[petsc-users] Segmentation violation in DMPlexDistribute on MacOS

[Maximilian Hartig]

> On 6. Nov 2018, at 15:53, Balay, Satish <balay at mcs.anl.gov> wrote:
> 
>> --with-cc=gcc-mp-6 --with-cxx=g++-mp-6 
> 
> Is it possible to use xcode compilers? I've seen wierd errors with mpich/openmpi and gcc on OSX - don't know how reliable they are on OSX.

Yes, using clang (Xcode) with gfortran from macports did indeed resolve the issue. Thank you.

Best,
Max

> 
> It would be a good test to check if the same error is reproduceable with them..
> 
> Satish
> 
> On Tue, 6 Nov 2018, Maximilian Hartig via petsc-users wrote:
> 
>> Hello petsc team,
>> 
>> I’ve run into an issue using DMPlexDistribute on Mac OS 10.14.1. Here’s my dilemma:
>> - Compiling with petsc in debug mode (—with-debugging=true); the problem does not occur
>> - On two other (linux) machines, the error does not occur
>> - valgrind is not available for Mac OS Mojave at this point in time and it is unclear until when it will be
>> - SEGV occurs with mesh from gmsh file and  DMPlexCreateBoxMesh copied from https://www.mcs.anl.gov/petsc/petsc-current/src/dm/impls/plex/examples/tutorials/ex1.c.html <https://www.mcs.anl.gov/petsc/petsc-current/src/dm/impls/plex/examples/tutorials/ex1.c.html>
>> - I use the lastest petsc on maint/ branch from git
>> - petsc itself compiles and runs its tests (make […] check)  without problems on one and two processors.
>> 
>> 
>> Here’s the code I run for testing:
>> 
>> #include <petscds.h>
>> #include <petscdmplex.h>
>> 
>> int main(int argc, char **args) {
>>    PetscErrorCode ierr;
>>    PetscPartitioner part;
>>    DM dm, distributedDm;
>>    const char help[] = "no help";
>> 
>>    PetscInitialize(&argc,&args,(char*)0,help);
>> 
>>    ierr = DMPlexCreateFromFile(PETSC_COMM_WORLD,"cylinder_smallring.msh",PETSC_TRUE,&dm); CHKERRQ(ierr);
>>    // ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD, 2, PETSC_TRUE, NULL, NULL, NULL, NULL, PETSC_TRUE, &dm); CHKERRQ(ierr);
>>    ierr = DMPlexGetPartitioner(dm, &part); CHKERRQ(ierr);
>>    ierr = PetscPartitionerSetFromOptions(part); CHKERRQ(ierr);
>>    // ierr = PetscPartitionerSetType(part, PETSCPARTITIONERPARMETIS); CHKERRQ(ierr);
>>    ierr = DMPlexDistribute(dm, 0, NULL, &distributedDm); CHKERRQ(ierr);
>>    if(distributedDm){
>>        ierr = DMDestroy(&dm); CHKERRQ(ierr);
>>        dm = distributedDm;
>>    }
>>    ierr = DMDestroy(&dm); CHKERRQ(ierr);
>> 
>>    PetscFinalize();
>>    return 0;
>> }
>> 
>> Here’s the error message:
>> 
>> scc-wkit-clx-237-216:cimply_playground maximilianhartig$ ~/petsc/arch-darwin-c/bin/mpiexec -np 2 ./meshTest
>> [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
>> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
>> [0]PETSC ERROR: to get more information on the crash.
>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>> [0]PETSC ERROR: Signal received
>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
>> [0]PETSC ERROR: Petsc Release Version 3.10.2, unknown 
>> [0]PETSC ERROR: ./meshTest on a arch-darwin-c named Maximilians-MacBook.local by maximilianhartig Tue Nov  6 11:02:14 2018
>> [0]PETSC ERROR: Configure options PETSC_ARCH=arch-darwin-c --with-debugging=false --download-mumps --download-chacoa --download-scalapack --download-mpich --with-fc=gfortran-mp-6 --download-triangle --with-cc=gcc-mp-6 --with-cxx=g++-mp-6 --download-fblaspack --download-parmetis --download-metis --download-hdf5 --download chaco
>> [0]PETSC ERROR: #1 User provided function() line 0 in  unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> 
>> 
>> I don’t know how to proceed with this and would be thankful for a pointer in the right direction.
>> Thanks,
>> 
>> Max
>> 
>>