Re: [galaxy-dev] BLAST only using single core

Thanks Peter, that was the hint I was needing. It looks like the solution for my LSF cluster was to use drmaa://-n 8/ in the universe_wsgi.ini and now I can see BLAST using 8 cores. It doesn’t scale perfectly so going higher isn't sensible but turnaround time for my test job has improved

Re: [galaxy-dev] BLAST only using single core

On Thu, Jul 21, 2016 at 10:35 AM, Shane Sturrock wrote: > > I’m just using the drmaa plugin so I’m guessing I need to either specify a > job runner for BLAST which sets GALAXY_SLOTS. The documentation isn’t > entirely clear although it seems I need to create a job_conf.xml

Re: [galaxy-dev] BLAST only using single core

Hi Peter, > On 21/07/2016, at 8:50 PM, Peter Cock wrote: > > Hi Shane, > > We've not touched anything on the BLAST+ wrapper here for > a while - the command line is always built using: > > -num_threads "\${GALAXY_SLOTS:-8}" > > That means use the environment

Re: [galaxy-dev] BLAST only using single core

Hi Shane, We've not touched anything on the BLAST+ wrapper here for a while - the command line is always built using: -num_threads "\${GALAXY_SLOTS:-8}" That means use the environment variable $GALAXY_SLOTS if set, defaulting to 8 threads if not. See:

[galaxy-dev] BLAST only using single core

Previously, the BLAST wrapper was able to use multiple cores but recently users have started complaining it has got really slow and when I look at the cluster a job is only using a single core. I don’t want jobs split across multiple cluster nodes, but each node has 16 cores so it would be good