[gmx-users] Parallel Gromacs Benchmarking with Opteron Dual-Core & Gigabit Ethernet

[Erik Lindahl]

Hi,

> I read at Gmx site that the DPPC system
> composed of 121,856 atoms. I saw the gmx topology files, it
> seems that Gmx makes data decomposition on input data to run in  
> parallel
> (in our simulation case using "-np 12" for execution
> on 3 nodes, the data space for every process is about 10156 atoms).
> I think that the DPPC system's size is not so big enough that someone
> can sense the scalability of parallel execution in the existence of
> Gigabit Eth. I mean to see the Cluster scalability in our  
> configuration,
> we should setup a bigger simulation. Pls correct me, if I'm in  
> mistake.

Well, you can always try different systems (genconf + edit topology),  
but the fact that you see low user CPU usage likely means the nodes  
are busy waiting for the communication (which probably counts as  
kernel/system usage).

Remember - compared to the benchmark numbers at www.gromacs.org, your  
bandwidth is 1/4 and the latency 4 times higher, since you have four  
cores sharing a single network connection.

Gromacs 4 should scale better on any hardware (significantly better  
with PME), but you'll probably never see great scaling with only 4- 
way shared gigabit ethernet.  It's available in the head branch of  
CVS for expert users/voluntary guinea-pigs, but entirely unsupported  
until we release it.

Cheers,

Erik