[gmx-users] best cluster for gromacs
Bert de Groot
bgroot at gwdg.de
Thu Aug 21 17:58:00 CEST 2003
we're about to renew our cluster and I'd like to share our thoughts, and
would very much appreciate if you could share your experience/thoughts too.
There have been some posts on this list about this issue, but there have
been some hardware developments since then, so I figured it would make sense
to post once again.
So far we've been very happy with our dual athlons (apart from a few stability
issues), but scaling is not that great, especially with PME. We have a few nodes
with myrinet, but even there most jobs run on maximally 2 dual nodes
(4 processors), because beyond that the scaling simply breaks. We've also
played with gigabit ethernet and the M-VIA protocol, but these only yield
marginal improvements, especially on the faster nodes.
Some points that we considered are:
-the latest generation of SCALI cards seem to have a quite promising
price/performance ratio. Does anyone have recent experience with SCALI?
-what about quad Xeon boards?
-any alternative to scali or myrinet for improved low latency networking?
-can we expect developments in gromacs in the near future that will
reduce the network load/improve scaling? (I don't want to push the developers
here, they're doing a splendid job. It's only to optimise the planning).
Dr. Bert de Groot
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany
tel: +49-551-2011306, fax: +49-551-2011089
email: bgroot at gwdg.de
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