<div dir="ltr">On Wed, Aug 21, 2013 at 9:19 AM, <span dir="ltr"><<a href="mailto:obonnefon@paca.inra.fr" target="_blank">obonnefon@paca.inra.fr</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><u></u>
<div style="font-family:Arial;font-size:14px">
<p>Hello,<br>
<br>
<br>
I need again your help.<br>
<br>
In the ex12.c, I have replaced the line :<br>
ierr = DMPlexCreateBoxMesh(comm, dim, interpolate, dm);CHKERRQ(ierr);<br>
by<br></p></div></blockquote><div>You probably want:</div><div><br></div><div>if (!rank) { <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div style="font-family:Arial;font-size:14px"><p>
ierr = DMPlexCreateFromCellList(comm,dim,obNbCells,obNbVertex,3,0,obCells,2,obVertex,dm);CHKERRQ(ierr);<br>
for (i=0;i<obNbBound;i++){<br>
ierr =DMPlexSetLabelValue(*dm, "marker", obBoundary[i]+obNbCells, 1);CHKERRQ(ierr);<br>
}<br></p></div></blockquote><div>} else {</div><div> ierr = DMCreate(comm, dm);CHKERRQ(ierr);</div><div> ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr);<br></div><div> ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr);</div>
<div>}</div><div><br></div><div>so that you have an empty mesh on proc 1. I should not crash, but I think its getting confused because</div><div>you have a weirdly specified mesh on all procs.</div><div><br></div><div> Matt</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="font-family:Arial;font-size:14px"><p>
<br>
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):<br>
<br>
Do you have any clue about this?<br>
<br>
Thanks.<br>
<br>
Olivier B<br>
<br>
Following, the error message:<br>
<br>
$ mpirun -np 2 ./ex12<br>
[1]PETSC ERROR: -----------------------------------------------------------------------<br>
[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<br>
[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<br>
[1]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a><br>
[1]PETSC ERROR: or try <a href="http://valgrind.org" target="_blank">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors<br>
[1]PETSC ERROR: likely location of problem given in stack below<br>
[1]PETSC ERROR: --------------------- Stack Frames ------------------------------------<br>
[1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,<br>
[1]PETSC ERROR: INSTEAD the line number of the start of the function<br>
[1]PETSC ERROR: is given.<br>
[1]PETSC ERROR: [1] PetscSFCreateEmbeddedSF line 863 /home/olivierb/SOFT/petsc-3.4.2/src/vec/is/sf/interface/sf.c<br>
[1]PETSC ERROR: [1] PetscSFDistributeSection line 1755 /home/olivierb/SOFT/petsc-3.4.2/src/vec/is/utils/vsectionis.c<br>
[1]PETSC ERROR: [1] DMPlexDistribute line 2771 /home/olivierb/SOFT/petsc-3.4.2/src/dm/impls/plex/plex.c<br>
[1]PETSC ERROR: [1] CreateMesh line 371 "unknowndirectory/"/home/olivierb/TP_PETSC/ex12.c<br>
[1]PETSC ERROR: --------------------- Error Message ------------------------------------<br>
[1]PETSC ERROR: Signal received!<br>
[1]PETSC ERROR: -----------------------------------------------------------------------<br>
[1]PETSC ERROR: Petsc Release Version 3.4.2, Jul, 02, 2013<br>
[1]PETSC ERROR: See docs/changes/index.html for recent updates.<br>
[1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<br>
[1]PETSC ERROR: See docs/index.html for manual pages.<br>
[1]PETSC ERROR: ------------------------------------------------------------------------<br>
[1]PETSC ERROR: ./ex12 on a arch-linux2-c-debug named pcbiom38 by olivierb Wed Aug 21 16:02:08 2013<br>
[1]PETSC ERROR: Libraries linked from /home/olivierb/BUILD/DEBUG/PETSC/lib<br>
[1]PETSC ERROR: Configure run at Tue Aug 20 11:32:52 2013--------------------------------------------------------------------------<br>
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 59.<br>
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>
You may or may not see output from other processes, depending onexactly when Open MPI kills them.--------------------------------------------------------------------------<br>
[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<br>
[1]PETSC ERROR: ------------------------------------------------------------------------<br>
[1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file--------------------------------------------------------------------------<br>
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).--------------------------------------------------------------------------<br>
<br>
<br></p>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
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