RE: AMBER: MPI is slower than single processor with water

From: Yu Chen <>
Date: Tue, 16 Jan 2007 15:23:23 -0500 (EST)

Hello Dr. Ross Walker;

I am from Dr. Summers' lab. Here is our system details(see below), so it's
the network, just wondering if we upgrade to Gigabit Network, will that be
enough for our current system?

28 nodes cluster, all with dual AMD Athlon MP 1800+ cpus, master node with
3G RAM, all nodes have 1G RAM. All are runing RedHat Enterprise Linux 3.
They all have 100MB NIC interface, one each on all nodes, two on master
node, one for outside, one for the cluster. And the switch is 3Com
10/100MB switch.

So if we just upgrade the network to Gigabit, including switch, will we
see some performance gain? Or should we really looking into Infiniband



On Tue, 16 Jan 2007, Ross Walker wrote:

> Dear Mike,
>> Protein MD and minimization calculations run much faster
>> with MPI than with a single processor, as expected,
>> EXCEPT when I include water (solvateoct with TIP3PBOX).
>> In this case, the calculations actually run a little
>> slower compared to using a single processor.
>> Is this a general problem when performing calculations
>> with many molecules, or have I misset (or have not used) a
>> necessary flag?
> This is a complicated issue that very much depends on your system setup and
> in particular the interconnect between your nodes. First of all if you are
> running GB or periodic PME calculations then you should compile and use
> PMEMD v9 which ships with Amber 9. This has been specifically optimized by
> Bob Duke to run efficiently in parallel.
> Secondly we really need to know more about your system. Not getting any
> speedup over a single processor is unusual. At the very least if you have a
> dual processor machine and you run a 2 processor job you should about a 1.9x
> speedup. The issue comes when communication must move out of the local node.
> If you have a very poor switch (such as a cheap 10GB switch which doesn't
> have a true non-blocking back plane) or even worse a hub at say only 100MBps
> speed then you will be lucky, on modern cpus, to see any speedup. This is
> especially true if you also use that same network for NFS traffic or other
> users of your cluster share it. If your cluster is bigger than a single
> switch such that you have multiple switches chained together and your
> queuing system doesn't ensure switch locality for your jobs then you might
> as well forget it. That said with a gigabit ethernet switch and single
> processor nodes you should at least be able to get to about 4 cpus or so.
> Ideally when building a cluster for running tightly integrated parallel
> calculations such as molecular dynamics you need a decent communication
> network such as myrinet or ideally infiniband. It also helps if you have all
> file system and management traffic routed over a different network to the
> mpi traffic.
> Note the problem is also a function of the speed of the individual cpus.
> Back in the day of 1GHz pentium 3's with a gigabit interconnect you could
> easily scale to between 8 or 16 cpus (depending on system size - typically
> the more atoms in your system the better scaling you get). This is because
> the ratio of compute speed to the interconnect speed was quite good. Now we
> have 3.8GHz machines with SSE2 that can do multiple floating point
> operations per clock cycle but people are still hooking them up with gigabit
> ethernet. Here the cpu is around 10 to 12 times quicker or more but the
> communication speed has remained the same - not good... Even worse they have
> 4 cpus per box and only one gigabit ethernet card which is like having only
> a 250MBps interconnect even before you take into account the extra overhead
> of packet collisions etc.
> So, hopefully the above helps a bit. It would be useful to know what the
> exact specs of your system are as well as the specs of the actual
> calculation you are trying to run and then we might be able to help out some
> more.
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
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Yu Chen
Howard Hughes Medical Institute
Chemistry Building, Rm 182
University of Maryland at Baltimore County
1000 Hilltop Circle
Baltimore, MD 21250

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Received on Wed Jan 17 2007 - 06:08:30 PST
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