Re: [AMBER] Using multiple CPU threads

From: David A Case <>
Date: Sat, 26 May 2018 09:19:21 -0400

On Sat, May 26, 2018, senal dinuka wrote:

> I am using Amber 16 along with Amber Tools 18 version. How would you use
> multiple threads for a single simulation when running on CPU. I have an
> Intel xeon system with 40 cores. So far my CPU runs use 2 cores only.

Basic approach is this:

mpirun -np xx sander.MPI <flags>


mpirun -np xx pmemd.MPI <flags>

Here "xx" is the number of MPI threads you wish to use. (Note that it
is not always true that more threads leads to faster performance: you
may wish to experiment.)

See note 8 on p. 24 of the reference manual for information on how to
install the parallel versions.

...hope this helps....dac

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Received on Sat May 26 2018 - 06:30:03 PDT
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