[Bioc-devel] reproducible with mclapply?
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]]
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--~--~---------~--~----~------------~-------~--~----~ 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]]