[AMBER] trpcage benchmark: reduce 32x or dimerize ?

From: Scott Brozell <sbrozell.comcast.net>
Date: Thu, 29 Apr 2021 21:26:12 -0400

Hi,

The GB 304 atoms TRPCage GPU benchmark emits
'Must have 32x more atoms than processors!'
when run on 8 nodes with 2 gpus each.

Based on comments in gb_parallel.F90, this looks arbitrary.
Has anyone tried the benchmark after disabling this check ?


Alternatively, do we have a canned protocol for creating a distant
dimer ? This would appear to be easy work for leap's translate
and combine commands. This is for benchmarking but i still want to
be cagey enough to avoid blow up, eg, spacetime folding as in a binary
neutron star death spiral: https://apod.nasa.gov/apod/ap171016.html
so advice on the distance, other comments, and suggestions are welcome.

That benchmark appears to stem from
http://ambermd.org/tutorials/basic/tutorial3/index.php
?

thanks,
scott


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Received on Thu Apr 29 2021 - 18:30:02 PDT
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