[Bioc-devel] reproducible with mclapply?

[Vincent Carey]

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
> -~----------~----~----~----~------~----~------~--~---
>

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