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 <[email protected]> wrote: > 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 >
