[petsc-users] DMPlexCreateExodusFromFile() does not work on macOS Sierra

[Matthew Knepley]

On Sat, Jan 21, 2017 at 10:38 PM, Fande Kong <fdkong.jd at gmail.com> wrote:

> Hi All,
>
> I upgraded the OS system to macOS Sierra, and observed that PETSc can not
> read the exodus file any more. The same code runs fine on macOS Capitan. I
> also tested the function DMPlexCreateExodusFromFile() against different
> versions of the GCC compiler such as GCC-5.4 and GCC-6, and neither of them
> work. I guess this issue is related to the external package *exodus*, and
> PETSc might not pick up the right enveriment variables for the *exodus.*
>
> This issue can be reproduced using the following simple code:
>

1) This is just a standard check. Have you reconfigured so that you know
ExodusII was built with the same compilers and system libraries?

2) If so, can you get a stack trace with gdb or lldb?

   Matt


> *static char help[] = " create mesh from exodus.\n\n";*
>
> *#include <petscdm.h>*
> *#include <petsc/private/dmpleximpl.h>*
>
> *#undef __FUNCT__*
> *#define __FUNCT__ "main"*
> *int main(int argc,char **argv)*
> *{*
> *  char                fineMeshFileName[2048];*
> *  DM                  dm;*
> *  MPI_Comm            comm;*
> *  PetscBool           flg;*
>
> *  PetscErrorCode      ierr;*
>
> *  ierr = PetscInitialize(&argc,&argv,(char *)0,help);CHKERRQ(ierr);*
> *  comm = PETSC_COMM_WORLD;*
> *  ierr =
> PetscOptionsGetString(NULL,NULL,"-file",fineMeshFileName,sizeof(fineMeshFileName),&flg);CHKERRQ(ierr);*
> *  if(!flg){*
> * SETERRQ(comm,PETSC_ERR_ARG_NULL,"please specify a fine mesh file \n");*
> *   }*
> *  ierr = DMPlexCreateExodusFromFile( comm,fineMeshFileName, PETSC_FALSE,
> &dm);CHKERRQ(ierr);*
> *  ierr = DMDestroy(&dm);CHKERRQ(ierr);*
> *  ierr = PetscFinalize();CHKERRQ(ierr);*
> *}*
>
>
> *LiviadeMacBook-Pro:partition livia$ ./DMPlexCreateExodusFromFile -file
> Tri3.exo *
> *[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
> <http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind>*
> *[0]PETSC ERROR: or try http://valgrind.org <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] DMPlexCreateExodusFromFile line 38
> /Users/livia/math/petsc/src/dm/impls/plex/plexexodusii.c*
> *[0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------*
> *[0]PETSC ERROR: Signal received*
> *[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> <http://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting.*
> *[0]PETSC ERROR: Petsc Release Version 3.7.5, unknown *
> *[0]PETSC ERROR: ./DMPlexCreateExodusFromFile on a arch-darwin-cxx-debug
> named LiviadeMacBook-Pro.local by livia Sat Jan 21 21:04:22 2017*
> *[0]PETSC ERROR: Configure options --with-clanguage=cxx
> --with-shared-libraries=1 --download-fblaslapack=1 --with-mpi=1
> --download-parmetis=1 --download-metis=1 --download-netcdf=1
> --download-exodusii=1 --download-hdf5=1 --with-debugging=yes
> --with-c2html=0 --download-hypre=1 --with-64-bit-indices=1
> --download-superlu_dist=1 PETSC_ARCH=arch-darwin-cxx-debug*
> *[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 log files of make and configuration are also attached.  If you have
> any idea on this issue, please let me know!
>
> Fande Kong,
>
>


-- 
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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