On 06/03/2014 10:17, Henric Winell wrote:
Hi,
I've implemented parallelization in one of my packages using the
'parallel' package -- many thanks for providing it!
In my package I'm importing 'parallel' and so added it to the
DESCRIPTION file's 'Import:' tag and also added a
'importFrom("parallel", ...)' statement in the NAMESPACE file.
Parallelization works nicely, but my package no longer passes any parts
of its (unparallelized) checks that depends on random number generation,
e.g., the simulated data in the check suite are no longer the same as
before parallelization was added. This seems to be due to 'parallel'
changing '.Random.seed' when loading its name space:
> set.seed(1)
> rs1 <- .Random.seed
> rnorm(1)
[1] -0.6264538
> set.seed(1)
> rs2 <- .Random.seed
> identical(rs1, rs2)
[1] TRUE
> loadNamespace("parallel")
<environment: namespace:parallel>
> rs3 <- .Random.seed
> identical(rs1, rs3)
[1] FALSE
> rnorm(1)
[1] -0.3262334
> set.seed(1)
> rs4 <- .Random.seed
> identical(rs1, rs4)
[1] TRUE
I've taken a look at the 'parallel' source code, and in a few places a
call to 'runif(1)' is issued. So, what effectively seems to happen when
'parallel' is loaded is
> set.seed(1)
> runif(1)
[1] 0.2655087
> rnorm(1)
[1] -0.3262334
which reproduces the above. But is this really necessary?
Yes, in the places it is used. Two are to do with setting up parallel
streams when called, and the other is only called if R_PARALLEL_PORT is
unset.
So set R_PARALLEL_PORT.
But your presumptions are wrong: R is perfectly entitled to use its
random number generator, as is other code running in the R interpreter.
Once your call returns you cannot expect the session state to remain
unchanged.
And more
importantly (at least to me): Can it somehow be avoided?
The current state of affairs is a bit unfortunate, since it implies that
a user just by loading the new parallelized version of my package can no
longer reproduce any subsequent results depending on random number
generation (unless a call to 'set.seed' was issued *after* attaching my
package).
I'd be most grateful for any help that you're able to provide here. Many
thanks!
Kind regards,
Henric Winell
sessionInfo()
R Under development (unstable) (2014-01-26 r64897)
See what the posting guide says about updating before posting ....
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=sv_SE.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.1.0 parallel_3.1.0 tools_3.1.0
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
