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

[Barry Smith]

 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
> >
> 
>