[Bioclusters] Any issues porting applications to OS X?

Dr Malay K Basu bioclusters@bioinformatics.org
Thu, 25 Mar 2004 14:10:04 -0500

On Thu, 2004-03-25 at 12:44, Chris Dwan (CCGB) wrote:

> The question is one of latency.  If your data motion tends to come in
> large bursts (get the blast target, write the output) then a little delay
> at the beginning of each transmission won't hurt too much.  Gigabit is
> fine.  Heck, some poor university folks get by mostly with 100 base-T.  :)
> If, on the other hand, your process needs to communicate small amounts of
> data, frequently (this particle moved out of my cell in the simulation,
> someone else better pick it up and send me an "ack") those litle hits for
> setting up a transmission will really add up.
> For the sequence based work with which I usually help out, I would almost
> always rather have the additional nodes.  That opinion will change as soon
> as I have to deal with any truly parallel, message passing jobs.

Question is it really necessary. Sure it will give you higher position
in top 500 list, but the price/performance ration IMHO is not worth
going in that direction. As someone already pointed out SGI Altrix is
cheaper than the home-brewed low-latency interconnect. For
bioinformatics is sure copper/fiber base networking is more than enough
(for sequence analysis it goes without saying). Real-time analysis
ofcourse will benefit from such low-latency interconnect. And
copper/fiber based networking has come a long way.