[gmx-users] GPU performance

[Benjamin Bobay]

Szilárd -

First, many thanks for the reply.

Second, I am glad that I am not crazy.

Ok so based on your suggestions, I think I know what the problem is/was.
There was a sander process running on 1 of the CPUs.  Clearly GROMACS was
trying to use 4 with "Using 4 OpenMP thread". I just did not catch that.
Sorry! Rookie mistake.

Which I guess leads me to my next question (sorry if its too naive):

(1) When running GROMACS (or a I guess any other CUDA based programs), its
best to have all the CPUs free, right? I guess based on my results I have
pretty much answered that question.  Although I thought that as long as I
have one CPU available to run the GPU it would be good: would setting
"-ntmpi 1 -ntomp 1" help or would I take a major hit in ns/day as well?

If I try the benchmarks again just to see (for fun) with "Using 4 OpenMP
thread", under top I have - so I think the CPU is fine :
PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
24791 bobayb    20   0 48.3g  51m 7576 R 299.1  0.2  11:32.90
mdrun


When I have a chance (after this sander run is done - hopefully soon) I can
try the benchmarks again.

Thanks again for the help!

Ben