[gmx-users] Using Gromacs on a cluster

[Mark Abraham]

Hi,

First, you'd want to know that your cluster has at least gigabit ethernet,
or preferably infiniband. Else you won't get value from parallelising over
nodes.

Then you'd want to be sure your science is best done with one large
relatively inefficient simulation, rather than several smaller, more
efficient simulations, each one taking longer for the same amount of
sampling.

Then you need to install and maintain an MPI library across all the nodes
(e.g. OpenMPI or MVAPICH2). Then work out how to construct the hostfile so
that when you run mpirun it knows how to log into each node and run
processes.

If your nodes have different CPU types, then you'll need also to manage
compiling GROMACS differently on each different kind of node, yet making
the correct compilation available on each.

Probably not worth it...

Mark

On Tue, Jun 21, 2016 at 2:13 PM bharat gupta <bharat.85.monu at gmail.com>
wrote:

> Hello Gromacs Users,
>
> I would like to know how to run the simulation on a cluster. I have cluster
> in my lab with 6 nodes having 16 cpus and 4 nodes having 8 cpus. What
> command do I have to use all the nodes? How do I know whether cpus from all
> nodes are being used??
>
> Thanks in advance for help
>
> --
> *Best Regards*
> Bharat
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