On Thu, 2008-12-18 at 21:23 +0530, Manik Mayur wrote: > I am not sure that mdrun_mpi or for that matter mdrun with options -np > 2 -multi 1 (I have a core 2 duo machine) is actually running the > process parallely, as the estimated time for completion for a > simulation is the same as without.
You don't need to supply the -np option to mdrun or grompp anymore, just run with mpirun -np 2 g_mdrun_mpi (options) > I have built open-mpi library, so do I have to make some changes at > its configuration level(even if I am using single machine with > multiple core processor)? Like adding localhost and the no. of nodes. > If yes, then can anybody help me with that. Are you using some other compiler than gcc? If not, there's no need to build anything yourself, just use the distribution provided versions. If you're running on a single node, you don't have to do anything, just run the MPI binary with mdrun. > Also, for the information, mdrum_mpi or mdrun with relevant options > shows NNODES=1. why? Because if you aren't running with mpirun -np the binary runs with only one core. And if you run a non-mpi binary with mpirun -np, you end up starting multiple copies of the simulation instead of a distributed one. -- ------------------------------------------------------ Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 ------------------------------------------------------ Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi ------------------------------------------------------ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
