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.
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. Also, for the information, mdrum_mpi or mdrun with relevant options shows NNODES=1. why? Thanks, Manik On Thu, Dec 18, 2008 at 1:24 PM, Jussi Lehtola <[email protected]>wrote: > On Thu, 2008-12-18 at 01:03 +0530, Chitrita Dutta Roy wrote: > > Can anyone give me a detailed notes on how to install gromacs 4 with > > mpi feature..I am using Intel Q9300 and fedora 10.It's very urgent as > > i am new to using gromacs plz give me as detailed note as possible.. > > Just install using yum: > > # yum -y install gromacs gromacs-mpi > > Due to some clashing names, all binaries have been renamed to start with > g_, i.e. mdrun is g_mdrun and so on. Everything is compiled both in > single and double precision, and MPI binaries are available of mdrun > (and once the Makefiles are updated I'll put in also the MPI enabled > analysis tools). > > Example: > g_mdrun single precision > g_mdrun_d double precision > g_mdrun_mpi single precision MPI > g_mdrun_mpi_d double precision MPI > -- > ------------------------------------------------------ > Jussi Lehtola, FM, Tohtorikoulutettava > Fysiikan laitos, Helsingin Yliopisto > [email protected], p. 191 50632 > ------------------------------------------------------ > Mr. Jussi Lehtola, M. Sc., Doctoral Student > Department of Physics, University of Helsinki, Finland > [email protected] > ------------------------------------------------------ > > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- _________________ HAPAX LEGOMENA
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