Clustalo Multi-core not working
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5.9 years ago
kgbenn123 ▴ 10

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?

multi-core processing clustalo • 2.0k views
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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.

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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.

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