[issm-support] ISSM compilation issues

[Morlighem, Mathieu (334H-Affiliate)]

Hi Jake,

I think you'll find the answer to your question on http://issm.jpl.nasa.gov/documentation/faq/matlab/
Basically, in some rare cases there might be a conflict of libraries between Matlab and PETSc.
One workaround is to use matlab in command line (matlab -nojvm)
and to never run ISSM in serial mode (never use md.cluster=none), which is extremely slow anyway.
Let us know if that does not fix your problem.

Regards,
Mathieu

----------------------------------------------
Mathieu Morlighem
Assistant Project Scientist
Department of Earth System Science
University of California, Irvine

(818) 354-4134 (JPL office)
(949) 824-1353 (UCI office)
(626) 429-5780 (cell)
Mathieu.Morlighem at uci.edu
________________________________________
From: issm-support-bounces at issm.ess.uci.edu [issm-support-bounces at issm.ess.uci.edu] On Behalf Of Jake Walter [jwalter at ucsc.edu]
Sent: Friday, April 06, 2012 5:07 PM
To: issm-support at issm.ess.uci.edu
Subject: [issm-support] ISSM compilation issues

Dear ISSM Support,

I am having trouble with the software on my Linux machine.  I am using a 64 bit installation for all the external packages and the install looks fine.  However, it crashes frequently in Matlab when running the example model, with an error message related to PETSC, an example is below.  Is there a more stable version that I should be using?  I have tried both versions 3.1 and 3.2 of PETSc and running Matlab 2012a.

Thanks so much for your help ahead of time.

Jake Walter


[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/petsc-as/documentation/troubleshooting.html#Signal[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: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 7, Mon Dec 20 14:26:37 CST 2010
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Unknown Name on a linux-gnu named love by jwalter Fri Apr  6 14:13:59 2012
[0]PETSC ERROR: Libraries linked from /soft/issm/issm/trunk/externalpackages/petsc/install/lib
[0]PETSC ERROR: Configure run at Thu Apr  5 14:20:09 2012
[0]PETSC ERROR: Configure options --prefix=/soft/issm/issm/trunk/externalpackages/petsc/install --with-mpi-dir=/soft/issm/issm/trunk/externalpackages/mpich2/install --PETSC_ARCH=linux-gnu-amd64 --PETSC_DIR=/soft/issm/issm/trunk/externalpackages/petsc/src --with-debugging=0 --with-shared=0 --download-mumps=yes --download-scalapack=yes --download-blacs=yes --download-blas=yes --download-f-blas-lapack=yes --download-parmetis=yes --FFLAGS=-I/soft/issm/issm/trunk/externalpackages/mpich2/install/include --download-plapack=yes --COPTFLAGS="-march=opteron -O2" --FOPTFLAGS="-march=opteron -O2" --CXXOPTFLAGS="-march=opteron -O2" --with-pic=1
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0


--
Jacob Walter
PhD Candidate
Dept. of Earth and Planetary Sciences
University of California, Santa Cruz
jwalter at ucsc.edu<mailto:jwalter at ucsc.edu>
http://es.ucsc.edu/~jwalter