From avraham.adler at gmail.com  Fri May 14 18:33:28 2010
From: avraham.adler at gmail.com (Avraham Adler)
Date: Fri, 14 May 2010 12:33:28 -0400
Subject: [Rd] Fwd:  Compiling R with ATLAS
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(Resent as plain text, sorry)

Thank you.

I am doing it this way as I really do not know much about Linux, and I
would not know how to re-compile Rblas and Rlapack with the ATLAS BLAS
and tuned LAPACK after I install the precompiled packages through
synaptic. This way, ostensibly, I should be compiling it from scratch
so it should work. Also, this way, I can compile R itself with
optimization and -march=native to squeeze out whatever speed I can
from my machine.

Any advice would be very much appreciated, and thank you for pointing
me to the correct list.

--Avi


On Fri, May 14, 2010 at 9:00 AM, Douglas Bates <bates at stat.wisc.edu> wrote:
>
> There is a Debian/Ubuntu specific list, R-SIG-Debian at R-project.org,
> which I am cc:'ing on this reply, that is a better location for this
> discussion.
>
> It appears that you may be going about things the hard way. ?There are
> Ubuntu packages for atlas and for R that can handle all of this for
> you. ?Take a look at http://cran.r-project.org/bin/linux/ubuntu for
> information on how to get started. ?It will probably be much easier to
> install the pre-compiled packages first and worry about compilation
> for customization later.
>
> On Thu, May 13, 2010 at 11:16 PM, Avraham Adler <avraham.adler at gmail.com> wrote:
> > Hello. I know almost nothing about Linux, so I apologize if the answer to
> > this is obvious.
> >
> > I am trying to compile R with ATLAS (successfully compiled 3.9.24 on Ubuntu
> > 10.04 64 bit). I configured with:
> >
> > ./configure --enable-R-shlib --enable-BLAS-shlib
> > --with-blas="-L/usr/local/atlas/lib -lf77blas -latlas"
> > --with-lapack="-L/usr/local/atlaslib -llapack -lcblas" --with-x
> >
> > and I get this error (from config.log):
> >
> > configure:28566: checking for dgemm_ in -L/usr/local/atlas/lib -lf77blas
> > -latlas
> > configure:28587: gcc -std=gnu99 -o conftest -g -O2 -fpic
> > -I/usr/local/include ?-L/usr/local/lib64 conftest.c -L/usr/local/atlas/lib
> > -lf77blas -latlas ?-lgfortran -lm -ldl -lm ?>&5
> > conftest.c: In function 'main':
> > conftest.c:193: warning: implicit declaration of function 'dgemm_'
> > /usr/local/atlas/lib/libf77blas.so: undefined reference to
> > `atl_f77wrap_zger2u_'
> > /usr/local/atlas/lib/libf77blas.so: undefined reference to
> > `atl_f77wrap_cger2c_'
> > /usr/local/atlas/lib/libf77blas.so: undefined reference to
> > `atl_f77wrap_zger2c_'
> > /usr/local/atlas/lib/libf77blas.so: undefined reference to
> > `atl_f77wrap_cger2u_'
> > collect2: ld returned 1 exit status
> > configure:28587: $? = 1
> >
> > I found the following e-mail in the archives <
> > http://www.mail-archive.com/r-devel at r-project.org/msg16853.html>, but it has
> > a different error, and the suggestion of switching out the BLAS later does
> > not seem to apply to ATLAS which requires two files, I think.
> >
> > Any advice would be very appreciated.
> >
> > Thank you.
> >
> > ? ? ? ?[[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >



[Rd] Fwd: Compiling R with ATLAS
Avraham Adler