[petsc-users] DMPlexCreateExodusFromFile() does not work on macOS Sierra
Matthew Knepley
knepley at gmail.com
Sun Jan 22 21:03:44 CST 2017
On Sun, Jan 22, 2017 at 8:40 PM, Fande Kong <fdkong.jd at gmail.com> wrote:
> Thanks, Matt.
>
> It is a weird bug.
>
> Do we have an alternative solution to this? I was wondering whether it is
> possible to read the ".exo" files without using the ExodusII. For example,
> can we read the ".exo" files using the netcdf only?
>
Well, ExodusII is only a think layer on NetCDF, just like other wrappers
are thin layers on HDF5. It is
really NetCDF that is failing. Can you switch compilers and see if that
helps?
Matt
> Fande Kong,
>
>
>
> On Sun, Jan 22, 2017 at 6:50 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
>
>> 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
>>
>
>
--
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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