Thank you both very much for the advice. It is obviously significantly more complicated than I first thought (although I /did/ manage to compile both ATLAS and R under windows following the instructions, go figure :). ) so I'll stop trying to bite off more than I can chew.
Thank you again, --Avraham On 5/28/10, Dirk Eddelbuettel <[email protected]> wrote: > > On 28 May 2010 at 10:02, Michael Rutter wrote: > | 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. > > Michael's advice is very, very good. Particularly if you are new to > this. Compiling Atlas _well_ is hard. > > And as Michael says, you don't have to. You system already does this. > > | > 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. > > Ubuntu 10.04 gives you prebuilt Atlas packages (albeit 3.6.0). Easiest > solution. > > You can take the Atlas packages from Debian (3.8.*) and rebuild locally. > > Or you can insinst on building all this yourself but it _is_ difficult. Few > of use here do this regularly, so few will be able to help. > > | > 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 > > In other words, complete failure... > > | > 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. > > I'd say start with the easy route as you can then proceed with your actual > modeling, estimation or data work. > > Dirk > > | > > | > 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 > | > | _______________________________________________ > | R-SIG-Debian mailing list > | [email protected] > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian > > -- > Regards, Dirk > -- Sent from my mobile device _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
