Entering edit mode
8.4 years ago
kgbenn123
▴
20
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?
What is
filein 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.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.