[petsc-users] DMPlexCreateExodusFromFile() does not work on macOS Sierra
Mark Adams
mfadams at lbl.gov
Mon Jan 23 07:55:51 CST 2017
And I trust you updated all system software (like gcc, NetCDF and
ExodusII). OSX upgrades are hell.
On Mon, Jan 23, 2017 at 12:36 AM, Matthew Knepley <knepley at gmail.com> wrote:
> On Sun, Jan 22, 2017 at 11:18 PM, Fande Kong <fdkong.jd at gmail.com> wrote:
>
>> Thanks, Matt,
>>
>> Clang does not have this issue. The code runs fine with clang.
>>
>
> Okay, it sounds like a gcc bug on Mac 10.6, or at least in the version you
> have.
>
> Matt
>
>
>> Fande,
>>
>> On Sun, Jan 22, 2017 at 8:03 PM, Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> 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
>>>
>>
>>
>
>
> --
> 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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