It means you are running a lot of parallel processes, but that does not translate into a linear increase in speed. So faster, but not 16X.
Warren Gallin On 2011-08-18, at 5:36 PM, Park, Jae Hyun nmn wrote: > Thank you, Warren. > Does that mean 16 times faster ? > > Jae H. Park > > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On > Behalf Of Warren Gallin > Sent: Thursday, August 18, 2011 7:26 PM > To: Discussion list for GROMACS users > Subject: 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 pa...@ornl.gov >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> hxxp://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> hxxp://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 gmx-users-requ...@gromacs.org. >> Can't post? Read hxxp://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > hxxp://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > hxxp://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 gmx-users-requ...@gromacs.org. > Can't post? Read hxxp://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
