Subject: [Viper-dev] viper failing on AMD64 ubuntu hardy64, included output

From: osman <[email-masked]>
Date: Sun, 22 Mar 2009 10:22:22 -0400

Hi,
I have installed the latest fenics using apt-get. But demos are failing
during the plot(u) calls. mesh plots are working, and if I comment out
plot calls, the scripts runs through without any problems. I was able to
look at the warped mesh of the gear (elasticity demo). But plot(u)
causes seg fault. Any ideas why this might be happening?

Thanks in advance
-osman

stargate:/home/osman/dolfin-doc/demo/pde/elasticity/python-bash-> python
demo.py
Solving linear variational problem
  Applying boundary conditions to linear system.
  Applying boundary conditions to linear system.
  Solving linear system of size 26688 x 26688 (PETSc LU solver,
umfpack).
Saved function v (unnamed function) to file elasticity.pvd in VTK
format.
[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 linux or man libgmalloc on Apple 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 2.3.3, Patch 3, Fri Jun 15
16:51:25 CDT 2007 HG revision: f051789beadcd36f77fb6111d20225e26ed7cc0d
[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 stargate by osman Sun
Mar 22 10:18:43 2009
[0]PETSC ERROR: Libraries linked
from /build/buildd/petsc-2.3.3/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Mon Mar 17 09:53:28 2008
[0]PETSC ERROR: Configure options --with-shared --with-dynamic
--with-debugging=0 --useThreads 0 --with-mpi-dir=/usr
--with-mpi-shared=1 --with-blas-lib=-lblas --with-lapack-lib=-llapack
--with-umfpack=1 --with-umfpack-include=/usr/include/suitesparse
--with-umfpack-lib="[/usr/lib/libumfpack.so,/usr/lib/libamd.so]"
--with-superlu=1 --with-superlu-include=/usr/include/superlu
--with-superlu-lib=/usr/lib/libsuperlu.so
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
[stargate:16794] MPI_ABORT invoked on rank 0 in communicator
MPI_COMM_WORLD with errorcode 59
Segmentation fault
stargate:/home/osman/dolfin-doc/demo/pde/elasticity/python-bash->

---

From: "Johannes Ring" <[email-masked]>
Date: Mon, 23 Mar 2009 08:28:55 +0100 (CET)

Hi Osman,

The packages works fine on a clean installation of Ubuntu Hardy on amd64.
Is it possible that you have some conflicting software under, e.g.,
/usr/local? Also try to run instant-clean and then re-run the demo and see
if that makes any difference.

Johannes

On Sun, March 22, 2009 15:22, osman wrote:
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
> find memory corruption errors
> _______________________________________________
> Viper-dev mailing list
> [email-masked]
> http://fenics.org/mailman/listinfo/viper-dev
>