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

[Dmitry Karpeyev]

On Sun Feb 22 2015 at 9:15:22 PM Barry Smith <bsmith at mcs.anl.gov> wrote:

>
> > On Feb 22, 2015, at 9:09 PM, David Knezevic <david.knezevic at akselos.com>
> wrote:
> >
> > Hi Dmitry,
> >
> > Thanks for the suggestion. I tried MatSetType(mat,MATMPIAIJ) followed by
> MatXAIJSetPreallocation(...), but unfortunately this still gives me the
> same error as before: "nnz cannot be greater than row length: local row 168
> value 24 rowlength 0".
> >
> > I gather that the idea here is that MatSetType builds a new matrix
> object, and then I should be able to pre-allocate for that new matrix
> however I like, right? Was I supposed to clear the matrix object somehow
> before calling MatSetType? (I didn't do any sort of clear operation.)
>
>   If the type doesn't change then MatSetType() won't do anything. You can
> try setting the type to BAIJ and then setting the type back to AIJ. This
> may/should clear out the matrix.
>
Ah, yes.  If the type is the same as before it does quit early, but
changing the type and then back will clear out and rebuild the matrix.   We
need
something like MatReset() to do the equivalent thing.

>
> >
> > As I said earlier, I'll make a dbg PETSc build, so hopefully that will
> help shed some light on what's going wrong for me.
>
I think it's always a good idea to have a dbg build of PETSc when you doing
things like these.

Dmitry.

>
>    Don't bother, what I suggested won't work.
>
>   Barry
>
>
> >
> > Thanks,
> > David
> >
> >
> >
> >
> > On Sun, Feb 22, 2015 at 6:02 PM, Dmitry Karpeyev <dkarpeev at gmail.com>
> wrote:
> > David,
> > It might be easier to just rebuild the whole matrix from scratch: you
> would in effect be doing all that with disassembling and resetting the
> preallocation.
> > MatSetType(mat,MATMPIAIJ)
> > or
> > PetscObjectGetType((PetscObject)mat,&type);
> > MatSetType(mat,type);
> > followed by
> > MatXAIJSetPreallocation(...);
> > should do.
> > Dmitry.
> >
> >
> > On Sun Feb 22 2015 at 4:45:46 PM Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> >  Do not call for SeqAIJ matrix. Do not call before the first time you
> have preallocated and put entries in the matrix and done the
> MatAssemblyBegin/End()
> >
> >   If it still crashes you'll need to try the debugger
> >
> >   Barry
> >
> > > On Feb 22, 2015, at 4:09 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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