Dear all,
This error came from a mistake I did ...
I compiled with the intel MPI version 4.1.0 by loading the correct
module .. However, when I tried to run MMPBSA.py.MPI I was loading by
mistake the module corresponding to intel mpi 4.0.3 ...
Its important to carefully double check that exactly the same MPI
version is used for compilation and running
Best wishes
Vlad
P.S. I am posting this just in case others will run into the same problems.
On 11/07/2013 07:34 PM, Vlad Cojocaru wrote:
> Dear all,
>
> I managed to compile AMBER/MMPBSA.py.MPI on 2 different clusters using
> the intel compiler and intel MPI2
> However, when I submit jobs via LSF, it appears as if the mpi4py cannot
> be imported on the compute nodes and I get the error below.
>
> mpi4py seems to build OK ( no error in mpi4py_install.log)
>
> Now I found this thread "http://archive.ambermd.org/201212/0204.html"
> and did what Jason suggested ... see the second traceback below
>
> Does anybody have any clue how to fix this ?
>
> Best and thanks,
> vlad
>
>
> Traceback (most recent call last):
> File
> "/usr/users/vcojoca/apps/cluster_intel/amber/12_tools-13_intel-13.0_impi-4.1.0/bin/MMPBSA.py.MPI",
> line 51, in <module>
> raise MMPBSA_Error('Could not import mpi4py package! Use serial
> version '
>
> Python 2.6.6 (r266:84292, Feb 21 2013, 19:26:11)
> [GCC 4.4.7 20120313 (Red Hat 4.4.7-3)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from mpi4py import MPI
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> ImportError: mpi4py/MPI.so: undefined symbol: MPI_Op_commutative
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Fri Nov 08 2013 - 01:30:04 PST
