[gmx-users] GRomacs 3.3.1 parallel run

[fabio tombolato]

Good morning, I started using Gromacs only few months ago doing MD on
proteins in membranes.
I' m using GRomacs 3.3.1 in parallel but I have some problems. I'm
doing my simulations on a 70  nodes cluster using 4 nodes (16
processors). the system uses PBS torque and SCALIMPI libraries.
When I run my jobs, the jobs start with no problems, even if there is
the following error message :
 Jul 30 15:56:05: (mdrun-5 at avogadro-60.n16.chimica.unipd.it)(2688)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-7 at avogadro-60.n16.chimica.unipd.it)(2690)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-0 at avogadro-22.n16.chimica.unipd.it)(4367)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-3 at avogadro-22.n16.chimica.unipd.it)(4370)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-2 at avogadro-22.n16.chimica.unipd.it)(4369)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-1 at avogadro-22.n16.chimica.unipd.it)(4368)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-4 at avogadro-60.n16.chimica.unipd.it)(2687)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-6 at avogadro-60.n16.chimica.unipd.it)(2689)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-11 at avogadro-61.n16.chimica.unipd.it)(698)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-15 at avogadro-62.n16.chimica.unipd.it)(32587)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-9 at avogadro-61.n16.chimica.unipd.it)(696)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-12 at avogadro-62.n16.chimica.unipd.it)(32584)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-13 at avogadro-62.n16.chimica.unipd.it)(32585)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-14 at avogadro-62.n16.chimica.unipd.it)(32586)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-8 at avogadro-61.n16.chimica.unipd.it)(695)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: (mdrun-10 at avogadro-61.n16.chimica.unipd.it)(697)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
NNODES=16, MYRANK=9, HOSTNAME=avogadro-61.n16.chimica.unipd.it
NNODES=16, MYRANK=11, HOSTNAME=avogadro-61.n16.chimica.unipd.it
NNODES=16, MYRANK=8, HOSTNAME=avogadro-61.n16.chimica.unipd.it
NNODES=16, MYRANK=10, HOSTNAME=avogadro-61.n16.chimica.unipd.it
NNODES=16, MYRANK=7, HOSTNAME=avogadro-60.n16.chimica.unipd.it
NNODES=16, MYRANK=5, HOSTNAME=avogadro-60.n16.chimica.unipd.it
NNODES=16, MYRANK=0, HOSTNAME=avogadro-22.n16.chimica.unipd.it
NNODES=16, MYRANK=4, HOSTNAME=avogadro-60.n16.chimica.unipd.it
NNODES=16, MYRANK=2, HOSTNAME=avogadro-22.n16.chimica.unipd.it
NNODES=16, MYRANK=15, HOSTNAME=avogadro-62.n16.chimica.unipd.it
NNODES=16, MYRANK=13, HOSTNAME=avogadro-62.n16.chimica.unipd.it
NNODES=16, MYRANK=6, HOSTNAME=avogadro-60.n16.chimica.unipd.it
NNODES=16, MYRANK=3, HOSTNAME=avogadro-22.n16.chimica.unipd.it
NNODES=16, MYRANK=1, HOSTNAME=avogadro-22.n16.chimica.unipd.it
NODEID=2 argc=12
NODEID=1 argc=12
NODEID=0 argc=12
NODEID=3 argc=12
                         :-)  G  R  O  M  A  C  S  (-:

                   Groningen Machine for Chemical Simulation

                            :-)  VERSION 3.3.1  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2006, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

          :-)  mdrun-0(mpi:4345 at avogadro-22.n16.chimica.unipd.it)  (-:

Option     Filename  Type         Description
......

When I want to delete a job, I use qdel; at this point the job
desappears from queue, but apparently the job is still running on the
processors. The output files are not updated and I have to enter the
nodes and force killing the processes with kill -9 .
This happens also if MD starts but crashes in a few seconds due for
example two overlapping atoms. The job desappears from queue but is
apparently running on nodes.
The error message is the following:

--- mpimon --- Aborting run after interrupt ---
Jul 30 15:57:07: (mpimon at avogadro-22.n16.chimica.unipd.it)(4345)
Mutable error: subMonitor-1 exits before allFinished is set
Jul 30 15:57:07: (mpimon at avogadro-22.n16.chimica.unipd.it)(4345)
Mutable error: subMonitor-3 exits before allFinished is set
Jul 30 15:57:07: (mpimon at avogadro-22.n16.chimica.unipd.it)(4345)
Mutable error: subMonitor-4 exits before allFinished is set
Jul 30 15:57:07: (mpimon at avogadro-22.n16.chimica.unipd.it)(4345)
Mutable error: subMonitor-2 exits before allFinished is set

What could be the origin of this problems?

Thank you very much

Fabio