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

Sun Jan 22 12:41:39 CST 2017

On Sat, Jan 21, 2017 at 10:47 PM, Matthew Knepley <knepley at gmail.com> wrote:

> 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?
>

0   libsystem_kernel.dylib         0x00007fffad8b8dda __pthread_kill + 10
1   libsystem_pthread.dylib       0x00007fffad9a4787 pthread_kill + 90
2   libsystem_c.dylib             0x00007fffad81e420 abort + 129
3   libpetsc.3.7.dylib             0x00000001100eb9ee
PetscAbortErrorHandler + 506 (errstop.c:40)
4   libpetsc.3.7.dylib             0x00000001100e631d PetscError + 916
(err.c:379)
5   libpetsc.3.7.dylib             0x00000001100ed830
PetscSignalHandlerDefault + 1927 (signal.c:160)
6   libpetsc.3.7.dylib             0x00000001100ed088
PetscSignalHandler_Private(int) + 630 (signal.c:49)
7   libsystem_platform.dylib       0x00007fffad997bba _sigtramp + 26
8   ???                           0x000000011ea09370 initialPoolContent +
19008
9   libnetcdf.7.dylib             0x000000011228fc62 utf8proc_map + 210
(dutf8proc.c:543)
10  libnetcdf.7.dylib             0x000000011228fd0f utf8proc_NFC + 38
(dutf8proc.c:568)
11  libnetcdf.7.dylib             0x00000001122a7928 NC_findattr + 110
(attr.c:341)
12  libnetcdf.7.dylib             0x00000001122a7a4e NC_lookupattr + 119
(attr.c:384)
13  libnetcdf.7.dylib             0x00000001122a93ef NC3_get_att + 47
(attr.c:1138)
14  libnetcdf.7.dylib             0x0000000112286126 nc_get_att_float + 90
(dattget.c:192)
15  libpetsc.3.7.dylib             0x00000001117f3a5b ex_open_int + 171
(ex_open.c:259)
16  libpetsc.3.7.dylib             0x0000000110c36609
DMPlexCreateExodusFromFile + 781 (plexexodusii.c:43)
17  DMPlexCreateExodusFromFile     0x000000010fed4cfc main + 397
(DMPlexCreateExodusFromFile.cpp:24)
18  libdyld.dylib                 0x00007fffad78a255 start + 1

>
>    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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