[Rd] boneheaded BLAS questions

Tomas Kalibera tom@@@k@||ber@ @end|ng |rom gm@||@com
Thu Mar 18 09:15:55 CET 2021

On 3/18/21 3:53 AM, Ben Bolker wrote:
> Thanks.  I know it's supposed to Just Work (and I definitely 
> appreciate all the work that's gone into making it Just Work 99% of 
> the time!).
>   I tried --with-lapack, no joy.
>   Will try to decipher the rules file tomorrow ...

This is documented in R Admin manual, section A.3, and there is also 
"configure --help".

On my Ubuntu 20.04, using "--with-blas --with-lapack" when a BLAS/LAPACK 
implementation is installed via "apt" works for me:

with libblas3, liblapack3 I get in R via sessionInfo()

BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

then I install libopenblas0 and get, after re-starting R (not rebuilding):

BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3


>   cheers
>    Ben
> On 3/17/21 10:25 PM, Dirk Eddelbuettel wrote:
>> Ben,
>> This stuff has worked unchanged since the 1990s when we had a 
>> _really_ far
>> sighted fellow in Debian come up with the 'switch the links' scheme 
>> which was
>> (and is) subsequently deployed by many numerical applications within 
>> Debian,
>> R and e.g. Octave included.
>> And I used this ability to switch over a decade ago in a 
>> never-quite-finished
>> paper which resulted in a package as well as a vignette as paper 
>> draft on
>> CRAN: gcbd [1] It used the ability to switch between implementation 
>> to time
>> and compare and benchmark the various BLAS and LAPACK libraries -- 
>> which was
>> then motivated by a comparison with GPUs. (The actual code / package is
>> stale-ish as some of the underlying packages have gone as eg the GPU 
>> one --
>> but the mechanics you are after still work the exact same way on 
>> Debian and
>> derivarives including Ubuntu and PopOS.)
>> (As a complete aside, the state of the art here is now one level up in
>> libraries based on flame/blis (a riff on blas) which can do a similar 
>> logical
>> switch _at runtime_ (rather than by flipping softlinks and restarting 
>> the
>> app). Julia and some other languages uses that, I think Fedora may 
>> have it in
>> its R build as well. Inaki may know more...)
>> That said, from the top of my head, I think you error may just be 
>> with the
>> second R compilation -- I always (i.e. for the Debian package) use both
>>    --with-blas --with-lapack
>> and not just --with-blas. And I do there is public: if you know where 
>> to look
>> you can see the exact invocation of the Debian build of the R package 
>> (which
>> Ubuntu and Pop and ... then shadow) [2]
>> Hth, Dirk
>> [1] https://cran.r-project.org/package=gcbd
>> [2] https://sources.debian.org/src/r-base/4.0.4-1/debian/rules/
>>      (and I apologise for how messy this still is)
> ______________________________________________
> R-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

More information about the R-devel mailing list