Re: [petsc-users] Matrix missing diagonal entry
Am Dienstag, 7. Oktober 2014, 08:34:55 schrieb Barry Smith: PETSc has this “extra” requirement that you provide values for the entire diagonal of the matrix, even those locations with zero. So make sure that you use MatSetValues() to put a zero on each diagonal entry that has zero. Thanks for that information. I came up with this scheme: _matCLU.assemble(MAT_FLUSH_ASSEMBLY); petsc::Vector zeros(_matCLU); // construct a vector like the given matrix MatDiagonalSet(_matCLU.matrix, zeros.vector, ADD_VALUES); _matCLU.assemble(MAT_FINAL_ASSEMBLY); (contains a bit of my petsc helper functions but should be clear I guess) To set all unset entries to zero. Do you see any problem with that? Best Regards, Florian Also from below you are using ICC that is incomplete cholesky factorization. If you want to use a direct solver you should select -pc_type cholesky Barry On Oct 7, 2014, at 8:14 AM, Florian Lindner mailingli...@xgm.de wrote: Hello, when I try to KSPSolve my matrix petsc prints out that a diagonal entry is missing: KSPSetOperators(solver, _matCLU.matrix, _matCLU.matrix ); KSPSolve(solver, vin.vector, vp.vector); And petsc is perfectly right about that specific entry being zero. So this may be more of a mathematical problem then pure petsc. The algorithm that I try to reimplement does the following: lu(_matrixCLU, _pivotsCLU); // Compute LU decomposition // Left out: Permutate in according to pivotsCLU forwardSubstitution(_matrixCLU, in, y); // CLU^-1 * in = y (lower triangle of CLU) backSubstitution(_matrixCLU, y, p); // CLU^-1 * y = p (upper triangle of CLU) multiply(_matrixA, p, out );// out = A * p (not relevant here) I want to replace to lu, forward- and backwardSubstituation by using a petsc KSP solver. Before doing any of these operations _matrixCLU and _matCLU are equal: === CLU Before LU === Dynamic Matrix of size 7 x 7 1. 0.3679 0.1353 0.3679 1. 0. 0. 0.3679 1. 0.3679 0.1353 1. 1. 0. 0.1353 0.3679 1. 0.3679 1. 1. 1. 0.3679 0.1353 0.3679 1. 1. 0. 1. 1. 1. 1. 1. 0. 0. 0. 0. 1. 1. 0. 0. 0. 0. 0. 0. 1. 1. 0. 0. 0. Mat Object:CLU 1 MPI processes type: seqsbaij row 0: (0, 1) (1, 0.367879) (2, 0.135335) (3, 0.367879) (4, 1) (5, 0) (6, 0) row 1: (1, 1) (2, 0.367879) (3, 0.135335) (4, 1) (5, 1) (6, 0) row 2: (2, 1) (3, 0.367879) (4, 1) (5, 1) (6, 1) row 3: (3, 1) (4, 1) (5, 0) (6, 1) row 4: row 5: row 6: LU decomposition of matrixCLU works, no rank deficiency (no 0 on the main diagonal after LU and I tested for full rank of matrixCLU). Petsc complains with this matrix: [0]PETSC ERROR: - Error Message -- [0]PETSC ERROR: Object is in wrong state [0]PETSC ERROR: Matrix is missing diagonal entry 4 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.5.2, unknown [0]PETSC ERROR: ../build/debug/binprecice on a arch-linux2-c-debug named helium by lindnefn Mon Oct 6 16:26:49 2014 [0]PETSC ERROR: Configure options [0]PETSC ERROR: #1 MatICCFactorSymbolic_SeqSBAIJ() line 2430 in /data2/scratch/lindner/petsc/src/mat/impls/sbaij/seq/sbaijfact2.c [0]PETSC ERROR: #2 MatICCFactorSymbolic() line 6266 in /data2/scratch/lindner/petsc/src/mat/interface/matrix.c [0]PETSC ERROR: #3 PCSetup_ICC() line 20 in /data2/scratch/lindner/petsc/src/ksp/pc/impls/factor/icc/icc.c [0]PETSC ERROR: #4 PCSetUp() line 902 in /data2/scratch/lindner/petsc/src/ksp/pc/interface/precon.c [0]PETSC ERROR: #5 KSPSetUp() line 305 in /data2/scratch/lindner/petsc/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #6 KSPSolve() line 417 in /data2/scratch/lindner/petsc/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #7 map() line 696 in src/mapping/PetRadialBasisFctMapping.hpp numerical equality test failed: 0.e+00 instead of 1.e+00 file: src/mapping/tests/PetRadialBasisFctMappingTest.cpp line: 196 statement: value==1.0 difference: 1.e+00 What's indeed perfectly right. But what is the best way to cope with that? Thanks, Florian
Re: [petsc-users] Matrix missing diagonal entry
Should be ok. On Oct 14, 2014, at 10:00 AM, Florian Lindner mailingli...@xgm.de wrote: Am Dienstag, 7. Oktober 2014, 08:34:55 schrieb Barry Smith: PETSc has this “extra” requirement that you provide values for the entire diagonal of the matrix, even those locations with zero. So make sure that you use MatSetValues() to put a zero on each diagonal entry that has zero. Thanks for that information. I came up with this scheme: _matCLU.assemble(MAT_FLUSH_ASSEMBLY); petsc::Vector zeros(_matCLU); // construct a vector like the given matrix MatDiagonalSet(_matCLU.matrix, zeros.vector, ADD_VALUES); _matCLU.assemble(MAT_FINAL_ASSEMBLY); (contains a bit of my petsc helper functions but should be clear I guess) To set all unset entries to zero. Do you see any problem with that? Best Regards, Florian Also from below you are using ICC that is incomplete cholesky factorization. If you want to use a direct solver you should select -pc_type cholesky Barry On Oct 7, 2014, at 8:14 AM, Florian Lindner mailingli...@xgm.de wrote: Hello, when I try to KSPSolve my matrix petsc prints out that a diagonal entry is missing: KSPSetOperators(solver, _matCLU.matrix, _matCLU.matrix ); KSPSolve(solver, vin.vector, vp.vector); And petsc is perfectly right about that specific entry being zero. So this may be more of a mathematical problem then pure petsc. The algorithm that I try to reimplement does the following: lu(_matrixCLU, _pivotsCLU); // Compute LU decomposition // Left out: Permutate in according to pivotsCLU forwardSubstitution(_matrixCLU, in, y); // CLU^-1 * in = y (lower triangle of CLU) backSubstitution(_matrixCLU, y, p); // CLU^-1 * y = p (upper triangle of CLU) multiply(_matrixA, p, out );// out = A * p (not relevant here) I want to replace to lu, forward- and backwardSubstituation by using a petsc KSP solver. Before doing any of these operations _matrixCLU and _matCLU are equal: === CLU Before LU === Dynamic Matrix of size 7 x 7 1. 0.3679 0.1353 0.3679 1. 0. 0. 0.3679 1. 0.3679 0.1353 1. 1. 0. 0.1353 0.3679 1. 0.3679 1. 1. 1. 0.3679 0.1353 0.3679 1. 1. 0. 1. 1. 1. 1. 1. 0. 0. 0. 0. 1. 1. 0. 0. 0. 0. 0. 0. 1. 1. 0. 0. 0. Mat Object:CLU 1 MPI processes type: seqsbaij row 0: (0, 1) (1, 0.367879) (2, 0.135335) (3, 0.367879) (4, 1) (5, 0) (6, 0) row 1: (1, 1) (2, 0.367879) (3, 0.135335) (4, 1) (5, 1) (6, 0) row 2: (2, 1) (3, 0.367879) (4, 1) (5, 1) (6, 1) row 3: (3, 1) (4, 1) (5, 0) (6, 1) row 4: row 5: row 6: LU decomposition of matrixCLU works, no rank deficiency (no 0 on the main diagonal after LU and I tested for full rank of matrixCLU). Petsc complains with this matrix: [0]PETSC ERROR: - Error Message -- [0]PETSC ERROR: Object is in wrong state [0]PETSC ERROR: Matrix is missing diagonal entry 4 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.5.2, unknown [0]PETSC ERROR: ../build/debug/binprecice on a arch-linux2-c-debug named helium by lindnefn Mon Oct 6 16:26:49 2014 [0]PETSC ERROR: Configure options [0]PETSC ERROR: #1 MatICCFactorSymbolic_SeqSBAIJ() line 2430 in /data2/scratch/lindner/petsc/src/mat/impls/sbaij/seq/sbaijfact2.c [0]PETSC ERROR: #2 MatICCFactorSymbolic() line 6266 in /data2/scratch/lindner/petsc/src/mat/interface/matrix.c [0]PETSC ERROR: #3 PCSetup_ICC() line 20 in /data2/scratch/lindner/petsc/src/ksp/pc/impls/factor/icc/icc.c [0]PETSC ERROR: #4 PCSetUp() line 902 in /data2/scratch/lindner/petsc/src/ksp/pc/interface/precon.c [0]PETSC ERROR: #5 KSPSetUp() line 305 in /data2/scratch/lindner/petsc/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #6 KSPSolve() line 417 in /data2/scratch/lindner/petsc/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #7 map() line 696 in src/mapping/PetRadialBasisFctMapping.hpp numerical equality test failed: 0.e+00 instead of 1.e+00 file: src/mapping/tests/PetRadialBasisFctMappingTest.cpp line: 196 statement: value==1.0 difference: 1.e+00 What's indeed perfectly right. But what is the best way to cope with that? Thanks, Florian
[petsc-users] Matrix missing diagonal entry
Hello, when I try to KSPSolve my matrix petsc prints out that a diagonal entry is missing: KSPSetOperators(solver, _matCLU.matrix, _matCLU.matrix ); KSPSolve(solver, vin.vector, vp.vector); And petsc is perfectly right about that specific entry being zero. So this may be more of a mathematical problem then pure petsc. The algorithm that I try to reimplement does the following: lu(_matrixCLU, _pivotsCLU); // Compute LU decomposition // Left out: Permutate in according to pivotsCLU forwardSubstitution(_matrixCLU, in, y); // CLU^-1 * in = y (lower triangle of CLU) backSubstitution(_matrixCLU, y, p); // CLU^-1 * y = p (upper triangle of CLU) multiply(_matrixA, p, out );// out = A * p (not relevant here) I want to replace to lu, forward- and backwardSubstituation by using a petsc KSP solver. Before doing any of these operations _matrixCLU and _matCLU are equal: === CLU Before LU === Dynamic Matrix of size 7 x 7 1. 0.3679 0.1353 0.3679 1. 0. 0. 0.3679 1. 0.3679 0.1353 1. 1. 0. 0.1353 0.3679 1. 0.3679 1. 1. 1. 0.3679 0.1353 0.3679 1. 1. 0. 1. 1. 1. 1. 1. 0. 0. 0. 0. 1. 1. 0. 0. 0. 0. 0. 0. 1. 1. 0. 0. 0. Mat Object:CLU 1 MPI processes type: seqsbaij row 0: (0, 1) (1, 0.367879) (2, 0.135335) (3, 0.367879) (4, 1) (5, 0) (6, 0) row 1: (1, 1) (2, 0.367879) (3, 0.135335) (4, 1) (5, 1) (6, 0) row 2: (2, 1) (3, 0.367879) (4, 1) (5, 1) (6, 1) row 3: (3, 1) (4, 1) (5, 0) (6, 1) row 4: row 5: row 6: LU decomposition of matrixCLU works, no rank deficiency (no 0 on the main diagonal after LU and I tested for full rank of matrixCLU). Petsc complains with this matrix: [0]PETSC ERROR: - Error Message -- [0]PETSC ERROR: Object is in wrong state [0]PETSC ERROR: Matrix is missing diagonal entry 4 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.5.2, unknown [0]PETSC ERROR: ../build/debug/binprecice on a arch-linux2-c-debug named helium by lindnefn Mon Oct 6 16:26:49 2014 [0]PETSC ERROR: Configure options [0]PETSC ERROR: #1 MatICCFactorSymbolic_SeqSBAIJ() line 2430 in /data2/scratch/lindner/petsc/src/mat/impls/sbaij/seq/sbaijfact2.c [0]PETSC ERROR: #2 MatICCFactorSymbolic() line 6266 in /data2/scratch/lindner/petsc/src/mat/interface/matrix.c [0]PETSC ERROR: #3 PCSetup_ICC() line 20 in /data2/scratch/lindner/petsc/src/ksp/pc/impls/factor/icc/icc.c [0]PETSC ERROR: #4 PCSetUp() line 902 in /data2/scratch/lindner/petsc/src/ksp/pc/interface/precon.c [0]PETSC ERROR: #5 KSPSetUp() line 305 in /data2/scratch/lindner/petsc/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #6 KSPSolve() line 417 in /data2/scratch/lindner/petsc/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #7 map() line 696 in src/mapping/PetRadialBasisFctMapping.hpp numerical equality test failed: 0.e+00 instead of 1.e+00 file: src/mapping/tests/PetRadialBasisFctMappingTest.cpp line: 196 statement: value==1.0 difference: 1.e+00 What's indeed perfectly right. But what is the best way to cope with that? Thanks, Florian
Re: [petsc-users] Matrix missing diagonal entry
PETSc has this “extra” requirement that you provide values for the entire diagonal of the matrix, even those locations with zero. So make sure that you use MatSetValues() to put a zero on each diagonal entry that has zero. Also from below you are using ICC that is incomplete cholesky factorization. If you want to use a direct solver you should select -pc_type cholesky Barry On Oct 7, 2014, at 8:14 AM, Florian Lindner mailingli...@xgm.de wrote: Hello, when I try to KSPSolve my matrix petsc prints out that a diagonal entry is missing: KSPSetOperators(solver, _matCLU.matrix, _matCLU.matrix ); KSPSolve(solver, vin.vector, vp.vector); And petsc is perfectly right about that specific entry being zero. So this may be more of a mathematical problem then pure petsc. The algorithm that I try to reimplement does the following: lu(_matrixCLU, _pivotsCLU); // Compute LU decomposition // Left out: Permutate in according to pivotsCLU forwardSubstitution(_matrixCLU, in, y); // CLU^-1 * in = y (lower triangle of CLU) backSubstitution(_matrixCLU, y, p); // CLU^-1 * y = p (upper triangle of CLU) multiply(_matrixA, p, out );// out = A * p (not relevant here) I want to replace to lu, forward- and backwardSubstituation by using a petsc KSP solver. Before doing any of these operations _matrixCLU and _matCLU are equal: === CLU Before LU === Dynamic Matrix of size 7 x 7 1. 0.3679 0.1353 0.3679 1. 0. 0. 0.3679 1. 0.3679 0.1353 1. 1. 0. 0.1353 0.3679 1. 0.3679 1. 1. 1. 0.3679 0.1353 0.3679 1. 1. 0. 1. 1. 1. 1. 1. 0. 0. 0. 0. 1. 1. 0. 0. 0. 0. 0. 0. 1. 1. 0. 0. 0. Mat Object:CLU 1 MPI processes type: seqsbaij row 0: (0, 1) (1, 0.367879) (2, 0.135335) (3, 0.367879) (4, 1) (5, 0) (6, 0) row 1: (1, 1) (2, 0.367879) (3, 0.135335) (4, 1) (5, 1) (6, 0) row 2: (2, 1) (3, 0.367879) (4, 1) (5, 1) (6, 1) row 3: (3, 1) (4, 1) (5, 0) (6, 1) row 4: row 5: row 6: LU decomposition of matrixCLU works, no rank deficiency (no 0 on the main diagonal after LU and I tested for full rank of matrixCLU). Petsc complains with this matrix: [0]PETSC ERROR: - Error Message -- [0]PETSC ERROR: Object is in wrong state [0]PETSC ERROR: Matrix is missing diagonal entry 4 [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.5.2, unknown [0]PETSC ERROR: ../build/debug/binprecice on a arch-linux2-c-debug named helium by lindnefn Mon Oct 6 16:26:49 2014 [0]PETSC ERROR: Configure options [0]PETSC ERROR: #1 MatICCFactorSymbolic_SeqSBAIJ() line 2430 in /data2/scratch/lindner/petsc/src/mat/impls/sbaij/seq/sbaijfact2.c [0]PETSC ERROR: #2 MatICCFactorSymbolic() line 6266 in /data2/scratch/lindner/petsc/src/mat/interface/matrix.c [0]PETSC ERROR: #3 PCSetup_ICC() line 20 in /data2/scratch/lindner/petsc/src/ksp/pc/impls/factor/icc/icc.c [0]PETSC ERROR: #4 PCSetUp() line 902 in /data2/scratch/lindner/petsc/src/ksp/pc/interface/precon.c [0]PETSC ERROR: #5 KSPSetUp() line 305 in /data2/scratch/lindner/petsc/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #6 KSPSolve() line 417 in /data2/scratch/lindner/petsc/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: #7 map() line 696 in src/mapping/PetRadialBasisFctMapping.hpp numerical equality test failed: 0.e+00 instead of 1.e+00 file: src/mapping/tests/PetRadialBasisFctMappingTest.cpp line: 196 statement: value==1.0 difference: 1.e+00 What's indeed perfectly right. But what is the best way to cope with that? Thanks, Florian
