[gmx-users] scaling of replica exchange

Valeria Losasso losasso at sissa.it
Wed Feb 23 07:51:19 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

Do you have any idea?
Thanks in advance


More information about the gromacs.org_gmx-users mailing list