[gmx-users] Re: Gromacs - LAM/MPI

Ken Chase math at velocet.ca
Fri Nov 8 22:24:50 CET 2002

On Fri, Nov 08, 2002 at 10:35:19PM +0100, David's all...
> On Fri, 2002-11-08 at 20:53, Paulo F. B. Goncalves wrote:
> > 
> > mpirun -v -c 12 -nger -lamd mdrun_mpi -np 12 -s ${MOL}_em.tpr -o
> > ${MOL}.trr -c ${MOL}.gro -v -g ${MOL}.log
> On normal (fast) ethernet you cannot scale to much more than two nodes
> for such small systems. The reason for this is partially the
> parallellization in gromacs, but mainly because the force calculation is
> so fast relative to the communication. I suggest you use your cluster
> for 8 two processor jobs while we work on imporved gromacs scaling.

If you dont scale well, say at only 30% at 12 nodes, what happens
when you run say 3 lam-mpi meshes instead, to soak up all the extra cpu?
I realise there's interupt time servicing the requests, as well as a
bit more latency from putting lots of data down the link (I saw 8-10
Mbps on fast ethernet on dual 1.33Ghz tbird machines for the d.dppc
benchmark with 4 dual nodes, and 18-25Mbps for the same config with GBE),
but you may end up with a factor of 2 better throughput - assuming you
have more than 1 job to run at a time of course!

Paulo: remember too, scaling is dependant on the ratio of CPU speed to
network, not just the raw network speed. I'd suspect P3-450s would scale
way better on fast ether than a Xeon 2.2Ghz.


> Please post future questions to the gromacs mailing list.
> -- 
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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Ken Chase, math at velocet.ca  *  Velocet Communications Inc.  *  Toronto, CANADA 

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