[petsc-users] Erro in solution

[Barry Smith]

   Danesh,

    Some of the PETSc solvers (like the default ILU) require that you put entries on all the diagonal locations of the matrix, even if they are zero. So you should explicitly put a 0 on the diagonal locations that have 0 and the issue will go away.

    Barry

On May 6, 2011, at 1:15 PM, Danesh Daroui wrote:

> 
> Dear PETSc users,
> 
> I have recently started to use PETSc in our code. As the first try, I
> assemble the matrix row by row and then put each non-zero element in
> each row into PETSc matrix. Then I start to solve the equation. I use
> PETSc on a multi-core machine, so I will not use MPI in my program. I
> compiled PETSc without MPI. The PETSc parts of my code are:
> 
> 
>        Mat Mp;
>        Vec xp, bp;
>        KSP ksp;
>        PetscErrorCode ierr;
> 
>        ierr=MatCreate(PETSC_COMM_WORLD, &Mp);
>        ierr=MatSetSizes(Mp, Msize, Msize, Msize, Msize);
>        ierr=MatSetType(Mp, MATSEQAIJ);
>        ierr=MatSetUp(Mp);
> 
>        ierr=VecCreate(PETSC_COMM_WORLD, &xp);
>        ierr=VecSetSizes(xp, Msize, Msize);
>        ierr=VecSetFromOptions(xp);
> 
>        ierr=VecCreate(PETSC_COMM_WORLD, &bp);
>        ierr=VecSetSizes(bp, Msize, Msize);
>        ierr=VecSetFromOptions(bp);
> 
> 	.
> 	.
> 	.
> 
> 	// each non zero element of row "i" and column "k" is put in 
> 	// PETSc matrix
> 	if (M_row[k]!=0.0)
> 		ierr=MatSetValues(Mp, 1, &i, 1, &k, &M_row[k],
> 					ADD_VALUES);
> 
> 
> 	ierr=MatAssemblyBegin(Mp, MAT_FINAL_ASSEMBLY);
> 	ierr=MatAssemblyEnd(Mp, MAT_FINAL_ASSEMBLY);
> 
> 	.
> 	.
> 	.
> 
> 	// copy right-hand-side to PETSc vector
> 	for (int i=0; i<Msize; ++i)
> 		VecSetValue(bp, i, b[i], INSERT_VALUES);
> 
> 	VecAssemblyBegin(bp);
> 	VecAssemblyEnd(bp);
> 
> 	ierr=KSPCreate(PETSC_COMM_WORLD, &ksp);
> 	ierr=KSPSetOperators(ksp, Mp, Mp, DIFFERENT_NONZERO_PATTERN);
> 	ierr=KSPSetTolerances(ksp, 1.e-2/Msize, 1.e-50, PETSC_DEFAULT, 
> 				PETSC_DEFAULT);
> 	ierr=KSPSetFromOptions(ksp);
> 	ierr=KSPSolve(ksp, bp, xp);
> 
> 
> 
> 
> 
> The problem is that whenever I run the code I get following output:
> 
> 
> 
> 
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Object is in wrong state!
> [0]PETSC ERROR: Matrix is missing diagonal entry 309!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 8, Thu Mar 17
> 13:37:48 CDT 2011
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Unknown Name on a linux-gnu named linux-sclt.site by dan
> Fri May  6 19:34:19 2011
> [0]PETSC ERROR: Libraries linked
> from /home/danesh/petsc-3.1-p8/linux-gnu-intel/lib
> [0]PETSC ERROR: Configure run at Fri May  6 15:50:26 2011
> [0]PETSC ERROR: Configure options PETSC_ARCH=linux-gnu-intel
> --with-scalar-type=complex --with-clanguage=c++ --with-mpi=0
> --with-cc=icc --with-fc=gfortran --with-cxx=icpc
> --with-blas-lapack-dir=/home/danesh/intel/mkl/lib/intel64/
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ_ilu0() line 1627 in
> src/mat/impls/aij/seq/aijfact.c
> [0]PETSC ERROR: MatILUFactorSymbolic_SeqAIJ() line 1731 in
> src/mat/impls/aij/seq/aijfact.c
> [0]PETSC ERROR: MatILUFactorSymbolic() line 5464 in
> src/mat/interface/matrix.c
> [0]PETSC ERROR: PCSetUp_ILU() line 204 in
> src/ksp/pc/impls/factor/ilu/ilu.c
> [0]PETSC ERROR: PCSetUp() line 795 in src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: KSPSetUp() line 237 in src/ksp/ksp/interface/itfunc.c
> [0]PETSC ERROR: KSPSolve() line 353 in src/ksp/ksp/interface/itfunc.c
> 
> 
> 
> I am sure that the matrix is correct and the system is not singular
> because the system can be solved using LAPACK's direct solver. I
> probably format the PETSc matrix incorrectly or some PETSc parameters
> are wrong. I would appreciate if you give me any clue about possible
> problem(s).
> 
> Regards,
> 
> Danesh
> 
>