What Is The Optimal Number Of Cpus For Newbler?

Question

[Casbon]

With 8 cpus, load doesn't even get above 2.

Answer 1

[Alastair Kerr]

I asked one of their devs this question last November. Then newbler only used a single CPU, but they had plans to implement multiple cores in the future (but no firm date). I do not know of any developments.

[Michael Schubert]

To work well with multiple CPUs there have to be a certain number of reasonably independent threads. But now, even 1 core is able to process multiple at the same time, thus you're approaching the limit quite quickly (unless you're using a massively parallel algorithm/application).

[Casbon]

Well it certainly supports multiple CPUs, but doesn't seem to work that well.

[Alastair Kerr]

Perhaps it was indeed the implementation rather than capability the dev was referring to then. Certainly when I was testing it out, it only used a core of my quad core machine.

Answer 2

[lexnederbragt]

In my experience, newbler (from version 2.3) manages to use a lot of the cpus it gets. However, cpu use is very dependent on the step in the assembly process. Read alignment is very cpu intensive, while building contigs/scaffold is a single cpu step. So, monitor cpu use and at the same time the standard output of newbler. might give you a better impression.