Re: [AMBER] Utilizing two different nodes simultaneously for one job

From: Jason Swails <>
Date: Tue, 1 Dec 2015 08:11:15 -0500

On Tue, Dec 1, 2015 at 1:35 AM, muhammad tahir ayub <>

> Dear Amber Users
> I am running md simulation of my protein
> Inhibitor of kappa B kinase beta IKKb, in our lab there is two nodes which
> contains 32 processors each, I want to run the md simulation on both the
> nodes.
> Is there any
> command to run the md simultaneously on both the nodes of cluster computer
> ​​
> .

​This is called "distributed" parallelism (because the system RAM is not
shared by all processors). MPI supports distributed parallelism, and is
the approach used by Amber to parallelize sander and pmemd.

So the answer is "yes", you need to figure out how to run an MPI program on
your cluster and then build Amber with MPI support. There are instructions
in the manual for building Amber in parallel. Note, however, that this is
an advanced topic. You should be fully comfortable running Amber in serial
before trying parallel calculations.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Dec 01 2015 - 05:30:04 PST
Custom Search