Hi Peter,

On 21/07/2016, at 8:50 PM, Peter Cock <p.j.a.cock@googlemail.com> 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 variable $GALAXY_SLOTS
if set, defaulting to 8 threads if not. See:


Galaxy itself should be setting $GALAXY_SLOTS via your
cluster configuration - and from your description this seems
to be set to 1 thread/slot only.

I suspect since I’m running an old configuration that my cluster setup isn’t optimal. I didn’t really want my users going nuts since our cluster is small (6 nodes, 16 cores each) so I wasn’t keen to give them too much power because and was happy that tools would only run on single cores although I’ve set things up as per the docs way back when so it uses multiple handlers and so on and with default_cluster_job_runner = drmaa:/// all in the galaxy.ini (universe_wsgi.ini actually)

Can you tell us more about how your Galaxy LSF is setup?
Have you got BLAST specific cluster job settings?

Nothing specific, but it would seem that the GALAXY_SLOTS variable has gone from being unset to set with the install I’ve got now and that would explain why BLAST has slowed down a lot.

(I don't use LSF so don't have the details to hand)

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 which sets local_slots to a value for runner drmaa unless there’s a way to set that in the galaxy.ini file instead.



On Wed, Jul 20, 2016 at 10:03 PM, Shane Sturrock <shane@biomatters.com> wrote:
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 if
they could be used. I’m still using the older 16.01 release and this has
been upgraded repeatedly over the last few years so I’m still using the
universe_wsg.ini file (sym linked to config/galaxy.ini) and I don’t have a
job_conf.xml set up. I’m using drmaa to drive an LSF cluster. BLAST is the
main issue here so I was wondering if there’s a way to pass the -num_threads
flag without breaking everything until I can build up a new server?

Dr. Shane Sturrock
NZGL BioIT Admin

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Dr. Shane Sturrock
NZGL BioIT Admin