[gmx-users] scaling of replica exchange

[Mark Abraham]

On 02/23/11, Fabio Affinito  <f.affinito at cineca.it> wrote:
> Hi Mark,
> I've checked with Valeria and the problem is actually on the setup of
> the system (unfair overlapping of the temperature distribution). So I
> think that the loss of efficiency should be of a factor between 2 or 3
> in her case and not more.
> 

That's going to affect the usefulness of doing replica-exchange, but not the computational performance when doing it. Doing exchanges that never/always succeed makes essentially no difference to the performance.

Mark


> On 02/23/2011 10:31 AM, Mark Abraham wrote:
> > 
> > 
> > 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.
> > 
> > Mark
> > 
> >> Valeria
> >>
> >>
> >>
> >> 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
> >> >
> 
> 
> -- 
> *********************************************
> Fabio Affinito, PhD
> CINECA
> SuperComputing Applications and Innovation Department - SCAI
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