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: ([EMAIL PROTECTED])(2688)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(2690)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(4367)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(4370)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(4369)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(4368)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(2687)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(2689)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(698)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(32587)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(696)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(32584)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(32585)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(32586)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(695)
Mutable error: Opening configfile: /opt/scali/etc/iba_params.conf
failed: No such file or directory
Jul 30 15:56:05: ([EMAIL PROTECTED])(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:[EMAIL PROTECTED]) (-:
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: ([EMAIL PROTECTED])(4345)
Mutable error: subMonitor-1 exits before allFinished is set
Jul 30 15:57:07: ([EMAIL PROTECTED])(4345)
Mutable error: subMonitor-3 exits before allFinished is set
Jul 30 15:57:07: ([EMAIL PROTECTED])(4345)
Mutable error: subMonitor-4 exits before allFinished is set
Jul 30 15:57:07: ([EMAIL PROTECTED])(4345)
Mutable error: subMonitor-2 exits before allFinished is set
What could be the origin of this problems?
Thank you very much
Fabio
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