[gmx-users] gromacs and cluster

[Florian Haberl]

hi


On Thursday 08 December 2005 11:08, 主月 ：） wrote:
> Hi:
> I've already installed GROMACS on the main node of my cluster(RH 9.0 OSCAR). And using the model in \share i can run md successfully. But with the pbsscript bellow the error came that is "qsub :directive error ...". How can i fix it. Thanks
> 
> 
> #!/bin/sh
> ### Job name
> #PBS  -N  pbsjob
> ### Output files
> #PBS �o pbsjob.out
> #PBS �e pbsjob.err
> ### Queue name
> #PBS �q workq
> ###CPU number
> #PBS  -l nodes=2:ppn=2
> ### Script command
> Cd  $PBS_O_WORKDIR
> Lamboot $PBS_NODEFILE
> mpirun C  mdrun
> Lamhalt
> exit 0
> 
> 
take a look on the documentation of your computer center
lamboot and lamhalt are not right here (i guess)

http://www.bo.infn.it/alice/introgrd/pbsabout/node18.html

Invalid directive, extra characters in #PBS -q infinite

$ qsub cpbs.cmd
qsub: directive error: -q infinite ###reset to use infinite queue

Directive lines cannot contain extra characters, like comments describing the directive action


a common pbs script is like:

#!/bin/sh
#PBS -l nodes=1:ppn=2
#PBS -q route
#PBS -l walltime=24:00:00

USE_PROG_MPI=gnu64
export USE_PROG_MPI


cd $PBS_O_WORKDIR

/opt/mpi/bin/mpirun -np 2 pathtomdrun -deffnm topol




> 
> 
> 祝 
> 
> 好
> 
> *************************************************
> Ji Qing（吉青）
> Institute of Chemistry, Chinese Academy of Sciences
> （中科院化学所）
> Tel: 0086-10-62562894  ，82618423
> *************************************************
> 
> 
Greetings,

Florian


-- 
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 Florian Haberl                        Universitaet Erlangen/ Nuernberg
                                       Computer-Chemie-Centrum   
                                       Naegelsbachstr. 25
                                       D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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