[Bioclusters] cluster or SMP

[Robert Olson]

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...

--bob


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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