On Sun, Jan 22, 2017 at 11:18 PM, Fande Kong <[email protected]> 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 <[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 >> > > -- 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
