[gmx-users] scaling of replica exchange
mark.abraham at anu.edu.au
Wed Feb 23 10:31:00 CET 2011
On 02/23/11, Valeria Losasso <losasso at sissa.it> wrote:
> 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.
They won't. The problem is that every 10 (or so) MD steps every processor does global communication to check nothing's gone wrong. That resulted from some unrelated bits of code trying to share the same machinery for efficiency, and treading on each others' toes.
> 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.
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