Bowtie -p/--threads parameter for increased performance

[thinkRNA]

Has any one been able to use the -p parameter to utilize multiple processors?

I have a 64 bit machine with 4 processors but the -p 2 doesn't use more than 1.

May be it requires different installation process(?) I will really appreciate any feedback from someone who got it to work.

Thanks in advance!
Priyam

[ffinkernagel]

How do you quantify that bowtie's only using one?
Works for me and bowtie 0.11.something, what are your other parameters?

[marloch]

I have always used Bowtie with the -p flag without problems (@ffinkernagel: just use a system monitor utility, e.g., "top" in Linux).

From Bowtie website:

To support the -p (multithreading) option, Bowtie needs the pthreads library. To compile Bowtie without pthreads (which disables -p), use make BOWTIE_PTHREADS=0.

[ffinkernagel]

@marloch: Sorry, that question was indeed not clearly stated. It was not meant to be 'how does one quantify multicore usage', but 'how does thinkRNA quantify multicore usage' - in order to exclude a simple artefact.

[thinkRNA]

I have always used Bowtie with the -p flag without problems (@ffinkernagel: just use a system monitor utility, e.g., "top" in Linux).

From Bowtie website:

To support the -p (multithreading) option, Bowtie needs the pthreads library. To compile Bowtie without pthreads (which disables -p), use make BOWTIE_PTHREADS=0.

I got it to work! Should have read the manual more closely.