[Bioc-devel] reproducible with mclapply?

[Kasper Daniel Hansen]

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 <stvjc at 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 <gcyu at 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 <
> stvjc at 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 <gcyu at 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 at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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