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.
Valeria On Wed, 23 Feb 2011, Mark Abraham wrote:
On 02/23/11, Valeria Losasso <[email protected]> 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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