Enis,
FYI, Unfortunately I am traveling out of the country today and further
investigation will need to wait until I return.
I will set a note to follow-up on this when I get back and let you know
more details so we can see just what is happening in more detail.
Expect to hear back from me in a
>
>
> Now we have what may be a CloudMan question: our working cluster has a
> head node and 4 workers. The head node is loaded up but the workers are
> idle. I would have thought jobs should be pushing out to the workers but we
> don't see any load on these machines.
>
> So are the jobs queued jus
Peter,
Thanks for the great information. I see where to tune the "split_size"
variable and also the READMEs :)
I'll do so more sleuthing, let the job run and observe. So far it is ~3hr
after job launch and still no load on the workers. I think from looking at
the /mnt/galaxy/tmp/job_working_dire
On Tue, May 3, 2016 at 9:23 PM, David Kovalic wrote:
> Peter,
>
> We made the modification to the config file, restarted galaxy and things
> seem to be working from the galaxy end. We see sub-job directories being
> created in /mnt/galaxy/tmp/job_working_directory. We think all of the
> required j
Peter,
We made the modification to the config file, restarted galaxy and things
seem to be working from the galaxy end. We see sub-job directories being
created in /mnt/galaxy/tmp/job_working_directory. We think all of the
required job chunks have been created (i.e. total sequences/1000 sub-job
di
Peter,
Thanks, I didn't see that, I was reading the paper and searching online.
Appreciate the help, we'll give it a go!
David
On Tue, May 3, 2016 at 2:16 PM Peter Cock wrote:
> Hi David,
>
> The NCBI BLAST+ wrappers have a tag setup,
> which becomes active if you have use_tasked_jobs = Tru
Hi David,
The NCBI BLAST+ wrappers have a tag setup,
which becomes active if you have use_tasked_jobs = True in
your config/galaxy.ini file (aka universe_wsgi.ini).
Specifically, the wrappers use this:
This is hard coded to break up the query FASTA file into batches
of 1000 sequences (e.g. a
BOF wiki page here, will add time and place once settled...
https://wiki.galaxyproject.org/Events/GCC2015/BoFs/DataSplittingAndParallelism
On Mon, Jul 6, 2015 at 6:22 PM, Peter Cock wrote:
> Hello all,
>
> Marco, Jon and I are going to try to get together during GCC2015
> for a BOF (a "Birds of
Hello all,
Marco, Jon and I are going to try to get together during GCC2015
for a BOF (a "Birds of a Feather" informal meeting) to talk about
Galaxy parallelisation (and collections). We've not yet picked a time,
but details should be on the wiki shortly...
https://wiki.galaxyproject.org/Events/G
Hi John,
Thanks for your reply.
I think for the time being, I will simply create a tool that creates an
interval file, and the parallelize on this interval file.
Though I agree, this would be a useful feature to include but I don't
think I am anywhere near ready to start dabbling in galaxy's
core
Hey Marco,
Thanks for the e-mail. This is an awesome idea, but I am worried it is
very hard to do this well in Galaxy. If you create symbolic links to
the original file - then Galaxy might delete the original file and the
derived files would all break without warning. Galaxy does have this
separat
Hi Roberto,
It looks like you are probably still using the default sqlite database. You’ll
want to update to using e.g. postgres when exploring these more database
intensive functions. See e.g.:
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_ser
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