[gmx-users] gromacs and cluster

[Oliver Beckstein]

>>
>> 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

If this is really a verbatim copy your PBS input file then I think you  
made the mistake of using a 'dash' character (looks a bit like '--')  
instead of the minus '-' in the options:

>> #PBS �o pbsjob.out
WRONG

correct:
#PBS -o pbsjob.out

>> #PBS �e pbsjob.err
WRONG

>> ### Queue name
>> #PBS �q workq
WRONG

>> ###CPU number
>> #PBS  -l nodes=2:ppn=2
CORRECT

>> ### Script command
>> Cd  $PBS_O_WORKDIR
>> Lamboot $PBS_NODEFILE
>> mpirun C  mdrun
>> Lamhalt
>> exit 0
And as already pointed out, the commands are almost certainly called  
'lamboot' ,'cd', anf 'lamhalt'. In UNIX case matters.

Oli

>>
>>
> 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
>
>
> --  
> ----------------------------------------------------------------------- 
> --------
>  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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--
Oliver Beckstein * oliver at biop.ox.ac.uk
     http://sansom.biop.ox.ac.uk/oliver/