On Mon, Feb 14, 2011 at 12:15:50PM -0000, Till B wrote: > Question #143963 on DOLFIN changed: > https://answers.launchpad.net/dolfin/+question/143963 > > Status: Answered => Open > > Till B is still having a problem: > I made the mesh with gmsh. It contains 227792 tetrahedra. > > In the program I do nothing more than apply boundary conditions, define the > variational problem and solve it. I took the iterative stokes demo and just > edited the definition of the mesh and added my boundary conditions. > Similarly to the other stokes demos I already prepared the subdomains in a > separate xml file. > > I accept that 1GB RAM is not much. But is there an amount of RAM that is > sufficient, no matter how large the mesh is?
No. > When I first asked about my memory problems, I understood that the > iterative solver has an upper bound for RAM consumption. Not an upper bound, just that it uses more memory than the iterative solvers. -- Anders > > 2011/2/14 Anders Logg <[email protected]> > > > Your question #143963 on DOLFIN changed: > > https://answers.launchpad.net/dolfin/+question/143963 > > > > Status: Open => Answered > > > > Anders Logg proposed the following answer: > > How large is your mesh? What kind of mesh is it? Triangles or > > tetrahedra? > > > > The storage of the mesh itself is very efficient in DOLFIN but > > depending on what other things you do in your program, you may well > > run out of memory. 1GB is not that much. > > > > > > > > On Mon, Feb 14, 2011 at 11:49:36AM -0000, Till B wrote: > > > 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]PETSCERROR: > > 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. > > > > > -------------------------------------------------------------------------- > > > > > > You received this question notification because you are a member of > > > DOLFIN Team, which is an answer contact for DOLFIN. > > > > > > _______________________________________________ > > > Mailing list: https://launchpad.net/~dolfin > > > Post to : [email protected] > > > Unsubscribe : https://launchpad.net/~dolfin > > > More help : https://help.launchpad.net/ListHelp > > > > > > If you still need help, you can reply to this email or go to the > > following page to enter your feedback: > > https://answers.launchpad.net/dolfin/+question/143963 > > > > You received this question notification because you are a direct > > subscriber of the question. > > > > You received this question notification because you are a member of > DOLFIN Team, which is an answer contact for DOLFIN. > > _______________________________________________ > Mailing list: https://launchpad.net/~dolfin > Post to : [email protected] > Unsubscribe : https://launchpad.net/~dolfin > More help : https://help.launchpad.net/ListHelp _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : [email protected] Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
