[petsc-users] DMPlexCreateExodusFromFile() does not work on macOS Sierra
Matthew Knepley
knepley at gmail.com
Sun Jan 22 23:36:53 CST 2017
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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