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

[Carsten Kutzner]

Hi Vivek,

if you use separate PME nodes (-npme) then one group of the processors  
will calculate the long-range (reciprocal space) part while the  
remaining processors do the short-range (direct space) part of the  
Coulomb forces. The goal is to choose the number of nodes in both  
groups such that the LR calculation takes the same amount of time as  
the SR calculation - otherwise one of the groups just does nothing for  
part of the time step.

Also it is advisable not to have too many nodes in the LR group - a  
quarter or a third is a good number as  pointed out by Justin and  
Berk. This you can achieve by shifting work between LR and SR part by  
enlarging the grid spacing and at the same time enlarging the Coulomb  
radius.

Carsten

On Nov 11, 2008, at 12:06 PM, vivek sharma wrote:

> Hi Carsten,
> I have also tried scaling gromacs for a number of nodes ....but was  
> not able to optimize it beyond 20 processor..on 20 nodes i.e. 1  
> processor per node..
> I am not getting the point of optimizing PME for the number of  
> nodes, is it like we can change the parameters for PME for MDS or  
> using some other coulomb type for the same, please explain.
> and suggest me the way to do it.
>
> With Thanks,
> Vivek
>
> 2008/11/10 Carsten Kutzner <ckutzne at gwdg.de>
> Hi,
>
> 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  
> networks",
> http://www3.interscience.wiley.com/journal/114205207/abstract?CRETRY=1&SRETRY=0
> 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.
>
> Carsten
>
>
> 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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