[petsc-users] Write binary to matrix

Fri Sep 23 10:56:44 CDT 2016

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> 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/d
>> ocumentation/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/softwar
>> e/petsc/arch-linux2-c-debug/lib/libpetsc.so.3.7(PetscError+0x374)
>> >     [0x7feed8d88750]
>> >     [neon:113111] [ 5] /data/scratch/lindnefn/softwar
>> e/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/softwar
>> e/petsc/arch-linux2-c-debug/lib/libpetsc.so.3.7(+0x860c95)
>> >     [0x7feed9547c95]
>> >     [neon:113111] [ 8] /data/scratch/lindnefn/softwar
>> e/petsc/arch-linux2-c-debug/lib/libpetsc.so.3.7(+0x861494)
>> >     [0x7feed9548494]
>> >     [neon:113111] [ 9] /data/scratch/lindnefn/softwar
>> e/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>>> 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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