[gmx-users] Gromacs installation on the cluster

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 15 11:14:05 CEST 2009

ram bio wrote:
> Dear Gromacs Users,
> About Gromacs installation on the cluster, we compiled it on both the
> login node and the computing nodes. I'd like to know which gromacs
> programs can be run on the login node without disturbing all other
> users and which ones must be run on the computing nodes (e.g. the MD
> program).

The exact answer depends on your workflows. mdrun will always be compute 
intensive and should almost always be run on the compute nodes (except 
maybe quickie EM runs). Almost everything else shouldn't need to be run 
on the compute nodes, except perhaps for the more compute-intensive 
analysis tools. Those include computing eigensystems and 
autocorrelations. If the I/O on the login node is much slower than on 
the compute nodes you may find advantages to shifting some analysis out 
there, but you have to weigh up the cost of writing scripts to do the 
work for you.


More information about the gromacs.org_gmx-users mailing list