[petsc-dev] Segfaults on DMPlexGenerate_Triangle

Dener, Alp adener at anl.gov
Thu May 31 12:55:15 CDT 2018

The latest master branch is segfaulting on three tao tests (two of which don’t actually use tao at all). The errors trace to DMPLex. The output is below:

[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]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: likely location of problem given in stack below
[0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[0]PETSC ERROR:       INSTEAD the line number of the start of the function
[0]PETSC ERROR:       is given.
[0]PETSC ERROR: [0] DMPlexGenerate_Triangle line 74 /Users/adener/Developer/petsc/src/dm/impls/plex/generators/triangle/trigenerate.c
[0]PETSC ERROR: [0] DMPlexGenerate line 155 /Users/adener/Developer/petsc/src/dm/impls/plex/plexgenerate.c
[0]PETSC ERROR: [0] DMPlexCreateBoxMesh_Simplex_Internal line 495 /Users/adener/Developer/petsc/src/dm/impls/plex/plexcreate.c
[0]PETSC ERROR: [0] DMPlexCreateBoxMesh line 1022 /Users/adener/Developer/petsc/src/dm/impls/plex/plexcreate.c
[0]PETSC ERROR: [0] CreateMesh line 54 /Users/adener/Developer/petsc/src/tao/examples/tutorials/ex1.c
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Signal received
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.9.2-548-ge8e5c7cd70  GIT Date: 2018-05-25 12:11:26 -0500
[0]PETSC ERROR: ./ex1 on a arch-darwin-c-debug named Calculon by adener Thu May 31 12:52:17 2018
[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-suitesparse --download-superlu --download-mumps --download-hdf5 --download-metis --download-parmetis --download-superlu_dist --download-triangle --download-netcdf --download-viennacl --download-chaco --download-ctetgen --download-exodusii --download-pnetcdf --with-fortran-interfaces=1 --download-p4est --download-pragmatic --download-eigen --download-scalapack
[0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59
system msg for write_line failure : Bad file descriptor

The specific tests that are failing are:

  *   tao_tutorial-ex1
  *   tao_tutorial-ex2
  *   tao_tutorial-ex3

These live under src/tao/examples/tutorials.

Is this just a local problem for me related to my configuration, or is there something actually broken here?


Alp Dener
Postdoctoral Appointee
Argonne National Laboratory
Mathematics and Computer Science Division
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