[gmx-users] infiniband question

[David van der Spoel]

Andrei Neamtu wrote:
> Hello gmx,
> 
> I have a question regarding infiniband interconnect: Is
> there any difference (in terms of performance) between integrated
> on-board infiniband (ex. Mellanox) and PCI-Express infiniband adaptors
> (due to pci-e limitations)? Which one is recomended. We are in a
> process of buying a cluster on which gromacs will be the main
> computational engine.
> Any help will be greatly appreciated!
> Thank you,
> Andrei

If you are buying a serious cluster then ask them to let you do 
benchmarks. the PCI bus can be a bottleneck, although the throughput is 
still quite OK. It also depends on how many cores are sharing the 
connection.


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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se