Could you include slightly more of that stack trace? You are only showing stuff in other libraries. I suspect that there are some logic problem when closing an h5 file in parallel.
Johan On Wed, Sep 17, 2014 at 6:01 PM, Martin Sandve Alnæs <[email protected]> wrote: > Here's a clue from gdb, does this ring any bells? > > (Have to go now, won't be able to reply tonight.) > > > io/python/test_XDMF.py:69: test_save_1d_scalar Building mesh (dist 0a) > Number of global vertices: 33 > Number of global cells: 32 > Building mesh (dist 1a) > ^C > Program received signal SIGINT, Interrupt. > 0x00007fffee8749a6 in opal_progress () from /usr/lib/libmpi.so.1 > (gdb) where > #0 0x00007fffee8749a6 in opal_progress () from /usr/lib/libmpi.so.1 > #1 0x00007fffee7c21f5 in ompi_request_default_wait_all () > from /usr/lib/libmpi.so.1 > #2 0x00007fffcab35302 in ompi_coll_tuned_sendrecv_actual () > from /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so > #3 0x00007fffcab3d2bf in ompi_coll_tuned_barrier_intra_two_procs () > from /usr/lib/openmpi/lib/openmpi/mca_coll_tuned.so > #4 0x00007fffee7cf56b in PMPI_Barrier () from /usr/lib/libmpi.so.1 > #5 0x00007fffbbf2ec73 in mca_io_romio_dist_MPI_File_close () > from /usr/lib/openmpi/lib/openmpi/mca_io_romio.so > #6 0x00007fffbbf0c1e0 in mca_io_romio_file_close () > from /usr/lib/openmpi/lib/openmpi/mca_io_romio.so > #7 0x00007fffee7bb056 in ?? () from /usr/lib/libmpi.so.1 > #8 0x00007fffee7bb481 in ompi_file_close () from /usr/lib/libmpi.so.1 > #9 0x00007fffee7eb0c5 in PMPI_File_close () from /usr/lib/libmpi.so.1 > #10 0x00007fffed554324 in ?? () from /usr/lib/x86_64-linux-gnu/libhdf5.so.7 > #11 0x00007fffed54b821 in H5FD_close () > from /usr/lib/x86_64-linux-gnu/libhdf5.so.7 > #12 0x00007fffed53b339 in ?? () from /usr/lib/x86_64-linux-gnu/libhdf5.so.7 > #13 0x00007fffed53c7ed in H5F_try_close () > from /usr/lib/x86_64-linux-gnu/libhdf5.so.7 > #14 0x00007fffed53caf4 in ?? () from /usr/lib/x86_64-linux-gnu/libhdf5.so.7 > #15 0x00007fffed5abde2 in H5I_dec_ref () > > > > > On 17 September 2014 17:17, Martin Sandve Alnæs <[email protected]> > wrote: > >> I'm trying to get the dolfin pytest branch running all tests in parallel >> but still have some issues that don't really seem pytest related. >> >> Running >> cd <dolfin>/test/unit/ >> mpirun -np 3 python -m pytest -s -v function/ io/ >> >> _sometimes_ hangs in one of the io tests, and it seems to always be in >> the construction of a FunctionSpace. I've observed this both in a test >> using a UnitIntervalMesh(32) and another test using a UnitSquareMesh(16,16). >> >> Any pointers? >> >> Martin >> > > > _______________________________________________ > fenics mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics > >
_______________________________________________ fenics mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics
