Roary parameters optimization (Noob question: CPUs X Threads)

Question

[hugo.avila]

I want to do pangenome analisys with raory, but i have a big dataset (~10k genomes) so i want to apply the maximum resources available in my server. In the roary manual it says that the flag -p set the number of threads to use.

The lscpu command provides the following output:

CPU(s): 64

Thread(s) per core: 2

Should I run roary with the flag -p (threads) "-p 128"?

Answer 1

[karl.stamm]

It's complicated. The only way to know for sure is to try various settings and measure the time they take. But for a shortcut, you're right that 128 is the absolute maximum. Usually something else begins bottlenecking and you'll get slower after some number down by 4 or 12. Try 8 and have a cup of tea.

[hugo.avila]

Tks ! i will try it.