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

[Barry Smith]

  Yeah try this.

> On Feb 22, 2015, at 5:02 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
> > >
> >
> >
>