Hi, its a problem of your cluster configuration, ask your local sysadmin.
On Tuesday, 31. July 2007 15:43, fabio tombolato wrote: > 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 Does this config file exist? > 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 . Normally qdel should send something like an TERM signal to the headnode (here NNODES=16, MYRANK=1, HOSTNAME=avogadro-22.n16.chimica.unipd.it) and all other nodes should close itself. > 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
