R SIG Debian - Dec 2023 - custom built R will not change BLAS/LAPACK with update-alternatives

What blas/lapack -dev libraries do you installed when you build?  I varied
this over the two+ decades for the Debian build but any consistent pair of
LAPACK and BLAS should work. From the aforementioned build log:

Get: 150 http://ftp.us.debian.org/debian sid/main amd64 libblas3 amd64 3.11.0-2
[149 kB]
Get: 151 http://ftp.us.debian.org/debian sid/main amd64 libblas-dev amd64
3.11.0-2 [158 kB]
[...]
Get: 227 http://ftp.us.debian.org/debian sid/main amd64 liblapack3 amd64
3.11.0-2 [2323 kB]
Get: 228 http://ftp.us.debian.org/debian sid/main amd64 liblapack-dev amd64
3.11.0-2 [4631 kB]
[...]
Setting up libblas3:amd64 (3.11.0-2) ...

update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to
provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu)
in auto mode

[...]
Setting up liblapack3:amd64 (3.11.0-2) ...

update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to
provide /usr/lib/x86_64-linux-gnu/liblapack.so.3
(liblapack.so.3-x86_64-linux-gnu) in auto mode


I use

  libblas-dev, liblapack-dev

as the Build-Depends in the chroot.  I think these are the generic one, they
provide a fallback. (And run-time I think I am defaulting to OpenBLAS most of
the time.)


FWIW I always found

  --with-blas="-lblas"
  --with-lapack="-llapack"

a little suspicious, but maybe that is just me if this works for you we are
where we wanted to be and all is good?

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

On Sat, 30-December-2023, at 22:45:12, Dirk Eddelbuettel <edd at
debian.org> wrote:
> What blas/lapack -dev libraries do you installed when you build?  I varied
> this over the two+ decades for the Debian build but any consistent pair of
> LAPACK and BLAS should work. From the aforementioned build log:
>
> Get: 150 http://ftp.us.debian.org/debian sid/main amd64 libblas3 amd64
3.11.0-2 [149 kB]
> Get: 151 http://ftp.us.debian.org/debian sid/main amd64 libblas-dev amd64
3.11.0-2 [158 kB]
> [...]
> Get: 227 http://ftp.us.debian.org/debian sid/main amd64 liblapack3 amd64
3.11.0-2 [2323 kB]
> Get: 228 http://ftp.us.debian.org/debian sid/main amd64 liblapack-dev amd64
3.11.0-2 [4631 kB]
> [...]
> Setting up libblas3:amd64 (3.11.0-2) ...
> update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to
provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu)
in auto mode
> [...]
> Setting up liblapack3:amd64 (3.11.0-2) ...
> update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3
to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3
(liblapack.so.3-x86_64-linux-gnu) in auto mode
>
> I use
>
>   libblas-dev, liblapack-dev
>
> as the Build-Depends in the chroot.  I think these are the generic one,
they
> provide a fallback.
I have those same four.  But right now also atlas and openblas (and this in
pthreads and openmp versions), and I don't build in a chroot (it is just for
my own consumption).  So this is the source of the differences: these extra ones
are picked (and then BLAS_LIBS set to "-lwhatever") before the generic
ones.

Mystery solved :-)  
> (And run-time I think I am defaulting to OpenBLAS most of
> the time.)
>
>
> FWIW I always found
>
>   --with-blas="-lblas"
>   --with-lapack="-llapack"
>
> a little suspicious, but maybe that is just me if this works for you we are
> where we wanted to be and all is good?
>
All is good. (Just for the sake of curiosity, and if you have the time: why did
you find those incantations suspicious?)

Thanks a lot again to both you and Ivan.

Best,

R.
> Dirk

-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-31
Facultad de Medicina 
Universidad Aut?noma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02 at gmail.com
       r.diaz at uam.es
       ramon.diaz at iib.uam.es

https://ligarto.org/rdiaz