http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind On Jul 31, 2013, at 12:49 PM, Chris Eldred <[email protected]> wrote:
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 [email protected] / [email protected]