[petsc-users] MatMPIAIJSetPreallocation: "nnz cannot be greater than row length"
David Knezevic
david.knezevic at akselos.com
Mon Feb 23 07:17:03 CST 2015
Hi Barry, hi Dmitry,
I set the matrix to BAIJ and back to AIJ, and the code got a bit further.
But I now run into the error pasted below (Note that I'm now using
"--with-debugging=1"):
PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
PETSC ERROR: Petsc has generated inconsistent data
PETSC ERROR: MPIAIJ Matrix was assembled but is missing garray
PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
PETSC ERROR: Petsc Release Version 3.5.2, Sep, 08, 2014
PETSC ERROR: ./example-dbg on a arch-linux2-c-debug named david-Lenovo by
dknez Mon Feb 23 08:05:44 2015
PETSC ERROR: Configure options --with-shared-libraries=1 --with-debugging=1
--download-suitesparse=1 --download-parmetis=1 --download-blacs=1
--download-scalapack=1 --download-mumps=1 --download-metis
--download-superlu_dist
--prefix=/home/dknez/software/libmesh_install/dbg_real/petsc
--download-hypre
PETSC ERROR: #1 MatCreateColmap_MPIAIJ_Private() line 361 in
/home/dknez/software/petsc-3.5.2/src/mat/impls/aij/mpi/mpiaij.c
PETSC ERROR: #2 MatSetValues_MPIAIJ() line 538 in
/home/dknez/software/petsc-3.5.2/src/mat/impls/aij/mpi/mpiaij.c
PETSC ERROR: #3 MatSetValues() line 1136 in
/home/dknez/software/petsc-3.5.2/src/mat/interface/matrix.c
PETSC ERROR: #4 add_matrix() line 765 in
/home/dknez/software/libmesh-src/src/numerics/petsc_matrix.C
--------------------------------------------------------------------------
This occurs when I try to set some entries of the matrix. Do you have any
suggestions on how I can resolve this?
Thanks!
David
On Sun, Feb 22, 2015 at 10:22 PM, Dmitry Karpeyev <dkarpeev at gmail.com>
wrote:
>
>
> 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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