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 _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
