Cufflinks Multithreading Not Working

[polarise]

Hi,

My Cufflinks installations (v.1.0.1 and v.1.0.3) do not respond to the -p <int> argument. How may I resolve this?

Any help will be appreciated.

Regards,

PK

[Thomas Doktor]

How do you know they're not responding to the -p option?
Do they output an error message or are you checking the use of multiple CPU's by the top command? What was the exact command you used?

[polarise]

How do you know they're not responding to the -p option?
Do they output an error message or are you checking the use of multiple CPU's by the top command? What was the exact command you used?

When the -p option was working as I think it should running Cufflinks took much shorter than it does. Also, the output would show that multiple chromosomes were being processed simultaneously. I have no recollection of whether there were multiple instances of Cufflinks shown in the table of process when it had worked in a previous version but presently I only have one such instance running at close to 100% even when I set -p 10.

No output error is given. The computation is OK albeit slow.

The exact command I used/I am using is:

cufflinks -o <dir> -G <GTF> -p 10 -u <bamfile>

Thanks for your assistance.

PK

[goudurix]

Dear all,
I run into the same problem. I have compiled cufflinks from source (and also tested with the binary version provided from the web site). I'm using cufflinks v1.3.0 and on a machine equipped with 2 Intel Xeon X5650 Processor (2.66GHz, 6C, 12M Cache, 6.40 GT/s QPI, 95W TDP, Turbo, HT). I'm using cufflinks with the following command.

cufflinks  -o cufflinks-g  -p 8 myDataset.bam  -g mm9.gtf

Any help would be really appreciated.
Thanks

[Gabriele Zoppoli]

problem with multithreading CuffLinks

Dear all,

did anybodody solve this issue? I notice from htop that only one core is indeed used...

I'm working with a dual core Intel® Xeon(R) CPU E5430 @ 2.66GHz × 8 workstation but the -p 8 (or any other number like 4) doesn't seem to make more than one physical CPU working, which is hideously slow...

[gesdys]

same problem here, only one core used and only sporadically 2.
it takes forever to analyze anything...