[gmx-users] Re: Re: Re: Question about parallazing Gromacs

[Qiao Baofu]

Thanks a lot!

2006/9/14, Cesar Araujo <cesar.araujo at oulu.fi>:
>
>
> > ------------------------------
> >
> > Message: 7
> > Date: Thu, 14 Sep 2006 09:27:45 +0200
> > From: "Qiao Baofu" <qiaobf at gmail.com>
> > Subject: Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao
> > Baofu)
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Message-ID:
> > <6a91f07b0609140027u68ac3085tb01120f19b854545 at mail.gmail.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi,
> >
> > Thanks. I have test different cpus. Our institute has two clusters: one
> is
> > each node has 4 cpu (A), one is one node has only 1 cpu (B).   I made
> > different tests on the two clusters and my local computer using the same
> > system. See the following result:
> >
> > A     (For 1 hour)
> >    # of cpus   ;    MD steps
> >      4             finished (200000steps for 26:21)
> >      8             finished (200000steps for 40:57)
> >     12             87950
> >     20             42749
> >     44             5962   !!!!!
> > B   (For 1 hour)
> >     # of cpu           ; MD steps
> >       1                156991  for 56:12
> >       2                179820
> >       3                200,000 for 54:20
> >       4                200,000 for 51:12
> > c. Local(single cpu), 200000 steps  For 1h52:38
> >
> > One can see that
> > 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local
> > computer.
> > 2. More than one nodes will decrease the performancs the gromacs,
> > 3. On cluster B, the more cpu used, the faster gromacs runs. But the
> > difference of speed is not apparent.
> > 4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node
> (4
> > cpus)
> >
> > I wonder if anyone can tell the bottlenack: the hardware on the cluster
> or
> > gromacs?
> >
> >
>
> Well, probably it is a combination of bottlenecks in both software and
> hardware.
> Both of them should be optimized to guarantee the best performance. From
> the
> hardware side the delays in inter-node communication across the network
> can
> be the reason. But also, it can be related with software issues related to
> the operating
> system and network configuration. I think that the first thing to do is
> work
> in cluster
> setup to achieve the best performance for your hardware configuration.
>
> In addition, take into account that inter-node communication between two
> CPU's
> inside the same machine should be faster than between two CPU's across the
> network.
>
> >From the software side (Gromacs) the algorithms should be optimized with
> regard
> to the parallel programming model. David said in a previous answer that
> they
> have detected some problems in the software implementation and they are
> working
> to solve that issue in the next version of Gromacs.
>
> Regards,
> -----------------------------------------------------------
> Cesar Araujo, Lic. of Chemistry
> Department of Molecular Endocrynology
> Oulu University Hospital
> FIN-90029 OYS, OULU, FINLAND
>
> phone: +358 8 3155632
> e-mail: cesar.araujo at oulu.fi
>
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-- 
Sincerely yours,
**********************************************
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**********************************************
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