[Bioclusters] General question on time consuming problems

Ian Korf iankorf at mac.com
Wed Apr 20 15:26:55 EDT 2005

Oh, harsh! The way I see it, inefficient coding creates jobs. If the 
"biologists" started writing space-efficient and time-efficient code, 
there would be no need for anyone on this list. Don't bite the hand 
that feeds :)

As for the question that Joe posed, I see a split between CPU-intensive 
and IO-intensive tasks. Neither CPU-intensive nor IO-intensive tasks 
are going away any time soon. I agree with Tim that the IO ones are 
harder to solve.


On Apr 20, 2005, at 7:27 AM, Tim Cutts wrote:

> On 20 Apr 2005, at 2:25 pm, Joe Landman wrote:
>> Hi folks:
>>  Are computational bottlenecks the major problem you are running into 
>> today?   What do you see in the future in terms of rate limiting 
>> efforts?  If you had an "infinitely fast" cluster (like a blue-gene 
>> from IBM), how would like impact your work/processes?
> The major bottlenecks are based around IO.  We have plenty of CPU 
> grunt.
> Scalable databases and parallel filesystems are what we need to sort 
> out now.  It's no use having infinite amounts of CPU power if you have 
> to force all the output through a very tiny pipe.
> A lot of this can be solved by programming expertise, but most 
> scientists aren't interested in coding for scalability, they're only 
> interested in quickly producing something which produces "the right 
> answer", whatever that means.
> Having scalable filesystems and databases would allow them to carry on 
> coding in their current less-than-perfect ways and still maintain some 
> half-decent performance.
> Tim
> -- 
> Dr Tim Cutts
> Informatics Systems Group, Wellcome Trust Sanger Institute
> GPG: 1024D/E3134233 FE3D 6C73 BBD6 726A A3F5  860B 3CDD 3F56 E313 4233
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