On 05/28/2010 01:27 AM, Avraham Adler wrote:
Hello. I am a Linux neophyte and know almost nothing about compiling,
so I would appreciate any help and advice y'all would care to offer.
I am trying to compile the 64 bit version of R using a tuned ATLAS and
LAPACK (ATLAS 3.9.24). I am running Ubunto 10.04 LTS (through wubi,
FWIW). The ATLAS and LAPACK files (atlas.so, f77blas.so, lapack.so,
and cblas.so) are sitting in the folder "/usr/local/atlas/lib"
(together with the static .a versions and some other files.
Following the R installation manual, I used the following configure string:
./configure --enable-R-shlib --enable-BLAS-shlib
--with-blas="-L/usr/local/atlas/lib -latlas -lf77blas"
--with-lapack="-L/usr/local/atlas/lib -llapack -lcblas" CFLAGS='-O3
-pipe -march=native' CXXFLAGS='-O3 -pipe -march=native'
R_PAPERSIZE='letter'
The configuration routine returns the following errors:
checking for cblas_cdotu_sub in vecLib framework... no
checking for dgemm_ in -L/usr/local/atlas/lib -latlas -lf77blas... no
checking for dgemm_... no
checking for ATL_xerbla in -latlas... no
checking for dgemm_ in -lblas... no
checking for dgemm_ in -lblas... (cached) no
checking for dgemm_ in -lblas... (cached) no
Looking at the config.log shows the following:
configure:28566: checking for dgemm_ in -L/usr/local/atlas/lib -latlas -lf77blas
configure:28587: gcc -std=gnu99 -o conftest -O3 -pipe -march=native
-fpic -I/usr/local/include -L/usr/local/lib64 conftest.c
-L/usr/local/atlas/lib -latlas -lf77blas -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
If I run "make" after this, R starts compiling and uses its own
built-in blas and lapack
I tried various different flavors of the configuration line including
using BLAS_LIBS and LAPACK_LIBS to pass the folder and libraries, and
nothing seems to work.
I do not know enough to know if the problem with my ATLAS libraries or
if the problem with my attempt at compiling R. If it makes a
difference, the ATLAS (3.9.24) needed to be compiled with the
--allow-multiple-definitions (-z multidef) option because of what may
be a bug
(see<http://sourceforge.net/tracker/?func=detail&aid=2998779&group_id=23725&atid=379483>
)
I do not know if I could follow the "Shared BLAS" route suggested for
ACML/Goto, as ATLAS requires two files (the f77blas library as well).
Also, I would like to use the tuned lapack.
I would very much appreciate any and everyones advice, as I have no
idea how to proceed.
Thank you,
--Avraham
Avraham,
As has been mentioned before, the R packages available on CRAN have been
built with support for BLAS. If you still want to compile your own, my
suggestion would be to google the following:
"checking for dgemm_... no"
OR
"warning: implicit declaration of function 'dgemm_'"
Make sure you use the quotes. You may find an answer to your problem there.
Michael
--
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter
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