[Bioclusters] cluster or SMP

Marcos de Carvalho operon at cbiot.ufrgs.br
Sat Sep 1 15:56:21 EDT 2007

Hi list,

I am in charge of the setup of a new bioinformatics lab in my university.  
However, I am wondering what would be the best for my current budget for  
the high-performance machine, that will do basically genome assemblies,  
gene finding and homology searches for at least 3 metagenomics projects  
(but it is probably that it will be used for other applications, like  
molecular dynamics). For this machine specifically I have about 23 000  
US$ and my first though was to build a cluster (which at current local  
prices could give me a 32 node diskless beowulf with E4400 chips or 16  
nodes with Q6600 chips). However, I saw some pretty good SMP machines  
(with a max of 8 dual core opterons), for about the same price.

  Taking off the fun of building the cluster, the relative easier  
administration of a SMP machine and their more general purpose application  
could justify their choose over a cluster? Even with 48 more cores, could  
the network be a serious bottleneck in comparison with the SMP machine?  
Does gigabit port trunking could be a solution for the network bottleneck?

  I am not in a hurry for this machine, so the time of building the cluster  
can be discarded.

Thanks in advance.



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