Using ATLAS with R is an old topic quite covered in the "R
Administration" manual (and by R's "configure" script
collection).
I still do not easily manage to build R properly on our new AMD
Opteron (2-processor).
I did work with the current Atlas 3.6.0, configured manually
(but "express" version) to build a threaded ATLAS version, and
successfully ran Atlas' own "make ptsanity_test arch=Linux_HAMMER64SSE2_2"
sanity check as well.
As it is known, this builds only static (*.a) versions of the
ATLAS libraries. However, after an R site search for (something
like) "ATLAS shared", I found Peter Dalgaard's message
http://finzi.psych.upenn.edu/R/Rhelp02/archive/7158.html
where PD confirmed it would work fine to link against the static
ATLAS libraries.
I didn't need (his suggestion of) using an explicit "-L..atlas_place...",
since these libraries are symbolically linked into
/usr/local/lib/ which is searched by default.
Now, R's configure (R-devel of 2004-02-24)
finds the ATLAS setup well behaved, reporting
>> R is now configured for x86_64-unknown-linux-gnu
>>
>> Source directory: ../R-devel
>> Installation directory: /usr/local
>>
>> C compiler: gcc -g -O2 -Wall -Wno-comment
>> C++ compiler: g++ -g -O2
>> Fortran compiler: g77 -g -O2 -Wall -fno-f90
>>
>> Interfaces supported: X11
>> External libraries: readline, BLAS(ATLAS)
^^^^^^^^^^^
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?
Thanks in advance for your share of experience here.
Martin
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