From mwkimpel at gmail.com  Wed Jun  4 04:17:33 2008
From: mwkimpel at gmail.com (Mark Kimpel)
Date: Tue, 3 Jun 2008 22:17:33 -0400
Subject: [Rd] benchmarking R installations
In-Reply-To: <18501.52730.350059.509071@cmath-5.math.ethz.ch>
References: <6b93d1830806022056o274e97c3i8d954748e17f6a81@mail.gmail.com>
	<20080603095219.G53049@xs7.xs4all.nl>
	<339D6E60-D926-4351-93DB-1E7C7D366800@r-project.org>
	<18501.52730.350059.509071@cmath-5.math.ethz.ch>
Message-ID: <6b93d1830806031917g39677670m8671ced32a7805fe@mail.gmail.com>

Thanks, once I get my new Intel installation running in tandem with a
gcc one, I'll report back. mark

On Tue, Jun 3, 2008 at 7:04 PM, Martin Maechler
<maechler at stat.math.ethz.ch> wrote:
>>>>>> "SU" == Simon Urbanek <simon.urbanek at r-project.org>
>>>>>>     on Tue, 3 Jun 2008 11:52:14 -0400 writes:
>
>    SU> On Jun 3, 2008, at 3:58 AM, Ludo Pagie wrote:
>
>    >> recently there was a post on R-help/Rd ?? with this link
>    >> on benchmarking different 'number crunching
>    >> packages'. They used a series of tests, although I didn't
>    >> check they used all the types you mentioned. I couldn't
>    >> find test code at first glance but myyebe it is available
>    >> on request???
>    >>
>    >> http://www.sciviews.org/benchmark/
>    >>
>
>    SU> It's quite outdated and doesn't work with the current R versions,
>
> Yes, that was the topic of the recent R-help post mentioned
> above.  And because of that I did post an updated version back to the
> list.
> Here's the posting, as found on http://search.r-project.org :
>    http://finzi.psych.upenn.edu/R/Rhelp02a/archive/130270.html
> and the R script here
>   https://stat.ethz.ch/pipermail/r-help/attachments/20080514/0ccea72b/attachment.pl
>
>    SU> but I have an updated version that works. I have put some
>    SU> benchmarks I'm aware of at
>
>    SU> http://r.research.att.com/benchmarks/
>
> That's cool!  Thanks, Simon!
> Martin
>
>    >> On Mon, 2 Jun 2008, Mark Kimpel wrote:
>    >>
>    >>> Recently I posted to this list with a question about
>    >>> using the Intel 10.1 compilers in building R and one
>    >>> response was basically, "why in the heck would you want
>    >>> to do that?" The answer is that my sysadmin believes
>    >>> that there will be a performance boost with the Intel
>    >>> vs. Gnu compilers on our Linux cluster, of which I am
>    >>> one of many users. Wanting to be a good citizen and use
>    >>> my machine time wisely, I'd of course like to use right
>    >>> tool to build the most efficient installation of R and
>    >>> associated packages.  BTW, we got R to compile nicely
>    >>> using the settings at the end of this post.
>    >>>
>    >>> Looking back on previous posts, however, it seems that
>    >>> there is no consensus as to how to benchmark R. I
>    >>> realize such a task is not trivial, nor controversial,
>    >>> but does anyone have a set of time-consuming tasks that
>    >>> can be used to compare R installations? It would seem
>    >>> logical that such a benchmark would include
>    >>> sub-benchmarks on file access, interpreted intensive
>    >>> tasks, C intensive tasks, BLAS intensive tasks, etc. You
>    >>> developers know more about this than I do, but I know
>    >>> enough to realize that there won't be one simple
>    >>> answer. Nevertheless, I'd like to make my usage
>    >>> decisions on something rather than anedotal claims.
>    >>>
>    >>> So, does anyone know of a good benchmarking script or
>    >>> would be willing to contribute one?
>    >>>
>    >>> And here are the settings we used to compile R with
>    >>> Intel 10.1 compilers:
>    >>>
>    >>> ../configure
>    >>> --prefix=/N/u/mkimpel/R_HOME/R-patched/R-build \
>    >>> --with-system-zlib=/usr/lib64
>    >>> --with-system-bzlib=/usr/lib64 \
>    >>> --with-mpi=/N/soft/linux-rhel4-x86_64/openmpi/1.2.5/intel-64
>    >>> --with- tcltk \
>    >>> --with-tcl-config=/N/soft/linux-rhel4-x86_64/tcl8.4.16/lib64/
>    >>> tclConfig.sh \
>    >>> --with-tk-config=/N/soft/linux-rhel4-x86_64/tk8.4.16/lib64/
>    >>> tkConfig.sh \ --without-x --without-readline
>    >>> --without-iconv \
>    >>> CC="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icc"
>    >>> \ CFLAGS="-O3 -no-prec-div -unroll" \
>    >>> F77="/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin/ifort"
>    >>> \ FFLAGS="-O3 -no-prec-div -unroll" \
>    >>> CXX="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icpc"
>    >>> \ CXXFLAGS="-O3 -no-prec-div -unroll" \
>    >>> FC="/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin/ifort"
>    >>> \ FCFLAGS="-O3 -no-prec-div -unroll" \
>    >>> OBJC="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icc"
>    >>> \ OBJCFLAGS="-O3 -no-prec-div -unroll" \
>    >>> --disable-R-profiling --disable-memory-profiling
>    >>> ##
>    >>> make all make install
>    >>>
>    >>> Mark
>    >>>
>    >>> --
>    >>> 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 (317) 663-0513
>    >>> Home (no voice mail please)
>    >>>
>    >>> ******************************************************************
>    >>>
>    >>> [[alternative HTML version deleted]]
>    >>>
>    >>> ______________________________________________
>    >>> R-devel at r-project.org mailing list
>    >>> https://stat.ethz.ch/mailman/listinfo/r-devel
>    >>>
>    >>
>> ______________________________________________
>    >> R-devel at r-project.org mailing list
>    >> https://stat.ethz.ch/mailman/listinfo/r-devel
>    >>
>    >>
>
> ______________________________________________
>    SU> R-devel at r-project.org mailing list
>    SU> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



-- 
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
(317) 663-0513 Home (no voice mail please)



[Rd] benchmarking R installations
Mark Kimpel