[Rd] ATLAS threaded 64 bit (Opteron) - need *.so?

[Douglas Bates]

Peter Dalgaard <p.dalgaard at biostat.ku.dk> writes:

> Martin Maechler <maechler at stat.math.ethz.ch> writes:
> 
> > and compilation (of course) goes fine till the crucial linking
> > stage :
> > 
> > gcc -shared   -o libRlapack.so dlapack0.lo dlapack1.lo dlapack2.lo dlapack3.lo cmplx.lo  -lf77blas -latlas -L/usr/lib64 -L/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3 -L/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../../lib64 -L/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../.. -L/lib/../lib64 -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm -lgcc_s
> > /usr/bin/ld: /usr/local/lib/libf77blas.a(xerbla.o): relocation R_X86_64_32 can not be used when making a shared object; recompile with -fPIC
> > /usr/local/lib/libf77blas.a: could not read symbols: Bad value
> > collect2: ld returned 1 exit status
> > 
> > and I'm stuck to some extent.
> > Note that the "recompile with -fPIC"  must related to the
> > contents of ATLAS' libf77blas.a itself (or to "xerbla.o" more
> > concretely), since all of R's  dlapack[0-3].lo are of course
> > compile with -fPIC.
> > 
> > I tend to conclude that I do need shared versions of ATLAS'
> > libraries?  If yes, I think I've seen instructions on how to
> > build these.  Where?
> > If these are really needed, I think I should add them to the
> > corresponding "R administration manual" section, right?
> 
> I don't think we actually got them written down (thank you for
> volunteering...) but it isn't terribly hard. There are just two basic
> tricks:
> 
> - add -fPIC all over the place during configure.
> 
> - after building you'll get a bunch of .a files. These can be
>   converted to .so using 
> 
>         ld -shared -o libfoo.so --whole-archive libfoo.a
> 
> One thing I haven't gotten around to yet is the ATLAS/LAPACK
> integration mentioned on
> http://math-atlas.sourceforge.net/errata.html#completelp

Have you tried configuring R with Goto's BLAS
                http://www.cs.utexas.edu/users/kgoto/

I haven't worked with Opteron or Athlon64 computers but I understand
that Goto's BLAS are very effective on those machines.  Furthermore
Goto's BLAS are (only) available as .so libraries so you don't need to
mess with creating the .so version.