[petsc-users] Write binary to matrix
Florian Lindner
mailinglists at xgm.de
Sun Sep 25 04:07:51 CDT 2016
Great! Thanks to you!
Am 23.09.2016 um 17:56 schrieb Hong:
> Florian:
> I pushed a fix in branch hzhang/fix_matview_mpisbaij (off petsc-maint)
> https://bitbucket.org/petsc/petsc/commits/d1654148bc9f02cde4d336bb9518a18cfb35148e
>
> After it is tested in our regression tests, it will be merged to
> petsc-maint and petsc-master.
> Thanks for reporting it!
>
> Hong
>
> On Fri, Sep 23, 2016 at 10:37 AM, Hong <hzhang at mcs.anl.gov
> <mailto:hzhang at mcs.anl.gov>> wrote:
>
> Florian:
> I can reproduce this error.
> This is a bug in PETSc library. I'll fix it and get back to you soon.
> Hong
>
>
> Am 22.09.2016 um 18:34 schrieb Hong:
> > Florian:
> > Would it work if replacing MATSBAIJ to MATAIJ or MATMPISBAIJ?
>
> MATAIJ works, but is not an option for my actual application.
>
> MATMPISBAIJ does not work. Not very suprisingly, since afaik
> setting it to MATSBAIJ and executing it on multiple MPI
> ranks actually results in MATMPISBAIJ.
>
> Best,
> Florian
>
>
> >
> > Hong
> >
> > 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
> <http://www.mcs.anl.gov/petsc/documentation/faq.html>
> > <http://www.mcs.anl.gov/petsc/documentation/faq.html
> <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>
> <mailto:mailinglists at xgm.de <mailto:mailinglists at xgm.de>>
> > <mailto:mailinglists at xgm.de <mailto:mailinglists at xgm.de>
> <mailto: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
> >
> >
>
>
>
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