[petsc-users] PetscBinaryRead and quad precision

Fri Jun 26 22:46:57 CDT 2015

Barry,

Thank you that kind of did the trick, although I have run into a couple
issues:

1) Is it expected for quad precision to have a significantly worse
performance than double precision in terms of wall-clock time? What took 60
seconds to solve with double precision now takes approximately 1500 seconds
to solve. I am guessing this has a lot to do with the fact that scalars are
now 16 bytes large as opposed to 8?

2) The program crashes at DMPlexDistribute() when I used two or more
processors. Here's the error log:

Input Error: Incorrect sum of 0.000000 for tpwgts for constraint 0.
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Error in external library
[0]PETSC ERROR: Error in METIS_PartGraphKway()
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.6-815-g2d9afd9  GIT
Date: 2015-06-26 18:48:28 -0500
[0]PETSC ERROR: ./main on a arch-linux2-quad-opt named pacotaco-xps by
justin Fri Jun 26 22:29:36 2015
[0]PETSC ERROR: Configure options --download-f2cblaslapack --download-metis
--download-mpich --download-parmetis --download-triangle --with-cc=gcc
--with-cmake=cmake --with-cxx=g++ --with-debugging=0 --with-fc=gfortran
--with-valgrind=1 PETSC_ARCH=arch-linux2-quad-opt
--with-precision=__float128
[0]PETSC ERROR: #1 PetscPartitionerPartition_ParMetis() line 1181 in
/home/justin/Software/petsc-dev/src/dm/impls/plex/plexpartition.c
[0]PETSC ERROR: #2 PetscPartitionerPartition() line 653 in
/home/justin/Software/petsc-dev/src/dm/impls/plex/plexpartition.c
[0]PETSC ERROR: #3 DMPlexDistribute() line 1505 in
/home/justin/Software/petsc-dev/src/dm/impls/plex/plexdistribute.c
[0]PETSC ERROR: #4 CreateMesh() line 762 in
/home/justin/Dropbox/DMPlex-nonneg/main.c
[0]PETSC ERROR: #5 main() line 993 in
/home/justin/Dropbox/DMPlex-nonneg/main.c
[0]PETSC ERROR: PETSc Option Table entries:
[0]PETSC ERROR: -al 1
[0]PETSC ERROR: -am 0
[0]PETSC ERROR: -at 0.001
[0]PETSC ERROR: -bcloc
0,1,0,1,0,0,0,1,0,1,1,1,0,0,0,1,0,1,1,1,0,1,0,1,0,1,0,0,0,1,0,1,1,1,0,1,0.45,0.55,0.45,0.55,0.45,0.55
[0]PETSC ERROR: -bcnum 7
[0]PETSC ERROR: -bcval 0,0,0,0,0,0,1
[0]PETSC ERROR: -binary_read_double
[0]PETSC ERROR: -dim 3
[0]PETSC ERROR: -dm_refine 1
[0]PETSC ERROR: -dt 0.001
[0]PETSC ERROR: -edges 3,3
[0]PETSC ERROR: -floc 0.25,0.75,0.25,0.75,0.25,0.75
[0]PETSC ERROR: -fnum 0
[0]PETSC ERROR: -ftime 0,99
[0]PETSC ERROR: -fval 1
[0]PETSC ERROR: -ksp_max_it 50000
[0]PETSC ERROR: -ksp_rtol 1.0e-10
[0]PETSC ERROR: -ksp_type cg
[0]PETSC ERROR: -log_summary
[0]PETSC ERROR: -lower 0,0
[0]PETSC ERROR: -mat_petscspace_order 0
[0]PETSC ERROR: -mesh datafiles/cube_with_hole4_mesh.dat
[0]PETSC ERROR: -mu 1
[0]PETSC ERROR: -nonneg 1
[0]PETSC ERROR: -numsteps 0
[0]PETSC ERROR: -options_left 0
[0]PETSC ERROR: -pc_type jacobi
[0]PETSC ERROR: -petscpartitioner_type parmetis
[0]PETSC ERROR: -progress 1
[0]PETSC ERROR: -simplex 1
[0]PETSC ERROR: -solution_petscspace_order 1
[0]PETSC ERROR: -tao_fatol 1e-8
[0]PETSC ERROR: -tao_frtol 1e-8
[0]PETSC ERROR: -tao_max_it 50000
[0]PETSC ERROR: -tao_monitor
[0]PETSC ERROR: -tao_type blmvm
[0]PETSC ERROR: -tao_view
[0]PETSC ERROR: -trans datafiles/cube_with_hole4_trans.dat
[0]PETSC ERROR: -upper 1,1
[0]PETSC ERROR: -vtuname figures/cube_with_hole_4
[0]PETSC ERROR: -vtuprint 1
[0]PETSC ERROR: ----------------End of Error Message -------send entire
error message to petsc-maint at mcs.anl.gov----------
application called MPI_Abort(MPI_COMM_WORLD, 76) - process 0
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 76) - process 0

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 12626 RUNNING AT pacotaco-xps
=   EXIT CODE: 76
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================

Know what's going on here?

Thanks,
Justin

On Fri, Jun 26, 2015 at 11:24 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>    We have an undocumented option -binary_read_double that will read in
> double precision from the file and place it into a quad precision array.
> This is exactly what you need
>
>    Barry
>
> Yes, we should fix up our binary viewers to allow  reading and writing
> generally for any precision but need a volunteer to do it.
>
>
>
> > On Jun 26, 2015, at 1:45 AM, Justin Chang <jychang48 at gmail.com> wrote:
> >
> > Hi all,
> >
> > I need to run simulations that rely on several of my custom binary
> datafiles (written in 32 bit int and 64 bit doubles). These date files were
> generated from MATLAB. In my PETSc code I invoke PetscBinaryRead(...) into
> these binary files, which gives me mesh data, auxiliaries, etc.
> >
> > However, when I now configure with quad precision
> (--with-precision=__float128 and --download-f2cblaslapack) my
> PetscBinaryRead() functions give me segmentation violation errors. I am
> guessing this is because I have binary files written in double precision
> but have PETSc which reads in quad precision, meaning I will be reading
> past the end of these files due to the larger strides.
> >
> > So my question is, is there a way to circumvent this issue? That is, to
> read double-precision binary data into a PETSc program configured with
> quad-precision? Otherwise I would have to rewrite or redo all of my
> datafiles, which I would prefer not to do if possible.
> >
> > Thanks,
> > Justin
> >
>
>
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