David van der Spoel
spoel at xray.bmc.uu.se
Mon Feb 4 11:54:52 CET 2002
On Mon, 4 Feb 2002, Andrea Bernini wrote:
> we are planning to build an 8 nodes cluster computer running
>Linux dedicated to GROMACS MD runs. In your experience, which fast
>ethernet switches (e.g. in terms of low latency) and ethernet adapters
>available on the market are better suitable for this very specific purpose?
Maybe it is useful to check the Beowulf mailing lists (www.beowulf.org)
Gigabit is usually not recommended with Linux, but a good backplane (i.e.
high bandwidth on the switch) could make some difference since in
principle all communication in gromacs happens simultaneously.
If you want to do parallel runs only, it may be worthwhile to in invest in
myrinet or scali (see www.gromacs.org for benchmarks). Otherwise you will
probably get more performace from 4 dual processor machines than 8 single
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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