On Sat, Jan 21, 2017 at 10:47 PM, Matthew Knepley <knep...@gmail.com> wrote:
> On Sat, Jan 21, 2017 at 10:38 PM, Fande Kong <fdkong...@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 > > 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 >