[Rd] different results on linux and windows
Klaus Nordhausen
klaus.nordhausen at uta.fi
Fri May 15 13:23:07 CEST 2009
Thanks a lot for all the replies! We managed now to solve our problem by
replacing the rand / srand functions by R's random number generator and
now the results on windows and linux agree.
Thanks again!
Klaus
Paul Gilbert wrote:
> I cannot say what the problem is in your code, but in general it is
> possible to get the same random sequences from Linux and Windows with
> R's Mersenne Twister generator. If you generate long sequences (say 10s
> of thousands) and then start doing comparisons involving remainders,
> like differencing the sums of two mean zero sequences, then differences
> between libraries will show up. I have found bigger differences between
> Linux variants than I have between Windows and most Linuxes.
>
> Paul Gilbert
>
> Klaus Nordhausen wrote:
>> Dear R experts,
>>
>> we are preparing an R-package to compute the Oja Median which contains
>> some C++ code in which random numbers are needed. To generate the random
>> numbers we use the following Mersenne-Twister implementation:
>>
>> // MersenneTwister.h
>> // Mersenne Twister random number generator -- a C++ class MTRand
>> // Based on code by Makoto Matsumoto, Takuji Nishimura, and Shawn Cokus
>> // Richard J. Wagner v1.0 15 May 2003 rjwagner at writeme.com
>>
>> the random seed for the Mersenne-Twister is provided by our R-function
>> which gives an (random) integer to the C++ function srand() which in
>> turn sets the seed in the code.
>>
>> Using the set.seed in R makes now the results reproducible, but the
>> results differ between windows and linux.
>>
>> Does anyone know what the problem there is?
>>
>> Our suspicion is that the reason is that some libraries are different
>> implemented on linux and windows (XP) compilers.
>>
>> After the program start we set the seed in row 447(vkm.cpp) with
>> srand(int);
>>
>> When the median will be calculated, an intern seed is set with unsigned
>> int seed = rand(); ( in row 100 (vkm.cpp)). This seed will be used
>> to calculate some random subsets and to
>> create a Mersenne Twister object with MTRand rr(seed); (row 156,
>> vkm.cpp).
>>
>> The MTRand Object rr is called with an unsigned Integer, so the
>> important function in the mersenneTwister.h class is in line 87:
>> MTRand( const uint32& oneSeed );
>>
>> According to that the Random Number Generator uses the methods
>> initialize(oneSeed); and reload(); (inside the method, beginning in
>> line 215)
>>
>> This both methods (line 283 and line 301) are using beside others
>> registers. Could it be that there is a different behavior between
>> Windows and Linux?
>>
>> We do not want to use only srand() since we might need more then the
>> number of pseudo random numbers that algorithm can provide.
>>
>> For those interested and which would like to see the code, a first
>> version of the package, called OjaMedian, is available as source file
>> and windows binary on my homepage:
>> http://www.uta.fi/~klaus.nordhausen/down.html
>>
>> The problem is in the ojaMedian function when the evolutionary algorithm
>> is used. Involved C++-files are mainly vkm.cpp and MersenneTwister.h.
>>
>> We would be very grateful for any advice on how to solve this problem.
>> (below is also a demonstration)
>>
>> Thank you very much in advance,
>>
>> Klaus
>>
>> Results on windows XP:
>>
>> Compiler used: gcc version 4.2.1-sjlj (mingw32-2)
>>
>>> library(OjaMedian)
>>> set.seed(1)
>>> testD <- rmvnorm(20,c(0,0))
>>> summary(testD)
>> V1 V2
>> Min. :-2.2147 Min. :-1.989352
>> 1st Qu.:-0.3844 1st Qu.:-0.399466
>> Median : 0.3597 Median :-0.054967
>> Mean : 0.1905 Mean :-0.006472
>> 3rd Qu.: 0.7590 3rd Qu.: 0.655663
>> Max. : 1.5953 Max. : 1.358680
>>> set.seed(1)
>>> ojaMedian(testD)
>> [1] 0.21423705 -0.05799643
>>> sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=Finnish_Finland.1252;LC_CTYPE=Finnish_Finland.1252;LC_MONETARY=Finnish_Finland.1252;LC_NUMERIC=C;LC_TIME=Finnish_Finland.1252
>>
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] OjaMedian_0.0-14 ICSNP_1.0-3 ICS_1.2-1 survey_3.14
>> [5] mvtnorm_0.9-5
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.9.0
>>>
>>
>> Results on Linux Kubuntu 8.10
>> result of: cat /proc/version:
>> Linux version 2.6.28-11-generic (buildd at palmer) (gcc version 4.3.3
>> (Ubuntu 4.3.3-5ubuntu4) ) #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009
>>
>>> library(OjaMedian)
>>> set.seed(1)
>>> testD <- rmvnorm(20,c(0,0))
>>> summary(testD)
>>
>> V1 V2
>> Min. :-2.2147 Min. :-1.989352
>> 1st Qu.:-0.3844 1st Qu.:-0.399466
>> Median : 0.3597 Median :-0.054967
>> Mean : 0.1905 Mean :-0.006472
>> 3rd Qu.: 0.7590 3rd Qu.: 0.655663
>> Max. : 1.5953 Max. : 1.358680
>>
>>> set.seed(1)
>>> ojaMedian(testD)
>>
>> (-0.501381, 0.193929)[1] 0.119149071 0.002732100
>>
>>> sessionInfo()
>>
>> R version 2.8.1 (2008-12-22)
>> i486-pc-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] OjaMedian_0.0-14 ICSNP_1.0-3 ICS_1.2-1 survey_3.14
>> [5] mvtnorm_0.9-5
>>
>>
>>
>>
>>
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--
Klaus Nordhausen
Researcher
Tampere School of Public Health
FIN-33014 University of Tampere
phone: +358 3 3551 4153
fax: +358 3 3551 4150
e-mail: Klaus.Nordhausen at uta.fi
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