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