Re: [AMBER] Running AmberTools21 on HPC cluster using distributed memory

From: David A Case <>
Date: Thu, 13 Jan 2022 09:18:26 -0500

On Thu, Jan 13, 2022, Manuel Fernandez Merino wrote:
>Thanks a lot for your answer.

I hope you read all of it, especially the part about asking for local help.
Some person knowledgeable about your cluster, and with access to it, might
be able to fix many of these things, but it's quite hard to do remotely.

>mpirun does not support recursive calls

This sounds like you are calling mpirun within mpirun. My guess is that
that you have "mpirun" in your DO_PARALLEL variable, and your queueing system
itself is invoking mpirun (via a command like "srun" or similar). You can
see how hard it is to figure things out based only on the final error.

Are you really planning to run nab programs in parallel on a
high-performance cluster via a job submission script? Same question for
cpptraj.MPI. If not, consider changing your test strategy. Many (most?)
Amber users would use a big cluster for pmemd jobs, and do the rest of
preparation and analysis on a local PC. I gave suggestions for that option
in my earlier email.

Also, can you run short parallel jobs via the command line, without
submitting them to the queueing system. Run a few tests, e.g. Run.dhfr.
If the codes work, you can ask for help on the job submission system from
a local administrator.

...good luck....dac

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Received on Thu Jan 13 2022 - 06:30:03 PST
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