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:
https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus...
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.
Can you tell us more about how your Galaxy LSF is setup?
Have you got BLAST specific cluster job settings?
(I don't use LSF so don't have the details to hand)
Peter
On Wed, Jul 20, 2016 at 10:03 PM, Shane Sturrock <shane(a)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
nzgl(a)biomatters.com
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