Index: /issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh =================================================================== --- /issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 12101) +++ /issm/trunk-jpl/configs/config-macosx64-larour-nopetsc.sh (revision 12102) @@ -1,28 +1,15 @@ #!/bin/sh -#petsc 3.2 -#mpich 1.4 +pythonversion=2.7 ./configure \ --prefix=$ISSM_TIER \ - --with-mpi-include=$ISSM_TIER/externalpackages/mpich2/install/include \ - --with-mpi-lib=" $ISSM_TIER/externalpackages/mpich2/install/lib/libpmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpich.a $ISSM_TIER/externalpackages/mpich2/install/lib/libmpl.a " \ --with-matlab-dir=$MATLAB_DIR \ + --with-python-dir=$ISSM_TIER/externalpackages/python/install\ + --with-python-version=$pythonversion \ + --with-python-numpy-dir=$ISSM_TIER/externalpackages/python/install/Python.framework/Versions/$pythonversion/lib/python$pythonversion/site-packages/numpy/core/include/numpy\ --with-triangle-dir=$ISSM_TIER/externalpackages/triangle/install \ - --with-metis-dir=$ISSM_TIER/externalpackages/metis/install \ - --with-chaco-dir=$ISSM_TIER/externalpackages/chaco/install \ - --with-fortran-lib="/usr/local/gfortran/lib/libgfortran.a" \ --with-math-lib="/usr/lib/libm.dylib" \ - --with-blas-lapack-dir=$ISSM_TIER/externalpackages/petsc/install/lib \ --with-graphics-lib="/usr/X11/lib/libX11.dylib" \ --with-cxxoptflags=" -fno-common -no-cpp-precomp -fexceptions -arch x86_64 -mmacosx-version-min=10.5 -O3 -DNDEBUG -w "\ - --with-numthreads=8 \ --with-gsl-dir=$ISSM_TIER/externalpackages/gsl/install -# --with-petsc-dir=$ISSM_TIER/externalpackages/petsc/install \ -# --with-petsc-arch=$ISSM_ARCH \ -# --with-plapack-lib="-L$ISSM_TIER/externalpackages/petsc/install/ -lPLAPACK" \ -# --with-plapack-include="-I$ISSM_TIER/externalpackages/petsc/install/include/ " \ -# --with-blacs-dir=$ISSM_TIER/externalpackages/petsc/install/ \ -# --with-scalapack-dir=$ISSM_TIER/externalpackages/petsc/install/ \ -# --with-mumps-dir=$ISSM_TIER/externalpackages/petsc/install/ -# --with-dakota-dir=$ISSM_TIER/externalpackages/dakota/install \ Index: /issm/trunk-jpl/externalpackages/nose/install-macosx64sh =================================================================== --- /issm/trunk-jpl/externalpackages/nose/install-macosx64sh (revision 12101) +++ /issm/trunk-jpl/externalpackages/nose/install-macosx64sh (revision 12102) @@ -1,10 +1,27 @@ #/bin/bash -#Install Python3 nose module +#Install Python nose module -rm -rf py3k +pythonversion=2 + +rm -rf src -svn checkout http://python-nose.googlecode.com/svn/branches/py3k -cd py3k +if [[ $pythonversion == "3" ]];then -python3.2 ./setup.py build -python3.2 ./setup.py install + svn checkout http://python-nose.googlecode.com/svn/branches/py3k + mv py3k src + + cd src + python ./setup.py build + python ./setup.py install +fi + +if [[ $pythonversion == "2" ]];then + + tar -zxvf nose-1.1.2.tar.gz + mv nose-1.1.2 src + rm -rf nose-1.1.2 + + cd src + python ./setup.py build + python ./setup.py install +fi Index: /issm/trunk-jpl/externalpackages/scipy/install-macosx64.sh =================================================================== --- /issm/trunk-jpl/externalpackages/scipy/install-macosx64.sh (revision 12101) +++ /issm/trunk-jpl/externalpackages/scipy/install-macosx64.sh (revision 12102) @@ -19,6 +19,6 @@ #install numpy cd numpy - python3.2 setup.py build - python3.2 setup.py install + python setup.py build + python setup.py install @@ -30,6 +30,6 @@ #install scipy cd scipy - python3.2 setup.py build - python3.2 setup.py install + python setup.py build + python setup.py install elif [[ $install == "3" ]];then Index: /issm/trunk-jpl/m4/issm_options.m4 =================================================================== --- /issm/trunk-jpl/m4/issm_options.m4 (revision 12101) +++ /issm/trunk-jpl/m4/issm_options.m4 (revision 12102) @@ -572,10 +572,5 @@ HAVE_METIS=no fi - - if test $HAVE_METIS = no; then - AC_MSG_ERROR([--with-metis-dir missing. Metis is needed to run ISSM]); - else - AC_MSG_RESULT($HAVE_METIS) - fi + AM_CONDITIONAL([METIS], [test x$HAVE_METIS = xyes]) dnl }}} dnl mpi{{{ @@ -603,4 +598,5 @@ fi fi + AM_CONDITIONAL([MPI], [test x$HAVE_MPI = xyes]) AC_MSG_RESULT($HAVE_MPI) dnl }}} @@ -1228,4 +1224,13 @@ fi + dnl check that if we have MPI, we have metis + if test "$HAVE_METIS" = "yes" && test "$HAVE_MPI" = "no" ; then + AC_MSG_ERROR([need mpi if using the metis partitioner!]); + fi + + + + + AC_MSG_RESULT(done) dnl }}} Index: /issm/trunk-jpl/src/Makefile.am =================================================================== --- /issm/trunk-jpl/src/Makefile.am (revision 12101) +++ /issm/trunk-jpl/src/Makefile.am (revision 12102) @@ -1,2 +1,2 @@ -EXTRA_DIST = perl pro py -SUBDIRS = c modules m +EXTRA_DIST = perl pro +SUBDIRS = c modules m py Index: /issm/trunk-jpl/src/c/Container/Constraints.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Constraints.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/Container/Constraints.cpp (revision 12102) @@ -48,6 +48,11 @@ /*figure out total number of constraints combining all the cpus (no clones here)*/ - MPI_Reduce(&localconstraints,&numberofconstraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); - MPI_Bcast(&numberofconstraints,1,MPI_INT,0,MPI_COMM_WORLD); + #ifdef _HAVE_MPI_ + MPI_Reduce(&localconstraints,&numberofconstraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); + MPI_Bcast(&numberofconstraints,1,MPI_INT,0,MPI_COMM_WORLD); + #else + numberofconstraints=localconstraints; + #endif + return numberofconstraints; Index: /issm/trunk-jpl/src/c/Container/Elements.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Elements.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/Container/Elements.cpp (revision 12102) @@ -125,4 +125,5 @@ /*Synchronize across cluster, so as to not end up with different sizes for each patch on each cpu: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&numvertices,&max_numvertices,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&max_numvertices,1,MPI_INT,0,MPI_COMM_WORLD); @@ -132,4 +133,5 @@ MPI_Bcast(&max_numnodes,1,MPI_INT,0,MPI_COMM_WORLD); numnodes=max_numnodes; + #endif /*Ok, initialize Patch object: */ @@ -191,7 +193,11 @@ /*Get rank of first cpu that has results*/ + #ifdef _HAVE_MPI_ if(this->Size()) rank=my_rank; else rank=num_procs; MPI_Allreduce (&rank,&minrank,1,MPI_INT,MPI_MIN,MPI_COMM_WORLD); + #else + minrank=my_rank; + #endif /*see what the first element of this partition has in stock (this is common to all partitions)*/ @@ -201,8 +207,11 @@ element->ListResultsInfo(&resultsenums,&resultssizes,&resultstimes,&resultssteps,&numberofresults); } + #ifdef _HAVE_MPI_ MPI_Bcast(&numberofresults,1,MPI_DOUBLE,minrank,MPI_COMM_WORLD); + #endif /*Get out if there is no results. Otherwise broadcast info*/ if(!numberofresults) return; + #ifdef _HAVE_MPI_ if(my_rank!=minrank){ resultsenums=(int*)xmalloc(numberofresults*sizeof(int)); @@ -215,4 +224,5 @@ MPI_Bcast(resultstimes,numberofresults,MPI_DOUBLE,minrank,MPI_COMM_WORLD); MPI_Bcast(resultssteps,numberofresults,MPI_INT,minrank,MPI_COMM_WORLD); + #endif /*Loop over all results and get nodal vector*/ @@ -273,5 +283,9 @@ local_nelem=this->Size(); + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)&local_nelem,(void*)&numberofelements,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); + #else + numberofelements=local_nelem; + #endif return numberofelements; Index: /issm/trunk-jpl/src/c/Container/Loads.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Loads.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/Container/Loads.cpp (revision 12102) @@ -63,6 +63,11 @@ /*figure out total number of loads combining all the cpus (no clones here)*/ + #ifdef _HAVE_MPI_ MPI_Reduce(&localloads,&numberofloads,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&numberofloads,1,MPI_INT,0,MPI_COMM_WORLD); + #else + numberofloads=localloads; + #endif + return numberofloads; Index: /issm/trunk-jpl/src/c/Container/Nodes.cpp =================================================================== --- /issm/trunk-jpl/src/c/Container/Nodes.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/Container/Nodes.cpp (revision 12102) @@ -83,8 +83,12 @@ * 0. This means the dofs between all the cpus are not unique. We now offset the dofs of eache * cpus by the total last dofs of the previus cpu, starting from 0. - * First: bet number of dofs for each cpu*/ + * First: get number of dofs for each cpu*/ alldofcount=(int*)xmalloc(num_procs*sizeof(int)); + #ifdef _HAVE_MPI_ MPI_Gather(&dofcount,1,MPI_INT,alldofcount,1,MPI_INT,0,MPI_COMM_WORLD); MPI_Bcast(alldofcount,num_procs,MPI_INT,0,MPI_COMM_WORLD); + #else + alldofcount[0]=dofcount; + #endif /* Every cpu should start its own dof count at the end of the dofcount from cpu-1*/ @@ -119,5 +123,9 @@ } } + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)truedofs,(void*)alltruedofs,numnodes*maxdofspernode,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + #else + alltruedofs[0]=truedofs[0]; + #endif /* Now every cpu knows the true dofs of everyone else that is not a clone*/ @@ -162,5 +170,9 @@ * dealt with by another cpu. We take the minimum because we are going to manage dof assignment in increasing * order of cpu rank. This is also why we initialized this array to num_procs.*/ + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)ranks,(void*)minranks,numnodes,MPI_INT,MPI_MIN,MPI_COMM_WORLD); + #else + for(i=0;iShowTrueDofs(truedofs); } + #ifdef _HAVE_MPI_ MPI_Allreduce((void*)truedofs,(void*)alltruedofs,numberofobjects*numberofdofsperobject,MPI_INT,MPI_MAX,MPI_COMM_WORLD); + #else + for(i=0;i -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - -/*Petsc includes: */ -#include "mex.h" - -#include "../../shared/shared.h" -#include - - -void PetscMatrixToDoubleMatrix(double** pmatrix, int* prows, int* pcols,Mat petsc_matrix){ - - int i,j,k; - - /*output: */ - double* matrix=NULL; - int rows,cols; - - /*intermediary: */ - int* idxm=NULL; - int* idxn=NULL; - - /*Some needed information: */ - MatGetSize(petsc_matrix,&rows,&cols); - - idxm=(int*)xmalloc(rows*sizeof(int)); - idxn=(int*)xmalloc(cols*sizeof(int)); - - for(i=0;i -#else -#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!" -#endif - -/*Petsc includes: */ -#include "petscmat.h" -#include "petscvec.h" -#include "petscksp.h" - -#include "mex.h" -#include "../../shared/shared.h" -#include - -void PetscVectorToDoubleVector(double** pvector, int* prows, Vec petsc_vector){ - - int i; - int rows; - int *idxm = NULL; - double *vector = NULL; - - /*output: */ - mxArray* dataref=NULL; - - /*Get size of vector: */ - if(petsc_vector){ - VecGetSize(petsc_vector,&rows); - if(rows){ - idxm=(int*)xmalloc(rows*sizeof(int)); - vector=(double*)xmalloc(rows*sizeof(double)); - for(i=0;imatrix->ToSerial(); - matrix->matrix->GetSize(&rows,cols); + matrix->matrix->GetSize(&rows,&cols); #endif Index: /issm/trunk-jpl/src/c/matlab/io/matlabio.h =================================================================== --- /issm/trunk-jpl/src/c/matlab/io/matlabio.h (revision 12101) +++ /issm/trunk-jpl/src/c/matlab/io/matlabio.h (revision 12102) @@ -72,10 +72,4 @@ int MatlabNArrayToNArray(bool** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); int MatlabNArrayToNArray(char** pmatrix,int* pmatrix_numel,int* pmatrix_ndims,int** pmatrix_size,const mxArray* mxmatrix); -int MatlabMatrixToPetscMatrix(Mat* matrix,int* prows,int* pcols, const mxArray* mxmatrix); - -/*Matlab to Petsc routines: */ -int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector); -void PetscMatrixToDoubleMatrix(double** pmatrix, int* prows, int* pcols,Mat matrix); -void PetscVectorToDoubleVector(double** pvector, int* prows, Vec vector); /*Matlab to SeqMat routines: */ @@ -83,3 +77,10 @@ SeqVec* MatlabVectorToSeqVec(const mxArray* dataref); +/*Matlab to Petsc routines: */ +#ifdef _HAVE_PETSC_ +int MatlabMatrixToPetscMatrix(Mat* matrix,int* prows,int* pcols, const mxArray* mxmatrix); +int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector); +#endif + + #endif /* _IO_H_ */ Index: /issm/trunk-jpl/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/ConstraintsStatex/RiftConstraintsState.cpp (revision 12102) @@ -32,7 +32,9 @@ } + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); found=mpi_found; + #endif return found; @@ -93,7 +95,9 @@ } + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); num_unstable_constraints=sum_num_unstable_constraints; + #endif /*Assign output pointers: */ @@ -131,7 +135,9 @@ /*Is there just one found? that would mean we have frozen! : */ + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); found=mpi_found; + #endif return found; @@ -189,7 +195,9 @@ } + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); found=mpi_found; + #endif return found; @@ -220,7 +228,9 @@ } + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); found=mpi_found; + #endif if (found){ @@ -279,7 +289,9 @@ } + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); num_unstable_constraints=sum_num_unstable_constraints; + #endif /*Assign output pointers: */ @@ -317,7 +329,9 @@ } + #ifdef _HAVE_MPI_ MPI_Reduce (&max_penetration,&mpi_max_penetration,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_max_penetration,1,MPI_DOUBLE,0,MPI_COMM_WORLD); max_penetration=mpi_max_penetration; + #endif /*feed max_penetration to inputs: */ @@ -354,7 +368,9 @@ } + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); num_unstable_constraints=sum_num_unstable_constraints; + #endif return num_unstable_constraints; Index: /issm/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalConstraintsState.cpp (revision 12102) @@ -36,7 +36,9 @@ } + #ifdef _HAVE_MPI_ MPI_Reduce (&num_unstable_constraints,&sum_num_unstable_constraints,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&sum_num_unstable_constraints,1,MPI_INT,0,MPI_COMM_WORLD); num_unstable_constraints=sum_num_unstable_constraints; + #endif /*Have we converged? : */ Index: /issm/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/ConstraintsStatex/ThermalIsPresent.cpp (revision 12102) @@ -28,7 +28,9 @@ } + #ifdef _HAVE_MPI_ MPI_Reduce (&found,&mpi_found,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&mpi_found,1,MPI_INT,0,MPI_COMM_WORLD); found=mpi_found; + #endif return found; Index: /issm/trunk-jpl/src/c/modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/DragCoefficientAbsGradientx/DragCoefficientAbsGradientx.cpp (revision 12102) @@ -27,7 +27,9 @@ /*Sum all J from all cpus of the cluster:*/ + #ifdef _HAVE_MPI_ MPI_Reduce (&J,&J_sum,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&J_sum,1,MPI_DOUBLE,0,MPI_COMM_WORLD); J=J_sum; + #endif /*Assign output pointers: */ Index: /issm/trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/ElementResponsex/ElementResponsex.cpp (revision 12102) @@ -37,6 +37,8 @@ /*Broadcast whether we found the element: */ + #ifdef _HAVE_MPI_ MPI_Allreduce ( &found,&sumfound,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); if(!sumfound)_error_("%s%i%s","could not find material with id",index," to compute ElementResponse"); + #endif /*Ok, we found the element, compute responseocity: */ @@ -46,6 +48,8 @@ /*Broadcast and plug into response: */ + #ifdef _HAVE_MPI_ MPI_Allreduce ( &cpu_found,&cpu_found,1,MPI_INT,MPI_MAX,MPI_COMM_WORLD); MPI_Bcast(&response,1,MPI_DOUBLE,cpu_found,MPI_COMM_WORLD); + #endif *presponse=response; Index: /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/GroundinglineMigrationx/GroundinglineMigrationx.cpp (revision 12102) @@ -156,6 +156,10 @@ vec_nodes_on_floatingice->Assemble(); + #ifdef _HAVE_MPI_ MPI_Allreduce(&local_nflipped,&nflipped,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); _printf_(VerboseConvergence()," Additional number of vertices allowed to unground: %i\n",nflipped); + #else + nflipped=local_nflipped; + #endif /*Avoid leaks: */ Index: /issm/trunk-jpl/src/c/modules/IceVolumex/IceVolumex.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/IceVolumex/IceVolumex.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/IceVolumex/IceVolumex.cpp (revision 12102) @@ -19,6 +19,10 @@ local_ice_volume+=element->IceVolume(); } + #ifdef _HAVE_MPI_ MPI_Reduce(&local_ice_volume,&total_ice_volume,1,MPI_DOUBLE,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&total_ice_volume,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + #else + total_ice_volume=local_ice_volume; + #endif /*Assign output pointers: */ Index: /issm/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/InputConvergencex/InputConvergencex.cpp (revision 12102) @@ -30,6 +30,8 @@ /*In parallel, we need to gather the converged status: */ + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)&num_notconverged,(void*)&total_notconverged,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); num_notconverged=total_notconverged; + #endif _printf_(VerboseConvergence()," #elements above convergence criterion = %i\n",num_notconverged); Index: /issm/trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MassFluxx/MassFluxx.cpp (revision 12102) @@ -59,6 +59,8 @@ } + #ifdef _HAVE_MPI_ MPI_Allreduce ( (void*)&mass_flux,(void*)&all_mass_flux,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD); mass_flux=all_mass_flux; + #endif /*Free ressources:*/ Index: /issm/trunk-jpl/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MaxAbsVxx/MaxAbsVxx.cpp (revision 12102) @@ -32,7 +32,9 @@ /*Figure out maximum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxabsvx,&node_maxabsvx,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxabsvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); maxabsvx=node_maxabsvx; + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MaxAbsVyx/MaxAbsVyx.cpp (revision 12102) @@ -33,7 +33,9 @@ /*Figure out maximum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxabsvy,&node_maxabsvy,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxabsvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); maxabsvy=node_maxabsvy; + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MaxAbsVzx/MaxAbsVzx.cpp (revision 12102) @@ -32,7 +32,9 @@ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxabsvz,&node_maxabsvz,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxabsvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); maxabsvz=node_maxabsvz; + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/modules/MaxVelx/MaxVelx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MaxVelx/MaxVelx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MaxVelx/MaxVelx.cpp (revision 12102) @@ -33,7 +33,9 @@ /*Figure out maximum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvel,&node_maxvel,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvel,1,MPI_DOUBLE,0,MPI_COMM_WORLD); maxvel=node_maxvel; + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/modules/MaxVxx/MaxVxx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MaxVxx/MaxVxx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MaxVxx/MaxVxx.cpp (revision 12102) @@ -32,7 +32,9 @@ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvx,&node_maxvx,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); maxvx=node_maxvx; + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/modules/MaxVyx/MaxVyx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MaxVyx/MaxVyx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MaxVyx/MaxVyx.cpp (revision 12102) @@ -32,7 +32,9 @@ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvy,&node_maxvy,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); maxvy=node_maxvy; + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/modules/MaxVzx/MaxVzx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MaxVzx/MaxVzx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MaxVzx/MaxVzx.cpp (revision 12102) @@ -33,7 +33,9 @@ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&maxvz,&node_maxvz,1,MPI_DOUBLE,MPI_MAX,0,MPI_COMM_WORLD ); MPI_Bcast(&node_maxvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); maxvz=node_maxvz; + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/modules/MeshPartitionx/MeshPartitionx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MeshPartitionx/MeshPartitionx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MeshPartitionx/MeshPartitionx.cpp (revision 12102) @@ -42,5 +42,7 @@ /*Partition using Metis:*/ if (num_procs>1){ + #ifdef _HAVE_METIS_ METIS_PartMeshNodalPatch(&numberofelements,&numberofnodes, index, &etype, &numflag, &num_procs, &edgecut, epart, npart); + #endif } else if (num_procs==1){ @@ -67,5 +69,7 @@ /*Partition using Metis:*/ if (num_procs>1){ + #ifdef _HAVE_METIS_ METIS_PartMeshNodalPatch(&numberofelements2d,&numberofnodes2d, index2d, &etype2d, &numflag, &num_procs, &edgecut, epart2d, npart2d); + #endif } else if (num_procs==1){ Index: /issm/trunk-jpl/src/c/modules/MinVelx/MinVelx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MinVelx/MinVelx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MinVelx/MinVelx.cpp (revision 12102) @@ -33,7 +33,9 @@ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvel,&node_minvel,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvel,1,MPI_DOUBLE,0,MPI_COMM_WORLD); minvel=node_minvel; + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MinVxx/MinVxx.cpp (revision 12102) @@ -32,7 +32,9 @@ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvx,&node_minvx,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvx,1,MPI_DOUBLE,0,MPI_COMM_WORLD); minvx=node_minvx; + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/modules/MinVyx/MinVyx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MinVyx/MinVyx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MinVyx/MinVyx.cpp (revision 12102) @@ -32,7 +32,9 @@ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvy,&node_minvy,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvy,1,MPI_DOUBLE,0,MPI_COMM_WORLD); minvy=node_minvy; + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/MinVzx/MinVzx.cpp (revision 12102) @@ -32,7 +32,9 @@ /*Figure out minimum across the cluster: */ + #ifdef _HAVE_MPI_ MPI_Reduce (&minvz,&node_minvz,1,MPI_DOUBLE,MPI_MIN,0,MPI_COMM_WORLD ); MPI_Bcast(&node_minvz,1,MPI_DOUBLE,0,MPI_COMM_WORLD); minvz=node_minvz; + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/modules/NodalValuex/NodalValuex.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/NodalValuex/NodalValuex.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/NodalValuex/NodalValuex.cpp (revision 12102) @@ -36,10 +36,16 @@ /*Broadcast whether we found the element: */ + #ifdef _HAVE_MPI_ MPI_Allreduce ( &found,&sumfound,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD); if(!sumfound)_error_("%s%i%s%s","could not find element with vertex with id",index," to compute nodal value ",EnumToStringx(natureofdataenum)); + #endif /*Broadcast and plug into response: */ + #ifdef _HAVE_MPI_ MPI_Allreduce ( &cpu_found,&cpu_found,1,MPI_INT,MPI_MAX,MPI_COMM_WORLD); MPI_Bcast(&value,1,MPI_DOUBLE,cpu_found,MPI_COMM_WORLD); + #else + value=cpu_found; + #endif *pnodalvalue=value; Index: /issm/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp =================================================================== --- /issm/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/modules/ParsePetscOptionsx/ParsePetscOptionsx.cpp (revision 12102) @@ -93,4 +93,5 @@ /*Ok, broadcast to other cpus: */ + #ifdef _HAVE_MPI_ MPI_Bcast(&numanalyses,1,MPI_INT,0,MPI_COMM_WORLD); if(my_rank!=0){ @@ -99,4 +100,5 @@ } MPI_Bcast(analyses,numanalyses,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif for(i=0;i namespace bamg { Index: /issm/trunk-jpl/src/c/objects/IoModel.cpp =================================================================== --- /issm/trunk-jpl/src/c/objects/IoModel.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/objects/IoModel.cpp (revision 12102) @@ -198,5 +198,7 @@ /*Ok, we have reached the end of the file. break: */ record_code=0; //0 means bailout + #ifdef _HAVE_MPI_ MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); /*tell others cpus we are bailing: */ + #endif break; } @@ -207,4 +209,5 @@ fread(&record_code,sizeof(int),1,this->fid); + #ifdef _HAVE_MPI_ /*Tell other cpus what we are doing: */ MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); /*tell other cpus what we are going to do: */ @@ -213,11 +216,13 @@ MPI_Bcast(&record_enum,1,MPI_INT,0,MPI_COMM_WORLD); MPI_Bcast(&record_length,1,MPI_INT,0,MPI_COMM_WORLD); + #endif - switch(record_code){ case 1: /*Read the boolean and broadcast it to other cpus:*/ if(fread(&booleanint,sizeof(int),1,this->fid)!=1) _error_(" could not read boolean "); + #ifdef _HAVE_MPI_ MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*create BoolParam: */ @@ -228,5 +233,7 @@ /*Read the integer and broadcast it to other cpus:*/ if(fread(&integer,sizeof(int),1,this->fid)!=1) _error_(" could not read integer "); + #ifdef _HAVE_MPI_ MPI_Bcast(&integer,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*create IntParam: */ @@ -237,5 +244,7 @@ /*Read the scalar and broadcast it to other cpus:*/ if(fread(&scalar,sizeof(double),1,this->fid)!=1) _error_(" could not read scalar "); + #ifdef _HAVE_MPI_ MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif /*create DoubleParam: */ @@ -246,5 +255,7 @@ /*We have to read a string from disk. First read the dimensions of the string, then the string: */ if(fread(&string_size,sizeof(int),1,this->fid)!=1) _error_(" could not read length of string "); + #ifdef _HAVE_MPI_ MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(string_size){ @@ -254,5 +265,7 @@ /*Read string, then broadcast: */ if(fread(string,string_size*sizeof(char),1,this->fid)!=1)_error_(" could not read string "); + #ifdef _HAVE_MPI_ MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); + #endif } else{ @@ -308,4 +321,5 @@ } } //}}} + #ifdef _HAVE_MPI_ else{ //cpu ~0 {{{2 for(;;){ //wait on cpu 0 @@ -377,4 +391,5 @@ } } //}}} + #endif } /*}}}*/ @@ -399,5 +414,7 @@ if(fread(&booleanint,sizeof(int),1,fid)!=1) _error_(" could not read boolean "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&booleanint,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*cast to bool: */ @@ -428,5 +445,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(&integer,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Assign output pointers: */ @@ -456,5 +475,7 @@ if(fread(&scalar,sizeof(double),1,fid)!=1)_error_(" could not read scalar "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&scalar,1,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif /*Assign output pointers: */ @@ -487,5 +508,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate string: */ @@ -498,5 +521,7 @@ if(fread(string,string_size*sizeof(char),1,fid)!=1)_error_(" could not read string "); } + #ifdef _HAVE_MPI_ MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); + #endif } else{ @@ -538,10 +563,14 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(my_rank==0){ if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix "); } - MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #ifdef _HAVE_MPI_ + MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate matrix: */ @@ -554,5 +583,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif } @@ -602,10 +633,14 @@ if(fread(&M,sizeof(int),1,fid)!=1) _error_("could not read number of rows for matrix "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(my_rank==0){ if(fread(&N,sizeof(int),1,fid)!=1) _error_("could not read number of columns for matrix "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate matrix: */ @@ -617,5 +652,7 @@ if(fread(matrix,M*N*sizeof(double),1,fid)!=1) _error_("could not read matrix "); } + #ifdef _HAVE_MPI_ MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif } @@ -652,5 +689,7 @@ if(fread(&numstrings,sizeof(int),1,fid)!=1) _error_(" could not read length of string array"); } + #ifdef _HAVE_MPI_ MPI_Bcast(&numstrings,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate string array: */ @@ -665,5 +704,7 @@ if(fread(&string_size,sizeof(int),1,fid)!=1) _error_(" could not read length of string "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&string_size,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(string_size){ string=(char*)xmalloc((string_size+1)*sizeof(char)); @@ -674,5 +715,7 @@ if(fread(string,string_size*sizeof(char),1,fid)!=1)_error_(" could not read string "); } + #ifdef _HAVE_MPI_ MPI_Bcast(string,string_size,MPI_CHAR,0,MPI_COMM_WORLD); + #endif } else{ @@ -717,5 +760,7 @@ if(fread(&numrecords,sizeof(int),1,fid)!=1) _error_("could not read number of records in matrix array "); } + #ifdef _HAVE_MPI_ MPI_Bcast(&numrecords,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(numrecords){ @@ -738,10 +783,14 @@ if(fread(&M,sizeof(int),1,fid)!=1) _error_("%s%i%s","could not read number of rows in ",i,"th matrix of matrix array"); } + #ifdef _HAVE_MPI_ MPI_Bcast(&M,1,MPI_INT,0,MPI_COMM_WORLD); + #endif if(my_rank==0){ if(fread(&N,sizeof(int),1,fid)!=1) _error_("%s%i%s","could not read number of columns in ",i,"th matrix of matrix array"); } + #ifdef _HAVE_MPI_ MPI_Bcast(&N,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Now allocate matrix: */ @@ -754,5 +803,7 @@ } + #ifdef _HAVE_MPI_ MPI_Bcast(matrix,M*N,MPI_DOUBLE,0,MPI_COMM_WORLD); + #endif } @@ -1047,11 +1098,15 @@ } } + #ifdef _HAVE_MPI_ MPI_Bcast(&found,1,MPI_INT,0,MPI_COMM_WORLD); if(!found)_error_("%s %s ","could not find data with name",EnumToStringx(data_enum)); + #endif /*Broadcast code and vector type: */ + #ifdef _HAVE_MPI_ MPI_Bcast(&record_code,1,MPI_INT,0,MPI_COMM_WORLD); MPI_Bcast(&vector_type,1,MPI_INT,0,MPI_COMM_WORLD); if(record_code==5) MPI_Bcast(&vector_type,1,MPI_INT,0,MPI_COMM_WORLD); + #endif /*Assign output pointers:*/ Index: /issm/trunk-jpl/src/c/objects/Patch.cpp =================================================================== --- /issm/trunk-jpl/src/c/objects/Patch.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/objects/Patch.cpp (revision 12102) @@ -120,9 +120,15 @@ int node_numrows; double *total_values = NULL; + #ifdef _HAVE_MPI_ MPI_Status status; + #endif /*First, figure out total number of rows combining all the cpus: */ + #ifdef _HAVE_MPI_ MPI_Reduce(&this->numrows,&total_numrows,1,MPI_INT,MPI_SUM,0,MPI_COMM_WORLD ); MPI_Bcast(&total_numrows,1,MPI_INT,0,MPI_COMM_WORLD); + #else + total_numrows=this->numrows; + #endif /*return if patch empty*/ @@ -140,4 +146,5 @@ /*Now, ask other nodes to send their values: */ + #ifdef _HAVE_MPI_ for (i=1;inumcols. Update the fields in the patch, to reflect this new @@ -159,7 +167,9 @@ this->values=total_values; } + #ifdef _HAVE_MPI_ else{ this->numrows=0; xfree((void**)&this->values); } + #endif }/*}}}*/ Index: /issm/trunk-jpl/src/c/solutions/issm.cpp =================================================================== --- /issm/trunk-jpl/src/c/solutions/issm.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/solutions/issm.cpp (revision 12102) @@ -42,12 +42,20 @@ if(ierr) _error_("Could not initialize Petsc"); #else + #ifdef _HAVE_MPI_ MPI_Init(&argc,&argv); #endif + #endif + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); start=MPI_Wtime(); + #else + start=(double)clock(); + #endif /*Size and rank: */ + #ifdef _HAVE_MPI_ MPI_Comm_rank(MPI_COMM_WORLD,&my_rank); MPI_Comm_size(MPI_COMM_WORLD,&num_procs); + #endif /*First process inputs*/ @@ -62,5 +70,9 @@ /*Create femmodel, using input file: */ + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); start_init=MPI_Wtime(); + #else + start_init=(double)clock(); + #endif femmodel=new FemModel(binfilename,outbinfilename,solution_type,analyses,numanalyses); @@ -82,8 +94,17 @@ femmodel->parameters->FindParam(&control_analysis,InversionIscontrolEnum); femmodel->parameters->FindParam(&tao_analysis,InversionTaoEnum); + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); finish_init=MPI_Wtime(); + #else + finish_init=(double)clock(); + #endif _printf_(true,"call computational core:\n"); + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); start_core=MPI_Wtime( ); + #else + start_core=(double)clock(); + #endif + if(dakota_analysis){ #ifdef _HAVE_DAKOTA_ @@ -106,6 +127,10 @@ solutioncore(femmodel); } + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); finish_core=MPI_Wtime( ); - + #else + finish_core=(double)clock(); + #endif + _printf_(true,"write results to disk:\n"); OutputResultsx(femmodel->elements, femmodel->nodes, femmodel->vertices, femmodel->loads, femmodel->materials, femmodel->parameters,femmodel->results); @@ -127,15 +152,26 @@ /*Get finish time and close*/ + #ifdef _HAVE_MPI_ MPI_Barrier(MPI_COMM_WORLD); finish = MPI_Wtime( ); _printf_(true,"\n %-34s %f seconds \n","FemModel initialization elapsed time:",finish_init-start_init); _printf_(true," %-34s %f seconds \n","Core solution elapsed time:",finish_core-start_core); _printf_(true,"\n %s %i hrs %i min %i sec\n\n","Total elapsed time:",int((finish-start)/3600),int(int(finish-start)%3600/60),int(finish-start)%60); + #else + finish=(double)clock(); + _printf_(true,"\n %-34s %f seconds \n","FemModel initialization elapsed time:",(finish_init-start_init)/CLOCKS_PER_SEC); + _printf_(true," %-34s %f seconds \n","Core solution elapsed time:",(finish_core-start_core)/CLOCKS_PER_SEC); + _printf_(true,"\n %s %i hrs %i min %i sec\n\n","Total elapsed time:",int((finish-start)/3600/CLOCKS_PER_SEC),int(int((finish-start)/CLOCKS_PER_SEC)%3600/60),(int(finish-start)/CLOCKS_PER_SEC)%60); + #endif + + #ifdef _HAVE_PETSC_ _printf_(true,"closing MPI and Petsc\n"); - #ifdef _HAVE_PETSC_ PetscFinalize(); #else + #ifdef _HAVE_MPI_ + _printf_(true,"closing MPI and Petsc\n"); MPI_Finalize(); + #endif #endif Index: /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp =================================================================== --- /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscMatrixToDoubleMatrix.cpp (revision 12102) @@ -10,4 +10,5 @@ #endif +#include /*Petsc includes: */ @@ -17,8 +18,5 @@ /*Petsc includes: */ -#include "mex.h" - -#include "../../shared/shared.h" -#include +#include "../../../shared/shared.h" Index: /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToDoubleVector.cpp =================================================================== --- /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToDoubleVector.cpp (revision 12101) +++ /issm/trunk-jpl/src/c/toolkits/petsc/patches/PetscVectorToDoubleVector.cpp (revision 12102) @@ -8,4 +8,6 @@ #endif +#include + /*Petsc includes: */ #include "petscmat.h" @@ -13,7 +15,5 @@ #include "petscksp.h" -#include "mex.h" -#include "../../shared/shared.h" -#include +#include "../../../shared/shared.h" void PetscVectorToDoubleVector(double** pvector, int* prows, Vec petsc_vector){ @@ -23,7 +23,4 @@ int *idxm = NULL; double *vector = NULL; - - /*output: */ - mxArray* dataref=NULL; /*Get size of vector: */ Index: /issm/trunk-jpl/src/c/toolkits/toolkits.h =================================================================== --- /issm/trunk-jpl/src/c/toolkits/toolkits.h (revision 12101) +++ /issm/trunk-jpl/src/c/toolkits/toolkits.h (revision 12102) @@ -20,6 +20,12 @@ #endif +#ifdef _HAVE_MPI_ #include "./mpi/mpiincludes.h" +#endif + +#ifdef _HAVE_METIS_ #include "./metis/metisincludes.h" +#endif + #include "./triangle/triangleincludes.h" #include "./toolkitsenums.h" Index: /issm/trunk-jpl/src/m/model/mesh/triangle.py =================================================================== --- /issm/trunk-jpl/src/m/model/mesh/triangle.py (revision 12102) +++ /issm/trunk-jpl/src/m/model/mesh/triangle.py (revision 12102) @@ -0,0 +1,55 @@ +from TriMesh import * +from numpy import * + +def triangle(md, domainname, resolution,riftname=''): + #TRIANGLE - create model mesh using the triangle package + # + # This routine creates a model mesh using TriMesh and a domain outline, to within a certain resolution + # where md is a @model object, domainname is the name of an Argus domain outline file, + # and resolution is a characteristic length for the mesh (same unit as the domain outline + # unit). Riftname is an optional argument (Argus domain outline) describing rifts. + # + # Usage: + # md=triangle(md,domainname,resolution) + # or md=triangle(md,domainname, resolution, riftname) + # + # Examples: + # md=triangle(md,'DomainOutline.exp',1000); + # md=triangle(md,'DomainOutline.exp',1000,'Rifts.exp'); + + + #Figure out a characteristic area. Resolution is a node oriented concept (ex a 1000m resolution node would + #be made of 1000*1000 area squares). + + #Check that mesh was not already run, and warn user: + if md.mesh.numberofelements != 0.: + choice = input('This model already has a mesh. Are you sure you want to go ahead? (y/n)') + if choice != 'y': + print 'no meshing done ... exiting' + return [] + + area = resolution**2. + + #Mesh using TriMesh + [md.mesh.elements,md.mesh.x,md.mesh.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,riftname,area) + + #Fill in rest of fields: + md.mesh.numberofelements = size(md.mesh.elements) + md.mesh.numberofvertices = size(md.mesh.x) + md.mesh.z = zeros(md.mesh.numberofvertices) + md.mesh.vertexonboundary = zeros(md.mesh.numberofvertices) + md.mesh.vertexonboundary[md.mesh.segments[:,0:2].astype(int)] = 1. + md.mesh.vertexonbed = ones(md.mesh.numberofvertices) + md.mesh.vertexonsurface = ones(md.mesh.numberofvertices) + md.mesh.elementonbed = ones(md.mesh.numberofelements) + md.mesh.elementonsurface = ones(md.mesh.numberofelements) + + #Now, build the connectivity tables for this mesh. + print "Node: NodeConnectivity not implemented yet!" + #md.mesh.vertexconnectivity = NodeConnectivity((md.mesh.elements), (md.mesh.numberofvertices)) + print "Node: ElementConnectivity not implemented yet!" + #md.mesh.elementconnectivity = ElementConnectivity((md.mesh.elements), (md.mesh.vertexconnectivity)) + + #type of model + md.mesh.dimension = 2. + return md Index: /issm/trunk-jpl/startup.py =================================================================== --- /issm/trunk-jpl/startup.py (revision 12101) +++ /issm/trunk-jpl/startup.py (revision 12102) @@ -82,4 +82,5 @@ from miscellaneous import * from private import * +from triangle import * #}}} Index: /issm/trunk-jpl/test/NightlyRun/test101.py =================================================================== --- /issm/trunk-jpl/test/NightlyRun/test101.py (revision 12101) +++ /issm/trunk-jpl/test/NightlyRun/test101.py (revision 12102) @@ -1,8 +1,9 @@ from model import * from TriMesh import * +from triangle import * -#md=model() -#md=triangle(md,'../Exp/Square.exp',150000); +md=model() +md=triangle(md,'../Exp/Square.exp',150000); -[index,x,y,segments,segmentmarkers]=TriMesh('../Exp/Square.exp',15000.0**2.0,True) -print(index,x,y,segments,segmentmarkers) +#[index,x,y,segments,segmentmarkers]=TriMesh('../Exp/Square.exp',15000.0**2.0,True) +#print(index,x,y,segments,segmentmarkers)