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]
