Mark, Thank you!!! It was non directly MPI, since I tried the fresh installation with intel and gcc but none worked, then i realized that my compilation of FFTW could be the problem (compiled with icc 11), then I recompiled FFTW with gcc and linking to this new fftw3.2.2 I recompiled gromacs booth with gcc and intel, booth compilations seems to work. Do you think that it could be any problem at mix gcc-fftw and intel mdrun??? I will continue the tests with the new gmx-tests and other TPRs.
Thanks Daniel 2009/10/30 Mark Abraham <[email protected]>: > Daniel Adriano Silva M wrote: >> >> Mark, >> >> I will test, but please tell me: do you think MPI linking problem >> could lead to problems with some dynamics and not with others as >> happens to me? and also note that all my test where made with mvapich2 >> (even that with one core). Please justin, what do you think about? > > For example, observing symptoms from buffer overruns can be sensitive to the > actual calculation being run because it can depend how the actual memory > gets laid out and used. So here, that might translate to the kind of system > being simulated, and the number of cores used. Such an overrun might be > present in the code all the time, or only exists after a linking mismatch, > or similar. > > Mark > >> Thanks >> Daniel >> >> 2009/10/30 Mark Abraham <[email protected]>: >>> >>> Daniel Adriano Silva M wrote: >>>> >>>> Dear Gromacs users, >>>> >>>> I am experimenting the next problem on an infiniband-cluster (8 >>>> intel-cores per node, GROMACS compiled with icc 11.1, all run through >>>> mvapich2): >>>> >>>> I have a molecule (protein 498aa, solvated or in vacuum I get the same >>>> problem at any box shape), when I try to SD minimize it with >>>> mvapich2-mdrun, it minimizes well with 1, 2 or 3 cores and reaches >>>> convergence in around 1000steps, however any further combination (4,5, >>>> ...n cores) makes it to immediately stop (less than 20 steps) with: >>>> >>>> "Steepest Descents converged to machine precision...". >>>> >>>> Further if I take "the 1 core minimized structure" and try to make a >>>> solvated-pr dynamics(2fs, MD, NTP, etc.) it also works with 1 >>>> processor, but with more cores it begins immediately to bring LINCS >>>> warnings: and dies: >>>> >>>> "Too many LINCS warnings" or "Water molecule starting at atom 16221 >>>> can not be settled" >>>> >>>> For a "long time" I had made another md simulations on this cluster >>>> with the same mdps and other proteic systems, and I only see this >>>> behavior with this particular protein, of course before send this >>>> mail I re-tested previuos-working tprs. >>>> Finally, the most suspicious is that I have another very similar >>>> 8-core box (with the same processors) but with gromacs gcc compiled, >>>> and it actually runs very well the same problematic molecule (even the >>>> same tpr) with mpi and 8-cores. >>>> What do you think??? Please, if you have some tpr to test something send >>>> it. >>> >>> I'd guess you're having some problem with (dynamic) linking of the MPI >>> library. Perhaps the version of some library has changed since recently, >>> etc. I'd suggest compiling two fresh copies of GROMACS with either icc >>> and >>> gcc on the troublesome machine and seeing what happens with them. >>> >>> Mark >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface >>> or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
