From: Robert McCarrick (rob.mccarrick_at_muohio.edu)
Date: Wed Apr 06 2011 - 11:19:16 CDT
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.
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
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