[AMBER] sander.MPI compiled with mvapich2 fails to exit upon completion

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Wed, 05 Jan 2011 18:44:44 +0100

Dear AMBER users,

Parallel jobs (sander.MPI + MVAPICH2) fail to exit upon completion. The
job appears to stall after it finishes ... The output is complete and
everything seems fine.
Of course, this is not nice if the sander job is part of a work flow.

Here are the details:
version: AMBER 11
mpi: MVAPICH2 1.6 (compiled specially for AMBER using the same compiler)
compiler: INTEL 11.0.073
arch: Linux x86_64, CentOS 5.5
cpu: AMD Opteron Istanbul
interconnection: Mellanox infiniband
Oracle Grid Engine used for controlling the jobs

The problem is not always reproducible and does not seem to occur with
OPENMPI (at least till now). However for some reason my version of AMBER
with OPENMPI scales worse that that with MVAPICH2 (that's why I prefer
using MVAPICH2).

If somebody else have seen this and knows how to elegantly fix (without
invoking "pkill" after every job) I would appreciate any advice.

Best wishes


Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
AMBER mailing list
Received on Wed Jan 05 2011 - 10:00:02 PST
Custom Search