Bowtie2 on Mac OSX Lion - multithreading possible?

[TabeaK]

Hiya!

I am running bowtie2 on a vanilla installation of Mac OSX Lion (i.e. I have not installed anything on top after the Macbook Pro came out of the box).

I am currently indexing my reference genome with bowtie2-build. In the MacOSX Activity monitor, I can see bowtie2 is only using one thread.

According to the developers, bowtie2 supports multithreading - but how do I get that to work under Mac OSX? I probably need to install additional libraries/tools, right? Thx in advance.

TabeaK

[knchess]

I don't think bowtie or bowtie2 support multithreading for indexing, just the alignment step. For the alignment step, there is an argument -p that lets you specify how many threads to use. It requires POSIX threads which I think is included in OS X.

[TabeaK]

Thank you, that is very helpful!

Didn't even occur to me that index building does not support multithreading.

Oh, well, it is running smoothly right now - just takes a while. Though my hardware is a bit suboptimal at the moment, admittedly.

Once I get to the alignment, I'll try the -p parameter. We'll see. And Lion IS supposed to have the POSIX library included, according to the Apple forums, anyway.

On a side note (showing my noob-status here...) - how many threads to use for alignment? Is that guided by the number of CPU cores? So 2 cores 2 threads, 4 cores 4 threads and so on?

Some of my native macbook applications go up to double digits in their thread usage, so I'm guessing my above assumption is wrong, as my Macbook has a 2.8Ghz Intel Core i7, which has what - 2cores?

[knchess]

Yeah indexing takes a while, but at least it only needs to be done once per genome then it's there.

Programs can use more threads than can be run at once if they wish. Generally that's done for convenience rather than performance, which is probably why those Mac apps are using double digit threads. Most i7 have 4 cores, but Intel has this tech called "hyper threading" so you can actually run twice as many threads concurrently. I don't know how much benefit running 8 threads vs 4 is but it won't hurt. 7 might be a good choice if you are also using the macbook at the same time, since your interactive stuff needs to be run at the same time too.

[GenoMax]

On a laptop you are probably going to be bottle-necked by the hard drive (i.e. it may not matter how many threads you use, if the disk can't keep up). You may want to watch the activity monitor for disk activity choosing different number of threads and then stop short of maxing out the disk throughput with an appropriate number of threads.

[TabeaK]

Hmm, so threads do not correspond to the cores then...I learn something new everyday, thanks guys!

I hadn't considered the disk activity, I'll check that. Cheers!