[petsc-users] import mesh.

[obonnefon at paca.inra.fr]

Hello,

I need again your help.

In the ex12.c, I have replaced the line :
    ierr = DMPlexCreateBoxMesh(comm, dim, interpolate,
dm);CHKERRQ(ierr);
by
    ierr =
DMPlexCreateFromCellList(comm,dim,obNbCells,obNbVertex,3,0,obCells,2,obVertex,dm);CHKERRQ(ierr);
       for (i=0;i<obNbBound;i++){
         ierr =DMPlexSetLabelValue(*dm, "marker",
obBoundary[i]+obNbCells, 1);CHKERRQ(ierr);
       }

The result works with one process (mpirun -np 1 ./ex12), but not with 2
(mpirun -np 2 ./ex12), it crashes during the partitioning (I'm using
chaco):

Do you have any clue about this?

Thanks.

Olivier B

Following, the error message:

$ mpirun -np 2 ./ex12
[1]PETSC ERROR:
-----------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[1]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X
to find memory corruption errors
[1]PETSC ERROR: likely location of problem given in stack below
[1]PETSC ERROR: ---------------------  Stack Frames
------------------------------------
[1]PETSC ERROR: Note: The EXACT line numbers in the stack are not
available,
[1]PETSC ERROR:       INSTEAD the line number of the start of the
function
[1]PETSC ERROR:       is given.
[1]PETSC ERROR: [1] PetscSFCreateEmbeddedSF line 863
/home/olivierb/SOFT/petsc-3.4.2/src/vec/is/sf/interface/sf.c
[1]PETSC ERROR: [1] PetscSFDistributeSection line 1755
/home/olivierb/SOFT/petsc-3.4.2/src/vec/is/utils/vsectionis.c
[1]PETSC ERROR: [1] DMPlexDistribute line 2771
/home/olivierb/SOFT/petsc-3.4.2/src/dm/impls/plex/plex.c
[1]PETSC ERROR: [1] CreateMesh line 371
"unknowndirectory/"/home/olivierb/TP_PETSC/ex12.c
[1]PETSC ERROR: --------------------- Error Message
------------------------------------
[1]PETSC ERROR: Signal received!
[1]PETSC ERROR:
-----------------------------------------------------------------------
[1]PETSC ERROR: Petsc Release Version 3.4.2, Jul, 02, 2013
[1]PETSC ERROR: See docs/changes/index.html for recent updates.
[1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[1]PETSC ERROR: See docs/index.html for manual pages.
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: ./ex12 on a arch-linux2-c-debug named pcbiom38 by olivierb
Wed Aug 21 16:02:08 2013
[1]PETSC ERROR: Libraries linked from /home/olivierb/BUILD/DEBUG/PETSC/lib
[1]PETSC ERROR: Configure run at Tue Aug 20 11:32:52
2013--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with
errorcode 59.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending onexactly
when Open MPI kills
them.--------------------------------------------------------------------------
[1]PETSC ERROR: Configure options --with-debugging=1 --download-fiat
--download-scientificpython --download-generator --download-triangle
--download-ctetgen --download-chaco
--prefix=/home/olivierb/BUILD/DEBUG/PETSC
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: User provided function() line 0 in unknown directory
unknown
file--------------------------------------------------------------------------
mpirun has exited due to process rank 1 with PID 4546 onnode pcbiom38
exiting without calling "finalize". This mayhave caused other processes in
the application to beterminated by signals sent by mpirun (as reported
here).--------------------------------------------------------------------------
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