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

[Steve Weston]

And you can get much better results using sqrt directly on the vector,
as it is intended to be called.  The sqrt function is so fast that it's
crazy to call it in parallel the way my vignette shows.  The
overhead kills you.  But I have this bad habit of using sqrt in my
parallel programming examples.  I actually put a footnote in the
vignette saying you should never do what I just did, but I can see
now that I wasn't nearly explicit enough.  I should probably include
a big disclaimer saying not to try this at home.

I'm pretty sure that the next version of foreach will issue warnings
if the tasks execute in less than a second.  But I'll definitely fix
the vignette.  Sorry about that.

- Steve



On Wed, Jul 15, 2009 at 12:54 PM, Mark Kimpel<mwkimpel at gmail.com> wrote:
> 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
>>
>> _______________________________________________
>> R-sig-hpc mailing list
>> R-sig-hpc at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>>
>



-- 
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