Question: Making Galaxy Tools run on multiple cores/treads?
1
gravatar for vebaev
21 months ago by
vebaev130
vebaev130 wrote:

Dear all,

I have been trying for some days to make Galaxy run tools on more than 1 core (e.g. Bowtie to use 8 or more cores on my machine with 48 cores) by modifying and activating the file jpb_conf.xml but without any luck.

I will appreciate if anyone already done it to point me to a tutorial of this method or to the other method on installing a job manager which is also I think out of mine knowledge?

ADD COMMENTlink modified 20 months ago by Jennifer Hillman Jackson25k • written 21 months ago by vebaev130
1

I guess you deleted your comment. Anyway, bowtie-build is single-threaded. For the others, make sure you restart Galaxy, since the job_conf.xml file is only parsed when Galaxy starts.

ADD REPLYlink written 20 months ago by Devon Ryan1.9k

Yes , I couldnt paste my file config correctly as typing from my iPad. I restarted it. Let me see if I can paste it now....


<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="8"/>
<plugin id="multilocal" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
</plugins>
<handlers>
<handler id="main"/>.
</handlers>

<destinations default="local">
<destination id="local" runner="local"/>
<destination id="multicore8" runner="multilocal">
<param id="local_slots">8</param>
</destination>
</destinations>

<tools>
<tool id="bowtie2" destination="multicore8"/>
<tool id="bowtie" destination="multicore8"/>
<tool id="bowtie-build" destination="multicore8"/>
<tool id="fastq_groomer_parallel" destination="multicore8"/>
<tool id="deeptools" destination="multicore8"/>
<tool id="cufflinks" destination="multicore8"/>
<tool id="cuffdiff" destination="multicore8"/>
<tool id="cuffmerge" destination="multicore8"/>
<tool id="tophat2" destination="multicore8"/>
</tools>
</job_conf>

ADD REPLYlink written 20 months ago by vebaev130

I don't see anything obviously wrong with that, just make sure you restart galaxy.

ADD REPLYlink written 20 months ago by Devon Ryan1.9k
2
gravatar for Devon Ryan
20 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

Make sure you're modifying job_conf.xml rather than jpb_conf.xml. Below is the relevant section of my job_conf.xml for running bowtie2:

 <destinations default="slurm">
    <destination id="slurm10threads" runner="slurm">
        <param id="request_cpus">10</param>
        <param id="embed_metadata_in_job">False</param>
        <param id="nativeSpecification">-p Galaxy -n 10</param>
        <env file="/data/galaxy/galaxy-central/galaxy_venv/bin/activate" />
    </destination>
</destinations>
<tools>
    <tool id="bowtie2" destination="slurm10threads"/>

If you're using the "local" job runner, then you'll need something like:

    <destination id="local" runner="local">
        <param id="local_slots">4</param>
    </destination>

And then either set destination to local or just make that the default.

ADD COMMENTlink written 20 months ago by Devon Ryan1.9k

Could you help me figure out why I can't seem to make the NCBI_blast_plus package run multi-threaded? I have tried using different tool IDs, "blast", "ncbi_blast_plus" and "ncbi_plast_plus_tools". But none seem to work... ? Thanks for your help.

<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
<job_conf>
    <plugins>
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
        <plugin id="multilocal" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="1"/>
    </plugins>
    <handlers>
       <handler id="main" />
    </handlers>

  <destinations default="local">
        <destination id="local" runner="local"/>
        <destination id="multicore4" runner="multilocal">
          <param id="local_slots">4</param>
       </destination>
  </destinations>
    <tools>
      <tool id="bowtie2" destination="multicore4" />
      <tool id="bowtie"  destination="multicore4" />
      <tool id="deeptools"  destination="multicore4" />
      <tool id="tophat2" destination="multicore4" />>
      <tool id="blast" destination="multicore4" />
    </tools>
</job_conf>
ADD REPLYlink modified 5 months ago • written 5 months ago by TWV20
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