Hi Szilárd, thank you for you reaction! I prepared a simple input which reproduces the behavior, see
https://owncloud.cesnet.cz/public.php?service=files&t=9e8fc3924fd109f6d48a552e20ceaf11 With -nt 1 it successfully finishes in ca 12 seconds, with -nt 2 it gets stuck after SETTLE citation. Regards, Jan 2015-06-15 21:51 GMT+02:00 Szilárd Páll <pall.szil...@gmail.com>: > On Sun, Jun 14, 2015 at 6:54 PM, Jan Jirsák <janjir...@gmail.com> wrote: >> Hi, >> >> I did the test and found out that -nt 8 is even slower than -nt 1 !! > > FYI: "-nt" is mostly backward compatibility option and for clarity > it's best to use either -ntmpi or -ntomp, depending on what you mean. > >> However, I think that simulation hasn't even properly started with 8 >> threads and got stuck somewhere in the beginning. >> >> Details: >> I used a short run (1000 steps) for testing. mdrun -nt 1 finished >> after ca 11 hours, whereas not a single checkpoint or run log record >> have been saved for mdrun -nt 8 (and simulation is still running). Not >> even starting energies were displayed - last record in a log file is a >> SETTLE citation. > > That's probably a stuck which should not happen and I'd consider that > a bug. Can you share your input files? > >> In top I noticed both processes used up to 100% CPU, but considerably >> differed in the use of memory. Relevant lines: >> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND >> 117710 jan 20 0 5313776 4.642g 9940 R 98.9 3.7 52:47.19 >> mdrun >> 117686 jan 20 0 547344 24456 8712 R 92.7 0.0 54:48.92 mdrun > > That definitely does not look good. > > BTW, in contrast with Mark's opinion I do think top is indicative. If > you wanted to use 8 cores and told mdrun to do so but you get load > only on one core, you can be (almost) certain that something is not > right. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.