Index: /issm/trunk/configs/linux64/linux64.sh =================================================================== --- /issm/trunk/configs/linux64/linux64.sh (revision 2041) +++ /issm/trunk/configs/linux64/linux64.sh (revision 2042) @@ -1,3 +1,3 @@ #!/bin/sh -./configure --prefix=$ISSM_DIR --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/externalpackages/fblaslapack/$ISSM_ARCH +./configure --prefix=$ISSM_DIR --with-matlab-dir=$MATLAB_DIR --with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install --with-metis-dir=$ISSM_DIR/externalpackages/metis/install --with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install --with-mpi-include=$ISSM_DIR/externalpackages/mpich2/install/include --with-mpi-lib="-L$ISSM_DIR/externalpackages/mpich2/install/lib/ -lmpich" --with-petsc-arch=$ISSM_ARCH --with-dakota-dir=$ISSM_DIR/externalpackages/dakota/install --with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/lib --with-plapack-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/lib --with-blacs-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/lib --with-scalapack-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/lib --with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install/$ISSM_ARCH/ --with-fortran-lib="-L/usr/lib/gcc/x86_64-redhat-linux/4.1.1/ -lgfortran" --with-graphics-lib=/usr/lib64/libX11.so Index: /issm/trunk/etc/cluster.rc =================================================================== --- /issm/trunk/etc/cluster.rc (revision 2041) +++ /issm/trunk/etc/cluster.rc (revision 2042) @@ -39,5 +39,5 @@ cluster_name=astrid -cluster_codepath=/u/astrid1/larour/issm/trunk/bin +cluster_codepath=/u/astrid-r1b/larour/issm/trunk/bin cluster_executionpath=/u/wilkes-r1b/larour/Testing/Execution Index: /issm/trunk/etc/environment.sh =================================================================== --- /issm/trunk/etc/environment.sh (revision 2041) +++ /issm/trunk/etc/environment.sh (revision 2042) @@ -29,6 +29,6 @@ #PETSC export PETSC_DIR -export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$PETSC_DIR/lib/$ISSM_ARCH" -export LD_RUN_PATH="$LD_RUN_PATH:$PETSC_DIR/lib/$ISSM_ARCH" +export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$PETSC_DIR/lib/" +export LD_RUN_PATH="$LD_RUN_PATH:$PETSC_DIR/lib" #SLEPC Index: /issm/trunk/m4/issm_options.m4 =================================================================== --- /issm/trunk/m4/issm_options.m4 (revision 2041) +++ /issm/trunk/m4/issm_options.m4 (revision 2042) @@ -275,30 +275,25 @@ if test -d "$PETSC_ROOT"; then - if test -d "$PETSC_ROOT/bmake/$PETSC_ARCH"; then - - PETSCINCL="-I$PETSC_ROOT/include -I$PETSC_ROOT/ -I$PETSC_ROOT/bmake/$PETSC_ARCH -I$PETSC_ROOT/src/mat/impls/dense/mpi/plapack/" - - case "${host_os}" in - *cygwin*) - PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetscksp.lib libpetscdm.lib libpetscmat.lib libpetscvec.lib libpetsc.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib" - ;; - *linux*) - PETSCLIB="-L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -lpetscsnes -lpetscts" - ;; - *darwin9.6.0*) - PETSCLIB="-L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -lpetscsnes -lpetscts" - ;; - esac - - - - AC_DEFINE([_HAVE_PETSC_],[1],[with Petsc in ISSM src]) - AC_SUBST([PETSCINCL]) - AC_SUBST([PETSCLIB]) - - HAVE_PETSC=yes - else - HAVE_PETSC=no - fi + PETSCINCL="-I$PETSC_ROOT/$PETSC_ARCH/include -I$PETSC_ROOT/include -I$PETSC_ROOT/ -I$PETSC_ROOT/bmake/$PETSC_ARCH -I$PETSC_ROOT/src/mat/impls/dense/mpi/plapack/" + + case "${host_os}" in + *cygwin*) + PETSCLIB="-link -LIBPATH:\"$PETSC_ROOT/lib/$PETSC_ARCH\" libpetscksp.lib libpetscdm.lib libpetscmat.lib libpetscvec.lib libpetsc.lib libpetscsnes.lib libpetscts.lib libmpiuni.lib" + ;; + *linux*) + PETSCLIB="-L$PETSC_ROOT/$PETSC_ARCH/lib -L$PETSC_ROOT/lib -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -lpetscsnes -lpetscts" + ;; + *darwin9.6.0*) + PETSCLIB="-L$PETSC_ROOT/lib/$PETSC_ARCH -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc -lpetscsnes -lpetscts" + ;; + esac + + + + AC_DEFINE([_HAVE_PETSC_],[1],[with Petsc in ISSM src]) + AC_SUBST([PETSCINCL]) + AC_SUBST([PETSCLIB]) + + HAVE_PETSC=yes else HAVE_PETSC=no @@ -476,5 +471,5 @@ HAVE_MUMPS=yes MUMPSINCL=-I"$MUMPS_ROOT/include" - MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps -lpord" + MUMPSLIB=-L"$MUMPS_ROOT/lib -ldmumps -lcmumps -lmumps_common -lpord -lparmetis" AC_DEFINE([_HAVE_MUMPS_],[1],[with Mumps in ISSM src]) Index: /issm/trunk/src/c/Makefile.am =================================================================== --- /issm/trunk/src/c/Makefile.am (revision 2041) +++ /issm/trunk/src/c/Makefile.am (revision 2042) @@ -615,5 +615,5 @@ endif -LDADD = ./libpISSM.a $(METISLIB) $(PETSCLIB) $(DAKOTALIB) $(SLEPCLIB) $(MUMPSLIB) $(PLAPACKLIB) $(MPILIB) $(X_LIBS) $(GRAPHICSLIB) $(BLASLAPACKLIB) $(MKLLIB) $(SCALAPACKLIB) $(BLACSLIB) $(FLIBS) +LDADD = ./libpISSM.a $(PETSCLIB) $(FLIBS) $(PLAPACKLIB) $(MUMPSLIB) $(SCALAPACKLIB) $(BLACSLIB) $(DAKOTALIB) $(METISLIB) $(BLASLAPACKLIB) $(MPILIB) $(MATHLIB) $(FORTRANLIB) $(GRAPHICSLIB) diagnostic_exe_SOURCES = parallel/diagnostic.cpp Index: /issm/trunk/src/c/Reduceloadfromgtofx/Reduceloadfromgtofx.cpp =================================================================== --- /issm/trunk/src/c/Reduceloadfromgtofx/Reduceloadfromgtofx.cpp (revision 2041) +++ /issm/trunk/src/c/Reduceloadfromgtofx/Reduceloadfromgtofx.cpp (revision 2042) @@ -36,5 +36,5 @@ /*Create G_mn'*/ - MatTranspose(G_mn,&tG_mn); + MatTranspose(G_mn,MAT_INITIAL_MATRIX,&tG_mn); /*Create G_mn' * pm*/ Index: /issm/trunk/src/c/Reducematrixfromgtofx/Reducematrixfromgton.cpp =================================================================== --- /issm/trunk/src/c/Reducematrixfromgtofx/Reducematrixfromgton.cpp (revision 2041) +++ /issm/trunk/src/c/Reducematrixfromgtofx/Reducematrixfromgton.cpp (revision 2042) @@ -50,5 +50,5 @@ //K_nn = K_nn + G_mn' * K_mn; - MatTranspose(Gmn,&tGmn); + MatTranspose(Gmn,MAT_INITIAL_MATRIX,&tGmn); MatMatMult(tGmn,Kmn,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&tGmnKmn); MatAXPY(Knn,a,tGmnKmn,DIFFERENT_NONZERO_PATTERN); Index: /issm/trunk/src/c/Solverx/Solverx.cpp =================================================================== --- /issm/trunk/src/c/Solverx/Solverx.cpp (revision 2041) +++ /issm/trunk/src/c/Solverx/Solverx.cpp (revision 2042) @@ -20,4 +20,5 @@ /*Solver*/ KSP ksp=NULL; + PC pc=NULL; int iteration_number; PetscTruth flag; @@ -39,25 +40,26 @@ PetscOptionsDetermineSolverType(&solver_type,solver_string); - if (solver_type==MUMPSPACKAGE_LU){ - /*Convert Kff to MATTAIJMUMPS: */ - MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==MUMPSPACKAGE_CHOL){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SPOOLESPACKAGE_LU){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SPOOLESPACKAGE_CHOL){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); - } - if (solver_type==SUPERLUDISTPACKAGE){ - /*Convert Kff to MATTSBAIJMUMPS: */ - MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff); - } - + /*obsolete? : */ +// if (solver_type==MUMPSPACKAGE_LU){ +// /*Convert Kff to MATTAIJMUMPS: */ +// MatConvert(Kff,MATAIJMUMPS,MAT_REUSE_MATRIX,&Kff); +// } +// if (solver_type==MUMPSPACKAGE_CHOL){ +// /*Convert Kff to MATTSBAIJMUMPS: */ +// MatConvert(Kff,MATSBAIJMUMPS,MAT_REUSE_MATRIX,&Kff); +// } +// if (solver_type==SPOOLESPACKAGE_LU){ +// /*Convert Kff to MATTSBAIJMUMPS: */ +// MatConvert(Kff,MATAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); +// } +// if (solver_type==SPOOLESPACKAGE_CHOL){ +// /*Convert Kff to MATTSBAIJMUMPS: */ +// MatConvert(Kff,MATSBAIJSPOOLES,MAT_REUSE_MATRIX,&Kff); +// } +// if (solver_type==SUPERLUDISTPACKAGE){ +// /*Convert Kff to MATTSBAIJMUMPS: */ +// MatConvert(Kff,MATSUPERLU_DIST,MAT_REUSE_MATRIX,&Kff); +// } +// /*Prepare solver*/ @@ -65,4 +67,10 @@ KSPSetOperators(ksp,Kff,Kff,DIFFERENT_NONZERO_PATTERN); KSPSetFromOptions(ksp); + + /*specific solver?: */ + KSPGetPC(ksp,&pc); + if (solver_type==MUMPSPACKAGE_LU){ + PCFactorSetMatSolverPackage(pc,MAT_SOLVER_MUMPS); + } /*If initial guess for solution, use it, except if we are using the MUMPS direct solver, where any initial Index: /issm/trunk/src/c/toolkits/petsc/patches/MatInvert.cpp =================================================================== --- /issm/trunk/src/c/toolkits/petsc/patches/MatInvert.cpp (revision 2041) +++ /issm/trunk/src/c/toolkits/petsc/patches/MatInvert.cpp (revision 2042) @@ -52,5 +52,5 @@ PCSetType(pc,PCLU); KSPSetUp(ksp); - PCGetFactoredMatrix(pc,&factored_matrix); + //PCGetFactoredMatrix(pc,&factored_matrix); //not found any replacement yet MatMatSolve(factored_matrix,identity,inv); Index: /issm/trunk/src/c/toolkits/petsc/patches/MatPartition.cpp =================================================================== --- /issm/trunk/src/c/toolkits/petsc/patches/MatPartition.cpp (revision 2041) +++ /issm/trunk/src/c/toolkits/petsc/patches/MatPartition.cpp (revision 2042) @@ -35,5 +35,5 @@ int lower_row,upper_row,range; int MA,NA; //matrixA dimensions - MatType type; + const char* type=NULL; int csize; Index: /issm/trunk/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp =================================================================== --- /issm/trunk/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp (revision 2041) +++ /issm/trunk/src/c/toolkits/petsc/patches/MatlabMatrixToPetscMatrix.cpp (revision 2042) @@ -27,4 +27,5 @@ int rows, cols; double* mxmatrix_ptr=NULL; + double* tmatrix=NULL; int ierr; int i,j; @@ -89,4 +90,12 @@ #endif + /*transpose, as Petsc now does not allows MAT_COLUMN_ORIENTED matrices in MatSetValues: */ + tmatrix=(double*)xmalloc(rows*cols*sizeof(double)); + for(i=0;i