Re: NAMD speed on MPICH2 Ubuntu 64 bit Cluster

From: Robert McCarrick (rob.mccarrick_at_muohio.edu)
Date: Thu Apr 07 2011 - 09:06:03 CDT

Hi Everyone,
Again, thanks for all of the useful comments. Interestingly, I tried
the NAMD-2.8b-x86_64 version (i.e. not the multicore or TCP versions)
and it seems to be performing more like expected. I always assumed
that there wouldn't be perfect scaling across the computers, but it
seemed weird to me that it was 2 times slower running on all 24 nodes
compared to just 6 on one computer. With the regular version of NAMD,
running across all four computers, it is twice as fast as running on
just one, which seems more reasonable. Perhaps I'm not calling the
multicore and TCP versions properly (I still have a lot to learn about
the software). Anyway, I will be taking all of your suggestions and
seeing what I can do to get it running as fast as possible. As of right
now, it looks like it's on the order of 20 times faster than the desktop
that they were using to run the simulations before, which is not too bad
for $2800 and a couple of days to get it up and running.
Rob

On Wed, 2011-04-06 at 18:01 -0400, Jim Phillips wrote:

> Hi Robert,
>
> What kind of switch are the nodes connected to? Any modestly priced
> unmanaged gigabit switch will easily beat your building network. Make
> sure the cards are actually connecting at gigabit speed and use netperf to
> be sure you're getting decent bandwidth.
>
> MPI will likely be slower than direct TCP or UDP (non-TCP). The default
> UDP network layer is now optimized for gigabit so TCP isn't necessarily
> faster any more and you should test both (which is why I keep them both).
>
> Try leaving one core idle per node to reduce OS interference. It's also
> good to benchmark one or two cores per node to see if you can scale across
> nodes at all.
>
> -Jim
>
>
> On Wed, 6 Apr 2011, Robert McCarrick wrote:
>
> > Axel,
> > Thanks so much for the reply. That's disappointing as this was just a
> > $2,800 build to speed up some calculations for one of the lab's here at
> > Miami (this is not my area at all, I just happen to be good with Linux).
> > In looking at the infiniband hardware, it would be about about triple
> > the cost of the cluster itself.
> >
> > What I will probably end up doing is writing my own little queuing
> > script that will take advantage of the fact that each computer is pretty
> > darn fast and the cluster could still run through a series of
> > experiments distributing the individual jobs to run on one of the
> > computers themselves using the 6 cores and the multicore optimized
> > version of NAMD. That way it will not have been a complete waste of
> > time money.
> > Rob
> >
> > On Wed, 2011-04-06 at 13:06 -0400, Axel Kohlmeyer wrote:
> >
> >>
> >>
> >> On Wed, Apr 6, 2011 at 12:19 PM, Robert McCarrick
> >> <rob.mccarrick_at_muohio.edu> wrote:
> >>
> >> Hi Everyone,
> >> Just to give more information on this. If I use the following
> >> command (with the TCP optimized version of NAMD for x86_64
> >> Linux):
> >>
> >> ./charmrun namd2 +p6 <configuration_file>
> >>
> >> I get a time of 0.0290901 s/step and I get 6 processes running
> >> on the main computer with a system load of 1.32. If I use the
> >> following command:
> >>
> >> ./charmrun namd2 +p24 <configuration_file>
> >>
> >> I get a time of 0.0497453 s/step and I get 6 processes on each
> >> of the four computers, but the system load on the main
> >> computer on which I executed the command has a load of 0.53
> >> and each of the other three computers have loads of about
> >> 0.01, indicating that they aren't really doing much of
> >> anything even though they have 6 namd processes running. I
> >> have a nodelist file and all of the computers can SSH to each
> >> other without a password. The directory in which the NAMD and
> >> configuration files are contained is mirrored on the other
> >> three computers via NFS (all of the user UIDs and GIDs and
> >> permissions are carrying over fine). I've been searching
> >> online and haven't found any way to address this. As
> >> mentioned in the previous email, I also compiled the
> >> mpi-Linux-x86_64 version and it doesn't seem to help the
> >> problem. Any help would be greatly appreciated.
> >>
> >>
> >>
> >>
> >> rob,
> >>
> >>
> >> TCP/IP networking doesn't give you great scaling, because of the high
> >> latencies.
> >> classical MD is quite sensitive to that, since you need to communicate
> >> multiple
> >> times in each time step and the computing effort for each step is
> >> rather small.
> >>
> >>
> >> now NAMD can do _some_ latency hiding, and thus does much better over
> >> TCP/IP than most other codes that i know. nevertheless, with 6 cores
> >> per node,
> >> you are really pushing the limit. you may benefit from the multi-core
> >> version
> >> that is now provided with version 2.8b1, as that will limit the
> >> communication
> >> to one task (instead of 6 tasks fighting for access to the network).
> >>
> >>
> >> if you really want good performance, you need to consider buying a
> >> fast
> >> low-latency interconnect. there are several of them with different
> >> properties
> >> and costs associated. the most popular currently seems to be
> >> infiniband,
> >> which seems to be a good match. i am seeing very good scaling behavior
> >> of NAMD (or rather charm++) using the IBVERBS library interface.
> >>
> >> cheers,
> >> axel.
> >>
> >>
> >>
> >> Thanks,
> >> Rob
> >>
> >>
> >>
> >> On Tue, 2011-04-05 at 14:51 -0400, Robert McCarrick wrote:
> >>
> >> > Hi Everyone,
> >> > I'm new to the cluster computer world. I've built a
> >> > four-computer cluster, each with a 6-core AMD Phenom
> >> > processor running Ubuntu Server 10.10 64 bit. I've tried
> >> > both the TCP optimized version on NAMD and compiling from
> >> > scratch with the mpi-Linux-X86_64 build of Charm. In all
> >> > cases, I'm getting about a 4-fold reduction in calculation
> >> > times when I run the job utilizing all four computers (i.e.
> >> > going from +p6 to +p24 causes a big slowdown). This seems
> >> > odd and I was wondering if anyone had any suggestions as to
> >> > where I might have gone wrong.
> >> > Rob
> >> > --
> >> > Robert M. McCarrick, Ph.D.
> >> > EPR Instrumentation Specialist
> >> > Department of Chemistry and Biochemistry
> >> > Miami University
> >> > 701 E. High Street
> >> > 101 Hughes Laboratories
> >> > Oxford, OH 45056
> >> > 513.529.0507 CW Room
> >> > 513.529.6829 Pulse Room
> >> > 513.529.5715 fax
> >> > rob.mccarrick_at_muohio.edu
> >> > http://epr.muohio.edu
> >>
> >>
> >> --
> >> Robert M. McCarrick, Ph.D.
> >> EPR Instrumentation Specialist
> >> Department of Chemistry and Biochemistry
> >> Miami University
> >> 701 E. High Street
> >> 101 Hughes Laboratories
> >> Oxford, OH 45056
> >> 513.529.0507 CW Room
> >> 513.529.6829 Pulse Room
> >> 513.529.5715 fax
> >> rob.mccarrick_at_muohio.edu
> >> http://epr.muohio.edu
> >>
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer
> >> akohlmey_at_gmail.com http://goo.gl/1wk0
> >>
> >> Institute for Computational Molecular Science
> >> Temple University, Philadelphia PA, USA.
> >
> >
> > --
> > Robert M. McCarrick, Ph.D.
> > EPR Instrumentation Specialist
> > Department of Chemistry and Biochemistry
> > Miami University
> > 701 E. High Street
> > 101 Hughes Laboratories
> > Oxford, OH 45056
> > 513.529.0507 CW Room
> > 513.529.6829 Pulse Room
> > 513.529.5715 fax
> > rob.mccarrick_at_muohio.edu
> > http://epr.muohio.edu
> >
> >

-- 
Robert M. McCarrick, Ph.D.
EPR Instrumentation Specialist
Department of Chemistry and Biochemistry
Miami University
701 E. High Street
101 Hughes Laboratories
Oxford, OH 45056
513.529.0507 CW Room
513.529.6829 Pulse Room
513.529.5715 fax
rob.mccarrick_at_muohio.edu
http://epr.muohio.edu

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