For what is worth, I agree with Dave Case on this.
Amber 20 has a new feature (shuttle transfer) where one can download to
the cpu only a subset of forces and coordinates. This is useful when one
needs to apply plumed restraints to just a subset of atoms in the system.
This new feature is in the code itself, so someone from the plumed
community should look into this.
Adrian
On 1/12/21 12:51 PM, David A Case wrote:
> [External Email]
>
> 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
> Plumed_force.inc" statement (line 752), then call gpu_upload_frc() after
> that.
>
> 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.]
>
> ....dac
>
>
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Jan 12 2021 - 10:00:02 PST
