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Re: Gbit or Firewire 800

With all fairness, we should add the Infiniband solution that VaTech used to the mix. However, the Infiniband solution will be expensive relative to the Gbit Ethernet. Considering the bio-informatics related number crunching and statistical computations that you'll be running (which generally is "embarassingly" parallel, i.e. the tasks assigned to each worker process/processor communicates very little with the other worker processes/processors), the Gbit Ethernet will be the most cost effective by far.

The main difference between the Gbit E-net and Infiniband is not as much the raw communication bandwidth as the pre-communication overhead latency. In the case of the Gbit E-net, this pre-communication overhead latency is dominated by the time it takes traversing through the E-net communication software stack to send and receive messages. The top selling point for technologies like Infiniband and MyriComm's Myrinet is much lower pre-communication overhead latency, which is a huge win in parallel applications in which the each worker process/processor communicates a lot with the other worker processes/processors. (A few example applications that have high inter-worker communication rates are computational fluid dynamics, weather prediction simulations, parallel digital signal processing, nuclear blast simulations, etc.)

In most parallel/distributed bioinformatic application, the application communicates relatively infrequently (as compared to the above examples), so it can absorb higher pre-communication overhead latencies. I agree with the others: go with the Gbit Ethernet.

-Albert


At 11:10 AM -0400 7/28/04, Michael Caplinger wrote:
If I could invest into a Workgroup Cluster from Apple, my first dilemma would be what interconnection to use. Should I connect all the nodes to a Gbit Ethernet switch using the 2 built in Gbit interface or use the the two 800 Mbit/s Firewire connection to daisy chain them or to connect them to a Firewire Hub ? The cluster would have minimum 12 nodes and do mostly bio-informatics related number crunching and statistical computation.

Go with the gigabit, it will be switched and the firewire would be shared bandwidth.

Mike Caplinger
System Administrator
Dept of Physics and Astronomy
University of Georgia
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References: 
 >Gbit or Firewire 800 (From: János <email@hidden>)
 >Re: Gbit or Firewire 800 (From: Sterling Anderson <email@hidden>)
 >Re: Gbit or Firewire 800 (From: Michael Caplinger <email@hidden>)



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