AMBER Archive (2004)

Subject: RE: AMBER: Problems with CPU scaling on cluster

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jul 15 2004 - 13:48:15 CDT

Dear Jacob,

> Thanks a LOT for your in-depth answer. I'll forward this to one of the
>cluster admins, and try running the jac benchmarks on various numbers of
>CPUs. As for the setup of the cluster it can be seen here:

> http://www.dcsc.sdu.dk/overview.php

>(we are using the new part of the cluster)

> Are there any obvious bottlenecks there with regards to amber you can
spot?

I suspect this is your problem:

6x up to 36-port gigabit ethernet switch

Depending on how those 6 switches are interlinked you could have a serious
bottle neck here. See if you can find out how they have configured these
switches, do they have a full speed backblane connecting all the switches or
have they just chained them together with gigabit? The problem comes if you
have say 8 cpus on one switch and 8 on another. If the switches do not have
a non blocking connection between them then you will have the equivalent of
a single 1Gbit link serving 8 machines...

One option would be to speak to the admins that control the queue system on
your cluster and see if they can configure it to guarantee that the 16 cpus
you are allocated for your job are all connected to the same switch, this
may improve things since you will not then be communicating over the, most
likely heavily contended, connections between the switches.

I hope this helps.
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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