[BiO BB] remove CTL-M and Buying a bioinformatics workstation

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Thu Sep 4 08:13:32 EDT 2003

On Thu, 4 Sep 2003, Yannick Wurm wrote:
> And Microsoft Word runs on it too :)


> Are the results shown surprising? The code for A/G Blast and HMMer seem 
> to be optimized for the G5, whereas the standard vanilla versions where 
> used on the linux boxes. Could optimization reduce the bias against the 
> xeon?

I hope so!

Did they run blast with the --number_of_cpus option set to 2 or 4?

The kernel level hyperthreading on the Xeon simulates 2n cpu's, but
I am not sure if this 'really' works (i.e. 4*2Gh from a 2*2Gh board).

Also I found the --number_of_cpus to be sub optimal in terms of cpu
usage. I prefer to simply start 4 jobs at the same time, so maby
this would improve the benchmark considerably (I got from ~50%
average usage on each cpu to ~100%).

Did they write jobs to /dev/null ?

if not the IO could be a (hidden?) factor.


> Yannick Wurm
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