[petsc-dev] Segfault in DMPlexDistribute

[Chris Eldred]

I am getting a segmentation fault when I try to distribute a DMPlex mesh:

[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[1]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC ERROR:
or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
corruption errors
[1]PETSC ERROR: likely location of problem given in stack below
[1]PETSC ERROR: ---------------------  Stack Frames
------------------------------------
[1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[1]PETSC ERROR:       INSTEAD the line number of the start of the function
[1]PETSC ERROR:       is given.
[1]PETSC ERROR: [1] PetscSFCreateEmbeddedSF line 863
/home/user/Desktop/LIBRARIES/petsc/src/vec/is/sf/interface/sf.c
[1]PETSC ERROR: [1] PetscSFDistributeSection line 1755
/home/user/Desktop/LIBRARIES/petsc/src/vec/is/utils/vsectionis.c
[1]PETSC ERROR: [1] DMPlexDistribute line 2771
/home/user/Desktop/LIBRARIES/petsc/src/dm/impls/plex/plex.c
[1]PETSC ERROR: --------------------- Error Message
------------------------------------
[1]PETSC ERROR: Signal received!
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: Petsc Development GIT revision:
dd831807ccae33b4bba0c6456b55575ff17239c3  GIT Date: 2013-06-03 14:26:06
-0600
[1]PETSC ERROR: See docs/changes/index.html for recent updates.
[1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[1]PETSC ERROR: See docs/index.html for manual pages.
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: ./test on a arch-linux2-cxx-debug named Puget-101334 by
user Wed Jul 31 12:44:44 2013
[1]PETSC ERROR: Libraries linked from
/home/user/Desktop/LIBRARIES/petsc/arch-linux2-cxx-debug/lib
[1]PETSC ERROR: Configure run at Mon Jun  3 14:29:12 2013
[1]PETSC ERROR: Configure options --download-boost --download-chaco
--download-ctetgen --download-f-blas-lapack --download-fiat
--download-generator --download-hdf5 --download-metis --download-ml
--download-mpich --download-parmetis --download-scientificpython
--download-triangle --with-clanguage=cxx --with-dynamic-loading
--with-openmp --with-pthreadclasses --with-shared-libraries --with-sieve
--with-threadcomm PETSC_ARCH=arch-linux2-cxx-debug
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
[cli_1]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1

I am building the mesh using DMPlexCreateFromCellList but I get the exact
same error occurring if I build it using DMPlexSetCone, etc. It is the
sample mesh from
http://www.mcs.anl.gov/petsc/petsc-as/documentation/tutorials/sieve.pdf(figure
2) so very simple.

Here is my relevant code:

cell_list = (/ 0 , 1 , 2  , 1 , 3 , 2 /)
vertex_coords = 0.0

call DMPlexCreateFromCellList(PETSC_COMM_WORLD, 2, 2, 4, 3,  1 , cell_list
, 2 , vertex_coords , dm,  ierr)
CHKERRQ(ierr)

call DMPlexDistribute(dm,'chaco',0,dm_distrib,ierr)
CHKERRQ(ierr)

I am running the code with mpirun -np 2 ./test (it also segfaults with
higher values for np).

Any ideas? The code works fine with mpirun -np 1 (presumably since it is
not actually attempting to distribute the mesh).

Thanks,
-Chris Eldred

--
Chris Eldred
DOE Computational Science Graduate Fellow
Graduate Student, Atmospheric Science, Colorado State University
B.S. Applied Computational Physics, Carnegie Mellon University, 2009
chris.eldred at gmail.com / celdred at atmos.colostate.edu
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