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 ==== > 1.0000 0.3679 0.1353 0.3679 1.0000 0.0000 0.0000 > 0.3679 1.0000 0.3679 0.1353 1.0000 1.0000 0.0000 > 0.1353 0.3679 1.0000 0.3679 1.0000 1.0000 1.0000 > 0.3679 0.1353 0.3679 1.0000 1.0000 0.0000 1.0000 > 1.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 > 0.0000 1.0000 1.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 1.0000 1.0000 0.0000 0.0000 0.0000 > > 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: 0.00000000000000000000e+00 instead of > 1.00000000000000000000e+00 > file: src/mapping/tests/PetRadialBasisFctMappingTest.cpp line: 196 > statement: value==1.0 > difference: 1.00000000000000000000e+00 > > > What's indeed perfectly right. But what is the best way to cope with that? > > Thanks, > Florian
