sarbani chattopadhyay wrote: > hi, > I am using gromacs to run MD simulations using "Intel dual core > machine OSX (version > 10.4.10) ".I downloaded the 'already compiled gromacs package'. Is there > any way to find > whether the simulation process makes optimum usage of the 2 processors.
Hi Sarbani, I assume you have the MPI version of Gromacs. You could for example run a 1000-step simulation on 1 CPU and afterwards on 2 CPUs. Gromacs prints performance numbers at the end of the md0.log file. You could then divide the ns/day value of your 2 CPU run by two times that value of the 1 CPU run and receive a measure for the scaling, which should not be much lower than 1.00 on a dual or quad core machine. Use longer runs for more reliable numbers. But a 10 minute run or so should suffice. > Is there any command to direct the 'mdrun' that takes the optimum > advantage of the > available processors? You might want to use the -shuffle and -sort options together with setting the number of CPUs by -np in the preprocessor grompp. > We have another machine which has "Xeon Quad Core ,the MAC version being > 10.4.10. > How to run gromacs making optimum usage of the 4 processors? mpirun -np 4 mdrun -s x.tpr Hope that helps, Regards, Carsten -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
