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

[David Knezevic]

P.S. Typo correction: I meant to say "I'm using a non-debug build".

David



On Sun, Feb 22, 2015 at 5:09 PM, David Knezevic <david.knezevic at akselos.com>
wrote:

> 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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