[petsc-users] Erro in solution

[Danesh Daroui]

Hi again,

The issue is solved and it was due to a bug in my code. But now the
problem is that PETSc is extremely slow when I try to solve even a small
equation. I fill the matrix and right-hand-side and call the solver as
below:

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 Msize is the size of right-hand-side vector. I use C++ and am
running PETSc in sequential mode so no MPI is used, but anyway, it
shouldn't be that slow! Am I right or I am missing something?

Thanks,

Danesh




On Sun, 2011-05-08 at 14:41 +0200, dan at ltu.se wrote:
> Hi,
> 
> I checked my code and there is no zero on the diagonal. I also modified the code
> so if there is any zero on the diagonal it will be stored anyway. After this
> change the problem still exists! I am not sure if I have called PETSc functions
> correctly or in correct sequence. But anyway, it returns the error:
> 
> [0]PETSC ERROR: Object is in wrong state!
> 
> 
> that and the rest of the error message is exactly as I posted before. Any idea
> to solve this problem?
> 
> Thanks,
> 
> D.
> 
> 
> 
> Quoting Barry Smith <bsmith at mcs.anl.gov>:
> 
> > 
> >    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
> > > 
> > > 
> > 
> > 
> >