On 02/23/11, Fabio Affinito <[email protected]> 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 * <[email protected]> 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 <[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 > >> > > > > -- > ********************************************* > Fabio Affinito, PhD > CINECA > SuperComputing Applications and Innovation Department - SCAI > Via Magnanelli, 6/3 > 40033 Casalecchio di Reno (Bologna) ITALY > +39/051/6171794 (Phone) > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >
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