[petsc-users] MatMPIAIJSetPreallocation: "nnz cannot be greater than row length"

[David Knezevic]

Hi Barry,

Thanks for your help, much appreciated.

I added a prototype for MatDisAssemble_MPIAIJ:
PETSC_INTERN PetscErrorCode MatDisAssemble_MPIAIJ(Mat);

and I added a call to MatDisAssemble_MPIAIJ before
MatMPIAIJSetPreallocation. However, I get a segfault on the call
to MatDisAssemble_MPIAIJ. The segfault occurs in both serial and parallel.

FYI, I'm using Petsc 3.5.2, and I'm not using a non-debug build (though I
could rebuild PETSc in debug mode if you think that would help figure out
what's happening here).

Thanks,
David



On Sun, Feb 22, 2015 at 1:13 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:


>   David,
>
>    This is an obscure little feature of MatMPIAIJ,   each time you change
> the sparsity pattern before you call the MatMPIAIJSetPreallocation you need
> to call  MatDisAssemble_MPIAIJ(Mat mat).    This is a private PETSc
> function so you need to provide your own prototype for it above the
> function you use it in.
>
>   Let us know if this resolves the problem.
>
>    Barry
>
> We never really intended that people would call
> MatMPIAIJSetPreallocation() AFTER they had already used the matrix.
>
>
> > On Feb 22, 2015, at 6:50 AM, David Knezevic <david.knezevic at akselos.com>
> wrote:
> >
> > Hi all,
> >
> > I've implemented a solver for a contact problem using SNES. The sparsity
> pattern of the jacobian matrix needs to change at each nonlinear iteration
> (because the elements which are in contact can change), so I tried to deal
> with this by calling MatSeqAIJSetPreallocation and
> MatMPIAIJSetPreallocation during each iteration in order to update the
> preallocation.
> >
> > This seems to work fine in serial, but with two or more MPI processes I
> run into the error "nnz cannot be greater than row length", e.g.:
> > nnz cannot be greater than row length: local row 528 value 12 rowlength 0
> >
> > This error is from the call to
> > MatSeqAIJSetPreallocation(b->B,o_nz,o_nnz); in
> MatMPIAIJSetPreallocation_MPIAIJ.
> >
> > Any guidance on what the problem might be would be most appreciated. For
> example, I was wondering if there is a problem with calling
> SetPreallocation on a matrix that has already been preallocated?
> >
> > Some notes:
> > - I'm using PETSc via libMesh
> > - The code that triggers this issue is available as a PR on the libMesh
> github repo, in case anyone is interested:
> https://github.com/libMesh/libmesh/pull/460/
> > - I can try to make a minimal pure-PETSc example that reproduces this
> error, if that would be helpful.
> >
> > Many thanks,
> > David
> >
>
>
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