From edd at debian.org  Tue Jun  3 17:16:35 2008
From: edd at debian.org (Dirk Eddelbuettel)
Date: Tue, 3 Jun 2008 15:16:35 +0000
Subject: [Rd] benchmarking R installations
In-Reply-To: <6b93d1830806030809w7139ee32g7b85a6210922784d@mail.gmail.com>
References: <6b93d1830806022056o274e97c3i8d954748e17f6a81@mail.gmail.com>
	<20080603041851.GA14088@eddelbuettel.com>
	<6b93d1830806030809w7139ee32g7b85a6210922784d@mail.gmail.com>
Message-ID: <20080603151634.GA5771@master.debian.org>

On Tue, Jun 03, 2008 at 11:09:28AM -0400, Mark Kimpel wrote:
> Dirk,
> 
> At the moment, our emphasis is getting an installation that will run Rmpi in
> batch mode. I imagine my sysadmin put that line in to minimize potential
> problems. To be honest, I didn't catch it, I was just glad to get a compile
> :)
> 
> As to the line that doesn't apply to the R install, I think you are
> referring to the "with mpi", which I think he also slipped in not realizing
> it should more properly go with the Rmpi install.

Right. I wasn't implying it would do harm.

As for the x11 choice: I prefer to keep the change vectors
minimal. Otherwise you go nuts trying to debug things.

But it's good to see that you now understand that you have to start
'at the top' with Intel icc, and once you have a working R with you
can start working towards packages.  It's like a port to a different
platform as you completely switch the toolchain.

Good luck and keep us posted. I have looking at icc on the TODO list
too (for my C++ code, though, given R's interactive nature I think
there are lower hanging fruits elsewhere...)

Lastly, as to the benchmarking: It's difficult. Ripley once snarled
that it is probably the application you want to run the most so
there you go ...

Dirk

> 
> Mark
> 
> On Tue, Jun 3, 2008 at 12:18 AM, Dirk Eddelbuettel <edd at debian.org> wrote:
> 
> > On Mon, Jun 02, 2008 at 11:56:16PM -0400, Mark Kimpel wrote:
> > > ../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
> > \
> >
> > There is no such option for R's configure.
> >
> > > --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 \
> >
> > So you never want your compute cluster to be able to do an interactive
> > plot under x11 ?
> >
> > Dirk
> >
> > --
> > Three out of two people have difficulties with fractions.
> >
> 
> 
> 
> -- 
> 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)
> 
> ******************************************************************

-- 
Three out of two people have difficulties with fractions.



[Rd] benchmarking R installations
Dirk Eddelbuettel