[petsc-users] Errors from large matrices

[Matthew Knepley]

On Sun, May 26, 2013 at 2:10 PM, Choi240 <choi240 at purdue.edu> wrote:

> Thank you for your fast reply. However, I was already using 64 bit pointer.
>

Then it sounds like you ar really out of memory. Also, make sure you are
checking all error codes
with CHKERRQ so you do not get follow-on errors.

   Matt


>
> -------- Original message --------
> Subject: Re: [petsc-users] Errors from large matrices
> From: Barry Smith <bsmith at mcs.anl.gov>
> To: Joon hee Choi <choi240 at purdue.edu>
> CC: petsc-users at mcs.anl.gov
>
>
>
> On May 26, 2013, at 6:19 AM, Joon hee Choi <choi240 at purdue.edu> wrote:
>
> > Hello all,
> >
> > I need to multiply a large seqaij matrix(X1) and a maij(or baij)
> matrix(CC). I set up X1 (size:4273949x108965941330383, nonzeros:143599552)
> and C (size:25495389x10, nonzeros:254953890) and created a maij matrix CC
> from C. However, I got errors such as out of memory and Caught signal
> number 11 SEGV: Segmentation Violation, probably memory access out of
> range. Is this memory problem, and do I have to change seqaij into mpiaij
> and use multi processors? Or do I have another methods fixing it? If you
> know the method, then please let me know it. Thank you.
>
> http://www.mcs.anl.gov/petsc/documentation/faq.html#with-64-bit-indices
>
>
> >
> > Joon
> >
> >
> > Code:
> >  ...
> >  ierr = MatCreate(PETSC_COMM_SELF, &X1); CHKERRQ(ierr);
> >  ierr = MatSetSizes(X1, PETSC_DECIDE, PETSC_DECIDE, I, J*K);
> CHKERRQ(ierr);
> >  ierr = MatSetBlockSizes(X1, I, J); CHKERRQ(ierr);
> >  ierr = MatSetType(X1, MATSEQAIJ); CHKERRQ(ierr);
> >  ierr = MatSeqAIJSetPreallocation(X1, 0, nnz); CHKERRQ(ierr);
> >
> >  for (int x=0; x<tups.size(); x++) {
> >       i = std::tr1::get<0>(tups[x]);
> >       j = std::tr1::get<2>(tups[x]) + std::tr1::get<1>(tups[x])*J;
> >       val = std::tr1::get<3>(tups[x]);
> >       ierr = MatSetValues(X1, 1, &i, 1, &j, &val, INSERT_VALUES);
> CHKERRQ(ierr);
> >  }
> >  ierr = MatAssemblyBegin(X1, MAT_FINAL_ASSEMBLY);
> >  ierr = MatAssemblyEnd(X1, MAT_FINAL_ASSEMBLY);
> >  ierr = PetscGetTime(&v1); CHKERRQ(ierr);
> >  ierr = PetscPrintf(PETSC_COMM_WORLD, "Setup Time: %2.1e \n", v1-v);
> CHKERRQ(ierr);
> >
> >  // Create a matrix C (K x R) with all values 1
> >  ierr = MatCreateSeqAIJ(PETSC_COMM_SELF, K, R, R, NULL, &C);
> CHKERRQ(ierr);
> >  for (k=0; k<K; k++) {
> >       for (r=0; r<R; r++) {
> >            ierr = MatSetValues(C, 1, &k, 1, &r, &one, INSERT_VALUES);
> CHKERRQ(ierr);
> >       }
> >  }
> >  ierr = MatAssemblyBegin(C, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
> >  ierr = MatAssemblyEnd(C, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
> >
> >  ierr = M...
>



-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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