MPI problems

Asked by Aron Wahlberg on 2010-02-23

I have recently installed dolfin 0.9.7 woth Dorsal. After solving some CGAL business (thanks Harish) I now bump into MPI issues. Anyone that recognize this?

>>> from dolfin import *
[Aron-Wahlbergs-MacBook-Pro.loca:63225] [NO-NAME] ORTE_ERROR_LOG: Unknown error: -127 in file /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_openmpi/work/openmpi-1.4.1/orte/mca/ess/singleton/ess_singleton_module.c at line 269
[Aron-Wahlbergs-MacBook-Pro.loca:63225] [NO-NAME] ORTE_ERROR_LOG: Unknown error: -127 in file /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_openmpi/work/openmpi-1.4.1/orte/mca/ess/singleton/ess_singleton_module.c at line 143
[Aron-Wahlbergs-MacBook-Pro.local:63225] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_openmpi/work/openmpi-1.4.1/orte/runtime/orte_init.c at line 132
--------------------------------------------------------------------------
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 A system-required executable either could not be found or was not executable by this user (-127) 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 "A system-required executable either could not be found or was not executable by this user" (-127) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[Aron-Wahlbergs-MacBook-Pro.local:63225] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!

Question information

Language:
English Edit question
Status:
Solved
For:
DOLFIN Edit question
Assignee:
No assignee Edit question
Solved by:
Harish Narayanan
Solved:
2010-02-23
Last query:
2010-02-23
Last reply:
2010-02-23

This question was reopened

Harish Narayanan (hnarayanan) said : #1

Is there some reason you are using openmpi from macports rather than just using what comes along with Mac OS X?

(I think it must have something to do with needing mpif77/mpif90, but I want to make sure.)

Aron Wahlberg (aron-simula) said : #2

I'm not completely sure actually. I can't remember when I installed it or for what reason, really. I checked with macports if it has any dependents but it doesn't. Do you suggest that I uninstall or deactivate it? Will that re-activate my pre-installed mac version of openMPI?

Aron

Best Harish Narayanan (hnarayanan) said : #3

Yes. Deactivate it, rebuild only DOLFIN (using your mac's default compilers) and hope for the best.

Aron Wahlberg (aron-simula) said : #4

Thanks Harish Narayanan, that solved my question.

Aron Wahlberg (aron-simula) said : #5

However, Now I get

>>> from dolfin import *
No module named vtk
*** Warning: Unable to import Viper, plotting disabled.
>>>

But I do have vtk-devel installed via macports and the lines in platforms/snowleopard.platform

Johannes Ring (johannr) said : #6

Are you sure you are using Python from MacPorts? Try to run 'which python'. It should give you '/opt/local/bin/python'. If you get '/usr/bin/python' instead, run the following commands to select Python from MacPorts:

  sudo port install python_select
  sudo python_select python26

Aron Wahlberg (aron-simula) said : #7

Yes, I am using MacPorts python.

Aron-Wahlbergs-MacBook-Pro:~ aron$ which python
/opt/local/bin/python
Aron-Wahlbergs-MacBook-Pro:~ aron$

Johannes Ring (johannr) said : #8

Maybe a re-installation of vtk-devel will help:

  sudo port uninstall vtk-devel
  sudo port install vtk-devel +py26

Harish Narayanan (hnarayanan) said : #9

You really should create separate questions. Changing the status of a solved question to unsolved and inserting another question in its place messes with the karma system.

Aron Wahlberg (aron-simula) said : #10

Thanks Harish Narayanan, that solved my question.