[R-sig-Debian] Compiling R-2.11.0 with ATLAS-tuned BLAS and LAPACK

[Dirk Eddelbuettel]

Hi Andrew,

On 2 June 2010 at 02:08, Andrew Piskorski wrote:
| Dirk, that reminds me.  I DO build R myself from scratch, but it often

I'm curious -- Why?

| ends up not using Atlas even though I told it "--with-blas".
| 
| In particular, I just built R 2.11.1 on an x86-64 server running
| Ubuntu 8.04.4 LTS (Hardy), and it doesn't want to use Atlas.  This
| machine has both these Atlas packages installed, although I'm not sure
| what the 3gf stuff is:
| 
|   ii  atlas3-base       3.6.0-20.6         Automatically Tuned Linear Algebra Software, 
|   ii  libatlas3gf-base  3.6.0-21.1ubuntu3  Automatically Tuned Linear Algebra Software, 
| 
| Below is my configure command and some of the relevant output.  Am I
| doing anything obviously wrong?  Or could this be some sort of
| limitation of the older Atlas packages on this machine?  Is R deciding
| not to use Atlas because of the "checking whether double complex BLAS
| can be used... no"?
| 
| ------------------------------------------------------------
| 
| LIBnn=lib r_arch=x86_64 LIBS=-lpthread ../configure  -with-x=yes --enable-R-shlib --enable-R-profiling --with-tcltk=/usr/lib/tcl8.4 --with-tcl-config=/usr/lib/tcl8.4/tclConfig.sh --enable-threads=posix --with-blas 

You could peek into my my obviously public configure call (by looking at
debian/rules), I use --with-blas and --with-lapack and you differ in at least
one.

I have also in the past (see commented-out code) had to say --with-blase=SOMETHING
for various values of something. 

As for the rest, I can only suggest the R Inst + Admin manual to you. 

You can also look into the code configure runs and try the tests by hand to
see if the library supports them ornot.

| checking build system type... x86_64-unknown-linux-gnu 
| checking host system type... x86_64-unknown-linux-gnu 
|  
| checking whether C99 double complex is compatible with Rcomplex... yes 
| yes 
| checking for cblas_cdotu_sub in vecLib framework... no 
| checking for dgemm_... no 
| checking for ATL_xerbla in -latlas... no 
| checking for dgemm_ in -lblas... yes 
| checking for dgemm_ in -ldgemm... no 
| checking for dgemm_ in -lblas... (cached) yes 
| checking for dgemm_ in -lessl... no 
| checking for dgemm_ in -lblas... (cached) yes 
| checking whether double complex BLAS can be used... no 
|  
|   C compiler:                gcc -std=gnu99  -g -O2 
|   Fortran 77 compiler:       gfortran  -g -O 
|   C++ compiler:              g++  -g -O2 
|   Fortran 90/95 compiler:    gfortran -g -O 
|   Obj-C compiler:              
|   Interfaces supported:      X11, tcltk 
|   External libraries:        readline 

No Blas. I get 

  External libraries:        readline, BLAS(generic), LAPACK(generic)

indicating that we use the generic interface permitting the plug-in use.

Hth, Dirk

|   Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo 
|   Options enabled:           shared R library, shared BLAS, R profiling, Java 
|   Recommended packages:      yes 
| 
| -- 
| Andrew Piskorski <atp at piskorski.com>
| http://www.piskorski.com/
| 
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-- 
  Regards, Dirk