[ssml] Unable to get CD-HIT-2D to create one thread per core

Tomer Altman taltman at AI.SRI.COM
Wed Jun 30 12:57:32 EDT 2010

To whomever it may concern,

I am trying to get CD-HIT-2D to make use of all of the cores on my 
machine. It seems that when I run the command with "-T 0", instead of 
running on all 8 cores, it is running only 4 threads: one per CPU. 
Running the program with "-T 8" didn't help, either.

When installing CD-HIT, I compiled using the openmp="yes" option.

The machine is running Ubuntu Linux:
absinthe:/tmp/blast-testing 34: uname -a
Linux absinthe 2.6.24-28-server #1 SMP Thu May 27 00:03:15 UTC 2010 
x86_64 GNU/Linux

Intel(R) Xeon(R) CPU           E5450  @ 3.00GHz
Four CPUs with two cores, each. Each core has hyperthreading.

Any insight into how to increase the number of threads per cd-hit-2d 
process would be greatly appreciated.


~Tomer Altman

Tomer Altman
taltman at ai.sri.com

Bioinformatics Research Group
Artificial Intelligence Center
SRI, International


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