[R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS
roy
ro|||n|or@|| @end|ng |rom gm@||@com
Wed Sep 30 10:41:12 CEST 2020
Thanks to all for the info and to Kasper for the complete options in
building R on macos. Using xcode clang/blas, I successfully built R 4.0.2
with the accelerate framework (or vecLib). I did some initial performance
tests using the scripts from
https://blog.revolutionanalytics.com/2014/10/revolution-r-open-mkl.html (a
cross product and a Cholesky factorization).
1. R 4.0.2 macos built with xcode/clang; without accelerate: cross
product: 151 secs elapsed / 151 secs user; factorization: 23 secs elapsed /
23 secs user
2. R 4.0.2 macos built with xcode/clang; with accelerate: cross
product: 1.7 secs elapsed / 6.3 secs user; factorization: 0.6 secs elapsed
/ 1.9 secs user
3. R 4.0.2 w/ MKL sequential via ubuntu/docker on mac: cross
product: 5 secs elapsed / 5 secs user; factorization: 0.94 secs elapsed /
0.9 secs user
4. R 4.0.2 w/ MKL parallel via ubuntu/docker on mac: cross
product: 2.8 secs elapsed / 5.3 secs user; factorization: 0.55 secs elapsed
/ 0.9 secs user
btw, these tests were done on:
- macos 10.15.7
- 2018 mac mini
- 3.6 GHZ, quad core, 16 GB memory
cheers, roy
On Wed, Sep 30, 2020 at 12:10 AM Simon Urbanek <simon.urbanek using r-project.org>
wrote:
>
>
> > On Sep 30, 2020, at 03:32, Prof Brian Ripley <ripley using stats.ox.ac.uk>
> wrote:
> >
> > On 29/09/2020 12:27, Kasper Daniel Hansen wrote:
> >> To use veclib you need
> >> --with-blas="-framework Accelerate"
> >
> > Details are in the R-admin manual, including that R fails one of its
> checks.
> >
> > Simon's calling this vecLib is a bit misleading. 'vecLib' was a
> vectorized library for PPC Macs, and the name lives on for a small part of
> the Accelerate framework. The part that supplies an enhanced BLAS is
> different, and is based on ATLAS for x86_64 CPUs.
> >
>
> This is just the way Apple names it (now on all platforms), the name has a
> long history and was related to PPC, but Apple chose not to change it even
> though it doesn't actually contain any PowerPC code anymore. Accelerate is
> just a stub that combines vecLib and vImage, and since R only uses vecLib
> it is sufficient to link to vecLib. I'm just referring to the actual
> framework involved and the vecLib framework itself contains all the
> libraries including LAPACK and BLAS (
> https://developer.apple.com/documentation/accelerate/veclib ).
>
> Cheers,
> Simon
>
>
> > Incidentally, on the configuration issue -- had you followed the posting
> guide and either read the current manual or tried R-patched you would not
> have encountered the problem (which AFAWK is very recent, from the Command
> Line Tools for Xcode 12, released only for rather recent versions of
> Catalina and pre-Big Sur about 10 days ago). Now documented at
> >
> >
> https://developer.apple.com/documentation/xcode-release-notes/xcode-12-release-notes
> >
> >> On Tue, Sep 29, 2020 at 9:53 AM roy <rollinforall using gmail.com> wrote:
> >>> Hi Simon,
> >>> Thanks for the info. I was totally unaware of ABI, vecLib, etc and
> that
> >>> Apple has blas, lapack, etc. But after reading up on this and
> re-reading
> >>> your email, I'm beginning to understand more about this.
> >>>
> >>> So, I would like to first checkout vecLib. From what you say, would I
> have
> >>> to do something like the following?
> >>>
> >>> ./configure --enable-BLAS-shlib --with-blas="-lBLAS" ...
> >>>
> >>> Is this also possible with LAPACK?
> >>>
> >>> tx again.
> >>> cheers, roy
> >>>
> >>>
> >>> On Mon, Sep 28, 2020 at 3:01 PM Simon Urbanek <
> simon.urbanek using r-project.org
> >>>>
> >>> wrote:
> >>>
> >>>> Rollin,
> >>>>
> >>>> it has been several years since I last tested MKL, so take it with a
> >>> grain
> >>>> of salt, but in general you don't necessarily have to build R with
> MKL in
> >>>> order to use it - you only need to use --enable-BLAS-shlib and link to
> >>> any
> >>>> ABI-compatible BLAS which can be vecLib as well. Then you can change
> the
> >>>> link from vecLib to MKL in the BLAS stub. Note that we only need the C
> >>> ABI,
> >>>> there are wrappers vecLibg95f.* which re-map the F entry points to C
> >>> entry
> >>>> points as to avoid Fortran ABI issues thus you don't care about the
> >>>> Fortran. However, historically, MKL has not been much more performant
> >>> than
> >>>> vecLib so it's unclear if it is worth the hassle. As with any
> accelerated
> >>>> BLAS, note that this may have effects on results in R.
> >>>>
> >>>> Cheers,
> >>>> Simon
> >>>>
> >>>>
> >>>>
> >>>>> On 28/09/2020, at 7:07 PM, rollin <rollinforall using gmail.com> wrote:
> >>>>>
> >>>>> I wanted to build R from source on macos (10.15.5) so I could include
> >>>>> Intel's MKL. So I first looked at building R from source without
> MKL.
> >>>>>
> >>>>> From the installation doc, I modified config.site to have the
> >>> following:
> >>>>>
> >>>>> CC=clang
> >>>>> OBJC=$CC
> >>>>> FC=/usr/local/bin/gfortran
> >>>>> CXX=clang++
> >>>>>
> >>>>>
> >>>>> I then ran configuration via the command:
> >>>>>
> >>>>> ./configure -C --enable-R-shlib --enable-memory-profiling
> >>>>> --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
> >>>>>
> >>>>
> >>>
> PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
> >>>>>
> >>>>>
> >>>>> And received the following information and error:
> >>>>>
> >>>>> checking if bzip2 version >= 1.0.6... no
> >>>>> checking whether bzip2 support suffices... configure: error: bzip2
> >>>> library
> >>>>> and headers are required
> >>>>>
> >>>>>
> >>>>> By looking at the log, I saw a compiler error due to an implicit
> >>>> function.
> >>>>> I then made the following change in config.site:
> >>>>>
> >>>>> CFLAGS='-Wno-implicit-function-declaration -g -O2''
> >>>>>
> >>>>>
> >>>>> And configure now ran without errors.
> >>>>>
> >>>>> However, when I looked at configuring to use MKL, I discovered that
> MKL
> >>>> on
> >>>>> macos does not support gnu fortran so, unless I purchase Intel's
> >>> Fortran
> >>>>> compiler, it looks like I'm sol.
> >>>>>
> >>>>> Has anyone built R with MKL on macos (10.15)? In any event, I wanted
> >>> to
> >>>> at
> >>>>> least note the issue and work around I encountered when building R on
> >>>>> macos with clang/xcode.
> >>>>>
> >>>>> [[alternative HTML version deleted]]
> >>>>>
> >>>>> _______________________________________________
> >>>>> R-SIG-Mac mailing list
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> >>>>
> >>>>
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
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> >>>
> >
> >
> > --
> > Brian D. Ripley, ripley using stats.ox.ac.uk
> > Emeritus Professor of Applied Statistics, University of Oxford
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
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