Running NAMD in MPI environment

From: 김민재 (
Date: Wed Feb 20 2019 - 09:58:42 CST


I am relatively new to NAMD, and I read the user guide on running NAMD in
Linux clusters. However, I needed some clarification on some things.

So, the supercomputer system I am accessing is a heterogeneous Linux
cluster, and it uses Infiniband. (It also has NVIDIA and AMD GPUs, so I was
wondering which NAMD Package I should use.) I need to follow this template
to submit a job to its queuing system:

   thorq -- add -- mode [ mode ] [ options ] executable _ file [ arg1 arg2
. . . ]

In the -- mode, I would specify the job type, which would be MPI and the
number of nodes I would like to use. However, I am currently stumped on
what I should type in the "executable_file" spot. The supercomputer center
people didn't seem to be familiar with NAMD, and they told me to insert a
binary file and type in input files afterwards. So, my question is should I
type in "charmrun" and then "ex.conf" ? Also, as questioned above, which
NAMD package should I use? The supercomputer user manual states that I can
use OpenCL or CUDA to write programs before running them, and that the
system supports MPI and SnuCL.

I would really appreciate help on this.

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