On Sun, Jan 22, 2017 at 8:40 PM, Fande Kong <[email protected]> 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 <[email protected]> > wrote: > >> On Sun, Jan 22, 2017 at 5:28 PM, Fande Kong <[email protected]> wrote: >> >>> On Sun, Jan 22, 2017 at 12:35 PM, Matthew Knepley <[email protected]> >>> wrote: >>> >>>> On Sun, Jan 22, 2017 at 12:41 PM, Fande Kong <[email protected]> >>>> wrote: >>>> >>>>> On Sat, Jan 21, 2017 at 10:47 PM, Matthew Knepley <[email protected]> >>>>> wrote: >>>>> >>>>>> On Sat, Jan 21, 2017 at 10:38 PM, Fande Kong <[email protected]> >>>>>> 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@5/lib/gcc/5/libgfortran.3.dylib (compatibility >>> version 4.0.0, current version 4.0.0)* >>> * /usr/local/opt/gcc@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@5/lib/gcc/5/libstdc++.6.dylib (compatibility >>> version 7.0.0, current version 7.21.0)* >>> * /usr/local/opt/gcc@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
