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
Valeria
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