Hi Jan, My computations aren't parallel, and I don't believe I have OpenMPI installed - I can't find the file SubsystemManager.cpp mentioned in the bitbucket issue.
I also get these 'MPI' crashes when I run the gmsh executable from the linux shell command line. I also get very similar when trying to use my own .py (which calls dolfin) from a different directory, which doesn't call the 'dolfin_parameters.xml' shown below. I have done the following to uninstall/reinstall Fenics: sudo apt-get remove fenics* sudo apt-get -purge autoremove fenics sudo apt-get update sudo add-apt-repository ppa:fenics-packages/fenics sudo apt-get update sudo apt-get install fenics sudo apt-get dist-upgrade (I also did this process with ipython, mayavi2 and gmsh.) Thank you, David What is your OpenMPI version? It could be https://bitbucket.org/fenics-project/dolfin/issue/384 Jan On Wed, 3 Dec 2014 16:27:25 +0000 David Holloway <[email protected]<mailto:[email protected]>> wrote: > Hi Jan, > > Thank you - here's a screen dump from trying to run a Fenics demo .py > > In [1]: run d1_p2D.py > Reading DOLFIN parameters from file "dolfin_parameters.xml". > [ubuntu:03039] *** Process received signal *** [ubuntu:03039] Signal: > Floating point exception (8) [ubuntu:03039] Signal code: Integer > divide-by-zero (1) [ubuntu:03039] Failing at address: 0xb74e7da0 > [ubuntu:03039] [ 0] [0xb77bb40c] [ubuntu:03039] [ 1] > /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2cda0) > [0xb74e7da0] [ubuntu:03039] > [ 2] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2e71c) [0xb74e971c] > [ubuntu:03039] [ 3] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2ea8b) > [0xb74e9a8b] [ubuntu:03039] > [ 4] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x98f6) [0xb74c48f6] > [ubuntu:03039] [ 5] > /usr/lib/i386-linux-gnu/libhwloc.so.5(hwloc_topology_load+0x1c6) > [0xb74c58ec] [ubuntu:03039] > [ 6] /usr/lib/libopen-rte.so.4(orte_odls_base_open+0x7b1) > [0xb770c881] [ubuntu:03039] > [ 7] /usr/lib/openmpi/lib/openmpi/mca_ess_hnp.so(+0x2445) > [0xb7797445] [ubuntu:03039] > [ 8] /usr/lib/libopen-rte.so.4(orte_init+0x1cf) [0xb76e1b3f] > [ubuntu:03039] [ 9] /usr/lib/libopen-rte.so.4(orte_daemon+0x256) > [0xb76fe1c6] [ubuntu:03039] [10] orted() [0x80485b3] [ubuntu:03039] > [11] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3) > [0xb7515a83] [ubuntu:03039] [12] orted() [0x80485f8] [ubuntu:03039] > *** End of error message *** [ubuntu:03035] [[INVALID],INVALID] > ORTE_ERROR_LOG: Unable to start a daemon on the local node in file > ess_singleton_module.c at line 343 [ubuntu:03035] [[INVALID],INVALID] > ORTE_ERROR_LOG: Unable to start a daemon on the local node in file > ess_singleton_module.c at line 140 [ubuntu:03035] [[INVALID],INVALID] > ORTE_ERROR_LOG: Unable to start a daemon on the local node in file > runtime/orte_init.c at line 128 > ---------------------------------------------------------------------- > ---- It looks like orte_init failed for some reason; your parallel > process is likely to abort. There are many reasons that a parallel > process can fail during orte_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): > > orte_ess_set_name failed > --> Returned value Unable to start a daemon on the local node > (-128) instead of ORTE_SUCCESS > ---------------------------------------------------------------------- > ---- > ---------------------------------------------------------------------- > ---- 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 "Unable to start a daemon on the local node" (-128) > instead of "Success" (0) > ---------------------------------------------------------------------- > ---- [ubuntu:3035] *** An error occurred in MPI_Init_thread > [ubuntu:3035] > *** on a NULL communicator [ubuntu:3035] *** Unknown error > [ubuntu:3035] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort > ---------------------------------------------------------------------- > ---- An MPI process is aborting at a time when it cannot guarantee > that all of its peer processes in the job will be killed properly. > You should double check that everything has shut down cleanly. > > Reason: Before MPI_INIT completed > Local host: ubuntu > PID: 3035 > ----------------------------------------------------------------------
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