For this situation, generate the permutation indexes outside of the mclapply, and the do mclapply over a list with the indices.
And btw., please don't use set.seed inside a package; that control should completely be left to the user. Best, Kasper On Wed, Jun 3, 2015 at 7:08 AM, Vincent Carey <st...@channing.harvard.edu> wrote: > This document indicates how to achieve reproducibility independent of the > underlying physical environment. > > http://cran.r-project.org/web/packages/doRNG/vignettes/doRNG.pdf > > Let me know if that satisfies the question. > > On Wed, Jun 3, 2015 at 5:32 AM, Yu, Guangchuang <g...@connect.hku.hk> > wrote: > > > Der Vincent, > > > > RNGkind("L'Ecuyer-CMRG") works as using mc.set.seed=FALSE. > > > > When mc.cores changes, the output is not reproducible. > > > > I think this issue is also of concern within the Bioconductor community > as parallel version of permutation test is commonly used now. > > > > Best Regards, > > > > Guangchuang > > > > > > > > On Wed, Jun 3, 2015 at 5:17 PM, Vincent Carey < > st...@channing.harvard.edu> > > wrote: > > > >> Hi, this question belongs on R-help, but perhaps > >> > >> > https://stat.ethz.ch/R-manual/R-devel/library/parallel/html/RngStream.html > >> > >> will be useful. > >> > >> Best regards > >> > >> On Wed, Jun 3, 2015 at 3:11 AM, Yu, Guangchuang <g...@connect.hku.hk> > >> wrote: > >> > >>> Dear all, > >>> > >>> I have an issue of setting seed value when using parallel package. > >>> > >>> > library("parallel") > >>> > library("digest") > >>> > > >>> > set.seed(0) > >>> > m <- mclapply(1:10, function(x) sample(1:10), > >>> + mc.cores=2) > >>> > digest(m, 'crc32') > >>> [1] "4827c80c" > >>> > > >>> > set.seed(0) > >>> > m <- mclapply(1:10, function(x) sample(1:10), > >>> + mc.cores=2) > >>> > digest(m, 'crc32') > >>> [1] "e95b9134" > >>> > >>> By default, set.seed() will be ignored since mclapply will set the seed > >>> internally. > >>> > >>> If we use mc.set.seed=FALSE to disable this feature. It works as > >>> indicated > >>> below: > >>> > >>> > set.seed(0) > >>> > m <- mclapply(1:10, function(x) sample(1:10), > >>> + mc.cores=2, mc.set.seed = FALSE) > >>> > digest(m, 'crc32') > >>> [1] "6bbada78" > >>> > > >>> > set.seed(0) > >>> > m <- mclapply(1:10, function(x) sample(1:10), > >>> + mc.cores=2, mc.set.seed = FALSE) > >>> > digest(m, 'crc32') > >>> [1] "6bbada78" > >>> > >>> The problems is that the results are also depending on the number of > >>> cores. > >>> > >>> > set.seed(0) > >>> > m <- mclapply(1:10, function(x) sample(1:10), > >>> + mc.cores=4, mc.set.seed = FALSE) > >>> > digest(m, 'crc32') > >>> [1] "a22e0aab" > >>> > >>> > >>> Any idea? > >>> > >>> Best Regards, > >>> Guangchuang > >>> -- > >>> --~--~---------~--~----~------------~-------~--~----~ > >>> Guangchuang Yu, PhD Candidate > >>> State Key Laboratory of Emerging Infectious Diseases > >>> School of Public Health > >>> The University of Hong Kong > >>> Hong Kong SAR, China > >>> www: http://ygc.name > >>> -~----------~----~----~----~------~----~------~--~--- > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> _______________________________________________ > >>> Bioc-devel@r-project.org mailing list > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >>> > >> > >> > > > > > > -- > > --~--~---------~--~----~------------~-------~--~----~ > > Guangchuang Yu, PhD Candidate > > State Key Laboratory of Emerging Infectious Diseases > > School of Public Health > > The University of Hong Kong > > Hong Kong SAR, China > > www: http://ygc.name > > -~----------~----~----~----~------~----~------~--~--- > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
