On Apr 10, 2013 3:34 AM, "Benjamin Bobay" <bgbo...@ncsu.edu> wrote: > > 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?
Some codes might treat the CPU as a "I/O, MPI and memory-serving co-processor" of the GPU; those codes will tend to be insensitive to the CPU config. GROMACS goes to great lengths to use all the hardware in a dynamically load-balanced way, so CPU load and config tend to affect the bottom line immediately. Mark > 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 -- 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
