[gmx-users] Question about parallazing Gromacs

Milan Melichercik melicher at cray.dbp.fmph.uniba.sk
Wed Sep 13 13:10:14 CEST 2006

Dňa St 13. September 2006 12:42 Qiao Baofu napísal:
> Hi all,
> I have a question about parallazing gromacs: I run the same system on a
> cluster of my institute and my local computer,
>      Cluster:* *dual processor boards AMD Opteron 270 (Dual-Core), 2.0 GHz
>      Local computer: AMD X86-64 Cpu, double precision
> 1. The cluster (nodes=3:ppn=4) runs  87950 MD steps  for one hour
> 2. The cluster (nodes=5:ppn=4) runs  42749 MD  steps  for one hour
> 3. The cluster (nodes=11:ppn=4) runs  5962 MD  steps  for one hour
> 3. My local computer runs  179090 MD steps  For 1hour 51 mintues.
> It is verry strange that the more cpus I use, the slowest the gromacs
> runs.!!
> Who knows what's wrong with my job?   And for paralleled gromacs, how many
> cpus is prefered?

As far as I know, the problem isn't your job but the interconnet between 
nodes, cause MD (and many other paralel computations) are very sensitive to 
the interconnect (network) bandwith and even more to the latencies - the 
processes need to transfer large amount of data to  the other nodes and till 
the other nodes don't have them, they cannot compute. The other problem can 
be related with the congestion of the network, so the switch (or generally 
network) isn't able to transfer so large amount of data and throw away some 
of them...
So (in the extreme case of the very slow net) you will have the fastest system 
by using only one node (and all of available CPU cores on it). I can't give 
you more specific answer cause I don't know your cluster. But the best 
result, I think, you can have simply by try the job on 1, 2, 3, etc. nodes...

Milan Melichercik

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