[gmx-users] Clovertown vs Woodcrest gromacs experiences?

Erik Lindahl lindahl at cbr.su.se
Fri Aug 24 09:56:32 CEST 2007


Quad-core is the way to go. I recently benchmarked the scaling of the  
CVS version, and with 8 independent jobs we get 85-97% throughput  
scaling, depending on the type of simulation. And you get essentially  
the same performance if you run two jobs using 4 cores each.

Even for a single simulation parallelizing over all 8 cores (lots of  
communication), the scaling is 70-90% with CVS.

However, unless you're in a rush you might want to wait until  
November when Intel is rumored to ship Harpertown (Penryn quad-core)  
with more cache, higher frequencies, and lower price. AMD will also  
release Barcelona (true quad-cores) in September, with higher  
frequencies expected in october/november.



On Aug 24, 2007, at 12:53 AM, Alan Chen wrote:

> If anyone has some gromacs benchmarks numbers they'd be willing to  
> share from clovertown
> quad cores. ..  we're having to decide between buying 3.0 ghz DPDC  
> woodcrest nodes (which
> we already have several of and are quite happy with) vs 2.66 ghz DP/ 
> QC clovertowns for the same price.
> I haven't seen any clovertown results in the benchmark page or in  
> past listserv messages. .
> Obviously, we don't  expect the clovertowns to scale perfectly for  
> single jobs due to the architecture, but I'm very
> curious how they do with multiple jobs on the same node - we tend  
> to run lots of independent trajectories of medium
> (~100,000 atom) sized systems in our lab.
> If anyone can share their experiences with gromacs on clovertown  
> XEON systems it would be greatly appreciated!
> Thanks!
> Alan Chen

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