For the record. gmx-4.6.4 hangs when number of threads is not a multiple of the number of nodes.
XAvier. On Nov 22, 2013, at 7:14 PM, XAvier Periole <x.peri...@rug.nl> wrote: > > Ok, tks. I'll try then :)) > > XAvier. > > On Nov 22, 2013, at 4:31 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > >> Hardware detection and management of the results is greatly improved since >> 4.6.1, so we would expect relevant changes, particularly if -pin off makes >> it work (very slowly) >> >> Mark >> On Nov 21, 2013 7:37 PM, "XAvier Periole" <x.peri...@rug.nl> wrote: >> >>> >>> For the record: >>> >>> I do not expect this issue to be affected by an update to gmx4.6.4 … >>> >>> But the problem is fixed by turning the pin option off. >>> >>> XAvier. >>> >>> On Nov 21, 2013, at 6:04 PM, Szilárd Páll <pall.szil...@gmail.com> wrote: >>> >>>> Hi, >>>> >>>> It's not expected, but instead of trying to figure out what the issues >>>> is with 4.6.1, you should really update to the latest version. If the >>>> problem persists with 4.6.4, we shall have a closer look. >>>> >>>> Cheers, >>>> -- >>>> Szilárd >>>> >>>> >>>> On Thu, Nov 21, 2013 at 11:38 AM, XAvier Periole <x.peri...@rug.nl> >>> wrote: >>>>> >>>>> Dears, >>>>> >>>>> When running on multiple nodes I get GMX-461 hanging if the number of >>> threads is not a multiple of the number of cores. >>>>> >>>>> example: with 11 nodes having 24 cores each, defining 253 threads (23 >>> threads per node) or 264 threads (24 threads per node) would work but >>> defining 256 threads would result in mdrun to hang for long time. >>>>> >>>>> That might be expected and not really an issue but that be nice if >>> anyone knows why. >>>>> >>>>> Thanks, >>>>> XAvier. >>>>> -- >>>>> 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. >>>> -- >>>> 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. >>> >>> -- >>> 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. >>> >> -- >> 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. > > -- > 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. -- 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.