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 independent of BiocParallel and/or have you tried it with the most recent BiocParallel implementation [https://github.com/Bioconductor/BiocParallel/]? /Henrik On Tue, Dec 4, 2012 at 12:38 PM, Henrik Bengtsson <h...@biostat.ucsf.edu> wrote: > Thanks. > > On Tue, Dec 4, 2012 at 3:47 AM, Vincent Carey > <st...@channing.harvard.edu> wrote: >> I have been booked up so no chance to deploy but I do have access to SGE and >> LSF so will try and will report ASAP. > > ...and I'll try it out on PBS (... but I most likely won't have time > to do this until the end of the year). > > Henrik > >> >> >> On Tue, Dec 4, 2012 at 4:08 AM, Hahne, Florian <florian.ha...@novartis.com> >> wrote: >>> >>> Hi Henrik, >>> I have now come up now with a relatively generic version of this >>> SGEcluster approach. It does indeed use BatchJobs under the hood and >>> should thus support all available cluster queues, assuming that the >>> necessary batchJobs routines are available. I could only test this on our >>> SGE cluster, but Vince wanted to try other queuing systems. Not sure how >>> far he got. For now the code is wrapped in a little package called >>> Qcluster with some documentation. If you want to I can send you a version >>> in a separate mail. Would be good to test this on other systems, and I am >>> sure there remain some bugs that need to be ironed out. In particular the >>> fault tolerance you mentioned needs to be addressed properly. Currently >>> the code may leave unwanted garbage if things fail in the wrong places >>> because all the communication is file-based. >>> Martin, I'll send you my updated version in case you want to include this >>> in biocParallel for others to contribute. >>> Florian >>> -- >>> >>> >>> >>> >>> >>> >>> On 12/4/12 5:46 AM, "Henrik Bengtsson" <h...@biostat.ucsf.edu> wrote: >>> >>> >Picking up this thread in lack of other places (= were should >>> >BiocParallel be discussed?) >>> > >>> >I saw Martin's updates on the BiocParallel - great. Florian's SGE >>> >scheduler was also mentioned; is that one built on top of BatchJobs? >>> >If so I'd be interested in looking into that/generalizing that to work >>> >with any BatchJobs scheduler. >>> > >>> >I believe there is going to be a new release of BatchJobs rather soon, >>> >so it's probably worth waiting until that is available. >>> > >>> >The main use case I'm interested in is to launch batch jobs on a >>> >PBS/Torque cluster, and then use multicore processing on each compute >>> >node. It would be nice to be able to do this using the BiocParallel >>> >model, but maybe it is too optimistic to get everything to work under >>> >same model. Also, as Vince hinted, fault tolerance etc needs to be >>> >addressed and needs to be addressed differently in the different >>> >setups. >>> > >>> >/Henrik >>> > >>> >On Tue, Nov 20, 2012 at 6:59 AM, Ramon Diaz-Uriarte <rdia...@gmail.com> >>> >wrote: >>> >> >>> >> >>> >> >>> >> On Sat, 17 Nov 2012 13:05:29 -0800,"Ryan C. Thompson" >>> >><r...@thompsonclan.org> wrote: >>> >> >>> >>> On 11/17/2012 02:39 AM, Ramon Diaz-Uriarte wrote: >>> >>> > In addition to Steve's comment, is it really a good thing that "all >>> >>>code >>> >>> > stays the same."? I mean, multiple machines vs. multiple cores are, >>> >>> > often, _very_ different things: for instance, shared vs. distributed >>> >>> > memory, communication overhead differences, whether or not you can >>> >>>assume >>> >>> > packages and objects to be automagically present in the slaves/child >>> >>> > process, etc. So, given they are different situations, I think it >>> >>> > sometimes makes sense to want to write different code for each >>> >>>situation >>> >>> > (I often do); not to mention Steve's hybrid cases ;-). >>> >>> > >>> >>> > >>> >>> > Since BiocParallel seems to be a major undertaking, maybe it would >>> >>> > be >>> >>> > appropriate to provide a flexible approach, instead of hard wiring >>> >>>the >>> >>> > foreach approach. >>> >>> Of course there are cases where the same code simply can't work for >>> >>>both >>> >>> multicore and multi-machine situations, but those generally don't fall >>> >>> into the category of things that can be done using lapply. Lapply and >>> >>> all of its parallelized buddies like mclapply, parLapply, and foreach >>> >>> are designed for data-parallel operations with no interdependence >>> >>> between results, and these kinds of operations generally parallelize >>> >>> as >>> >>> well across machines as across cores, unless your network is not fast >>> >>> enough (in which case you would choose not to use multi-machine >>> >>> parallelism). If you want a parallel algorithm for something like the >>> >>> disjoin method of GRanges, you might need to write some special >>> >>> purpose >>> >>> code, and that code might be very different for multicore vs >>> >>>multi-machine. >>> >> >>> >>> So yes, sometimes there is a fundamental reason that you have to >>> >>> change >>> >>> the code to make it run on multiple machines, and neither foreach nor >>> >>> any other parallelization framework will save you from having to >>> >>>rewrite >>> >>> your code. But often there is no fundamental reason that the code has >>> >>>to >>> >>> change, but you end up changing it anyway because of limitations in >>> >>>your >>> >>> parallelization framework. This is the case that foreach saves you >>> >>>from. >>> >> >>> >> >>> >> >>> >> Hummm... I guess you are right, and we are talking about "often" or >>> >>"most >>> >> of the time", which is where all this would fit. Point taken. >>> >> >>> >> >>> >> Best, >>> >> >>> >> R. >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> -- >>> >> Ramon Diaz-Uriarte >>> >> Department of Biochemistry, Lab B-25 >>> >> Facultad de Medicina >>> >> Universidad Autónoma de Madrid >>> >> Arzobispo Morcillo, 4 >>> >> 28029 Madrid >>> >> Spain >>> >> >>> >> Phone: +34-91-497-2412 >>> >> >>> >> Email: rdia...@gmail.com >>> >> ramon.d...@iib.uam.es >>> >> >>> >> http://ligarto.org/rdiaz >>> >> >>> >> _______________________________________________ >>> >> Bioc-devel@r-project.org mailing list >>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
