On Tue, 3 Nov 2015 20:32:40 +0000 Emil Eriksen <[email protected]> wrote: > Hi all, > > i have some problems running examples which uses MPI, e.g. the > "d1_p2D.py" example. Examples not using MPI, e.g. the > "alg_newton_np.py" example runs just fine.
These files are from outdated, unmaintained FEniCS tutorial. Start rather with documented demos included in DOLFIN source tree or on FEniCS website http://fenicsproject.org/documentation/dolfin/1.6.0/python/demo/index.html Jan > > Trying to isolate the problem, i booted an Ubuntu 14.04 LTS live > installation from USB and updated all packages > > sudo apt-get update > sudo apt-get upgrade > sudo apt-get dist-upgrade > > Next i added the official FEniCS repository > > sudo add-apt-repository ppa:fenics-packages/fenics > > and installed FEniCS using the Synaptic Package Manager. Now > "alg_newton_np.py" runs, but "d1_p2D.py" gives the error listed > below. Printing the > > ompi_info > > i can see that I have version 1.6.5 of Open MPI (latest version on > default Ubuntu repo). Do you have any idea of what i might be doing > wrong? > > Cheers, > emher > > Reading DOLFIN parameters from file "dolfin_parameters.xml". > [ubuntu:11850] mca: base: component_find: unable to > open /usr/lib/openmpi/lib/openmpi/mca_paffinity_hwloc: perhaps a > missing symbol, or compiled for a different version of Open MPI? > (ignored) [ubuntu:11850] mca: base: component_find: unable to > open /usr/lib/openmpi/lib/openmpi/mca_carto_auto_detect: perhaps a > missing symbol, or compiled for a different version of Open MPI? > (ignored) [ubuntu:11850] mca: base: component_find: unable to > open /usr/lib/openmpi/lib/openmpi/mca_carto_file: perhaps a missing > symbol, or compiled for a different version of Open MPI? (ignored) > [ubuntu:11850] mca: base: component_find: unable to > open /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap: perhaps a missing > symbol, or compiled for a different version of Open MPI? (ignored) > [ubuntu:11850] mca: base: component_find: unable to > open /usr/lib/openmpi/lib/openmpi/mca_shmem_posix: perhaps a missing > symbol, or compiled for a different version of Open MPI? (ignored) > [ubuntu:11850] mca: base: component_find: unable to > open /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing > symbol, or compiled for a different version of Open MPI? (ignored) > -------------------------------------------------------------------------- > It looks like opal_init failed for some reason; your parallel process > is likely to abort. There are many reasons that a parallel process > can fail during opal_init; some of which are due to configuration or > environment problems. This failure appears to be an internal > failure; here's some additional information (which may only be > relevant to an Open MPI developer): > > opal_shmem_base_select failed > --> Returned value -1 instead of OPAL_SUCCESS > -------------------------------------------------------------------------- > [ubuntu:11850] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file > runtime/orte_init.c at line 79 > -------------------------------------------------------------------------- > It looks like MPI_INIT failed for some reason; your parallel process > is likely to abort. There are many reasons that a parallel process > can fail during MPI_INIT; some of which are due to configuration or > environment problems. This failure appears to be an internal > failure; here's some additional information (which may only be > relevant to an Open MPI developer): > > ompi_mpi_init: orte_init failed > --> Returned "Error" (-1) instead of "Success" (0) > -------------------------------------------------------------------------- > *** An error occurred in MPI_Init_thread > *** on a NULL communicator > *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort > [ubuntu:11850] Local abort before MPI_INIT completed successfully; > not able to aggregate error messages, and not able to guarantee that > all other processes were killed! > _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
