Hi, Your job scheduler and/or MPI launcher is most likely to blame. The fact that mdrun warns about the logical core (hardware thread) mismatch means that the OpenMP runtime thinks that you should be using one thread per rank. This typically means that the MPI launcher or job scheduler set an affinity mask for each rank and likely mdrun also skipped pinning threads because of this.
This should however alone not cause nodes to be empty, but rather it would cause ranks to overlap and run on the same core. In any case, you should pass the correct ranks/node threads/rank settigns to your launchers; to ensure correct rank placement you'll have to either set up affinities through the scheduler or let mdrun do it. Cheers, -- Szilárd On Fri, Jan 15, 2016 at 9:25 AM, Chunlei ZHANG <chunleizhang....@gmail.com> wrote: > Dear GMX developers and users, > > I have a cluster of 24 nodes, each having two 10-core intel CPUs. > Gromacs 5.1 is compiled by using intel mpi (version 5.1.1) and mkl. > > I can successfully run a simulation by using pure MPI (480 MPI processes). > But the performance is not good and the log file of mdrun suggests using > fewer MPI processes. > I try to launch 240 MPI processes, each using 2 openMP threads, by the > command: > mpirun -ppn 20 -np 240 gmx_mpi mdrun -ntomp 2 > > But only a fraction of the nodes are running mdrun and the log file says: > > Number of logical cores detected (20) does not match the number reported by > OpenMP (1). > Consider setting the launch configuration manually! > > Does anyone know how to solve this problem? > Thanks in advance. > > Best, > Chunlei > -- > 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.