[petsc-users] DMPlexCreateExodusFromFile() does not work on macOS Sierra
Matthew Knepley
knepley at gmail.com
Sun Jan 22 19:50:26 CST 2017
On Sun, Jan 22, 2017 at 5:28 PM, Fande Kong <fdkong.jd at gmail.com> wrote:
> On Sun, Jan 22, 2017 at 12:35 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
>
>> On Sun, Jan 22, 2017 at 12:41 PM, Fande Kong <fdkong.jd at gmail.com> wrote:
>>
>>> 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
>>>
>>
>> This is a NetCDF error on ex_open_int(). My guess is that your NetCDF
>> build is old and when it calls the system DLL
>> you bomb. Can you do a completely new build, meaning either reclone PETSc
>> somewhere else, or delete the whole
>> $PETSC_DIR/$PETSC_ARCH/externalpackage directory and reconfigure/build?
>>
>> Thanks,
>>
>> Matt
>>
>>
>
> Hi Matt,
>
> Thanks for reply. I recloned PETSc (the old petsc folder is deleted
> completely) and reconfigure. And still has the same issue. I also checked
> if the binary is complied against any other netcdf. The binary is actually
> complied against the right netcdf installed through PETSc.
>
You can see that this crash happens on the call to
int CPU_word_size = 0, IO_word_size = 0, exoid = -1;
float version;
exoid = ex_open(filename, EX_READ, &CPU_word_size, &IO_word_size,
&version);
which means the fault is not in PETSc, but rather in ExodusII for your
machine. We could definitely
confirm this if you made a 5 line program that only called this, but I
don't see why it should be different.
I am not sure what to do, since I am not in control of anything about
ExodusII. Can you report this to
their dev team? It is strange since Blaise has not reported this, and I
know he uses it all the time.
Thanks,
Matt
> *LiviadeMacBook-Pro:partition livia$ otool -L DMPlexCreateExodusFromFile*
> *DMPlexCreateExodusFromFile:*
> * /Users/livia/math/petsc/arch-darwin-cxx-debug/lib/libpetsc.3.7.dylib
> (compatibility version 3.7.0, current version 3.7.5)*
> *
> /Users/livia/math/petsc/arch-darwin-cxx-debug/lib/libsuperlu_dist.5.dylib
> (compatibility version 5.0.0, current version 5.1.3)*
> * /Users/livia/math/petsc/arch-darwin-cxx-debug/lib/libparmetis.dylib
> (compatibility version 0.0.0, current version 0.0.0)*
> * /Users/livia/math/petsc/arch-darwin-cxx-debug/lib/libmetis.dylib
> (compatibility version 0.0.0, current version 0.0.0)*
> * /Users/livia/math/petsc/arch-darwin-cxx-debug/lib/libnetcdf.7.dylib
> (compatibility version 10.0.0, current version 10.0.0)*
> * /Users/livia/math/petsc/arch-darwin-cxx-debug/lib/libhdf5_hl.8.dylib
> (compatibility version 9.0.0, current version 9.1.0)*
> * /Users/livia/math/petsc/arch-darwin-cxx-debug/lib/libhdf5.8.dylib
> (compatibility version 9.0.0, current version 9.1.0)*
> * /opt/X11/lib/libX11.6.dylib (compatibility version 10.0.0, current
> version 10.0.0)*
> * /Users/livia/math/mpich-3.2_install/lib/libmpifort.12.dylib
> (compatibility version 14.0.0, current version 14.0.0)*
> * /usr/local/opt/gcc at 5/lib/gcc/5/libgfortran.3.dylib (compatibility
> version 4.0.0, current version 4.0.0)*
> * /usr/local/opt/gcc at 5/lib/gcc/5/libquadmath.0.dylib (compatibility
> version 1.0.0, current version 1.0.0)*
> * /Users/livia/math/mpich-3.2_install/lib/libmpicxx.12.dylib
> (compatibility version 14.0.0, current version 14.0.0)*
> * /usr/local/opt/gcc at 5/lib/gcc/5/libstdc++.6.dylib (compatibility version
> 7.0.0, current version 7.21.0)*
> * /usr/local/opt/gcc at 5/lib/gcc/5/libgcc_s.1.dylib (compatibility version
> 1.0.0, current version 1.0.0)*
> * /Users/livia/math/mpich-3.2_install/lib/libmpi.12.dylib (compatibility
> version 14.0.0, current version 14.0.0)*
> * /Users/livia/math/mpich-3.2_install/lib/libpmpi.12.dylib (compatibility
> version 14.0.0, current version 14.0.0)*
> * /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 1238.0.0)*
> * /usr/local/lib/gcc/5/libgcc_s.1.dylib (compatibility version 1.0.0,
> current version 1.0.0)*
>
>
>
>
>
>>
>>>
>>
>>>> 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
>>>>
>>>
>>>
>>
>>
>> --
>> 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
>>
>
>
--
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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