[Bioclusters] cluster or SMP

Robert Olson olson at mcs.anl.gov
Tue Sep 4 11:38:40 EDT 2007

We recently obtained a pair of 8-core Mac Pro machines with 16 G of  
RAM. We have had a 48-node dual-G5 Mac cluster for a couple years.

It takes a fair bit of work and understanding of local vs remote file  
system issues to make the cluster work efficiently. However, we have  
seen *immediate* increases in productivity for the folks that started  
using the SMP boxes; the increase in amount of memory and the fact  
that it is trivial to efficiently use the multiple processors made a  
world of difference.

What we're probably going to do moving forward is make sure we have  
cycles available on SMP boxes for folks to use, and run our  
production batch-oriented tasks that we can take the time to optimize  
for it on the cluster.

As far as network goes; we've got 2TB of local disk on each of these  
machines (3 750G drives), so we have essentially zero network use for  
the work being done on them at the moment...


On Sep 1, 2007, at 2:56 PM, Marcos de Carvalho wrote:

> 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.
> Regards,
> Marcos
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