Re: [AMBER] Troubleshooting long idle times in pmemd.MPI

From: David A Case <>
Date: Sat, 1 May 2021 13:02:18 -0400

On Thu, Apr 29, 2021, Kevin Keane wrote:

>We recently upgraded our cluster from RedHat 7 to RedHat 8, and we use
>Amber 16/AmberTools 17. We recompiled Amber during the migration.
>Ever since the upgrade, we noticed that Amber jobs take dramatically longer
>than they used to.
>The CPU times remain normal (in the example below, about 9 minutes), but
>the wall time needed was about 70 minutes. This job ran on two CPUs...

Do you see the same degradation on serial jobs? That might help provide a

I'm not sure how relevant this is, but the supplied MPI libraries for CentOS
don't work well with Amber, and we recommend buidling MPI from source there:

It's possible that similar limitations apply to RedHat as well. (We don't
have a regular testing scheme for RedHat.)


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Received on Sat May 01 2021 - 10:30:03 PDT
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