instructing cufflinks to use more than one thread

[MatthewVC]

I have a dual core computer (athlon X2 6000+), which can run one thread per core, according to the manufacturer.
However, when I run cufflinks with the -p2 option to tell it to use two threads, only one CPU is used at a time. When I open the system monitor to look at CPU use, the use will vary between 100% for CPU1 and 0% for CPU2, then the opposite, changing every 20 seconds or so. Am I using the -p option incorrectly? or does cufflinks generally use only one core at a time?

Thanks,
Matt

[john_mu]

I have noticed this too when I ran it on our cluster.

At the time I guessed it was just because not all of the pipeline was multi-threaded, so it will only start to use the additional cores are some later time.

Did you sit around and watch it at different time intervals?

Otherwise, we'll have to wait for Cole Trapnell to reply.

[MatthewVC]

I watched it for an hour or two, then went to bed. The pattern of switching CPUs was roughly the same the entire time.

In the morning, the program wasn't using any CPU time, as it was "processing packets" for regions of chromosomes. It's been stuck on the mitochondrial chromosome for quite some time now (~24hr). I'm starting to wonder if the program is frozen or fubared somehow.

[john_mu]

I watched it for an hour or two, then went to bed. The pattern of switching CPUs was roughly the same the entire time.

In the morning, the program wasn't using any CPU time, as it was "processing packets" for regions of chromosomes. It's been stuck on the mitochondrial chromosome for quite some time now (~24hr). I'm starting to wonder if the program is frozen or fubared somehow.

Switching of CPUs is normal and not due to cufflinks. That is just your computer balancing the load on both cores so that one side does not get too hot.

Give it another day, for me it took about 2-3 days.