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 ...
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)
>
Ben, possibly useful project related to this https://github.com/staticfloat/libblastrampoline which is what Dirk referred to as the Julia state of art. It is actually much more complex than it sounds because of differences in naming and ABI between BLAS implementations, so simple switches don't work. Dirk has the luxury of having control over what he compiles, but that is not always the case (like with Accelerate or MKL) ... Cheers, Simon> On 18/03/2021, at 3:53 PM, Ben Bolker <bbolker at gmail.com> 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 ... > > 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 at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
On 17 March 2021 at 22:53, 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!). And for what it is worth, the aforementioned 'switching from within' solution is using FlexiBLAS (not BLIS as I had said in the previous email), and was described in an R application R here: https://www.enchufa2.es/archives/switch-blas-lapack-without-leaving-your-r-session.html That won't help for you tried on your Debian-based system though, and I would (in the near-term) try that. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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 Best Tomas> > ? 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 at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel