[Bioclusters] Any issues porting applications to OS X?

Chris Dwan (CCGB) bioclusters@bioinformatics.org
Thu, 25 Mar 2004 11:44:49 -0600 (CST)

> >> On the topic on low latency interconnects, how many of you are running
> >> your
> >> clusters with such interconnets? Especially in the area of
> >> bioinformatics.
> >> We are using quadrics on one IA32 cluster and Myrinet on IA32, IA64
> >> and G5.
> >> With occasional mpi jobs that uses these interconnects, I do not see
> >> other
> >> jobs requiring it.
>  From what I have seen so far, expensive interconnects are not really
> necessary of a large portion of bioinformatics work. Gigabit on copper
> is more than enough for most type of work. We use gigabit on copper for
> connecting execution nodes to the switch and gigabit on fiber for
> connecting NAS to the switch. It saves lots of money and works great.

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.

-Chris Dwan