No subject


Wed Jan 12 20:38:46 GMT 2011


the -a flag for the single request (via a web page) is a very powerful
combo. Both can be easily done with SGE, using the -b y "blastall -a 4
blabla" :-)

My own .02 cents and best regards

Sylvain

On 22/05/10 13:42, "[NAME]" <[ADDRESS]> wrote:

> hi masters:
> 
> I just installed Rocks clusters 5.3(the lastest) with default SGE package on a
> small 2 nodes cluster for testing purpose. Everything seems working. But the
> ncbi blast is not working with performance double as expecting.
> 
> example here a long time ago, seems blast is working with SGE very well
> already.
> http://developers.sun.com/solaris/articles/integrating_blast.html
> 
> follow the instruction to create the job, it submit to one node only.
> 
> i try qsub with array option (-t 1-2), job is dispatch to 2 nodes to utilize
> all cpus. but the execution time do not even reduce a second, compare to
> running job in one node. (the test run is 15 min with 1000 seq blastx)
> 
> i try other option -pe orte 4, then qstat could see the job also spread to 2
> nodes, but one of the host the cpu do not boost up at all. so the performance
> is still same as before.
> 
> 
> I google and seems all other people are happy and quiet. Do I need to config
> or setup anything?
> 
> I install Rocks 5.3 with default setting. only config i did was to add 'execd'
> into the qmaster host to make it exec node also. (as instruction in Rocks
> guide.)
> 
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