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[Till B <question143963@xxxxxxxxxxxxxxxxxxxxx>]

Question #143963 on DOLFIN changed:
https://answers.launchpad.net/dolfin/+question/143963

Till B posted a new comment:
Hi again!

So I finally got XUbuntu running on a virtual machine. I installed Fenics from the Fenics ppa repositories. Now the iterative Stokes demo works. But when I put my own mesh in, I get memory problems again. In addition Petsc produces errors. My virtual machine has around 1.2 gig RAM, more is not possible. Does this mean that Fenics is in general not suitable for larger meshes?
Here is the output:

till@virtual-python:~/Desktop/sf_winshared/test$ python demo.py
Assembling linear system and applying boundary conditions...
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Out of memory. This could be due to allocating
[0]PETSC ERROR: too large an object or bleeding by not properly
[0]PETSC ERROR: destroying unneeded objects.
[0]PETSC ERROR: Memory allocated 0 Memory used by process 878977024
[0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
[0]PETSC ERROR: Memory requested 1131238140!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 10, Tue Nov 24 16:38:09 CST 2009
[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 virtual-python by till Mon Feb 14 10:56:04 2011
[0]PETSC ERROR: Libraries linked from /build/buildd/petsc-3.0.0.dfsg/linux-gnu-c-opt/lib
[0]PETSC ERROR: Configure run at Thu Dec 31 09:53:25 2009
[0]PETSC ERROR: Configure options --with-shared --with-debugging=0 --useThreads 0 --with-fortran-interfaces=1 --with-mpi-dir=/usr/lib/openmpi --with-mpi-shared=1 --with-blas-lib=-lblas-3gf --with-lapack-lib=-llapackgf-3 --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 --with-spooles=1 --with-spooles-include=/usr/include/spooles --with-spooles-lib=/usr/lib/libspooles.so --with-hypre=1 --with-hypre-dir=/usr --with-scotch=1 --with-scotch-include=/usr/include/scotch --with-scotch-lib=/usr/lib/libscotch.so
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
[0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2986 in src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: MatCreateSeqAIJ() line 2863 in src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Null argument, when expecting valid pointer!
[0]PETSC ERROR: Trying to zero at a null pointer!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 10, Tue Nov 24 16:38:09 CST 2009
[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 virtual-python by till Mon Feb 14 10:56:04 2011
[0]PETSC ERROR: Libraries linked from /build/buildd/petsc-3.0.0.dfsg/linux-gnu-c-opt/lib
[0]PETSC ERROR: Configure run at Thu Dec 31 09:53:25 2009
[0]PETSC ERROR: Configure options --with-shared --with-debugging=0 --useThreads 0 --with-fortran-interfaces=1 --with-mpi-dir=/usr/lib/openmpi --with-mpi-shared=1 --with-blas-lib=-lblas-3gf --with-lapack-lib=-llapackgf-3 --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 --with-spooles=1 --with-spooles-include=/usr/include/spooles --with-spooles-lib=/usr/lib/libspooles.so --with-hypre=1 --with-hypre-dir=/usr --with-scotch=1 --with-scotch-include=/usr/include/scotch --with-scotch-lib=/usr/lib/libscotch.so
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: PetscMemzero() line 189 in src/sys/utils/memc.c
[0]PETSC ERROR: MatZeroEntries_SeqAIJ() line 727 in src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: MatZeroEntries() line 4796 in src/mat/interface/matrix.c
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Null argument, when expecting valid pointer!
[0]PETSC ERROR: Trying to zero at a null pointer!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 10, Tue Nov 24 16:38:09 CST 2009
[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 virtual-python by till Mon Feb 14 10:56:04 2011
[0]PETSC ERROR: Libraries linked from /build/buildd/petsc-3.0.0.dfsg/linux-gnu-c-opt/lib
[0]PETSC ERROR: Configure run at Thu Dec 31 09:53:25 2009
[0]PETSC ERROR: Configure options --with-shared --with-debugging=0 --useThreads 0 --with-fortran-interfaces=1 --with-mpi-dir=/usr/lib/openmpi --with-mpi-shared=1 --with-blas-lib=-lblas-3gf --with-lapack-lib=-llapackgf-3 --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 --with-spooles=1 --with-spooles-include=/usr/include/spooles --with-spooles-lib=/usr/lib/libspooles.so --with-hypre=1 --with-hypre-dir=/usr --with-scotch=1 --with-scotch-include=/usr/include/scotch --with-scotch-lib=/usr/lib/libscotch.so
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: PetscMemzero() line 189 in src/sys/utils/memc.c
[0]PETSC ERROR: MatZeroEntries_SeqAIJ() line 727 in src/mat/impls/aij/seq/aij.c
[0]PETSC ERROR: MatZeroEntries() line 4796 in src/mat/interface/matrix.c
Computing Dirichlet boundary values, topological search [=>           ] 8.2%
Computing Dirichlet boundary values, topological search [==>          ] 16.5%
Computing Dirichlet boundary values, topological search [===>         ] 28.9%
Computing Dirichlet boundary values, topological search [=====>       ] 41.2%
Computing Dirichlet boundary values, topological search [======>      ] 53.6%
Computing Dirichlet boundary values, topological search [========>    ] 65.9%
Computing Dirichlet boundary values, topological search [==========>  ] 78.3%
Computing Dirichlet boundary values, topological search [===========> ] 90.7%
Computing Dirichlet boundary values, topological search [=============] 100.0%
Computing Dirichlet boundary values, topological search [=============] 100.0%
[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 3.0.0, Patch 10, Tue Nov 24 16:38:09 CST 2009
[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 virtual-python by till Mon Feb 14 10:56:04 2011
[0]PETSC ERROR: Libraries linked from /build/buildd/petsc-3.0.0.dfsg/linux-gnu-c-opt/lib
[0]PETSC ERROR: Configure run at Thu Dec 31 09:53:25 2009
[0]PETSC ERROR: Configure options --with-shared --with-debugging=0 --useThreads 0 --with-fortran-interfaces=1 --with-mpi-dir=/usr/lib/openmpi --with-mpi-shared=1 --with-blas-lib=-lblas-3gf --with-lapack-lib=-llapackgf-3 --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 --with-spooles=1 --with-spooles-include=/usr/include/spooles --with-spooles-lib=/usr/lib/libspooles.so --with-hypre=1 --with-hypre-dir=/usr --with-scotch=1 --with-scotch-include=/usr/include/scotch --with-scotch-lib=/usr/lib/libscotch.so
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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 on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

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