[gmx-users] Re: Running Gromacs in Clusters

Dr. Vitaly Chaban vvchaban at gmail.com
Wed Nov 7 23:06:10 CET 2012

> I've tried your suggestions and had no sucess. I've got "no resources
> available" error but I checked out and 50% of the nodes are available.
> Perhaps, could be a library problem? Here, I compiled gromacs with MPI-LAM
> 7. Are you using another one?

I would suggest that the problem is within your submission system,
PBS, rather than within MPI, since "no resources available" is not a
MPI error. I am pretty sure that you cannot run any other software
parallel among nodes on your cluster.

You need to read the documentation for your queueing system or get in
touch with your sysadmin.

Did you try just "nodes=X" with no cores?

There might be a forbiddance for using multiple nodes according to
your cluster setup, perhaps.

Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark

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