REMD on GPU cluster

From: Michael Feig (
Date: Mon Apr 13 2015 - 17:09:05 CDT

Basically my question is how to run NAMD with REMD across multiple nodes
each with 1 or 2 GPUs.


I have seen previous posts but I am unsure about how exactly to go about it.


More specifically, for optimal performance it seems that I would want each
replica use 1 GPU plus maybe 10 CPU cores. If I then wanted to run 10
replicas, would I simply request 10 GPUs and 100 cores (or 10 GPU nodes
exclusively) and then use mpirun? How will NAMD figure out which cores
'belong' to which GPU or do I not need to worry about it? Does anybody have
experience with REMD on such a cluster with a recent NAMD version (2.10 or





Michael Feig, Ph.D.


Biochemistry & Molecular Biology; Chemistry

Michigan State University <>


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