[R-sig-hpc] The foreach, iterators and doMC packages

[Mark Kimpel]

I'm having trouble getting these packages to work as I believe they
should. I have a new Debian Lenny box running on an Intel i7 with 12
GB of memory and wrote a test script to see how much performance
increase I could achieve with foreach. For this purpose, I used code
extracted from the vignette. Below is the code, the system.time
output, and sessionInfo(). I should add that I've run this multiple
times and always achieved similar results. These last were achieved
after doing init 1 to get me into a strict terminal mode and avoid the
GUI.

As you can see, the results seem to be the opposite of what one would
expect. The fastest time, by an order of magnitude, is achieved by a
simple for loop, and %do% slightly outperforms %dopar%

How can this be explained?
Mark
####################################
require(foreach)
require(multicore)
require(doMC)
registerDoMC(cores=5)
z <- 30000


for.each.do.time <- system.time(
            a <- foreach(i = 1:z, .combine = "c") %do% sqrt(i)
            )
#
for.each.do.par.time <- system.time(
            b <- foreach(i = 1:z, .combine = "c") %dopar% sqrt(i)
            )

#
c <- rep(0,z)
loop.time <- system.time(
            for (i in 1:length(c))
            c[i] <- sqrt(i)
            )
#
out <- rbind(unclass(for.each.do.time), unclass(for.each.do.par.time),
unclass(loop.time))
out
"user.self"	"sys.self"	"elapsed"	"user.child"	"sys.child"
25.713	0	25.712	0	0
25.918	0.016	26.015	0.192	0.192
0.207999999999998	0	0.206000000000003	0	0
#
"R.version.platform" "x86_64-unknown-linux-gnu"
"R.version.arch" "x86_64"
"R.version.os" "linux-gnu"
"R.version.system" "x86_64, linux-gnu"
"R.version.status" ""
"R.version.major" "2"
"R.version.minor" "9.1"
"R.version.year" "2009"
"R.version.month" "06"
"R.version.day" "26"
"R.version.svn rev" "48839"
"R.version.language" "R"
"R.version.version.string" "R version 2.9.1 (2009-06-26)"
"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"
"basePkgs1" "stats"
"basePkgs2" "graphics"
"basePkgs3" "grDevices"
"basePkgs4" "datasets"
"basePkgs5" "utils"
"basePkgs6" "methods"
"basePkgs7" "base"



------------------------------------------------------------
Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail

"The real problem is not whether machines think but whether men do."
-- B. F. Skinner
******************************************************************



On Wed, Jul 1, 2009 at 10:56 PM, Steve
Weston<steve at revolution-computing.com> wrote:
> There have been several announcements of three new packages that I've
> recently uploaded to CRAN: foreach, iterators, and doMC.  You can read
> one description on David Smith's blog, at:
>
>    http://blog.revolution-computing.com
> or:
>    http://bit.ly/tygLz
>
> You can also read the vignette that I wrote for foreach on a CRAN
> website.
>
> I would like to mention that one of the goals of the foreach package is
> to make it easy to write an R package that allows the end user to choose
> what parallel computing engine to use.  That's useful because the user
> may already have and use a parallel computing system, and not want to
> install and maintain yet another one.  (The foreach and iterators packages
> themselves are trivial to install, since they provide a framework for using
> parallel computing systems such as multicore and nws.)
>
> Currently, only the doMC "parallel backend" for multicore is publicly
> available on CRAN, but I'm hoping to get a chance to write and release
> other backend packages, to support MPI and shared memory, for example.
>
> I'd love to hear from R package authors on how to improve foreach
> so that it's a more attractive platform on which to develop parallel
> applications.  Especially if you've had difficulty using parallel
> computing systems in the past.
>
> --
> Steve Weston
> REvolution Computing
> One Century Tower | 265 Church Street, Suite 1006
> New Haven, CT  06510
> P: 203-777-7442 x266 | www.revolution-computing.com
>
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