Thanks for your suggestions, Rose.
On Wed, Sep 14, 2011 at 1:14 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> > Thanks, Jason. It works if I specify a host file. But there is
> > another
> > issue: qstat -f showed that the job was running on other nodes.
> > Actually
> > sander.MPI is running on the nodes I specified. Will this probably
> > mess up
> > the PBS queue system?
>
> Yes it will - it will annoy other people who might be using those other
> nodes. Any properly configured cluster should not actually let you do this.
> I.e. you should not be able to access nodes not allocated to your specific
> job by the queuing system. I suggest talking to the admin of your cluster
> to
> find out:
>
> 1) Why you could run on different nodes from the ones PBS allocated. This
> is
> bad from both a usability perspective and also a security one.
>
> 2) What the correct procedure is for running MPI jobs on your specific
> cluster.
>
> He/she should be in a much better position to advise you on this than we
> can
> given the huge number of degrees of freedom in how one sets up a cluster.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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Received on Wed Sep 14 2011 - 11:30:03 PDT
