[molpro-user] how to run molpro across an opteron cluster

Reuti reuti at staff.uni-marburg.de
Fri Dec 10 01:22:15 GMT 2004

Hi Seth,

I put some hints online at the SGE mailing list:


just follow the whole thread back.

1) Recompile Global Arrays to use an rsh in the $PATH (not ssh directly, this 
should be handled by SGE)
2) Change SGE to use ssh (passwordless), this will be used by the rsh-wrapper 
in the qrsh
3) Prepare a PE with a hostlist in the PBS_NODEFILE format, i.e. not unique or 
with no. of CPUs but with one line per used CPU (like mpich without shared 
4) Create the same scratch directory on all nodes (you can use the $TMPDIR name 
of SGE in your jobscript and create it on all the node in the machines file)

5) Run the job

6) Remove scratch directories on the nodes

CU - Reuti

Quoting Dr Seth OLSEN <s.olsen1 at uq.edu.au>:

> Hi Molpro Users,
> I have built parallel Molpro to run on an 64bit Opteron node running Fedora
> Core 2.    Each node in the cluster has 2 cpus, each of which represents one 
> slot in the context of the Sun Grid Engine queuing system which manages the
> job load on the cluster.  We are currently working on creating a parallel
> environment which will allow molpro jobs to use both slots on a single node. 
> Is there anyone on the list with experience in similar matters?  After this,
> we will work on getting molpro jobs to run across nodes.  Regarding this, I
> have some questions about how parallel molpro does machine-machine
> communications.  How does Molpro do internode communication?  Right now, the
> nodes of the cluster are set up to speak with each other via ssh.  What must
> be done to get molpro to work across nodes in that environment?
> Cheers,
> Seth Olsen
> ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms
> Dr Seth Olsen, PhD
> Postdoctoral Fellow, Computational Systems Biology Group
> Centre for Computational Molecular Science
> Chemistry Building,
> The University of Queensland
> Qld 4072, Brisbane, Australia
> tel (617) 33653732
> fax (617) 33654623
> email: s.olsen1 at uq.edu.au
> Web: www.ccms.uq.edu.au 
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