Hi, I see degrading scaling when going from 96 to 192 cores on a cray for my system. I have periodic molecules and do umbrella sampling (with small deviations from the reference) which might affect the performance. My code is based on 4.5.5 without performance-critical modifications.
Erik 9 nov 2012 kl. 03.06 skrev Szilárd Páll: > 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 ----------------------------------------------- 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
