[petsc-users] Write binary to matrix

[Florian Lindner]

Hey,

this code reproduces the error when run with 2 or more ranks.

#include <petscmat.h>
#include <petscsys.h>

int main(int argc, char *argv[])
{
  PetscInitialize(&argc, &argv, "", NULL);

  Mat matrix;
  MatCreate(PETSC_COMM_WORLD, &matrix);
  MatSetType(matrix, MATSBAIJ);
  MatSetSizes(matrix, 10, 10, PETSC_DETERMINE, PETSC_DETERMINE);
  MatSetFromOptions(matrix);
  MatSetUp(matrix);

  MatAssemblyBegin(matrix, MAT_FINAL_ASSEMBLY);
  MatAssemblyEnd(matrix, MAT_FINAL_ASSEMBLY);

  PetscViewer viewer;
  PetscViewerBinaryOpen(PETSC_COMM_WORLD, "test.mat", FILE_MODE_WRITE, &viewer);
  MatView(matrix, viewer);
  PetscViewerDestroy(&viewer);
  MatDestroy(&matrix);

  PetscFinalize();
}


The complete output is:


lindnefn at neon /data/scratch/lindnefn/aste (git)-[master] % mpic++ petsc.cpp -lpetsc &&  mpirun -n 2 ./a.out

[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: No support for this operation for this object type
[0]PETSC ERROR: Cannot get subcomm viewer for binary files or sockets unless SubViewer contains the rank 0 process
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.7.3, unknown
[0]PETSC ERROR: ./a.out on a arch-linux2-c-debug named neon by lindnefn Thu Sep 22 16:10:34 2016
[0]PETSC ERROR: Configure options --with-debugging=1 --download-petsc4py=yes --download-mpi4py=yes
--download-superlu_dist --download-parmetis --download-metis
[0]PETSC ERROR: #1 PetscViewerGetSubViewer_Binary() line 46 in
/data/scratch/lindnefn/software/petsc/src/sys/classes/viewer/impls/binary/binv.c
[0]PETSC ERROR: #2 PetscViewerGetSubViewer() line 43 in
/data/scratch/lindnefn/software/petsc/src/sys/classes/viewer/interface/dupl.c
[0]PETSC ERROR: #3 MatView_MPISBAIJ_ASCIIorDraworSocket() line 900 in
/data/scratch/lindnefn/software/petsc/src/mat/impls/sbaij/mpi/mpisbaij.c
[0]PETSC ERROR: #4 MatView_MPISBAIJ() line 926 in /data/scratch/lindnefn/software/petsc/src/mat/impls/sbaij/mpi/mpisbaij.c
[0]PETSC ERROR: #5 MatView() line 901 in /data/scratch/lindnefn/software/petsc/src/mat/interface/matrix.c
WARNING! There are options you set that were not used!
WARNING! could be spelling mistake, etc!
Option left: name:-ksp_converged_reason (no value)
Option left: name:-ksp_final_residual (no value)
Option left: name:-ksp_view (no value)
[neon:113111] *** Process received signal ***
[neon:113111] Signal: Aborted (6)
[neon:113111] Signal code:  (-6)
[neon:113111] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36cb0) [0x7feed8958cb0]
[neon:113111] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x37) [0x7feed8958c37]
[neon:113111] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x148) [0x7feed895c028]
[neon:113111] [ 3]
/data/scratch/lindnefn/software/petsc/arch-linux2-c-debug/lib/libpetsc.so.3.7(PetscTraceBackErrorHandler+0x563)
[0x7feed8d8db31]
[neon:113111] [ 4] /data/scratch/lindnefn/software/petsc/arch-linux2-c-debug/lib/libpetsc.so.3.7(PetscError+0x374)
[0x7feed8d88750]
[neon:113111] [ 5] /data/scratch/lindnefn/software/petsc/arch-linux2-c-debug/lib/libpetsc.so.3.7(+0x19b2f6) [0x7feed8e822f6]
[neon:113111] [ 6]
/data/scratch/lindnefn/software/petsc/arch-linux2-c-debug/lib/libpetsc.so.3.7(PetscViewerGetSubViewer+0x4f1)
[0x7feed8e803cb]
[neon:113111] [ 7] /data/scratch/lindnefn/software/petsc/arch-linux2-c-debug/lib/libpetsc.so.3.7(+0x860c95) [0x7feed9547c95]
[neon:113111] [ 8] /data/scratch/lindnefn/software/petsc/arch-linux2-c-debug/lib/libpetsc.so.3.7(+0x861494) [0x7feed9548494]
[neon:113111] [ 9] /data/scratch/lindnefn/software/petsc/arch-linux2-c-debug/lib/libpetsc.so.3.7(MatView+0x12b6)
[0x7feed971c08f]
[neon:113111] [10] ./a.out() [0x400b8b]
[neon:113111] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7feed8943f45]
[neon:113111] [12] ./a.out() [0x4009e9]
[neon:113111] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 113111 on node neon exited on signal 6 (Aborted).
--------------------------------------------------------------------------

Thanks,
Florian



Am 22.09.2016 um 13:32 schrieb Matthew Knepley:
> On Thu, Sep 22, 2016 at 5:42 AM, Florian Lindner <mailinglists at xgm.de <mailto:mailinglists at xgm.de>> wrote:
> 
>     Hello,
> 
>     I want to write a MATSBAIJ to a file in binary, so that I can load it later using MatLoad.
> 
>     However, I keep getting the error:
> 
>     [5]PETSC ERROR: No support for this operation for this object type!
>     [5]PETSC ERROR: Cannot get subcomm viewer for binary files or sockets unless SubViewer contains the rank 0 process
>     [6]PETSC ERROR: PetscViewerGetSubViewer_Binary() line 46 in
>     /data/scratch/lindnefn/software/petsc/src/sys/classes/viewer/impls/binary/binv.c
> 
> 
> Do not truncate the stack.
> 
> Run under valgrind.
> 
>   Thanks,
> 
>      Matt
>  
> 
>     The rank 0 is included, as you can see below, I use PETSC_COMM_WORLD and the matrix is also created like that.
> 
>     The code looks like:
> 
>     PetscErrorCode ierr = 0;
>     PetscViewer viewer;
>     PetscViewerBinaryOpen(PETSC_COMM_WORLD, filename.c_str(), FILE_MODE_WRITE, &viewer); CHKERRV(ierr);
>     MatView(matrix, viewer); CHKERRV(ierr);
>     PetscViewerDestroy(&viewer);
> 
>     Thanks,
>     Florian
> 
> 
> 
> 
> -- 
> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any
> results to which their experiments lead.
> -- Norbert Wiener