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. Thanks Daniel Silva _______________________________________________ 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
