[gmx-users] GPU performance
bgbobay at ncsu.edu
Wed Apr 10 03:34:19 CEST 2013
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
When I have a chance (after this sander run is done - hopefully soon) I can
try the benchmarks again.
Thanks again for the help!
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