Question: Single and Multi threading on one machine
gravatar for jasperkoehorst
3.2 years ago by
jasperkoehorst10 wrote:

I am trying to set up galaxy tools either single or multithreaded on a 24 core machine.

So what I would like to achieve is to have a maximum of 20 single core workers running and if a multi threaded job is started of lets say 6 cores then I can have a maximum of 20-6 = 14 single core runners and 1 multi core runner.

However I am having a very hard time to get this working and am probably missing something.

My multi threaded tool command looks like:

<command interpreter="python3.4"> '-input' '$input' '--seqtype' '$seqtype' '-f' 'TSV' '--applications' '$appl' '-output' '$outfile' -sourcedb XYZ '-num_threads' \${GALAXY_SLOTS:-6}

My job_conf.xml file looks like this:

        <plugin id="local" type="runner" load="" workers="20"/>
        <handler id="main"/>
    <destinations default="single">
        <destination id="single" runner="local">
        <param id="local_slots">20</param>

I digged a bit in the code and noticed:

            slots_statement = 'GALAXY_SLOTS="%d"; export GALAXY_SLOTS; GALAXY_SLOTS_CONFIGURED="1"; export GALAXY_SLOTS_CONFIGURED;' % ( int( slots ) )

Which is set to one as 1 runner is running, but shouldnt it in theory not be set to 6 as it consumes 6 slots cores?


threading multi • 1.5k views
ADD COMMENTlink modified 3.2 years ago by jmchilton1.1k • written 3.2 years ago by jasperkoehorst10
gravatar for jmchilton
3.2 years ago by
United States
jmchilton1.1k wrote:

What is 1 in this context - GALAXY_SLOTS or GALAXY_SLOTS_CONFIGURED? In your example GALAXY_SLOTS should be set to 20 which should cause all 20 of the local runner threads to each use 20 cores - this is not great.

Have you looked at this answer

Adapting it to your 20 core machine - you might want to have say two 8 core threads and 4 single core threads That would look something like this:

        <plugin id="local" type="runner" load="" workers="4"/>
        <plugin id="multilocal" type="runner" load="" workers="2"/>
    <destinations default="local">
        <destination id="local" runner="local"/>
        <destination id="multicore8" runner="multilocal">
          <param id="local_slots">8</param>
    <tool id="bowtie2" destination="multicore8" />
    <tool id="bowtie"  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" />


There are some things you can do to work through different permutations in this file - but ultimately Galaxy isn't a resource manager and you should probably install something like SLURM or Condor to make most effective use of your resources.

ADD COMMENTlink written 3.2 years ago by jmchilton1.1k
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