Hi Rafael, I'd agree with RM, take a look at some of the explicit parallelization packages (I find snowfall has less overhead on my typing than Rmpi does) if you're planning to run over multiple trees. This will let you run on multiple cores or on clusters. Here's quick example based on my understanding of your question: https://github.com/cboettig/sandbox/blob/master/r-sig-phylo/parallel.md
-Carl On Wed, Mar 21, 2012 at 9:06 AM, Brian O'Meara <bome...@utk.edu> wrote: > The multicore package has been rolled into the built-in R package parallel > in R >=2.14.0, with slight changes. There's a task view on parallelization > that might help: > http://cran.r-project.org/web/views/HighPerformanceComputing.html . I've > found the foreach package helpful for parallelization, too. It's especially > good if you still think in terms of for loops (as I do, sadly, though I'm > working on it). > > Brian > > _______________________________________ > Brian O'Meara > Assistant Professor > Dept. of Ecology & Evolutionary Biology > U. of Tennessee, Knoxville > http://www.brianomeara.info > > Students wanted: Applications due Dec. 15, annually > Postdoc collaborators wanted: Check NIMBioS' website > Calendar: http://www.brianomeara.info/calendars/omeara > > > On Wed, Mar 21, 2012 at 11:58 AM, Rafael Rubio de Casas <r...@nescent.org > >wrote: > > > Dear all, > > I have been trying to come up with easy ways to split diversitree runs > > among processors when using multiple trees. It seems that the multicore > > package would be a good way of doing it, but I have failed to use > > multicore with diversitree functions. Essentially, I cannot figure out > > how to tell multicore that the function takes two set of objects, one > > containing the likelihood functions and another one containing the > > parameters. Does anybody have experience and/or advice doing this? Any > > guidance would be most welcome. > > Other alternatives for splitting diversitree jobs among processors would > > also be highly appreciated. > > Thanks in advance, > > Rafa > > -- > > National Evolutionary Synthesis Center > > *NESCent <http://www.nescent.org/>* > > 2024 W. Main Street, Suite A200 > > Durham, NC27705 > > r...@nescent.org <mailto:r...@duke.edu> > > 919.668.9107 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-phylo mailing list > > R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- Carl Boettiger UC Davis http://www.carlboettiger.info/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
