[ssml] Unable to get CD-HIT-2D to create one thread per core
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
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.
taltman at ai.sri.com
Bioinformatics Research Group
Artificial Intelligence Center
More information about the ssml-general