Hi, With a fast network like Cray's you can easily get to 400-500 atoms/core core with 4.5 (that's 400+ cores for your system), perhaps even further. With 4.6 this improves quite a bit (up to 2-3x).
-- Szilárd On Wed, Nov 7, 2012 at 5:19 PM, Erik Marklund <[email protected]> wrote: > Hi, > > Sure you can go beyond 24 cores. I'm currently simulating ~170 000 atoms > on 192 cores at ~45 ns a day. with half the number of processors I get ~27 > ns a day. It will of course depend on the hardware, particular algorithms, > run parameters, and on the system details. > > Erik > > 7 nov 2012 kl. 16.51 skrev Marcelo Depolo: > > > Good afternoon, > > > > > > I wonder if anyone has experience running Gromacs in MPI. I'm > paralleling the > > processes and want to know how many processors reduces the computation > time to > > the minimum. I am currently using 24 processors for a system of 170 000 > > atoms and obtaining a simulation of 50ns in 15 days. There's a way to > > reduce more this computational time? > > > > Thanks in advance! > > -- > > Marcelo Depólo Polêto > > Departamento de Bioquímica e Biologia Molecular > > Universidade Federal de Viçosa - UFV > > *Website: http://opensourcebioinformatics.com/site/* > > -- > > 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 > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > [email protected] > http://www2.icm.uu.se/molbio/elflab/index.html > > -- > 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
