Re: [AMBER] pmemd.MPI with a single-entry group file?

From: David A Case <>
Date: Thu, 22 Mar 2018 21:52:30 -0400

On Thu, Mar 22, 2018, Kevin Keane wrote:
> I am trying to get Amber to work on our MPI cluster for one of our
> researchers, and am running into a problem. Please forgive if I get any
> chemical terminology wrong; I'm an IT guy.
> I am calling pmemd.MPI with a group file to take advantage of our cluster,
> such as this:
> /opt/amber/amber16/bin/pmemd.MPI -ng 8 -groupfile <filename>

A group file allows you to run multiple independent simulations from a
single program instance. Each "replica" gets the same number
of MPI threads (which is why the number of threads must be a multiple
of the number of groups.

First, you need to use mpirun (or its equivalent) to start pmemd.MPI:

mpirun -np 16 /opt/amber/amber16/bin/pmemd.MPI -ng 8 -groupfile <filename>

This will assign two MPI threads to each of the 8 groups. I'm frankly
not sure what will happen if you run pmemd.MPI without using mpirun.
It may actually work (giving one MPI thread per replica), but that's
almost by accident, since the code wasn't designed that way. Even if
you must want one thread per replica, it's better to use mpirun with the
number of threads set equal to the number of groups.

> When I have a group with only one element, pmemd.MPI fails with the error
> message that the file mdin is missing,

It doesn't really make much sense to set "-ng 1", since you could just put
the single line of the group file onto the command line.

I suppose that the "-ng 1" case should do what you expect, and
effectively treat the group file as the rest of the command line. And
it's arguably a bug that it doesn't do so. But I'm guessing no one
ever tried or tested what happens with -ng 1.

There are examples and further details in Section 17.11 of the Amber
2017 Reference Manual. But for now, you'll have to special case the
situation where the "number of replicas" is 1: just run pmemd.MPI in
the usual manner (not via multipmemd and group files).

...good luck...dac

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Received on Thu Mar 22 2018 - 19:00:02 PDT
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