376) ++++ ../trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp (revision 23377) +@@ -348,7 +348,7 @@ + old_wh_input = basalelement->GetInput(EplHeadOldEnum); _assert_(old_wh_input); + } + if(smb_model==SMBgradientscomponentsEnum){ +- surface_runoff_input = basalelement->GetInput(SmbRunoffEnum); ++ surface_runoff_input = basalelement->GetInput(SmbRunoffEnum); _assert_(surface_runoff_input); + } + + /* Start looping on the number of gaussian points: */ +@@ -362,7 +362,8 @@ + + /*Loading term*/ + basal_melt_input->GetInputValue(&water_load,gauss); +- surface_runoff_input->GetInputValue(&runoff_value,gauss); ++ if(surface_runoff_input) surface_runoff_input->GetInputValue(&runoff_value,gauss); ++ else runoff_value = 0.; + scalar = Jdet*gauss->weight*(water_load+runoff_value); + //scalar = Jdet*gauss->weight*(water_load)/epl_transmitivity; + if(dt!=0.) scalar = scalar*dt; +Index: ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23376) ++++ ../trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp (revision 23377) +@@ -406,7 +406,8 @@ + active_element_input->GetInputValue(&active_element); + if(!active_element){ + basal_melt_input->GetInputValue(&water_load,gauss); +- surface_runoff_input->GetInputValue(&runoff_value,gauss); ++ if(surface_runoff_input) surface_runoff_input->GetInputValue(&runoff_value,gauss); ++ else runoff_value = 0.; + scalar = Jdet*gauss->weight*(water_load+runoff_value); + //scalar = Jdet*gauss->weight*(water_load)/sediment_transmitivity; + if(dt!=0.) scalar = scalar*dt; Index: /issm/oecreview/Archive/23185-23389/ISSM-23377-23378.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23377-23378.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23377-23378.diff (revision 23390) @@ -0,0 +1,70 @@ +Index: ../trunk-jpl/src/m/classes/clusters/stallo.py +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/stallo.py (revision 23377) ++++ ../trunk-jpl/src/m/classes/clusters/stallo.py (revision 23378) +@@ -105,23 +105,20 @@ + executable='issm_ocean.exe' + #write queuing script + shortname=modelname[0:min(12,len(modelname))] ++ timeobj=datetime.timedelta(minutes=self.time) ++ m,s=divmod(timeobj.total_seconds(), 60) ++ h,m=divmod(m, 60) ++ d,h=divmod(h, 60) ++ timestring="%02d-%02d:%02d:%02d" % (d, h, m, s) ++ + fid=open(modelname+'.queue','w') +- + fid.write('#!/bin/bash -l\n') + fid.write('#SBATCH --job-name=%s \n' % shortname) +- if self.queue=='devel': +- fid.write('#SBATCH --qos %s \n' % self.queue) +- else: +- fid.write('#SBATCH --partition %s \n' % self.queue) ++ fid.write('#SBATCH --qos=%s \n' % self.queue) + fid.write('#SBATCH --nodes=%i \n' % self.numnodes) + fid.write('#SBATCH --ntasks-per-node=%i \n' % self.cpuspernode) +- timeobj=datetime.timedelta(minutes=self.time) +- m,s=divmod(timeobj.total_seconds(), 60) +- h,m=divmod(m, 60) +- d,h=divmod(h, 60) +- timestring="%02d-%02d:%02d:%02d" % (d, h, m, s) + fid.write('#SBATCH --time={}\n'.format(timestring)) #walltime is minutes +- fid.write('#SBATCH --mem-per-cpu={}MB\n'.format(int(1000*self.mem)))# mem is in MB (to keep it integral) ++ fid.write('#SBATCH --mem-per-cpu={}MB\n'.format(int(1000*self.mem)))# mem is in MB + if (np.mod(self.np,16)+np.mod(self.np,20))==0: + fid.write('#SBATCH --ntask=%i\n' % self.np) + fid.write('#SBATCH --account=%s\n' % self.accountname) +Index: ../trunk-jpl/src/m/classes/clusters/stallo.m +=================================================================== +--- ../trunk-jpl/src/m/classes/clusters/stallo.m (revision 23377) ++++ ../trunk-jpl/src/m/classes/clusters/stallo.m (revision 23378) +@@ -97,16 +97,17 @@ + executable='issm_ocean.exe'; + end + ++ days=floor(cluster.time/(60*24)); ++ hours=floor((cluster.time-(days*60*24))/60); ++ minutes=floor(mod((cluster.time-(days*60*24)-(hours*60)),60)); ++ + %write queuing script + fid=fopen([modelname '.queue'],'w'); + fprintf(fid,'#!/bin/bash -l\n'); + fprintf(fid,'#SBATCH --job-name=%s \n',modelname); +- fprintf(fid,'#SBATCH --qos %s \n',cluster.queue); ++ fprintf(fid,'#SBATCH --qos=%s \n',cluster.queue); + fprintf(fid,'#SBATCH --nodes=%i \n',cluster.numnodes); + fprintf(fid,'#SBATCH --ntasks-per-node=%i \n',cluster.cpuspernode); +- days=floor(cluster.time/(60*24)); +- hours=floor((cluster.time-(days*60*24))/60); +- minutes=floor(mod((cluster.time-(days*60*24)-(hours*60)),60)); + fprintf(fid,'#SBATCH --time=%02i-%02i:%02i:00 \n',days,hours,minutes); + fprintf(fid,'#SBATCH --mem-per-cpu=%iMB\n',1000*cluster.mem); % mem in MB + if (mod(cluster.np,16)+mod(cluster.np,20))==0, +@@ -115,6 +116,7 @@ + fprintf(fid,'#SBATCH --account=%s\n',cluster.accountname); + fprintf(fid,'#SBATCH --output %s/%s/%s.outlog \n',cluster.executionpath,dirname,modelname); + fprintf(fid,'#SBATCH --error %s/%s/%s.errlog \n\n',cluster.executionpath,dirname,modelname); ++ + fprintf(fid,'export ISSM_DIR="%s/../"\n',cluster.codepath);%FIXME + fprintf(fid,'module purge\n'); + fprintf(fid,'module load CMake/3.8.0-GCCcore-6.3.0\n'); Index: /issm/oecreview/Archive/23185-23389/ISSM-23378-23379.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23378-23379.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23378-23379.diff (revision 23390) @@ -0,0 +1,26 @@ +Index: ../trunk-jpl/test/NightlyRun/test455.py +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test455.py (revision 23378) ++++ ../trunk-jpl/test/NightlyRun/test455.py (revision 23379) +@@ -23,7 +23,7 @@ + md.flowequation.fe_HO=i + md=solve(md,'Stressbalance') + field_names =field_names+['Vx'+i,'Vy'+i,'Vz'+i,'Vel'+i,'Pressure'+i] +- field_tolerances=field_tolerances+[6e-08,6e-08,6e-08,6e-08,3e-13] ++ field_tolerances=field_tolerances+[7e-08,6e-08,6e-08,6e-08,3e-13] + field_values=field_values+[\ + md.results.StressbalanceSolution.Vx,\ + md.results.StressbalanceSolution.Vy,\ +Index: ../trunk-jpl/test/NightlyRun/test455.m +=================================================================== +--- ../trunk-jpl/test/NightlyRun/test455.m (revision 23378) ++++ ../trunk-jpl/test/NightlyRun/test455.m (revision 23379) +@@ -13,7 +13,7 @@ + md.flowequation.fe_HO=i{1}; + md=solve(md,'Stressbalance'); + field_names ={field_names{:},['Vx' i{1}],['Vy' i{1}],['Vz' i{1}],['Vel' i{1}],['Pressure' i{1}]}; +- field_tolerances={field_tolerances{:},6e-08,6e-08,6e-08,6e-08,3e-13}; ++ field_tolerances={field_tolerances{:},7e-08,6e-08,6e-08,6e-08,3e-13}; + field_values={field_values{:},... + (md.results.StressbalanceSolution.Vx),... + (md.results.StressbalanceSolution.Vy),... Index: /issm/oecreview/Archive/23185-23389/ISSM-23379-23380.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23379-23380.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23379-23380.diff (revision 23390) @@ -0,0 +1,52 @@ +Index: ../trunk-jpl/src/c/analyses/LevelsetAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/LevelsetAnalysis.cpp (revision 23379) ++++ ../trunk-jpl/src/c/analyses/LevelsetAnalysis.cpp (revision 23380) +@@ -130,7 +130,7 @@ + /*activate formulation: */ + femmodel->SetCurrentConfiguration(LevelsetAnalysisEnum); + +- if(VerboseSolution()) _printf0_("call computational core:\n"); ++ if(VerboseSolution()) _printf0_(" call computational core:\n"); + if(stabilization==4){ + solutionsequence_fct(femmodel); + } +Index: ../trunk-jpl/src/c/analyses/ExtrapolationAnalysis.cpp +=================================================================== +--- ../trunk-jpl/src/c/analyses/ExtrapolationAnalysis.cpp (revision 23379) ++++ ../trunk-jpl/src/c/analyses/ExtrapolationAnalysis.cpp (revision 23380) +@@ -64,7 +64,7 @@ + /*activate formulation: */ + femmodel->SetCurrentConfiguration(ExtrapolationAnalysisEnum); + +- if(VerboseSolution()) _printf0_("extrapolation of " << EnumToStringx(extvar_enum) << ": call computational core:\n"); ++ if(VerboseSolution()) _printf0_(" extrapolation of " << EnumToStringx(extvar_enum) << ":\n"); + solutionsequence_linear(femmodel); + + if(save_results){ +Index: ../trunk-jpl/src/c/cores/balancethickness_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/balancethickness_core.cpp (revision 23379) ++++ ../trunk-jpl/src/c/cores/balancethickness_core.cpp (revision 23380) +@@ -20,7 +20,7 @@ + /*recover parameters: */ + femmodel->parameters->FindParam(&save_results,SaveResultsEnum); + +- if(VerboseSolution()) _printf0_("call computational core:\n"); ++ if(VerboseSolution()) _printf0_(" call computational core:\n"); + solutionsequence_linear(femmodel); + + if(save_results){ +Index: ../trunk-jpl/src/c/cores/balancevelocity_core.cpp +=================================================================== +--- ../trunk-jpl/src/c/cores/balancevelocity_core.cpp (revision 23379) ++++ ../trunk-jpl/src/c/cores/balancevelocity_core.cpp (revision 23380) +@@ -26,7 +26,7 @@ + femmodel->parameters->SetParam(DrivingStressYEnum,InputToSmoothEnum); + solutionsequence_linear(femmodel); + +- if(VerboseSolution()) _printf0_("call computational core:\n"); ++ if(VerboseSolution()) _printf0_(" call computational core:\n"); + femmodel->SetCurrentConfiguration(BalancevelocityAnalysisEnum); + solutionsequence_linear(femmodel); + Index: /issm/oecreview/Archive/23185-23389/ISSM-23387-23388.diff =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-23387-23388.diff (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-23387-23388.diff (revision 23390) @@ -0,0 +1,494 @@ +Index: ../trunk-jpl/examples/Pig2/Pig.par +=================================================================== +--- ../trunk-jpl/examples/Pig2/Pig.par (nonexistent) ++++ ../trunk-jpl/examples/Pig2/Pig.par (revision 23388) +@@ -0,0 +1,118 @@ ++% Parameters to change/Try ++friction_coefficient = 10; % default [10] ++Temp_change = 0; % default [0 K] ++ ++%Name and Coordinate system ++md.miscellaneous.name='PIG'; ++md.mesh.epsg=3031; ++ ++%NetCdf Loading ++disp(' Loading SeaRISE data from NetCDF'); ++ncdata='../Data/Antarctica_5km_withshelves_v0.75.nc'; ++x1 = ncread(ncdata,'x1'); ++y1 = ncread(ncdata,'y1'); ++usrf = ncread(ncdata,'usrf')'; ++topg = ncread(ncdata,'topg')'; ++temp = ncread(ncdata,'presartm')'; ++smb = ncread(ncdata,'presprcp')'; ++gflux = ncread(ncdata,'bheatflx_fox')'; ++ ++%Geometry ++disp(' Interpolating surface and ice base'); ++md.geometry.base = InterpFromGridToMesh(x1,y1,topg,md.mesh.x,md.mesh.y,0); ++md.geometry.surface = InterpFromGridToMesh(x1,y1,usrf,md.mesh.x,md.mesh.y,0); ++clear usrf, topg; ++ ++disp(' Constructing thickness'); ++md.geometry.thickness=md.geometry.surface-md.geometry.base; ++ ++%ensure hydrostatic equilibrium on ice shelf: ++di=md.materials.rho_ice/md.materials.rho_water; ++ ++%Get the node numbers of floating nodes ++pos=find(md.mask.groundedice_levelset<0); ++ ++%apply a flotation criterion on the precedingly defined nodes and ++%redefine base and thickness accordingly ++md.geometry.thickness(pos)=1/(1-di)*md.geometry.surface(pos); ++md.geometry.base(pos)=md.geometry.surface(pos)-md.geometry.thickness(pos); ++md.geometry.hydrostatic_ratio=ones(md.mesh.numberofvertices,1); %For Dakota ++ ++%Set min thickness to 1 meter ++pos0=find(md.geometry.thickness<=1); ++md.geometry.thickness(pos0)=1; ++md.geometry.surface=md.geometry.thickness+md.geometry.base; ++md.geometry.bed=md.geometry.base; ++md.geometry.bed(pos)=md.geometry.base(pos)-1000; ++ ++%Initialization parameters ++disp(' Interpolating temperatures'); ++md.initialization.temperature=InterpFromGridToMesh(x1,y1,temp,md.mesh.x,md.mesh.y,0)+273.15+Temp_change; ++clear temp; ++ ++disp(' Loading velocities data from NetCDF'); ++nsidc_vel='../Data/Antarctica_ice_velocity.nc'; ++xmin = ncreadatt(nsidc_vel,'/','xmin'); ++ymax = ncreadatt(nsidc_vel,'/','ymax'); ++spacing = ncreadatt(nsidc_vel,'/','spacing'); ++nx = double(ncreadatt(nsidc_vel,'/','nx')); ++ny = double(ncreadatt(nsidc_vel,'/','ny')); ++velx = double(ncread(nsidc_vel,'vx')); ++vely = double(ncread(nsidc_vel,'vy')); ++% Read coordinates ++xmin = strtrim(xmin); ++xmin = str2num(xmin(1:end-2)); ++ymax = strtrim(ymax); ++ymax = str2num(ymax(1:end-2)); ++spacing = strtrim(spacing); ++spacing = str2num(spacing(1:end-2)); ++% Build the coordinates ++x2=xmin+(0:1:nx)'*spacing; ++y2=(ymax-ny*spacing)+(0:1:ny)'*spacing; ++ ++disp(' Set observed velocities') ++md.initialization.vx=InterpFromGridToMesh(x2,y2,flipud(velx'),md.mesh.x,md.mesh.y,0); ++md.initialization.vy=InterpFromGridToMesh(x2,y2,flipud(vely'),md.mesh.x,md.mesh.y,0); ++md.initialization.vz=zeros(md.mesh.numberofvertices,1); ++md.initialization.vel=sqrt(md.initialization.vx.^2+md.initialization.vy.^2); ++clear velx vely; ++ ++disp(' Set Pressure'); ++md.initialization.pressure=md.materials.rho_ice*md.constants.g*md.geometry.thickness; ++ ++disp(' Construct ice rheological properties'); ++md.materials.rheology_n=3*ones(md.mesh.numberofelements,1); ++md.materials.rheology_B=paterson(md.initialization.temperature); ++ ++%Forcings ++disp(' Interpolating surface mass balance'); ++mass_balance=InterpFromGridToMesh(x1,y1,smb,md.mesh.x,md.mesh.y,0); ++md.smb.mass_balance=mass_balance*md.materials.rho_water/md.materials.rho_ice; ++clear smb; ++ ++disp(' Set geothermal heat flux'); ++md.basalforcings.geothermalflux=InterpFromGridToMesh(x1,y1,gflux,md.mesh.x,md.mesh.y,0); ++clear gflux; ++ ++%Friction and inversion set up ++disp(' Construct basal friction parameters'); ++md.friction.coefficient=friction_coefficient*ones(md.mesh.numberofvertices,1); ++md.friction.p=ones(md.mesh.numberofelements,1); ++md.friction.q=ones(md.mesh.numberofelements,1); ++ ++%no friction applied on floating ice ++pos=find(md.mask.groundedice_levelset<0); ++md.friction.coefficient(pos)=0; ++md.groundingline.migration='SubelementMigration'; ++ ++md.inversion=m1qn3inversion(); ++md.inversion.vx_obs=md.initialization.vx; ++md.inversion.vy_obs=md.initialization.vy; ++md.inversion.vel_obs=md.initialization.vel; ++ ++disp(' Set boundary conditions'); ++md=SetMarineIceSheetBC(md); ++md.basalforcings.floatingice_melting_rate = zeros(md.mesh.numberofvertices,1); ++md.basalforcings.groundedice_melting_rate = zeros(md.mesh.numberofvertices,1); ++md.thermal.spctemperature = md.initialization.temperature; ++md.masstransport.spcthickness = NaN*ones(md.mesh.numberofvertices,1); +Index: ../trunk-jpl/examples/Pig2/runme.m +=================================================================== +--- ../trunk-jpl/examples/Pig2/runme.m (nonexistent) ++++ ../trunk-jpl/examples/Pig2/runme.m (revision 23388) +@@ -0,0 +1,231 @@ ++steps=[1:8]; ++ ++if any(steps==1) %Mesh Generation #1 ++ ++ %Mesh parameters ++ domain =['./DomainOutline.exp']; ++ hinit=5000; % element size for the initial mesh ++ hmax=40000; % maximum element size of the final mesh ++ hmin=4000; % minimum element size of the final mesh ++ gradation=1.7; % maximum size ratio between two neighboring elements ++ err=8; % maximum error between interpolated and control field ++ ++ % Generate an initial uniform mesh (resolution = hinit m) ++ md=bamg(model,'domain',domain,'hmax',hinit); ++ ++ % Get necessary data to build up the velocity grid ++ nsidc_vel='../Data/Antarctica_ice_velocity.nc'; ++ xmin = strsplit(ncreadatt(nsidc_vel,'/','xmin')); xmin = str2num(xmin{2}); ++ ymax = strsplit(ncreadatt(nsidc_vel,'/','ymax')); ymax = str2num(ymax{2}); ++ spacing = strsplit(ncreadatt(nsidc_vel,'/','spacing')); spacing = str2num(spacing{2}); ++ nx = double(ncreadatt(nsidc_vel,'/','nx')); ++ ny = double(ncreadatt(nsidc_vel,'/','ny')); ++ vx = double(ncread(nsidc_vel,'vx')); ++ vy = double(ncread(nsidc_vel,'vy')); ++ ++ % Build the coordinates ++ x=xmin+(0:1:nx)'*spacing; ++ y=(ymax-ny*spacing)+(0:1:ny)'*spacing; ++ ++ % Interpolate velocities onto coarse mesh ++ vx_obs=InterpFromGridToMesh(x,y,flipud(vx'),md.mesh.x,md.mesh.y,0); ++ vy_obs=InterpFromGridToMesh(x,y,flipud(vy'),md.mesh.x,md.mesh.y,0); ++ vel_obs=sqrt(vx_obs.^2+vy_obs.^2); ++ clear vx vy x y; ++ ++ % Adapt the mesh to minimize error in velocity interpolation ++ md=bamg(md,'hmax',hmax,'hmin',hmin,'gradation',gradation,'field',vel_obs,'err',err); ++ ++ % Plot and save model ++ plotmodel(md,'data','mesh') ++ save ./Models/PIG_Mesh_generation md; ++end ++ ++if any(steps==2) %Masks #2 ++ ++ md = loadmodel('./Models/PIG_Mesh_generation'); ++ ++ % Load SeaRISe dataset for Antarctica http://websrv.cs.umt.edu/isis/index.php/Present_Day_Antarctica ++ searise='../Data/Antarctica_5km_withshelves_v0.75.nc'; ++ ++ %read thickness mask from SeaRISE ++ x1=double(ncread(searise,'x1')); ++ y1=double(ncread(searise,'y1')); ++ thkmask=double(ncread(searise,'thkmask')); ++ ++ %interpolate onto our mesh vertices ++ groundedice=double(InterpFromGridToMesh(x1,y1,thkmask',md.mesh.x,md.mesh.y,0)); ++ groundedice(groundedice<=0)=-1; ++ clear thkmask; ++ ++ %fill in the md.mask structure ++ md.mask.groundedice_levelset=groundedice; %ice is grounded for mask equal one ++ md.mask.ice_levelset=-1*ones(md.mesh.numberofvertices,1);%ice is present when negatvie ++ ++ plotmodel(md,'data',md.mask.groundedice_levelset,'title','grounded/floating','data',md.mask.ice_levelset,'title','ice/no-ice') ++ ++ save ./Models/PIG_SetMask md; ++end ++ ++if any(steps==3) %Parameterization #3 ++ ++ md = loadmodel('./Models/PIG_SetMask'); ++ md = setflowequation(md,'SSA','all'); ++ md = parameterize(md,'./Pig.par'); ++ ++ save ./Models/PIG_Parameterization md; ++end ++ ++if any(steps==4) %Rheology B inversion ++ ++ md = loadmodel('./Models/PIG_Parameterization'); ++ ++ % Control general ++ md.inversion.iscontrol=1; ++ md.inversion.maxsteps=40; ++ md.inversion.maxiter=40; ++ md.inversion.dxmin=0.1; ++ md.inversion.gttol=1.0e-6; ++ md.verbose=verbose('control',true); ++ ++ % Cost functions ++ md.inversion.cost_functions=[101 103 502]; ++ md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,3); ++ md.inversion.cost_functions_coefficients(:,1)=1000; ++ md.inversion.cost_functions_coefficients(:,2)=1; ++ md.inversion.cost_functions_coefficients(:,3)=1.e-16; ++ ++ % Controls ++ md.inversion.control_parameters={'MaterialsRheologyBbar'}; ++ md.inversion.min_parameters=md.materials.rheology_B; ++ md.inversion.max_parameters=md.materials.rheology_B; ++ pos = find(md.mask.groundedice_levelset<0); ++ md.inversion.min_parameters(pos) = cuffey(273); ++ md.inversion.max_parameters(pos) = cuffey(200); ++ ++ % Additional parameters ++ md.stressbalance.restol=0.01; ++ md.stressbalance.reltol=0.1; ++ md.stressbalance.abstol=NaN; ++ ++ % Solve ++ md.cluster=generic('name',oshostname,'np',2); ++ mds=extract(md,md.mask.groundedice_levelset<0); ++ mds=solve(mds,'Stressbalance'); ++ ++ % Update model rheology_B accordingly ++ md.materials.rheology_B(mds.mesh.extractedvertices)=mds.results.StressbalanceSolution.MaterialsRheologyBbar; ++ plotmodel(md,'data',md.materials.rheology_B) ++ ++ % Save model ++ save ./Models/PIG_Control_B md; ++end ++ ++if any(steps==5) %drag inversion ++ ++ md = loadmodel('./Models/PIG_Control_B'); ++ ++ % Cost functions ++ md.inversion.cost_functions=[101 103 501]; ++ md.inversion.cost_functions_coefficients=ones(md.mesh.numberofvertices,3); ++ md.inversion.cost_functions_coefficients(:,1)=2000; ++ md.inversion.cost_functions_coefficients(:,2)=1; ++ md.inversion.cost_functions_coefficients(:,3)=8e-7; ++ ++ % Controls ++ md.inversion.control_parameters={'FrictionCoefficient'}; ++ md.inversion.min_parameters=1*ones(md.mesh.numberofvertices,1); ++ md.inversion.max_parameters=200*ones(md.mesh.numberofvertices,1); ++ ++ % Solve ++ md=solve(md,'Stressbalance'); ++ ++ % Update model friction fields accordingly ++ md.friction.coefficient=md.results.StressbalanceSolution.FrictionCoefficient; ++ ++ %Plot and save ++ plotmodel(md,... ++ 'data',md.initialization.vel,'title','Observed velocity',... ++ 'data',md.results.StressbalanceSolution.Vel,'title','Modeled Velocity',... ++ 'data',md.geometry.base,'title','Bed elevation',... ++ 'data',md.results.StressbalanceSolution.FrictionCoefficient,'title','Friction Coefficient',... ++ 'colorbar#all','on','colorbartitle#1-2','(m/yr)',... ++ 'caxis#1-2',([1.5,4000]),... ++ 'colorbartitle#3','(m)', 'log#1-2',10); ++ save ./Models/PIG_Control_drag md; ++end ++ ++if any(steps==6) %Transient Run #1 ++ ++ md = loadmodel('../Pig/Models/PIG_Control_drag'); ++ ++ md.inversion.iscontrol=0; ++ md.transient.ismasstransport=1; ++ md.transient.isstressbalance=1; ++ md.transient.isgroundingline=1; ++ md.transient.ismovingfront=0; ++ md.transient.isthermal=0; ++ md.verbose.solution=1; ++ md.timestepping.time_step=0.1; ++ md.timestepping.final_time=10; ++ md.transient.requested_outputs={'default','IceVolume','IceVolumeAboveFloatation'}; ++ ++ %Set melt to 25 m/yr under floating ice ++ md.basalforcings.groundedice_melting_rate=zeros(md.mesh.numberofvertices,1); ++ md.basalforcings.floatingice_melting_rate=25*ones(md.mesh.numberofvertices,1); ++ ++ ++ md=solve(md,'Transient'); ++ time = cell2mat({md.results.TransientSolution(:).time}); ++ V_control = cell2mat({md.results.TransientSolution(:).IceVolumeAboveFloatation}); ++ plot(time,V_control); legend({'Control run'}); ++ ++ % Save model ++ save ./Models/PIG_Transient md; ++end ++ ++if any(steps==7) %High Melt #2 ++ md = loadmodel('./Models/PIG_Transient'); ++ ++ %Set melt to 60 m/yr under floating ice ++ md.basalforcings.floatingice_melting_rate=60*ones(md.mesh.numberofvertices,1); ++ ++ md=solve(md,'Transient'); ++ V_melt = cell2mat({md.results.TransientSolution(:).IceVolumeAboveFloatation}); ++ plot(time,[V_control',V_melt']); legend({'Control run','High melt'}); ++ ++ save ./Models/PIG_HighMelt md; ++end ++ ++if any(steps==8) %Ice Front retreat ++ md = loadmodel('./Models/PIG_Transient'); ++ ++ pos = find(ContourToNodes(md.mesh.x,md.mesh.y,'FrontRetreat.exp',2)); ++ md.mask.ice_levelset(pos) = +1; %Deactivate nodes in retreated area ++ ++ md=solve(md,'Transient'); ++ V_retreat = cell2mat({md.results.TransientSolution(:).IceVolumeAboveFloatation}); ++ plot(time,[V_control',V_melt',V_retreat']); legend({'Control run','High melt','Retreat'}); ++ ++ save ./Models/PIG_FrontRetreat md; ++end ++ ++if any(steps==9) %High surface mass balance #3 ++ %Load model from PIG_Transient ++ %... ++ ++ %Change surface mass balance (x2) ++ %... ++ ++ %Solve ++ %... ++ ++ %Get volume time series ++ %... ++ ++ %plot ++ plot(time,[V_control',V_melt',V_retreat',V_smb']); legend({'Control run','High melt','Retreat','SMB'}); ++ ++ %Save model ++ save ./Models/PIG_SMB md; ++end + +Property changes on: ../trunk-jpl/examples/Pig2/runme.m +___________________________________________________________________ +Added: svn:executable +## -0,0 +1 ## ++* +\ No newline at end of property +Index: ../trunk-jpl/examples/Pig2/DomainOutline.exp +=================================================================== +--- ../trunk-jpl/examples/Pig2/DomainOutline.exp (nonexistent) ++++ ../trunk-jpl/examples/Pig2/DomainOutline.exp (revision 23388) +@@ -0,0 +1,101 @@ ++## Name: ++## Icon:0 ++# Points Count Value ++95 25000.000000 ++# X pos Y pos ++-1712113.0179281300 -349656.0205056490 ++-1711509.1917759699 -349354.1074295690 ++-1709240.6586108401 -349354.1074295690 ++-1707080.1508345299 -348922.0058743060 ++-1705459.7700022999 -347193.5996532570 ++-1703083.2114483600 -345249.1426545770 ++-1701138.7544496800 -344168.8887664210 ++-1698438.1197292900 -343952.8379887900 ++-1698006.0181740201 -341900.3556012940 ++-1693793.0280102200 -340279.9747690600 ++-1691092.3932898301 -339631.8224361670 ++-1688391.7585694401 -339415.7716585360 ++-1686447.3015707601 -340063.9239914290 ++-1683530.6160727399 -341036.1524907690 ++-1682558.3875734000 -343304.6856558960 ++-1682134.7209454600 -344182.1487658350 ++-1682126.2860181299 -345681.2442098390 ++-1681072.0444963200 -345932.4393879640 ++-1680634.4718407800 -346682.5639403050 ++-1680571.9614614199 -348557.8753211580 ++-1677446.4424933300 -348370.3441830730 ++-1675508.6207331200 -349495.5310115840 ++-1676616.9911885399 -353567.0975933760 ++-1672991.8601872099 -353799.6175753630 ++-1668839.1631938200 -353999.1991486380 ++-1667132.2298986400 -355121.4651541420 ++-1666069.5534494901 -357496.8595698890 ++-1662944.0344814099 -358309.4945015920 ++-1660756.1712037399 -358747.0671571240 ++-1657922.9836098100 -361682.8074238540 ++-1656579.2228470000 -364003.8487410000 ++-1653004.8841628900 -364748.0635758530 ++-1653442.4568184200 -361622.5446077650 ++-1651129.5727820301 -355684.0585683980 ++-1648929.2928810001 -350845.9692010000 ++-1646260.7698359799 -347802.2804785470 ++-1644571.8968503401 -341785.6704672340 ++-1643503.3064999001 -340869.0986596620 ++-1643190.7546030900 -336680.9032424240 ++-1642690.6715682000 -335243.1645171040 ++-1641913.0916588283 -332341.0814454452 ++-1640683.9739821283 -330436.6112348017 ++-1637816.0327364956 -328532.1410241582 ++-1635241.2508976001 -328652.8685499910 ++-1631765.4107996500 -327017.1790921330 ++-1625934.5618617306 -322342.6128395668 ++-1620608.3852626982 -320438.1426289233 ++-1616101.6204481323 -320438.1426289233 ++-1611594.8556335662 -320914.2601815842 ++-1607907.5026034669 -321866.4952869060 ++-1602991.0318966676 -324723.2006028712 ++-1599713.3847588014 -327579.9059188365 ++-1593977.5022675355 -328532.1410241582 ++-1590699.8551296694 -334721.6692087495 ++-1589259.8391499999 -338300.0840570000 ++-1588627.0898328500 -343572.9950327750 ++-1588056.6000060199 -345432.3563530700 ++-1586993.9235568701 -347432.6884926460 ++-1589259.8391499999 -349315.9832070000 ++-1585493.6744521901 -352996.1122558430 ++-1585118.6121760199 -354496.3613605250 ++-1585861.9157163899 -356240.3342513760 ++-1586368.8197632500 -358747.0671571240 ++-1587889.0972700799 -360996.6006787950 ++-1586681.3716600600 -363935.4286441500 ++-1585806.2263489999 -365748.2296456410 ++-1586743.8820394201 -368373.6655788350 ++-1586056.2678664399 -370123.9562009640 ++-1585493.6744521901 -371124.1222707520 ++-1586243.7990045301 -373562.0270658610 ++-1414257.6683934701 -327460.5482541260 ++-1412220.4351378100 -325972.8942023180 ++-1404515.9240538401 -296165.1737279960 ++-1387984.9332285200 -267002.0106682320 ++-1360067.9373810000 -107884.1934940000 ++-1423274.3497420000 -81217.9259650000 ++-1402446.7987670000 -45916.9921070000 ++-1478343.8065599999 60338.8188030000 ++-1503760.4789370000 36334.1837800000 ++-1528509.5619775900 63667.6809196406 ++-1623055.4918765700 62841.1506965373 ++-1725734.5897359999 -61372.6193030000 ++-1719614.6457630000 -69022.5492690000 ++-1759088.2843859999 -114004.1374660000 ++-1755416.3180020000 -117064.1094530000 ++-1761230.2647760001 -126856.0198080000 ++-1758170.2927900001 -130527.9861920000 ++-1762148.2563720001 -135423.9413700000 ++-1764902.2311590000 -131445.9777880000 ++-1769798.1863370000 -134199.9525750000 ++-1775000.1387139999 -131445.9777880000 ++-1794277.9622269999 -153477.7760890000 ++-1712576.7101950001 -225081.1205660000 ++-1729939.5891459100 -335652.4567604720 ++-1712113.0179281300 -349656.0205056490 ++ +Index: ../trunk-jpl/examples/Pig2/FrontRetreat.exp +=================================================================== +--- ../trunk-jpl/examples/Pig2/FrontRetreat.exp (nonexistent) ++++ ../trunk-jpl/examples/Pig2/FrontRetreat.exp (revision 23388) +@@ -0,0 +1,17 @@ ++## Name:FrontRetreat ++## Icon:0 ++# Points Count Value ++11 1.000000 ++# X pos Y pos ++-1626858.6376043619 -327176.4356578548 ++-1605190.4936934854 -325911.1425827671 ++-1604716.0087903275 -316263.2828852235 ++-1607088.4333061168 -312625.5652943464 ++-1612465.9288752396 -311676.5954880306 ++-1618476.0709819060 -312467.4036599604 ++-1624011.7281854146 -313890.8583694341 ++-1626858.6376043619 -315788.7979820656 ++-1627807.6074106777 -319268.3539385567 ++-1628756.5772169936 -322589.7482606619 ++-1626858.6376043619 -327176.4356578548 ++ Index: /issm/oecreview/Archive/23185-23389/ISSM-DocReview-23185-23389.tex =================================================================== --- /issm/oecreview/Archive/23185-23389/ISSM-DocReview-23185-23389.tex (revision 23390) +++ /issm/oecreview/Archive/23185-23389/ISSM-DocReview-23185-23389.tex (revision 23390) @@ -0,0 +1,67 @@ +\documentclass[]{report} % list options between brackets +\usepackage{graphicx} % list packages between braces + +% type user-defined commands here + +\begin{document} + +\title{JPL EXPORT ADMINISTRATION \\ DOCUMENT REVIEW RECORD} % type title between braces +\author{Tom Scavo} % type author(s) between braces +\date{October 27, 1995} % type date between braces +%\maketitle + + +\begin{center} +\begin{tabular}{ |c|c| } +\hline +JPL EXPORT ADMINISTRATION \\ +\textit{ DOCUMENT REVIEW RECORD} \\ +\hline +\end{tabular} +\end{center} + +\hfill Log \#: \underline{\input{LogNumber}} + +\vspace{1cm} +\noindent (Note: This form and process do not replace the procedures described in JPL Policy relating to review and approval of proposals and contractual +documents. This process is intended to document the review and coordination of requests to ascertain the export control ramifications relating to specific +documents. Export Administration signature does not convey authority to export or release the "Exporter of Record" from any export laws or regulations.)\\ + +\noindent \textbf{Program:} \underline{ISSM: Ice Sheet System Model} \\ \\ +\noindent \textbf{Person Requesting or Initiating Export}: \underline{Dr. Eric Larour}\\ \\ +\noindent \textbf{Date Received}: \underline{\input{Date}}\\ \\ +\noindent \textbf{Document Title/Description}: ISSM changes from revision \input{r1} to revision \input{r2} \\ \\ +\noindent \textbf{Release to:} \underline{http://issm.ess.uci.edu/svn/issm/issm/trunk on ISSM svn repository}\\ \\ +\noindent \textbf{JPL Intranet:} \underline{murdo.jpl.nasa.gov/proj/ice/larour/issm-uci/trunk-jpl}\\ \\ + +\noindent \textbf{Disposition: 6 } +Does not contain export-controlled information. May be released/disclosed as requested subject to +Company guidelines on protection of proprietary information (if applicable). \\ + +\noindent \textbf{Comments:} see table of changes below. \\ \\ +\noindent \textbf{Reviewed by ISSM Export Transfer Liaison:} Dr. Eric Larour \hfill \textbf{Date:} \input{Date} \\ +\includegraphics[scale=1]{signature} + +\noindent JPL Export Administration Form TBS – June 29, 2011 + +\begin{center} +\line(1,0){250} +\end{center} + +\noindent \textbf{Disposition:} \\ +1: Public Domain Information (Ref ITAR Section 120.11) \\ +2: Qualifies for ITAR Exemption \\ +3: Covered by Department of State License/Agreement Number \\ +4: Covered by Department of Commerce validated license or exception \\ +5: New License Required \\ +6: Does not contain export-controlled information. May be released/disclosed as requested subject + to Company guidelines on protection of proprietary information (if applicable). \\ +7: Other (specify) +\begin{center} +\line(1,0){250} +\end{center} + + +\input{log} + +\end{document} Index: /issm/oecreview/Archive/23185-23389/LogNumber.tex =================================================================== --- /issm/oecreview/Archive/23185-23389/LogNumber.tex (revision 23390) +++ /issm/oecreview/Archive/23185-23389/LogNumber.tex (revision 23390) @@ -0,0 +1,1 @@ +23185-23389 Index: /issm/oecreview/Archive/23185-23389/Makefile =================================================================== --- /issm/oecreview/Archive/23185-23389/Makefile (revision 23390) +++ /issm/oecreview/Archive/23185-23389/Makefile (revision 23390) @@ -0,0 +1,8 @@ +TARGET=ISSM-DocReview-23185-23389 + +all: + pdflatex -interaction=errorstopmode -file-line-error -halt-on-error $(TARGET).tex + rm -rf *.log *.aux + +clean: + rm -rf *.log *.aux Index: /issm/oecreview/Archive/23185-23389/log.tex =================================================================== --- /issm/oecreview/Archive/23185-23389/log.tex (revision 23390) +++ /issm/oecreview/Archive/23185-23389/log.tex (revision 23390) @@ -0,0 +1,1141 @@ +\noindent \textbf{Change \#1} with diff file ISSM-23185-23186.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/exp/exptool.m\\ +Export determination: 6. \\ +Rationale: CHG: minor\\ +\vspace{3em} + +\noindent \textbf{Change \#2} with diff file ISSM-23187-23188.diff: \\ +Function name: \\ +M /issm/trunk-jpl M /issm/trunk-jpl/src M /issm/trunk-jpl/src/m/mesh/triangle.m D /issm/trunk-jpl/src/m/modules/Triangle.m\\ +Export determination: 6. \\ +Rationale: merged trunk and trunk-jpl\\ +\vspace{3em} + +\noindent \textbf{Change \#3} with diff file ISSM-23190-23191.diff: \\ +Function name: \\ +M /issm/trunk-jpl M /issm/trunk-jpl/src M /issm/trunk-jpl/test\\ +Export determination: 6. \\ +Rationale: Block revision 23189 from being merged into trunk-jpl\\ +\vspace{3em} + +\noindent \textbf{Change \#4} with diff file ISSM-23191-23192.diff: \\ +Function name: \\ +M /issm/trunk-jpl/configure.ac\\ +Export determination: 6. \\ +Rationale: CHG: new revision number of ISSM\\ +\vspace{3em} + +\noindent \textbf{Change \#5} with diff file ISSM-23192-23193.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/mesh/triangle.py M /issm/trunk-jpl/src/m/mesh/triangle2dvertical.m D /issm/trunk-jpl/src/m/modules/Triangle.py\\ +Export determination: 6. \\ +Rationale: CHG: removing Triangle.py as well\\ +\vspace{3em} + +\noindent \textbf{Change \#6} with diff file ISSM-23193-23194.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test421.m M /issm/trunk-jpl/test/NightlyRun/test421.py\\ +Export determination: 6. \\ +Rationale: CHG: relaxing tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#7} with diff file ISSM-23194-23195.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/mesh/triangle.py\\ +Export determination: 6. \\ +Rationale: BUG: forgot to import Triangle\_python\\ +\vspace{3em} + +\noindent \textbf{Change \#8} with diff file ISSM-23197-23198.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/solutionsequences/solutionsequence\_nonlinear.cpp M /issm/trunk-jpl/src/c/solutionsequences/solutionsequence\_schurcg.cpp\\ +Export determination: 6. \\ +Rationale: NEW: added preconditioned Schur CG solution sequence for FS 3D\\ +\vspace{3em} + +\noindent \textbf{Change \#9} with diff file ISSM-23198-23199.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/solutionsequences/solutionsequence\_nonlinear.cpp\\ +Export determination: 6. \\ +Rationale: CHG: Removed personal troubleshooting commands\\ +\vspace{3em} + +\noindent \textbf{Change \#10} with diff file ISSM-23199-23200.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/StressbalanceAnalysis.h\\ +Export determination: 6. \\ +Rationale: NEW: Added routine to calculate local contribution to the Schur preconditioner\\ +\vspace{3em} + +\noindent \textbf{Change \#11} with diff file ISSM-23204-23205.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/solutionsequences/solutionsequence\_schurcg.cpp\\ +Export determination: 6. \\ +Rationale: CHG: Fixed bug in the SchurCG solver for nonzero Dirichlet B.C.\\ +\vspace{3em} + +\noindent \textbf{Change \#12} with diff file ISSM-23205-23206.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/solutionsequences/convergence.cpp M /issm/trunk-jpl/src/c/solutionsequences/solutionsequence\_schurcg.cpp\\ +Export determination: 6. \\ +Rationale: CHG: Reduced SchurCG storage req. by storing preconditioner in Kff. Added adjusted routine to check for convergence.\\ +\vspace{3em} + +\noindent \textbf{Change \#13} with diff file ISSM-23206-23207.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: CHG: PressureMassMatrix and SchurPreconditioner can now also be constructed in 2D\\ +\vspace{3em} + +\noindent \textbf{Change \#14} with diff file ISSM-23207-23208.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: CHG: Combined 2D \& 3D case for MassMatrix \& SchurPrecond into one\\ +\vspace{3em} + +\noindent \textbf{Change \#15} with diff file ISSM-23210-23211.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/clusters/stallo.py\\ +Export determination: 6. \\ +Rationale: BUG:updating Stallo cluster file\\ +\vspace{3em} + +\noindent \textbf{Change \#16} with diff file ISSM-23211-23212.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/contrib/defleurian/netCDF/export\_netCDF.py M /issm/trunk-jpl/src/m/contrib/defleurian/paraview/enveloppeVTK.py M /issm/trunk-jpl/src/m/contrib/defleurian/paraview/exportVTK.py\\ +Export determination: 6. \\ +Rationale: CHG:updating export routines\\ +\vspace{3em} + +\noindent \textbf{Change \#17} with diff file ISSM-23212-23213.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/solutionsequences/solutionsequence\_schurcg.cpp\\ +Export determination: 6. \\ +Rationale: CHG: make sure code compile with PETSc 3.4\\ +\vspace{3em} + +\noindent \textbf{Change \#18} with diff file ISSM-23214-23215.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test290.m M /issm/trunk-jpl/test/NightlyRun/test290.py\\ +Export determination: 6. \\ +Rationale: CHG: Easing tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#19} with diff file ISSM-23215-23216.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/adjointstressbalance\_core.cpp M /issm/trunk-jpl/src/c/cores/stressbalance\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: Added SchurCG switch to control method\\ +\vspace{3em} + +\noindent \textbf{Change \#20} with diff file ISSM-23216-23217.diff: \\ +Function name: \\ +M /issm/trunk-jpl/m4/issm\_options.m4\\ +Export determination: 6. \\ +Rationale: BUG: Minor: extra backslash in m1qn3 lib path.\\ +\vspace{3em} + +\noindent \textbf{Change \#21} with diff file ISSM-23217-23218.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/control\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: Added SchurCG compatibility to control\_core.cpp\\ +\vspace{3em} + +\noindent \textbf{Change \#22} with diff file ISSM-23218-23219.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/control\_core.cpp\\ +Export determination: 6. \\ +Rationale: BUG: use brackets to protect case\\ +\vspace{3em} + +\noindent \textbf{Change \#23} with diff file ISSM-23219-23220.diff: \\ +Function name: \\ +M /issm/trunk-jpl/etc/environment.sh\\ +Export determination: 6. \\ +Rationale: CHG: libprepend mpich\\ +\vspace{3em} + +\noindent \textbf{Change \#24} with diff file ISSM-23220-23221.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/solutionsequences/solutionsequence\_schurcg.cpp\\ +Export determination: 6. \\ +Rationale: CHG: added switch to MatCreateSubMatrix for PETSc 3.5+\\ +\vspace{3em} + +\noindent \textbf{Change \#25} with diff file ISSM-23221-23222.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/FemModel.cpp M /issm/trunk-jpl/src/c/classes/Profiler.cpp M /issm/trunk-jpl/src/c/classes/Profiler.h M /issm/trunk-jpl/src/c/cores/masstransport\_core.cpp M /issm/trunk-jpl/src/c/cores/stressbalance\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: added core solution profiling\\ +\vspace{3em} + +\noindent \textbf{Change \#26} with diff file ISSM-23222-23223.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/FemModel.cpp M /issm/trunk-jpl/src/c/classes/Profiler.h\\ +Export determination: 6. \\ +Rationale: CHG: moved core profiling to md.debug.profiling\\ +\vspace{3em} + +\noindent \textbf{Change \#27} with diff file ISSM-23223-23224.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test2084.m\\ +Export determination: 6. \\ +Rationale: CHG: Eased tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#28} with diff file ISSM-23224-23225.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test2084.m\\ +Export determination: 6. \\ +Rationale: CHG: Eased tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#29} with diff file ISSM-23227-23228.diff: \\ +Function name: \\ +A /issm/trunk-jpl/externalpackages/codipack A /issm/trunk-jpl/externalpackages/codipack/install.sh\\ +Export determination: 6. \\ +Rationale: NEW: added codipack\\ +\vspace{3em} + +\noindent \textbf{Change \#30} with diff file ISSM-23228-23229.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/Profiler.h M /issm/trunk-jpl/src/c/cores/thermal\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: added thermal core solution profiling\\ +\vspace{3em} + +\noindent \textbf{Change \#31} with diff file ISSM-23229-23230.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/FemModel.cpp\\ +Export determination: 6. \\ +Rationale: CHG: added output for thermal core solution profiling\\ +\vspace{3em} + +\noindent \textbf{Change \#32} with diff file ISSM-23230-23231.diff: \\ +Function name: \\ +A /issm/trunk-jpl/src/m/classes/clusters/stallo.m M /issm/trunk-jpl/src/m/classes/clusters/stallo.py\\ +Export determination: 6. \\ +Rationale: NEW: adding matlab stallo and updating py\\ +\vspace{3em} + +\noindent \textbf{Change \#33} with diff file ISSM-23231-23232.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/modules/Chaco.py M /issm/trunk-jpl/src/m/modules/Scotch.py M /issm/trunk-jpl/src/m/partition/partitioner.py M /issm/trunk-jpl/src/m/qmu/dakota\_in\_write.py M /issm/trunk-jpl/src/m/qmu/dakota\_out\_parse.py M /issm/trunk-jpl/src/m/qmu/process\_qmu\_response\_data.m M /issm/trunk-jpl/src/wrappers/Chaco/Chaco.cpp M /issm/trunk-jpl/src/wrappers/python/io/FetchPythonData.cpp M /issm/trunk-jpl/src/wrappers/python/io/pythonio.h A /issm/trunk-jpl/test/NightlyRun/test234.py A /issm/trunk-jpl/test/NightlyRun/test235.py A /issm/trunk-jpl/test/NightlyRun/test413.py A /issm/trunk-jpl/test/NightlyRun/test414.py A /issm/trunk-jpl/test/NightlyRun/test417.py A /issm/trunk-jpl/test/NightlyRun/test444.py\\ +Export determination: 6. \\ +Rationale: NEW: added Dakota/QMU Chaco tests (234,235,413,414,417,444), minor bug fixes, left out 418 due to unresolved memory issues\\ +\vspace{3em} + +\noindent \textbf{Change \#34} with diff file ISSM-23232-23233.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/FemModel.cpp M /issm/trunk-jpl/src/c/classes/Profiler.h M /issm/trunk-jpl/src/c/cores/damage\_core.cpp M /issm/trunk-jpl/src/c/cores/esa\_core.cpp M /issm/trunk-jpl/src/c/cores/gia\_core.cpp M /issm/trunk-jpl/src/c/cores/hydrology\_core.cpp M /issm/trunk-jpl/src/c/cores/movingfront\_core.cpp M /issm/trunk-jpl/src/c/cores/sealevelrise\_core.cpp M /issm/trunk-jpl/src/c/cores/smb\_core.cpp M /issm/trunk-jpl/src/c/cores/transient\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: added core solution profiling\\ +\vspace{3em} + +\noindent \textbf{Change \#35} with diff file ISSM-23233-23234.diff: \\ +Function name: \\ +A /issm/trunk-jpl/externalpackages/adjointmpi A /issm/trunk-jpl/externalpackages/adjointmpi/install.sh\\ +Export determination: 6. \\ +Rationale: NEW: added adjointmpi for codipack\\ +\vspace{3em} + +\noindent \textbf{Change \#36} with diff file ISSM-23234-23235.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/linux64\_ross\_dakota\\ +Export determination: 6. \\ +Rationale: CHG: Adding Python tests for Dakota\\ +\vspace{3em} + +\noindent \textbf{Change \#37} with diff file ISSM-23235-23236.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test2084.m M /issm/trunk-jpl/test/NightlyRun/test2084.py\\ +Export determination: 6. \\ +Rationale: CHG: fixed 2084 so that python and matlab versions test names and tolerances match\\ +\vspace{3em} + +\noindent \textbf{Change \#38} with diff file ISSM-23236-23237.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/numberedcostfunction.m\\ +Export determination: 6. \\ +Rationale: CHG: updated numberedcostfunction\\ +\vspace{3em} + +\noindent \textbf{Change \#39} with diff file ISSM-23237-23238.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/toolkits/issm/IssmToolkitUtils.cpp\\ +Export determination: 6. \\ +Rationale: CHG: added check to avoid crash\\ +\vspace{3em} + +\noindent \textbf{Change \#40} with diff file ISSM-23238-23239.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/mesh/triangle.py\\ +Export determination: 6. \\ +Rationale: BUG: no more Triangle module\\ +\vspace{3em} + +\noindent \textbf{Change \#41} with diff file ISSM-23239-23240.diff: \\ +Function name: \\ +M /issm/trunk-jpl/m4/issm\_options.m4\\ +Export determination: 6. \\ +Rationale: CHG: integrating CoDIPack changes\\ +\vspace{3em} + +\noindent \textbf{Change \#42} with diff file ISSM-23240-23241.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/Numberedcostfunction.cpp M /issm/trunk-jpl/src/c/cores/controladm1qn3\_core.cpp M /issm/trunk-jpl/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp M /issm/trunk-jpl/src/c/modules/ModelProcessorx/ModelProcessorx.h M /issm/trunk-jpl/src/c/shared/MemOps/MemOps.cpp M /issm/trunk-jpl/src/c/toolkits/issm/IssmMpiSparseMat.h\\ +Export determination: 6. \\ +Rationale: CHG: integrating changes from CoDiPack's branche\\ +\vspace{3em} + +\noindent \textbf{Change \#43} with diff file ISSM-23241-23242.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/Makefile.am A /issm/trunk-jpl/src/c/toolkits/codipack A /issm/trunk-jpl/src/c/toolkits/codipack/CoDiPackCommon.hpp A /issm/trunk-jpl/src/c/toolkits/codipack/CoDiPackGlobal.h A /issm/trunk-jpl/src/c/toolkits/codipack/ampi\_interface.cpp A /issm/trunk-jpl/src/c/toolkits/codipack/codipackincludes.h M /issm/trunk-jpl/src/c/toolkits/toolkits.h\\ +Export determination: 6. \\ +Rationale: CHG: integrating CoDiPack's changes\\ +\vspace{3em} + +\noindent \textbf{Change \#44} with diff file ISSM-23242-23243.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/Elements/Element.cpp M /issm/trunk-jpl/src/c/classes/ExternalResults/GenericExternalResult.h M /issm/trunk-jpl/src/c/classes/FemModel.cpp M /issm/trunk-jpl/src/c/cores/control\_core.cpp M /issm/trunk-jpl/src/c/cores/controlvalidation\_core.cpp M /issm/trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp M /issm/trunk-jpl/src/c/modules/ModelProcessorx/CreateParameters.cpp M /issm/trunk-jpl/src/c/modules/SurfaceMassBalancex/Gembx.cpp M /issm/trunk-jpl/src/c/shared/Enum/EnumDefinitions.h M /issm/trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp M /issm/trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp\\ +Export determination: 6. \\ +Rationale: CHG: integrating CoDiPack's changes\\ +\vspace{3em} + +\noindent \textbf{Change \#45} with diff file ISSM-23243-23244.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/modules/SurfaceMassBalancex/Gembx.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixing compilation\\ +\vspace{3em} + +\noindent \textbf{Change \#46} with diff file ISSM-23244-23245.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/shared/Numerics/extrema.cpp M /issm/trunk-jpl/src/c/shared/Numerics/isnan.cpp M /issm/trunk-jpl/src/c/shared/Numerics/isnan.h M /issm/trunk-jpl/src/c/shared/Numerics/numerics.h M /issm/trunk-jpl/src/c/shared/Numerics/recast.h M /issm/trunk-jpl/src/c/shared/Numerics/types.h\\ +Export determination: 6. \\ +Rationale: CHG: integrating changes from CoDiPack's branche\\ +\vspace{3em} + +\noindent \textbf{Change \#47} with diff file ISSM-23245-23246.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/autodiff.js M /issm/trunk-jpl/src/m/classes/autodiff.m M /issm/trunk-jpl/src/m/classes/autodiff.py\\ +Export determination: 6. \\ +Rationale: CHG: added field for CoDiPack\\ +\vspace{3em} + +\noindent \textbf{Change \#48} with diff file ISSM-23246-23247.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/wrappers/javascript/Makefile.am M /issm/trunk-jpl/src/wrappers/matlab/Makefile.am M /issm/trunk-jpl/src/wrappers/python/Makefile.am\\ +Export determination: 6. \\ +Rationale: CHG: integrated CoDiPack changes\\ +\vspace{3em} + +\noindent \textbf{Change \#49} with diff file ISSM-23247-23248.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/linux64\_ross\_dakota\\ +Export determination: 6. \\ +Rationale: CHG: Disabling Python tests for Dakota again until Nathan can have a look\\ +\vspace{3em} + +\noindent \textbf{Change \#50} with diff file ISSM-23248-23249.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test2084.m M /issm/trunk-jpl/test/NightlyRun/test2084.py\\ +Export determination: 6. \\ +Rationale: CHG: Adjusted tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#51} with diff file ISSM-23249-23250.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test215.m M /issm/trunk-jpl/test/NightlyRun/test215.py\\ +Export determination: 6. \\ +Rationale: CHG: Adjusted tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#52} with diff file ISSM-23250-23251.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/ad\_core.cpp M /issm/trunk-jpl/src/c/cores/adgradient\_core.cpp M /issm/trunk-jpl/src/c/cores/controladm1qn3\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: final changes from CoDiPack\\ +\vspace{3em} + +\noindent \textbf{Change \#53} with diff file ISSM-23251-23252.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/FemModel.cpp M /issm/trunk-jpl/src/c/classes/IoModel.cpp M /issm/trunk-jpl/src/c/toolkits/gsl/DenseGslSolve.cpp M /issm/trunk-jpl/src/c/toolkits/mpi/issmmpi.cpp M /issm/trunk-jpl/src/c/toolkits/mpi/issmmpi.h M /issm/trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp\\ +Export determination: 6. \\ +Rationale: CHG: final changes from CoDiPack\\ +\vspace{3em} + +\noindent \textbf{Change \#54} with diff file ISSM-23252-23253.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/classes/FemModel.cpp M /issm/trunk-jpl/src/c/classes/IoModel.cpp M /issm/trunk-jpl/src/c/cores/controlm1qn3\_core.cpp M /issm/trunk-jpl/src/c/cores/transient\_core.cpp M /issm/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp M /issm/trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp\\ +Export determination: 6. \\ +Rationale: CHG: compile the code with CoDiPack in\\ +\vspace{3em} + +\noindent \textbf{Change \#55} with diff file ISSM-23253-23254.diff: \\ +Function name: \\ +M /issm/trunk-jpl/externalpackages/codipack/install.sh\\ +Export determination: 6. \\ +Rationale: CHG: get trunk instead\\ +\vspace{3em} + +\noindent \textbf{Change \#56} with diff file ISSM-23254-23255.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/FemModel.cpp M /issm/trunk-jpl/src/c/classes/FemModel.h M /issm/trunk-jpl/src/c/classes/Options/GenericOption.h M /issm/trunk-jpl/src/c/classes/Params/Parameters.cpp M /issm/trunk-jpl/src/c/classes/Params/Parameters.h M /issm/trunk-jpl/src/c/toolkits/mpi/issmmpi.h\\ +Export determination: 6. \\ +Rationale: CHG: fixing compilation for CoDiPack\\ +\vspace{3em} + +\noindent \textbf{Change \#57} with diff file ISSM-23255-23256.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/IoModel.cpp M /issm/trunk-jpl/src/c/cores/controlad\_core.cpp M /issm/trunk-jpl/src/c/modules/FloatingiceMeltingRatePicox/FloatingiceMeltingRatePicox.cpp M /issm/trunk-jpl/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp M /issm/trunk-jpl/src/c/shared/Elements/PrintArrays.cpp M /issm/trunk-jpl/src/c/shared/Elements/elements.h M /issm/trunk-jpl/src/c/toolkits/mpi/issmmpi.h M /issm/trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/objects/PetscMat.h M /issm/trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.cpp M /issm/trunk-jpl/src/c/toolkits/petsc/objects/PetscVec.h\\ +Export determination: 6. \\ +Rationale: CHG: fixing some more errors related to CoDiPack compilation\\ +\vspace{3em} + +\noindent \textbf{Change \#58} with diff file ISSM-23256-23257.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/geometry.py M /issm/trunk-jpl/src/m/qmu/preqmu.py\\ +Export determination: 6. \\ +Rationale: BUG: fixed preqmu.py causing directory error in consecutive Dakota/QMU tests, minor formatting issue in geometry.py\\ +\vspace{3em} + +\noindent \textbf{Change \#59} with diff file ISSM-23257-23258.diff: \\ +Function name: \\ +A /issm/trunk-jpl/test/NightlyRun/test420.py\\ +Export determination: 6. \\ +Rationale: NEW: added test420.py\\ +\vspace{3em} + +\noindent \textbf{Change \#60} with diff file ISSM-23258-23259.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test417.py A /issm/trunk-jpl/test/NightlyRun/test418.py\\ +Export determination: 6. \\ +Rationale: NEW: added test418.py to test on Jenkins, fails on my computer due to a memory issue.\\ +\vspace{3em} + +\noindent \textbf{Change \#61} with diff file ISSM-23259-23260.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/linux64\_ross\_dakota\\ +Export determination: 6. \\ +Rationale: CHG: Added Python tests back to Ubuntu Dakota build. Working on Mac version now.\\ +\vspace{3em} + +\noindent \textbf{Change \#62} with diff file ISSM-23260-23261.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/linux64\_ross\_python\\ +Export determination: 6. \\ +Rationale: CHG: Attempting to bring Python build test suite reporting online\\ +\vspace{3em} + +\noindent \textbf{Change \#63} with diff file ISSM-23261-23262.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/linux64\_ross\_python\\ +Export determination: 6. \\ +Rationale: CHG: Attempting to bring Python build test suite reporting online\\ +\vspace{3em} + +\noindent \textbf{Change \#64} with diff file ISSM-23262-23263.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/linux64\_ross\_python\\ +Export determination: 6. \\ +Rationale: CHG: Attempting to bring Python build test suite reporting online\\ +\vspace{3em} + +\noindent \textbf{Change \#65} with diff file ISSM-23263-23264.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/linux64\_ross\_python\\ +Export determination: 6. \\ +Rationale: CHG: Attempting to bring Python build test suite reporting online (testing to see if something fishy is going on here)\\ +\vspace{3em} + +\noindent \textbf{Change \#66} with diff file ISSM-23264-23265.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/linux64\_ross\_python\\ +Export determination: 6. \\ +Rationale: CHG: Attempting to bring Python build test suite reporting online (apparently something fishy is not going on here)\\ +\vspace{3em} + +\noindent \textbf{Change \#67} with diff file ISSM-23265-23266.diff: \\ +Function name: \\ +A /issm/trunk-jpl/src/m/classes/clusters/tetralith.m\\ +Export determination: 6. \\ +Rationale: NEW: new cluster script\\ +\vspace{3em} + +\noindent \textbf{Change \#68} with diff file ISSM-23266-23267.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/toolkits/gsl/DenseGslSolve.cpp M /issm/trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixing handling of external functions in codipack\\ +\vspace{3em} + +\noindent \textbf{Change \#69} with diff file ISSM-23267-23268.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controladm1qn3\_core.cpp M /issm/trunk-jpl/src/c/modules/ModelProcessorx/Autodiff/CreateParametersAutodiff.cpp\\ +Export determination: 6. \\ +Rationale: NEW: integrating CoDiPack in m1qn3, still crashes after first it\\ +\vspace{3em} + +\noindent \textbf{Change \#70} with diff file ISSM-23268-23269.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controladm1qn3\_core.cpp M /issm/trunk-jpl/src/c/cores/controlm1qn3\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: minor cosmetics\\ +\vspace{3em} + +\noindent \textbf{Change \#71} with diff file ISSM-23269-23270.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/runme.py\\ +Export determination: 6. \\ +Rationale: FIX: fixed runme.py bug causing default behavior to run no tests rather than all tests (except those explicitly excluded)\\ +\vspace{3em} + +\noindent \textbf{Change \#72} with diff file ISSM-23270-23271.diff: \\ +Function name: \\ +A /issm/trunk-jpl/src/m/partition/AreaAverageOntoPartition.py\\ +Export determination: 6. \\ +Rationale: FIX: forgot to add AreaAverageOntoPartition.py when I uploaded the Dakota/QMU tests\\ +\vspace{3em} + +\noindent \textbf{Change \#73} with diff file ISSM-23271-23272.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test2084.m M /issm/trunk-jpl/test/NightlyRun/test2084.py\\ +Export determination: 6. \\ +Rationale: CHG: Adjusted tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#74} with diff file ISSM-23272-23273.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test2084.m M /issm/trunk-jpl/test/NightlyRun/test2084.py\\ +Export determination: 6. \\ +Rationale: CHG: Adjusted tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#75} with diff file ISSM-23273-23274.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/macosx\_pine-island\_dakota\\ +Export determination: 6. \\ +Rationale: CHG: Activating Python Dakota tests\\ +\vspace{3em} + +\noindent \textbf{Change \#76} with diff file ISSM-23274-23275.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/macosx\_pine-island\_dakota\\ +Export determination: 6. \\ +Rationale: CHG: Deactivating Python Dakota tests until I can get Python stable on Pine Island\\ +\vspace{3em} + +\noindent \textbf{Change \#77} with diff file ISSM-23275-23276.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/macosx\_pine-island M /issm/trunk-jpl/jenkins/macosx\_pine-island\_dakota M /issm/trunk-jpl/jenkins/macosx\_pine-island\_dakota\_static M /issm/trunk-jpl/jenkins/macosx\_pine-island\_examples M /issm/trunk-jpl/jenkins/macosx\_pine-island\_static\\ +Export determination: 6. \\ +Rationale: CHG: Activating Python Dakota tests on Pine Island; adjusting all Mac configs to match number of cores available on Pine Island\\ +\vspace{3em} + +\noindent \textbf{Change \#78} with diff file ISSM-23276-23277.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/macosx\_pine-island\_dakota\\ +Export determination: 6. \\ +Rationale: CHG: Activating Python Dakota tests on Pine Island; adjusting all Mac configs to match number of cores available on Pine Island\\ +\vspace{3em} + +\noindent \textbf{Change \#79} with diff file ISSM-23277-23278.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/macosx\_pine-island\_dakota\\ +Export determination: 6. \\ +Rationale: CHG: Adjusting path to Python\\ +\vspace{3em} + +\noindent \textbf{Change \#80} with diff file ISSM-23278-23279.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test211.js M /issm/trunk-jpl/test/NightlyRun/test211.m M /issm/trunk-jpl/test/NightlyRun/test211.py\\ +Export determination: 6. \\ +Rationale: CHG: Easing tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#81} with diff file ISSM-23279-23280.diff: \\ +Function name: \\ +M /issm/trunk-jpl/externalpackages/adjointmpi/install.sh\\ +Export determination: 6. \\ +Rationale: CHG: switching to other branch\\ +\vspace{3em} + +\noindent \textbf{Change \#82} with diff file ISSM-23280-23281.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/toolkits/mpi/issmmpi.h M /issm/trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp\\ +Export determination: 6. \\ +Rationale: CHG: switching to new branch of AdjointMPI\\ +\vspace{3em} + +\noindent \textbf{Change \#83} with diff file ISSM-23281-23282.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controladm1qn3\_core.cpp\\ +Export determination: 6. \\ +Rationale: NEW: CoDiPack now works with 1 cpu\\ +\vspace{3em} + +\noindent \textbf{Change \#84} with diff file ISSM-23282-23283.diff: \\ +Function name: \\ +A /issm/trunk-jpl/test/NightlyRun/test702.py\\ +Export determination: 6. \\ +Rationale: NEW: added test702.py\\ +\vspace{3em} + +\noindent \textbf{Change \#85} with diff file ISSM-23283-23284.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/macosx\_pine-island\_dakota\\ +Export determination: 6. \\ +Rationale: BUG: Correcting path to numpy dir\\ +\vspace{3em} + +\noindent \textbf{Change \#86} with diff file ISSM-23284-23285.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/modules/MeshPartition.m M /issm/trunk-jpl/src/m/modules/MeshPartition.py\\ +Export determination: 6. \\ +Rationale: BUG: fixed new implementation\\ +\vspace{3em} + +\noindent \textbf{Change \#87} with diff file ISSM-23285-23286.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/modules/CoordinateSystemTransformx/CoordinateSystemTransformx.cpp M /issm/trunk-jpl/src/c/modules/CoordinateSystemTransformx/CoordinateSystemTransformx.h M /issm/trunk-jpl/src/c/modules/ModelProcessorx/CreateNodes.cpp\\ +Export determination: 6. \\ +Rationale: CHG: enable compilation with proj.4\\ +\vspace{3em} + +\noindent \textbf{Change \#88} with diff file ISSM-23286-23287.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controlm1qn3\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: minor error message:\\ +\vspace{3em} + +\noindent \textbf{Change \#89} with diff file ISSM-23287-23288.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/wrappers/DistanceToMaskBoundary/DistanceToMaskBoundary.cpp M /issm/trunk-jpl/src/wrappers/IssmConfig/IssmConfig.cpp\\ +Export determination: 6. \\ +Rationale: CHG: added some variables\\ +\vspace{3em} + +\noindent \textbf{Change \#90} with diff file ISSM-23288-23289.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/wrappers/DistanceToMaskBoundary/DistanceToMaskBoundary.cpp\\ +Export determination: 6. \\ +Rationale: CHG: added error message for now\\ +\vspace{3em} + +\noindent \textbf{Change \#91} with diff file ISSM-23289-23290.diff: \\ +Function name: \\ +A /issm/trunk-jpl/jenkins/linux64\_ross\_codi\\ +Export determination: 6. \\ +Rationale: CHG: added codi test\\ +\vspace{3em} + +\noindent \textbf{Change \#92} with diff file ISSM-23290-23291.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test3015.m\\ +Export determination: 6. \\ +Rationale: CHG: added codi test\\ +\vspace{3em} + +\noindent \textbf{Change \#93} with diff file ISSM-23291-23292.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/linux64\_ross\_codi\\ +Export determination: 6. \\ +Rationale: CHG: fixing codipack\\ +\vspace{3em} + +\noindent \textbf{Change \#94} with diff file ISSM-23292-23293.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/linux64\_ross\_codi M /issm/trunk-jpl/test/NightlyRun/test3480.m M /issm/trunk-jpl/test/NightlyRun/test3481.m\\ +Export determination: 6. \\ +Rationale: CHG: make some test work with CODIPACK\\ +\vspace{3em} + +\noindent \textbf{Change \#95} with diff file ISSM-23293-23294.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controladm1qn3\_core.cpp M /issm/trunk-jpl/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp M /issm/trunk-jpl/src/c/modules/SetControlInputsFromVectorx/SetControlInputsFromVectorx.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixing memory leaks\\ +\vspace{3em} + +\noindent \textbf{Change \#96} with diff file ISSM-23294-23295.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/toolkits/issm/IssmMpiSparseMat.h\\ +Export determination: 6. \\ +Rationale: BUG: Daniel's suggestion makes ISSM hang\\ +\vspace{3em} + +\noindent \textbf{Change \#97} with diff file ISSM-23305-23306.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/Params/Parameters.cpp M /issm/trunk-jpl/src/c/classes/Params/Parameters.h\\ +Export determination: 6. \\ +Rationale: CHG: FindParamAndMakePassive should always be compiled\\ +\vspace{3em} + +\noindent \textbf{Change \#98} with diff file ISSM-23306-23307.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controlm1qn3\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: extending m1qn3 to AD compilation\\ +\vspace{3em} + +\noindent \textbf{Change \#99} with diff file ISSM-23307-23308.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controlm1qn3\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: scaling factor should be double, not active\\ +\vspace{3em} + +\noindent \textbf{Change \#100} with diff file ISSM-23308-23309.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/toolkits/petsc/objects/PetscSolver.cpp\\ +Export determination: 6. \\ +Rationale: CHG: added VerboseSolver output for number of PETSc KSP iterations\\ +\vspace{3em} + +\noindent \textbf{Change \#101} with diff file ISSM-23309-23310.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controlm1qn3\_core.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixing compilation\\ +\vspace{3em} + +\noindent \textbf{Change \#102} with diff file ISSM-23310-23311.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/Params/Parameters.cpp M /issm/trunk-jpl/src/c/classes/Params/Parameters.h\\ +Export determination: 6. \\ +Rationale: CHG: forgot to commit vector passive\\ +\vspace{3em} + +\noindent \textbf{Change \#103} with diff file ISSM-23311-23312.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/control\_core.cpp M /issm/trunk-jpl/src/c/cores/controlm1qn3\_core.cpp M /issm/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.cpp M /issm/trunk-jpl/src/c/modules/GetVectorFromControlInputsx/GetVectorFromControlInputsx.h\\ +Export determination: 6. \\ +Rationale: CHG: trying to simplify m1qn3 core to merge with ad\\ +\vspace{3em} + +\noindent \textbf{Change \#104} with diff file ISSM-23315-23316.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controladm1qn3\_core.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixing CoDiPack\\ +\vspace{3em} + +\noindent \textbf{Change \#105} with diff file ISSM-23316-23317.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controladm1qn3\_core.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixing CoDiPack\\ +\vspace{3em} + +\noindent \textbf{Change \#106} with diff file ISSM-23317-23318.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/analyses/EnthalpyAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/SmbAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/ThermalAnalysis.cpp M /issm/trunk-jpl/src/c/classes/Elements/Element.cpp M /issm/trunk-jpl/src/c/classes/Elements/Element.h M /issm/trunk-jpl/src/c/classes/Materials/Matpar.cpp M /issm/trunk-jpl/src/c/cores/transient\_core.cpp M /issm/trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp M /issm/trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h A /issm/trunk-jpl/src/c/shared/Elements/PddSurfaceMassBalanceSicopolis.cpp M /issm/trunk-jpl/src/c/shared/Elements/elements.h M /issm/trunk-jpl/src/c/shared/Enum/EnumDefinitions.h M /issm/trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp A /issm/trunk-jpl/src/m/classes/SMBpddSicopolis.m A /issm/trunk-jpl/test/Archives/Archive245.arch A /issm/trunk-jpl/test/NightlyRun/test245.m\\ +Export determination: 6. \\ +Rationale: NEW: SICOPOLIS PDD scheme\\ +\vspace{3em} + +\noindent \textbf{Change \#107} with diff file ISSM-23318-23319.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controlvalidation\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: make validation core work for AD (youhou)\\ +\vspace{3em} + +\noindent \textbf{Change \#108} with diff file ISSM-23319-23320.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/classes/IoModel.cpp\\ +Export determination: 6. \\ +Rationale: CHG: improved error message\\ +\vspace{3em} + +\noindent \textbf{Change \#109} with diff file ISSM-23320-23321.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/modules/ModelProcessorx/Control/UpdateElementsAndMaterialsControl.cpp\\ +Export determination: 6. \\ +Rationale: CHG: better error message\\ +\vspace{3em} + +\noindent \textbf{Change \#110} with diff file ISSM-23321-23322.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/shared/Elements/PddSurfaceMassBalanceSicopolis.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixed ADOLC compilation\\ +\vspace{3em} + +\noindent \textbf{Change \#111} with diff file ISSM-23322-23323.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/shared/Elements/PddSurfaceMassBalanceSicopolis.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixed ADOLC compilation\\ +\vspace{3em} + +\noindent \textbf{Change \#112} with diff file ISSM-23323-23324.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/shared/Elements/PddSurfaceMassBalanceSicopolis.cpp\\ +Export determination: 6. \\ +Rationale: CHG: error message IF adolc\\ +\vspace{3em} + +\noindent \textbf{Change \#113} with diff file ISSM-23324-23325.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/controlvalidation\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: fixing ADOLC\\ +\vspace{3em} + +\noindent \textbf{Change \#114} with diff file ISSM-23325-23326.diff: \\ +Function name: \\ +D /issm/trunk-jpl/externalpackages/README\\ +Export determination: 6. \\ +Rationale: DEL not needed anymore\\ +\vspace{3em} + +\noindent \textbf{Change \#115} with diff file ISSM-23327-23328.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/shared/Enum/EnumDefinitions.h\\ +Export determination: 6. \\ +Rationale: BUG: Moved Enums to right locations in EnumDefinitons.h\\ +\vspace{3em} + +\noindent \textbf{Change \#116} with diff file ISSM-23328-23329.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/SmbAnalysis.cpp M /issm/trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp\\ +Export determination: 6. \\ +Rationale: BUG: use correct Enum\\ +\vspace{3em} + +\noindent \textbf{Change \#117} with diff file ISSM-23329-23330.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp M /issm/trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp\\ +Export determination: 6. \\ +Rationale: CHG: missing files in r23327 (Sychronized)\\ +\vspace{3em} + +\noindent \textbf{Change \#118} with diff file ISSM-23330-23331.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/linux64\_caladan\_ad M /issm/trunk-jpl/jenkins/linux64\_caladan\_ampi M /issm/trunk-jpl/jenkins/linux64\_ross\_ad M /issm/trunk-jpl/jenkins/linux64\_ross\_ampi M /issm/trunk-jpl/jenkins/linux64\_ross\_codi\\ +Export determination: 6. \\ +Rationale: CHG: remove metis from installation\\ +\vspace{3em} + +\noindent \textbf{Change \#119} with diff file ISSM-23331-23332.diff: \\ +Function name: \\ +A /issm/trunk-jpl/src/m/classes/cfdragcoeffabsgrad.m\\ +Export determination: 6. \\ +Rationale: Adding matlab file for cost function for drag\\ +\vspace{3em} + +\noindent \textbf{Change \#120} with diff file ISSM-23332-23333.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/plot/applyoptions.m M /issm/trunk-jpl/src/m/plot/googlemaps.m\\ +Export determination: 6. \\ +Rationale: CHG: multiple tries for Google maps\\ +\vspace{3em} + +\noindent \textbf{Change \#121} with diff file ISSM-23333-23334.diff: \\ +Function name: \\ +A /issm/trunk-jpl/src/m/classes/SMBpddSicopolis.py M /issm/trunk-jpl/src/m/qmu/helpers.py A /issm/trunk-jpl/test/NightlyRun/test245.py\\ +Export determination: 6. \\ +Rationale: NEW: added python version of test 245\\ +\vspace{3em} + +\noindent \textbf{Change \#122} with diff file ISSM-23334-23335.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/plot/googlemaps.m\\ +Export determination: 6. \\ +Rationale: CHG: fixed typo\\ +\vspace{3em} + +\noindent \textbf{Change \#123} with diff file ISSM-23335-23336.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: CHG: specialization for SpatialLinearFloatingMeltRateEnum at the wrong place\\ +\vspace{3em} + +\noindent \textbf{Change \#124} with diff file ISSM-23336-23337.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/FreeSurfaceBaseAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: CHG: allow FS with other melt parameterizations\\ +\vspace{3em} + +\noindent \textbf{Change \#125} with diff file ISSM-23337-23338.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/cores/stressbalance\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: need melting rates for vz\\ +\vspace{3em} + +\noindent \textbf{Change \#126} with diff file ISSM-23338-23339.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: BUG: do not load melting rate, it is bmb's job\\ +\vspace{3em} + +\noindent \textbf{Change \#127} with diff file ISSM-23339-23340.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test701.m M /issm/trunk-jpl/test/NightlyRun/test701.py M /issm/trunk-jpl/test/NightlyRun/test702.m M /issm/trunk-jpl/test/NightlyRun/test702.py\\ +Export determination: 6. \\ +Rationale: CHG: FS now needs Bmb\\ +\vspace{3em} + +\noindent \textbf{Change \#128} with diff file ISSM-23340-23341.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: BUG: still need to keep grounded ice melt rate\\ +\vspace{3em} + +\noindent \textbf{Change \#129} with diff file ISSM-23341-23342.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/StressbalanceVerticalAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: CHG: vertanalysis requires melt rates\\ +\vspace{3em} + +\noindent \textbf{Change \#130} with diff file ISSM-23342-23343.diff: \\ +Function name: \\ +M /issm/trunk-jpl/m4/issm\_options.m4\\ +Export determination: 6. \\ +Rationale: CHG: added a check on numthreads, make sure it is an int\\ +\vspace{3em} + +\noindent \textbf{Change \#131} with diff file ISSM-23345-23346.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/StressbalanceAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: CHG: make friction PISM work for SB\\ +\vspace{3em} + +\noindent \textbf{Change \#132} with diff file ISSM-23348-23349.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/toolkits/mumps/MumpsSolve.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixed solver in parallel with CoDiPack\\ +\vspace{3em} + +\noindent \textbf{Change \#133} with diff file ISSM-23349-23350.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/toolkits/mpi/issmmpi.cpp\\ +Export determination: 6. \\ +Rationale: CHG: integrating MeDiPack\\ +\vspace{3em} + +\noindent \textbf{Change \#134} with diff file ISSM-23350-23351.diff: \\ +Function name: \\ +M /issm/trunk-jpl/m4/issm\_options.m4 M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/cores/controlm1qn3\_core.cpp M /issm/trunk-jpl/src/c/toolkits/codipack/ampi\_interface.cpp\\ +Export determination: 6. \\ +Rationale: CHG: integrating MeDiPack\\ +\vspace{3em} + +\noindent \textbf{Change \#135} with diff file ISSM-23351-23352.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test211.js M /issm/trunk-jpl/test/NightlyRun/test211.m M /issm/trunk-jpl/test/NightlyRun/test211.py\\ +Export determination: 6. \\ +Rationale: CHG: relaxing tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#136} with diff file ISSM-23352-23353.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/toolkits/mpi/issmmpi.h\\ +Export determination: 6. \\ +Rationale: CHG: integrating MeDiPack\\ +\vspace{3em} + +\noindent \textbf{Change \#137} with diff file ISSM-23353-23354.diff: \\ +Function name: \\ +A /issm/trunk-jpl/externalpackages/medipack A /issm/trunk-jpl/externalpackages/medipack/install.sh\\ +Export determination: 6. \\ +Rationale: NEW: added MeDiPack\\ +\vspace{3em} + +\noindent \textbf{Change \#138} with diff file ISSM-23354-23355.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/groundingline.m\\ +Export determination: 6. \\ +Rationale: BUG: checks not needed when we are not in a transient solution with a grounding line migration\\ +\vspace{3em} + +\noindent \textbf{Change \#139} with diff file ISSM-23355-23356.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/groundingline.js M /issm/trunk-jpl/src/m/classes/groundingline.py\\ +Export determination: 6. \\ +Rationale: CHG: same change in grounding line for python and js\\ +\vspace{3em} + +\noindent \textbf{Change \#140} with diff file ISSM-23357-23358.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/Makefile.am M /issm/trunk-jpl/src/c/shared/Numerics/types.h M /issm/trunk-jpl/src/c/toolkits/mpi/issmmpi.cpp M /issm/trunk-jpl/src/c/toolkits/mpi/issmmpi.h M /issm/trunk-jpl/src/wrappers/matlab/Makefile.am M /issm/trunk-jpl/src/wrappers/python/Makefile.am\\ +Export determination: 6. \\ +Rationale: CHG: integrating MeDiPack but not working yet\\ +\vspace{3em} + +\noindent \textbf{Change \#141} with diff file ISSM-23358-23359.diff: \\ +Function name: \\ +M /issm/trunk-jpl/m4/issm\_options.m4\\ +Export determination: 6. \\ +Rationale: CHG: added check that we don't have both adjointmpi and medipack\\ +\vspace{3em} + +\noindent \textbf{Change \#142} with diff file ISSM-23359-23360.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test3480.m M /issm/trunk-jpl/test/NightlyRun/test3481.m\\ +Export determination: 6. \\ +Rationale: CHG: now CoDiPack can run in parallel\\ +\vspace{3em} + +\noindent \textbf{Change \#143} with diff file ISSM-23361-23362.diff: \\ +Function name: \\ +A /issm/trunk-jpl/externalpackages/adjointmpi/install-pleiades.sh\\ +Export determination: 6. \\ +Rationale: CHG: added install-pleiades.sh\\ +\vspace{3em} + +\noindent \textbf{Change \#144} with diff file ISSM-23363-23364.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/mesh/planet/gmsh/gmshplanet.m\\ +Export determination: 6. \\ +Rationale: BUG: Typo in missing gmsh error message\\ +\vspace{3em} + +\noindent \textbf{Change \#145} with diff file ISSM-23365-23366.diff: \\ +Function name: \\ +A /issm/trunk-jpl/src/m/classes/SMBgradientscomponents.m A /issm/trunk-jpl/src/m/classes/SMBgradientscomponents.py M /issm/trunk-jpl/src/m/classes/clusters/stallo.m M /issm/trunk-jpl/src/m/classes/clusters/stallo.py M /issm/trunk-jpl/src/m/classes/taoinversion.py M /issm/trunk-jpl/src/m/contrib/defleurian/paraview/enveloppeVTK.py M /issm/trunk-jpl/src/m/solve/WriteData.py\\ +Export determination: 6. \\ +Rationale: NEW: adding a smb scheme that compute runoff separately (also fixing stallo cluster)\\ +\vspace{3em} + +\noindent \textbf{Change \#146} with diff file ISSM-23366-23367.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/SmbAnalysis.cpp M /issm/trunk-jpl/src/c/classes/Elements/Element.cpp M /issm/trunk-jpl/src/c/classes/Elements/Element.h M /issm/trunk-jpl/src/c/classes/Materials/Matpar.cpp M /issm/trunk-jpl/src/c/cores/transient\_core.cpp M /issm/trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.cpp M /issm/trunk-jpl/src/c/modules/SurfaceMassBalancex/SurfaceMassBalancex.h M /issm/trunk-jpl/src/c/shared/Enum/EnumDefinitions.h M /issm/trunk-jpl/src/c/shared/Enum/EnumToStringx.cpp M /issm/trunk-jpl/src/c/shared/Enum/StringToEnumx.cpp M /issm/trunk-jpl/src/c/shared/io/Marshalling/IoCodeConversions.cpp\\ +Export determination: 6. \\ +Rationale: NEW: adding a smb scheme that compute runoff separately (smbcore is called two times in transient to provide runoff to hydro model\\ +\vspace{3em} + +\noindent \textbf{Change \#147} with diff file ISSM-23367-23368.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: BUG:commenting debugging message\\ +\vspace{3em} + +\noindent \textbf{Change \#148} with diff file ISSM-23368-23369.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: BUG:commenting debugging message\\ +\vspace{3em} + +\noindent \textbf{Change \#149} with diff file ISSM-23369-23370.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/runme.py M /issm/trunk-jpl/test/NightlyRun/test101.m\\ +Export determination: 6. \\ +Rationale: BUG:partial fix, issues remain in Hydro\\ +\vspace{3em} + +\noindent \textbf{Change \#150} with diff file ISSM-23370-23371.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp M /issm/trunk-jpl/src/c/classes/Params/Parameters.cpp M /issm/trunk-jpl/src/c/cores/hydrology\_core.cpp M /issm/trunk-jpl/src/c/cores/transient\_core.cpp\\ +Export determination: 6. \\ +Rationale: BUG:partial fix, issues remain in Hydro\\ +\vspace{3em} + +\noindent \textbf{Change \#151} with diff file ISSM-23371-23372.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test101.m\\ +Export determination: 6. \\ +Rationale: BUG:reverting unwanted commit\\ +\vspace{3em} + +\noindent \textbf{Change \#152} with diff file ISSM-23372-23373.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/MasstransportAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixing user included bug\\ +\vspace{3em} + +\noindent \textbf{Change \#153} with diff file ISSM-23373-23374.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixing AD compilation and many other tests\\ +\vspace{3em} + +\noindent \textbf{Change \#154} with diff file ISSM-23374-23375.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/toolkits/mpi/issmmpi.h\\ +Export determination: 6. \\ +Rationale: CHG: minor\\ +\vspace{3em} + +\noindent \textbf{Change \#155} with diff file ISSM-23375-23376.diff: \\ +Function name: \\ +M /issm/trunk-jpl/jenkins/jenkins.sh\\ +Export determination: 6. \\ +Rationale: CHG: do not show files everytime\\ +\vspace{3em} + +\noindent \textbf{Change \#156} with diff file ISSM-23376-23377.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: BUG: fixed crash with input not always provided\\ +\vspace{3em} + +\noindent \textbf{Change \#157} with diff file ISSM-23377-23378.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp\\ +Export determination: 6. \\ +Rationale: CHG: fixing NR\\ +\vspace{3em} + +\noindent \textbf{Change \#158} with diff file ISSM-23378-23379.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/m/classes/clusters/stallo.m M /issm/trunk-jpl/src/m/classes/clusters/stallo.py\\ +Export determination: 6. \\ +Rationale: CHG:uniformisation of stallo cluster\\ +\vspace{3em} + +\noindent \textbf{Change \#159} with diff file ISSM-23379-23380.diff: \\ +Function name: \\ +M /issm/trunk-jpl/test/NightlyRun/test455.m M /issm/trunk-jpl/test/NightlyRun/test455.py\\ +Export determination: 6. \\ +Rationale: CHG: Relaxed tolerances\\ +\vspace{3em} + +\noindent \textbf{Change \#160} with diff file ISSM-23380-23381.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/ExtrapolationAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/LevelsetAnalysis.cpp M /issm/trunk-jpl/src/c/cores/balancethickness\_core.cpp M /issm/trunk-jpl/src/c/cores/balancevelocity\_core.cpp\\ +Export determination: 6. \\ +Rationale: CHG: cosmetics\\ +\vspace{3em} + +\noindent \textbf{Change \#161} with diff file ISSM-23384-23385.diff: \\ +Function name: \\ +A /issm/trunk-jpl/externalpackages/petsc/install-3.9-macosx64.sh\\ +Export determination: 6. \\ +Rationale: CHG: adding installation script for Denis\\ +\vspace{3em} + +\noindent \textbf{Change \#162} with diff file ISSM-23387-23388.diff: \\ +Function name: \\ +M /issm/trunk-jpl/src/c/analyses/HydrologyDCEfficientAnalysis.cpp M /issm/trunk-jpl/src/c/analyses/HydrologyDCInefficientAnalysis.cpp M /issm/trunk-jpl/src/c/solutionsequences/solutionsequence\_hydro\_nonlinear.cpp\\ +Export determination: 6. \\ +Rationale: CHG: streamlining in EPL activation and dealing with frozen nodes EffectivPressure\\ +\vspace{3em} + +\noindent \textbf{Change \#163} with diff file ISSM-23388-23389.diff: \\ +Function name: \\ +A /issm/trunk-jpl/examples/Pig2 A /issm/trunk-jpl/examples/Pig2/DomainOutline.exp A /issm/trunk-jpl/examples/Pig2/FrontRetreat.exp A /issm/trunk-jpl/examples/Pig2/Models A /issm/trunk-jpl/examples/Pig2/Pig.par A /issm/trunk-jpl/examples/Pig2/runme.m\\ +Export determination: 6. \\ +Rationale: NEW: new tutorial for NIMS\\ +\vspace{3em} + Index: /issm/oecreview/Archive/23185-23389/r1.tex =================================================================== --- /issm/oecreview/Archive/23185-23389/r1.tex (revision 23390) +++ /issm/oecreview/Archive/23185-23389/r1.tex (revision 23390) @@ -0,0 +1,1 @@ +23185 Index: /issm/oecreview/Archive/23185-23389/r2.tex =================================================================== --- /issm/oecreview/Archive/23185-23389/r2.tex (revision 23390) +++ /issm/oecreview/Archive/23185-23389/r2.tex (revision 23390) @@ -0,0 +1,1 @@ +23389