Hi, I'd like to pick up the discussion on a BatchJobs backend for
BiocParallel where it was left back in Dec 2012 (Bioc-devel thread
'BiocParallel'
[https://stat.ethz.ch/pipermail/bioc-devel/2012-December/003918.html]).
Florian, would you mind sharing your BatchJobs backend code? Is it
independe
On Thu, Jun 6, 2013 at 1:56 PM, Henrik Bengtsson wrote:
> Hi, I'd like to pick up the discussion on a BatchJobs backend for
> BiocParallel where it was left back in Dec 2012 (Bioc-devel thread
> 'BiocParallel'
> [https://stat.ethz.ch/pipermail/bioc-devel/2012-December/003918.html]).
>
> Florian,
And here is the on-going development of the backend:
https://github.com/mllg/BiocParallel/tree/batchjobs
Not sure how well it's been tested.
Kudos to Michel Lang for making so much progress so quickly.
Michael
On Thu, Jun 6, 2013 at 1:59 PM, Dan Tenenbaum wrote:
> On Thu, Jun 6, 2013 at 1:56
Great - this looks promising already.
What's your test system(s), beyond standard SSH and multicore
clusters? I'm on a Torque/PBS system.
I'm happy to test, give feedback etc. I don't see an 'Issues' tab on
the GitHub page. Michel, how do you prefer to get feedback?
/Henrik
On Thu, Jun 6, 2
We're regularly running BatchJobs itself on an LSF cluster. Works great.
On Thu, Jun 6, 2013 at 5:48 PM, Henrik Bengtsson wrote:
> Great - this looks promising already.
>
> What's your test system(s), beyond standard SSH and multicore
> clusters? I'm on a Torque/PBS system.
>
> I'm happy to tes
Hi Henrik,
Sorry for the late response. Suggestions and feedback are always
welcome. I just forgot to enable the issue tracker (now enabled).
For prototyping I usually use Interactive/Multicore, but I'll
regularly test on our local clusters which use Torque or Slurm,
respectively.
Michel
2013/6
This slipped under my radar, sorry. Guess there already is some
considerable work going on right now to bring queued clusters closer into
the Bioconductor world. If my first attempt on this is still of any help I
am happy to share it, of course. Just let me know.
Michael: I tried to install your Bi
Hi Florian,
Yes you're absolutely right. The fork currently depends on some
functions which are not yet included in the CRAN build. For now you
can get the latest development version on
http://batchjobs.googlecode.com. We'll upload a new version of
BatchJobs soon. I've documented this as an issue
Thanks for the info, the package now installs. Looks pretty cool. Attached
is my first hack at this from a couple of months ago. In a way it is very
similar to what you guys are doing, only that It predates the times of a
formal registry for parallel backends. I just tried to make it look like a
cl
