[gmx-users] scaling of replica exchange
lcbllcc at gmail.com
Wed Feb 23 08:33:40 CET 2011
> 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.
> Do you have any idea?
> Thanks in advance
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