[Bioc-devel] reproducible with mclapply?

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]]

--
--~--~---------~--~----~------------~-------~--~----~
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]]