[gmx-users] GRomacs 3.3.1 parallel run

Tue Jul 31 16:11:21 CEST 2007

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: (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

Does this config file exist?

> 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 .

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: (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
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Greetings,

Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
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