Using mpi4py with python3.5

Question

I am trying to using mpi4py with python3.5 I have installed openMPI, and then the mpi4py module, on Ubuntu 16.04.

I get the following error when I try and import mpi4py:

Python 3.5.2 (default, Jul  5 2016, 12:43:10) 
[GCC 5.4.0 20160609] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from mpi4py import MPI
[ubuntu:31733] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap: /usr/lib/openmpi/lib/openmpi/mca_shmem_mmap.so: undefined symbol: opal_show_help (ignored)
[ubuntu:31733] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_posix: /usr/lib/openmpi/lib/openmpi/mca_shmem_posix.so: undefined symbol: opal_shmem_base_framework (ignored)
[ubuntu:31733] mca: base: component_find: unable to open /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv: /usr/lib/openmpi/lib/openmpi/mca_shmem_sysv.so: undefined symbol: opal_show_help (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
--------------------------------------------------------------------------
--------------------------------------------------------------------------
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):

  opal_init failed
  --> Returned value Error (-1) 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: ompi_rte_init failed
  --> Returned "Error" (-1) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init_thread
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)
[ubuntu:31733] Local abort before MPI_INIT completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed

How can I resolve this?

try installing msmpi before installing mpi4py

hsinghal
– hsinghal

2018-11-13 12:25:26 +00:00
Commented Nov 13, 2018 at 12:25 — hsinghal
– hsinghal, Commented Nov 13, 2018 at 12:25

218 · Accepted Answer · 2016-08-09 16:41:04Z

3

I solved this by doing the following:

Remove existing installs:

sudo apt-get remove openmpi-bin
sudo apt-get remove python3-mpi4py

Reinstall

sudo apt-get install libopenmpi-dev
sudo pip3 install mpi4py
sudo apt install openmpi-bin

answered Aug 9, 2016 at 16:41

218

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