Scott,
is seems like 304 atoms spread over 16 GPUs is not an efficient case... is
this something other than single MD? I would think the best you could do
would be a single GPU. Even then it's not using the GPU efficiently, see
for example Dave Cerutti's work to do multiple MD runs of trp-cage on a
single GPU.
Carlos
On Thu, Apr 29, 2021 at 9:27 PM Scott Brozell <sbrozell.comcast.net> wrote:
> 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 Fri Apr 30 2021 - 07:00:02 PDT
