On Mon, 16 Feb 2009, Tiago Marques wrote:
I must ask, doesn't anybody on this list run like 16 cores on two nodes well, for a code and job that completes like in a week?
For GROMACS and other MD programs, the way a job runs depends on a lot of factors that define the simulation: the size of the molecular system, the force field in use, the cutoff distances, etc. Furthermore, what you call a job actually contains a very important variable - the number of MD steps, which can make the total runtime go from seconds to months (or more). Asking for someone who runs in the same conditions as you probably means that he/she has already done the simulations you are about to begin, meaning from a scientific point of view that you would better invest your time in something else as he/she would publish first ;-)
I have found several MD codes to scale rather poorly when used on clusters composed of 8-core nodes, especially when those 8 cores are coming from 2 quad-core Intel CPUs; the poor scaling was also with InfiniBand (Mellanox ConnectX), so IB will not magically solve your problems. The setup that seemed to me like a good compromise was with 4-core nodes, when these 4 cores come from 2 dual-core CPUs, associated with Myrinet or IB.
You have to understand that, the way most MD programs are done this days, the MD simulations of small molecular systems are simply not going to scale, the communication dominates the total runtime. Communication through shared memory is still the best way to scale such a job, so having a node with as many cores a possible and running a job to use all of them is probably going to give you the best performance.
-- Bogdan Costescu IWR, University of Heidelberg, INF 368, D-69120 Heidelberg, Germany Phone: +49 6221 54 8240, Fax: +49 6221 54 8850 E-mail: bogdan.coste...@iwr.uni-heidelberg.de _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
