The cpu using question when I run the cufflinks.

Question: The cpu using question when I run the cufflinks.

4.2 years ago by

wukai199010 • 0

United States

wukai199010 • 0 wrote:

My question is, my "cufflinks" using the 100% cpu before the others run the "blastx", but now, the "cufflinks" just using 6.7% cpu, and the others using the 90% cpu, why? It's not not fair.

cufflinks • 1.3k views

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modified 4.2 years ago by Bjoern Gruening ♦ 5.1k • written 4.2 years ago by wukai199010 • 0

4.2 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi,

actually this is a admin problem. Are you running Galaxy with a queueing system? Galaxy supports several scheduling systems that will manage your jobs and create Queues. If you have to many jobs on one cluster, like in your case, the Blast Jobs have to wait until your cufflinks job is finished.

Please tell your Galaxy admin to look use such a scheduler and you will be fine :)

Cheers,

Bjoern

ADD COMMENT • link written 4.2 years ago by Bjoern Gruening ♦ 5.1k

Hi,

Thanks!

I running the program on my local clusters' one node directly, and I don't using the "qsub".

Blastx is running by others in my institute. So, why he can get the more computing resource?

Best,

Kai Wu

ADD REPLY • link written 4.2 years ago by wukai199010 • 0

Everything is executed at once without any queueing, so your OS is responsible for managing resources. At this point it is out of scope for Galaxy. Sorry. Try to use a scheduling system. Slurm maybe?

ADD REPLY • link written 4.2 years ago by Bjoern Gruening ♦ 5.1k

4.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Your question is a bit difficult to understand.

If you are talking about a local or cloud Galaxy with an associated cluster/set of nodes actually executing the jobs, then you are probably seeing the resources used by Galaxy based on interactions with the database itself.

Best, Jen, Galaxy team

ADD COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks for your answer.

I running the program on my local cluster's one node.

So, it's the program's problem?

ADD REPLY • link written 4.2 years ago by wukai199010 • 0

Please see Bjoern's reply - it has the right suggestions for a solution. Take care, Jen, Galaxy team

ADD REPLY • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k

Ok, thanks!

ADD REPLY • link written 4.2 years ago by wukai199010 • 0

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