[petsc-users] DMPlexCreateExodusFromFile() does not work on macOS Sierra
Fande Kong
fdkong.jd at gmail.com
Sun Jan 22 23:18:32 CST 2017
Thanks, Matt,
Clang does not have this issue. The code runs fine with clang.
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
>
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