[petsc-users] PetscSFReduceBegin does not work correctly on openmpi-1.4.3 with 64 integers

[Matthew Knepley]

On Mon, Sep 10, 2012 at 10:47 PM, fdkong <fd.kong at foxmail.com> wrote:

>
> >> Hi all,
> >>
> >> The function PetscSFReduceBegin runs well on MPICH, but does not work
> >> on  openmpi-1.4.3, with 64 integers. Anyone knows why?
> >>
>
> >1) What error are you seeing? There are no errors in the build.
>
> Yes, There are no errors in the build and configure. But when I ran my
> code involved the function PetscSFReduceBegin on supercomputer, I got the
> error below:
>

Can you run src/sys/sf/examples/tutorials/ex1? There are several tests in
the makefile there. I suspect
that your graph is not correctly specified.

   Matt


> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSCERROR: or try
> http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
> corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 3, Wed Aug 29 11:26:24
> CDT 2012
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: ./linearElasticity on a arch-linu named node0353 by
> fako9399 Mon Sep 10 16:50:42 2012
> [0]PETSC ERROR: Libraries linked from
> /projects/fako9399/petsc-3.3-p3/arch-linux264-cxx-opt/lib
> [0]PETSC ERROR: Configure run at Mon Sep 10 13:58:46 2012
> [0]PETSC ERROR: Configure options --known-level1-dcache-size=32768
> --known-level1-dcache-linesize=32 --known-level1-dcache-assoc=0
> --known-memcmp-ok=1 --known-sizeof-char=1 --known-sizeof-void-p=8
> --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8
> --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8
> --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-sizeof-MPI_Comm=8
> --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --with-clanguage=cxx
> --with-shared-libraries=1 --with-dynamic-loading=1
> --download-f-blas-lapack=1 --with-batch=1 --known-mpi-shared-libraries=0
> --with-mpi-shared=1 --download-parmetis=1 --download-metis=1
> --with-64-bit-indices=1
> --with-netcdf-dir=/projects/fako9399/petsc-3.3-p3/externalpackage/netcdf-4.1.3install
> --download-exodusii=1 --with-debugging=no --download-ptscotch=1
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: User provided function() line 0 in unknown directory
> unknown file
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 59.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 0 with PID 1517 on
> node node0353 exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
>
> I had done some debugs, and then found the error came from the
> function PetscSFReduceBegin.
>
> >2) Please do not send logs to petsc-users, send them to
> >petsc-maint at mcs.anl.gov
>
> Ok, Thanks.
>
> >  Matt
>
>
> >> Maybe this link could help us guess why?
> >> http://www.open-mpi.org/community/lists/devel/2005/11/0517.php
> >>
> >> I attached the configure.log and make.log files.
> >> ------------------
> >> Fande Kong
> >> ShenZhen Institutes of Advanced Technology
> >> Chinese Academy of Sciences
> >>
> >>
>



-- 
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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