[Bioc-devel] reproducible with mclapply?

[Yu, Guangchuang]

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]]