Question: (Closed) Galaxy tool multi-threading
gravatar for TWV
8 months ago by
TWV20 wrote:

I have a local instance of galaxy running on a PC with 4 cores (8 threads). When I run a blast, bowtie2 or other similar job, they only ever use 1 thread.

I have read that it is possible to setup which tools should use how many jobs by editing config/job_conf.xml. I adapted the setup made in to be used on my PC:

        <plugin id="local" type="runner" load="" workers="4"/>
        <plugin id="multilocal" type="runner" load="" workers="1"/>
       <handler id="main" />

  <destinations default="local">
        <destination id="local" runner="local"/>
        <destination id="multicore4" runner="multilocal">
          <param id="local_slots">4</param>

      <tool id="bowtie2" destination="multicore4" />
      <tool id="bowtie"  destination="multicore4" />
      <tool id="deeptools"  destination="multicore4" />
      <tool id="cufflinks" destination="multicore4" />
      <tool id="cuffdiff"  destination="multicore4" />
      <tool id="cuffmerge" destination="multicore4" />
      <tool id="tophat2" destination="multicore4" />

If I am no mistaken, this way 4 cores will be reserved for 4 single-threaded jobs, and the other 4 are reserved for the listed tools which will be run one job at a time with 4 cores, am I right? Did I miss or misunderstand something?

thread multithread jobs • 327 views
ADD COMMENTlink written 8 months ago by TWV20

Also related:

ADD REPLYlink modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson25k

Hello TWV!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


PS: Please review that reply and the linked conversation at the galaxy-dev mailing list. I missed that this was addressed already in other posts. All (most) are linked now.
ADD REPLYlink modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson25k
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