[gmx-users] Gromacs 4 Scaling Benchmarks...

Carsten Kutzner ckutzne at gwdg.de
Mon Nov 10 13:44:26 CET 2008


most likely the Ethernet is the problem here. I compiled some numbers  
for the DPPC
benchmark in the paper "Speeding up parallel GROMACS on high-latency  
which are for version 3.3, but PME will behave similarly. If you did  
not already use
separate PME nodes, this is worth a try, since on Ethernet the  
performance will drastically
depend on the number of nodes involved in the FFT. I also have a tool  
which finds the
optimal PME settings for a given number of nodes, by varying the  
number of PME nodes
and the fourier grid settings. I can send it to you if you want.


On Nov 9, 2008, at 10:30 PM, Yawar JQ wrote:

> I was wondering if anyone could comment on these benchmark results  
> for the d.dppc benchmark?
> Nodes	Cutoff (ns/day)	PME (ns/day)
> 4	1.331	0.797
> 8	2.564	1.497
> 16	4.5	1.92
> 32	8.308	0.575
> 64	13.5	0.275
> 128	20.093	-
> 192	21.6	-
> It seems to scale relatively well up to 32-64 nodes without PME.  
> This seems slightly better than the benchmark results for Gromacs 3  
> on www.gromacs.org.
> Can someone comment on the magnitude of the performance hit and lack  
> of scaling with PME is worrying me.
> For the PME runs, I set rlist,rvdw,rouloumb=1.2 and the rest set to  
> the defaults. I can try it with some other settings, larger spacing  
> for the grid, but I'm not sure how much more that would help. Is  
> there a more standardized system I should use for testing PME scaling?
> This is with GNU compilers and parallelization with OpenMPI 1.2. I'm  
> not sure what we're using for the FFTW The compute nodes are Dell  
> m600 blades w/ 16GB of RAM and dual quad core Intel Xeon 3GHz  
> processors. I believe it's all ethernet interconnects.
> Thanks,
> YQ
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