[R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS

[Simon Urbanek]

> 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]]
>>>>> 
>>>>> _______________________________________________
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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
> 
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