Question: Clustalo Multi-core not working
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gravatar for kgbenn123
2.8 years ago by
kgbenn12310
kgbenn12310 wrote:

Does anyone know how to ensure clustalo is running multi-core processing? When I run it with a "--threads=8" flag, it ends up using one thread -- in fact it bounces from core to core, but only ever 1 at a time. Mayhaps I'm reading "top" wrong, but I'm pretty sure it's not working. I have gcc 4.9.3, I'm using openmp (even though according to clustalo documentation, you shouldn't have to force multi-core processing), and I don't see multiple cores being used or a difference in wall-clock time.

time (clustalo -i file -o test --threads=8 -fopenmp)

Am I just doing something wrong, or has anyone else experienced this problem with Clustalo?

ADD COMMENTlink written 2.8 years ago by kgbenn12310

What is file in this example? You won't likely see any difference if this is a very small input set. Also, not every step of the algorithms will use multiple cores so you will need a non-trivial data set to see any differences. The last thing I would look at is the syntax. This is minor and likely unrelated, but it's not clear what the parentheses are doing here.

ADD REPLYlink written 2.8 years ago by SES8.2k

442kb set of 350 fasta seqs

So I am getting a consistent difference of 10 seconds faster (3:40 vs. 3:50) but I was doubting it because top wasn't showing all cores being utilized.

ADD REPLYlink written 2.8 years ago by kgbenn12310
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