Hi, On Jan 17, 2011, at 4:11 PM, Arnau Cordomi wrote:
> Dear Gromacs Users, > > We normally run gromacs 4.0.x mdrun with OpenMPI in a 24 core > shared-memory server (SunFire X4450). > i. e. the command we use for a 12 core run is : mpirun -np 12 mdrun -v > -c output_md.gro > This is working great so far. > > Now we are trying to use gromacs 4.5.x and I found this on the > release notes > (http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x) > : > > “Running on a multi-core node now uses thread-based parallelization to > automatically spawn the optimum number of threads in the default > build. MPI is now only required for parallelization over the network.” > > So, I guess now instead of “mpirun -np 12 mdrun -v -c output_md.gro” > we should use “mdrun -nt 12 -v -c output_md.gro” and expect the same > performance. Am I right? Right. > > Also, is this “automatically spawn the optimum number of threads” > reliable ? Does that mean that if the recommended number is 4 cores > (threads) there’s no way to make it run faster even if specifying -nt > 12 or 24 ? You should use the number of logical cores you have. This is normally the number of physical cores, unless you use some kind of hyperthreading or simultaneous multiprocessing in which case -nt is twice the number of physical cores. mdrun reads the number of threads from your system via sysconf(). Carsten > > Any advice will be welcome. > Thanks in advance. > > Best Regards, > Arnau > > Cordomí > -- > 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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
