[gmx-users] scaling of replica exchange

Valeria Losasso losasso at sissa.it
Wed Feb 23 09:02:29 CET 2011

Thank you Mark. I found one message of this month concerning this topic, 
and there are some small suggestions. I don't think that such a changes 
can restore a factor of 26, but it could be worth to try to see what 
happens. I will let you know.


On Wed, 23 Feb 2011, Mark Abraham wrote:

> On 02/23/11, Valeria Losasso <losasso at sissa.it> wrote:
>       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
> There have been two threads on this topic in the last month or so, please check the archives. The implementation of
> multi-simulations scales poorly. The scaling of replica-exchange itself is not great either. I have a working version under
> final development that scales much better. Watch this space.
> Mark

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