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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
