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

[K.A. Feenstra]

Ken Chase wrote:
> 
[...]
> 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!

I'd rather run three 4-CPU jobs. I'd suggest you run a series of benchmarks
of a few hours to see what would actually give you the best overall 
performance. My guess is, from the scaling behavior of Gromacs, that 
3x12CPU on 12 CPU's would be slower than 3x4CPU on 12 CPU's.

> 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.

Right! 
You could also use e.g. Amber, which scales better than Gromacs, for 
a similar reason: Amber's single CPU performance is about a factor of 
ten lower than Gromacs's!


-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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