Indeed, gromacs (non-mpi) will use all the resources available. If you do not want that you can control de number of threads created with the -nt option of mdrun.
regards Felipe ----Mensaje original---- De: [email protected] Fecha: 18-ago-2011 19:26 Para: "Discussion list for GROMACS users"<[email protected]> Asunto: Re: [gmx-users] more than 100% CPU I believe that the current version of GROMACS supports threading, which does not require mpi. So mdrun is running threads at 100% of the activity of each of your 16 nodes, hence 1600%. Warren Gallin On 2011-08-18, at 5:19 PM, Park, Jae Hyun nmn wrote: > Hi GMX users, > > I installed GMX 4.5.3 recently. > But, when I just execute mdrun (without mpi, I did not installed mpi-version > of mdrun), the use of CPU appears more than 100% (?top? command in LINUX). > How is it possible? > For example, I am using 16-node machine. And if I simply run ?mdrun?, then > use of CPU is 1600%!!. > The simulation runs well and the results looks reasonable. > Is there anybody who can teach me what is happening? I would deeply > appreciate. > > Best, > Jae H. Park > > ======================= > Jae Hyun Park, Ph. D. > Physics Division > Oak Ridge National Laboratory > PO. Box 2008, MS-6372 > Oak Ridge, TN 37831 > Phone (865) 241-1482 > E-mail [email protected] > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
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