[Bioclusters] Related question (was: a dedicated cluster to mpiblast the nr database)

Joe Landman bioclusters@bioinformatics.org
Fri, 05 Dec 2003 09:00:30 -0500

This raises an interesting question ...

Tim Cutts wrote:


>We've done this recently, comparing 32-bit BLAST on Linux/x86, with 4GB
>RAM, against various vendors' quad-CPU-64-bit-32GB-RAM performance
>monsters.  For BLAST, in particular, I don't think big machines are
>worth it.  The 20-40% speed advantage is much smaller than the price
>penalty.  Buy lots of little ones instead.  If you need a more generic

I am curious about this.  I agree with Tim on this, but I have not been 
able to quantify this for myself, even from an estimation point of view.

What speed advantage would be worth such a price penalty?  Or better 
put,  for every $1000USD over in price per unit from the base, how much 
additional performance would be needed to justify the cost?   Is the 
idea to keep the price performance the same (e.g. for 10x the price, you 
get 10x the performance), or should it be a different function.

Another similar question is, if these larger boxen were 1/10 their 
current price, would people buy 10x more?  Less than that?  More than 
that?  That is, is this the analysis bottleneck?

note:  I have my own thoughts on this, but I would like to hear other 
peoples thoughts.  This is relevant for both something I am working on 
writing, and from the point of view of a vendor wanting to make sure we 
are working towards the right goals.

>high performance compute resource which requires much larger amounts of
>memory (and there are plenty of bioinformatics tasks which do, it's just
>that BLAST isn't really one of them), that's when you start considering
>the big memory boxes.

Quite true.  I do see big clusters being used for a number of apps which 
map reasonable well onto them.  You need the heavy metal for some tasks 
(big memory/big I/O).  Some things simply cannot be done well on 
distributed shared nothing machines. 

>Just my 2

Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615