Ok, the redmine is filled up and anybody who has time to help finding the issue is welcome :) I can't do much more!
As an alternative a colleague suggested that I could potentially get around the problem by using a compilation combining Open-MP or thread-MPI for each replica running on one node (shared memory=no need of decomposition) and MPI across nodes. Would it work? But I might have a problem, the CG uses shifted potentials and they seem not to be implemented with OpenMP and thread-MPI is not compatible with MPI … Any other solution one could imagine? XAvier. On May 9, 2013, at 1:01 PM, XAvier Periole <x.peri...@rug.nl> wrote: > > I finally could reproduce the problem in gmx461 and have fled up a red mine > report. > > I hope we can fix this easily but I am not sure how things go go from now! > Someone will get the bug assigned and fix it when ever possible or something > else? > > Thank you all for the help, > XAvier. > > On May 2, 2013, at 10:15 PM, XAvier Periole <x.peri...@rug.nl> wrote: > >> >> I'll look at the 4.6.1 version next week, I could install it but I got a >> conflict between the environmental variable defining openMP variable but I >> turned it off during compilation … >> >> You could try to run on particle decomposition to see if you get a problem … >> it should one quite quick. >> >> On May 2, 2013, at 2:36 PM, Michael Shirts <mrshi...@gmail.com> wrote: >> >>> Both. So if 4.6.1 doesn't work, I want to know so we can patch it >>> before 4.6.2 comes out. If it does work, then there is probably stuff >>> that can be backported. >>> >>> On Thu, May 2, 2013 at 8:32 AM, XAvier Periole <x.peri...@rug.nl> wrote: >>>> >>>> You mean working with or working on the code? >>>> >>>> I'll try gmx-4.6.1 >>>> >>>> On May 2, 2013, at 2:26 PM, Michael Shirts <mrshi...@gmail.com> wrote: >>>> >>>>> Quick check here -- is 4.6 behaving correctly? I actually spent some >>>>> time working on REMD in 4.6, and it seems to be behaving correctly in >>>>> my hands with temperature and pressure control. >>>>> >>>>> Thanks for any additional info on this! >>>>> >>>>> On Thu, May 2, 2013 at 8:18 AM, Mark Abraham <mark.j.abra...@gmail.com> >>>>> wrote: >>>>>> On Thu, May 2, 2013 at 12:58 PM, XAvier Periole <x.peri...@rug.nl> wrote: >>>>>> >>>>>>> >>>>>>> I saw that redmine report, which could be related but it seems to happen >>>>>>> only for runs done outside the domain and particle decompositions. >>>>>>> >>>>>>> I'll fill up a red mine. >>>>>>> >>>>>>> Anything I could do to help speeding the fix? >>>>>>> >>>>>> >>>>>> What'd be really nice is some thought on how one can demonstrate that the >>>>>> implementation of the exchange matches what would be expected from the >>>>>> theory. For T-exchange under NVT, it is sufficient to rescale velocities >>>>>> and quantities derived from them by the correct factor. That includes >>>>>> various things like T-coupling history and integrator half-step >>>>>> quantities >>>>>> (and does REMD with leap-frog make sense anyway?). For NPT, there's >>>>>> probably also some P-coupling quantities to scale, and the box to >>>>>> exchange. >>>>>> Anything I've missed? Hopefully virial contributions don't matter either >>>>>> way? >>>>>> >>>>>> Perhaps a decent first step is to hack the code to do a "self exchange," >>>>>> by >>>>>> clearing the entire state and rebuilding with what would/should be >>>>>> received >>>>>> from an exchange with a hypothethetical replica in an identical >>>>>> pre-exchange state. Only if the code can do that (i.e. mdrun -reprod >>>>>> produces a trajectory indistinguishable from a run that does not attempt >>>>>> this self exchange) is it worth considering proper state exchanges, and >>>>>> the >>>>>> process of making the code do the former should illustrate what is >>>>>> required >>>>>> for the latter. >>>>>> >>>>>> Mark >>>>>> -- >>>>>> 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 >>>> >>>> -- >>>> 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 >> >> -- >> 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 -- 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
