Hi Valeria, > Dear all, > I am making some tests to start using replica exchange molecular dynamics > on my system in water. The setup is ok (i.e. one replica alone runs > correctly), but I am not able to parallelize the REMD. Details follow: > > - the test is on 8 temperatures, so 8 replicas > - Gromacs version 4.5.3 > - One replica alone, in 30 minutes with 256 processors, makes 52500 steps. > 8 replicas with 256x8 = 2048 processors, make 300 (!!) steps each = 2400 > in total (I arrived to these numbers just to see some update of the log > file: since I am running on a big cluster, I can not use more than half an > hour for tests with less than 512 processors) > - I am using mpirun with options -np 256 -s md_.tpr -multi 8 -replex 1000 I think that with this option you are using 256/8=32 cpu for each replica. If you want use 256 for each replica you cna try set up -np option equal to 256x8 = 2048.
Luca > > Do you have any idea? > Thanks in advance > > Valeria -- 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
