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?