[Bioclusters] Re: [GE users] ideal load threshold for cluster nodes.

Joe Landman landman at scalableinformatics.com
Fri Jul 14 16:34:27 EDT 2006

Hi Jinal:

Jinal Jhaveri wrote:
> Hi All,
> I am using load_avg=2.0 as a load threshold for our SGE nodes. I avoid 
> using the np_load_avg (load per processor) as it is mis-interpreted on 
> intel machines with hyperthreading enabled. Can anyone (especialy in 
> Bioinformatics setting running jobs like blast,interpro) share their 
> experience on what load threshold works best for them?

Unless you have a really good reason for running HT, I would probably 
suggest disabling it.  Our tests with BLAST a few years ago showed no 
real benefit.  You do get benefit from bigger caches and faster memory 
systems, but not HT.

With that in mind, I would probably stick to the load average == number 
of cores in system.


> Thank you!
> --Jinal
> ps. Apologies for cross posting but I realized that both SGE gurus and 
> Bio-cluster people might be able to answer this question.
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Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
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