[gmx-users] gromacs and cluster

[Mark Abraham]

Ö÷Ô £º£© 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

This is not a GROMACS problem - please look at your PBS documentation,
or get some help from someone who has experience running any sort of
parallel job on it. We can't know the quirks of your PBS installation.

That said, I think the "-l nodes=2:ppn=2" PBS directive is your most
likely source of a PBS problem, but that directive is highly
installation-specific. Capitalizing "Cd", "Lamboot" and "Lamhalt" is
almost certainly not right either.

Mark

> #!/bin/sh
> ### Job name
> #PBS  -N  pbsjob
> ### Output files
> #PBS ¨Co pbsjob.out
> #PBS ¨Ce pbsjob.err
> ### Queue name
> #PBS ¨Cq workq
> ###CPU number
> #PBS  -l nodes=2:ppn=2
> ### Script command
> Cd  $PBS_O_WORKDIR
> Lamboot $PBS_NODEFILE
> mpirun C  mdrun
> Lamhalt
> exit 0
> 
> 
> 
> 
> ×£ 
> 
> ºÃ
> 
> *************************************************
> Ji Qing£¨¼ªÇࣩ
> Institute of Chemistry, Chinese Academy of Sciences
> £¨ÖпÆÔº»¯Ñ§Ëù£©
> Tel: 0086-10-62562894  £¬82618423
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