[Beowulf] Southampton's RPi cluster is cool but too many cables?

Ellis H. Wilson III ellis at cse.psu.edu
Tue Sep 25 08:26:05 PDT 2012


On 09/25/2012 11:17 AM, Prentice Bisbal wrote:
> Where did you get that data-point from? I've been told a single genome
> sequence takes up about 6 GB of data, and I think that's after it's been
> processed.
>
> According to this article,  raw sequence can take up between 2-30 TB,
> and a processed one 1.5 GB. (Disclaimer: I only read the executive summary)

At 2TB and a 6 hour lifespan for this thing to pull in the genome, 
you're talking about around 90MB/s to process, and at 30TB now we're 
talking about near to 1.4GB/s to process.  Since it states that the 
laptop is doing the processing of the genome, I have serious doubts that 
this thing could a) do the processing fast enough to boil the data down, 
b) offload the data fast enough via USB or whatever it's connected with 
(even gigabit ethernet is only barely fast enough) or c) have 2-30TB of 
storage inside of it ;D.

So even ignoring where the data points come from or the reality of the 
size of a genome, I'm upper-bounding the data it actually pulls in to 
something at most at like 500GB.  And that's still probably too optimistic.

Very interested to hear more about the specifics of this thing, if 
anyone can find a solid number on it.

Best,

ellis


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