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, 2013 at 5:21 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > 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 <dtene...@fhcrc.org> wrote: >> >> On Thu, Jun 6, 2013 at 1:56 PM, Henrik Bengtsson <h...@biostat.ucsf.edu> >> 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, 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/]? >> > >> >> You should be aware that there is Google Summer of Code project in >> progress to address this. >> >> http://www.bioconductor.org/developers/gsoc2013/ (towards the bottom) >> >> Dan >> >> >> > /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 > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
