Set Priority for local copy of Galaxy

Question: Set Priority for local copy of Galaxy

4.4 years ago by

ahdee • 30

United States

ahdee • 30 wrote:

Hi all,

I have a local copy of Galaxy installed on my humble i7 8-core box. Is there a way to set the priority so that when its running a workflow it does not freeze up my entire system. I tried lowering priorities for several programs but different programs are called so it makes it difficult to pinpoint which one to set. So for example is there a way to have Galaxy and any other program it calls with a given set of priority, such as low?

thank in advance.

Alex

system-priority galaxy local • 1.0k views

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modified 4.4 years ago by Dannon Baker ♦ 3.7k • written 4.4 years ago by ahdee • 30

4.4 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi Alex,

I'm just guessing but if you are running Galaxy without a job scheduler, all programs are a child of your main Galaxy process. Under that assumption you can give your Galaxy python process a nice-value and it should pass it to all sub-processes.

It's worth a try :)

Cheers,

Bjoern

ADD COMMENT • link modified 4.4 years ago • written 4.4 years ago by Bjoern Gruening ♦ 5.1k

Bjoern, awesome, so I guess each of the process priority that is spawn will inherit the parent's priority. Is there a way to tell which python is the Galaxy one? thanks.

ADD REPLY • link written 4.4 years ago by ahdee • 30

4.4 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

Bjoern's suggestion is worth a try, but you can also look into configuring a your job config to use fewer workers, limiting the number of concurrently running child processes being handled by Galaxy. See https://wiki.galaxyproject.org/Admin/Config/Jobs for more details, but in short, you want to create this job_conf.xml file and change the default number of local workers from 4 to 2 (or even 1, if you just want one core being utilized by Galaxy's job running).

ADD COMMENT • link written 4.4 years ago by Dannon Baker ♦ 3.7k

Thank Dannon; this is exactly what I was working for. Quick question, does worker # equal to hardware cores or hyperthread? I have an i7 which is technically 4 but has 8 with hypethreading, for example if I set that to 4 will that utilized 4/8 or all 8? thanks!

ADD REPLY • link written 4.4 years ago by ahdee • 30

4 local workers would run 4 concurrent jobs. Depending on the tool, it's important to note that it's possible to use multiple processes per job -- that is to say that this isn't a firm process limit, but rather the number of concurrent jobs Galaxy will try to run with the local runner. For example, bowtie with the -p 4 option would use 4 parallel processes (but this would be one galaxy job).

ADD REPLY • link written 4.4 years ago by Dannon Baker ♦ 3.7k

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