Compiling R with ATLAS
(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]]
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