Re: [AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40%

From: David A Case <>
Date: Tue, 12 Jan 2021 12:51:06 -0500

On Tue, Jan 12, 2021, Amanda Buyan wrote:
>I hope you are able to help me with something. We have successfully
>installed Amber20, along with the PLUMED package and libraries. One of our
>students as well as me have been using Amber20 with PLUMED, but we have
>noticed that the performance of Amber20 has decreased with the addition
>of PLUMED. Has anyone else had this issue? Could it be an issue with my
>installation of either Amber or PLUMED?
>Some other specs that you might need: we are using pmemd.cuda (no MPI
>option), plumed2.5, and we are loading the single CPU plumed library.

A few days ago, I chastized Bill Ross for guessing, but here goes anyway:

I think running plumed with pmemd.cuda is expected to slow down GPU runs.
As far as I can tell, the plumed part is all done on the CPU, so the GPU
has to communicate with the CPU every time it need plumed functionality.

Look at the PLUMED section in runmd.F90, starting at about line 743. It has
to call gpu_download_crd() and gpu_download_frc() before the "include" statement (line 752), then call gpu_upload_frc() after

This would be expected to slow things down, probably by quite a bit,
depending on the size of the system.

[Caveat: above is based on a cursory reading of the code; I've not run
plumed calculations myself. I hope others with more direct experience will
chime in.]


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Received on Tue Jan 12 2021 - 10:00:02 PST
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