------------------------------
Message: 7
Date: Thu, 14 Sep 2006 09:27:45 +0200
From: "Qiao Baofu" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Re: Question about parallazing Gromacs (Qiao
Baofu)
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
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: [EMAIL PROTECTED]
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