[petsc-users] Segmentation violation in DMPlexDistribute on MacOS

[Balay, Satish]

> --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.

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
> 
>