[gmx-users] scaling of replica exchange

[Luca]

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