Re: [R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS
On Tue, Sep 29, 2020 at 4:32 PM Prof Brian Ripley 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. It may be worth mentioning that python and homebrew have removed all dependency on Accelerate due to bugs and Apple's (lack of) maintenance: https://github.com/scipy/scipy/wiki/Dropping-support-for-Accelerate ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS
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 wrote: > > > > On Sep 30, 2020, at 03:32, Prof Brian Ripley > 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 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.urba...@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 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 > >
Re: [R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS
> On Sep 30, 2020, at 03:32, Prof Brian Ripley 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 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 >>> >>> 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 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 > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>> [[alternative HTML version deleted]] >>> >>>
Re: [R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS
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. 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 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 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 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=$CC FC=/usr/local/bin/gfortran CXX=clang++ I then ran configuration via the command: ./configure -C --enable-R-shlib --enable-memory-profiling --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig And received the following information and error: checking if bzip2 version >= 1.0.6... no checking whether bzip2 support suffices... configure: error: bzip2 library and headers are required By looking at the log, I saw a compiler error due to an implicit function. I then made the following change in config.site: CFLAGS='-Wno-implicit-function-declaration -g -O2'' And configure now ran without errors. However, when I looked at configuring to use MKL, I discovered that MKL on macos does not support gnu fortran so, unless I purchase Intel's Fortran compiler, it looks like I'm sol. Has anyone built R with MKL on macos (10.15)? In any event, I wanted to at least note the issue and work around I encountered when building R on macos with clang/xcode. [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS
To use veclib you need
--with-blas="-framework Accelerate"
My full building script on OS X is currently
../${SRCDIR}/configure SHELL='/bin/bash' \
--prefix=/usr/local/R/${R_VERSION} --disable-R-framework\
CC="/usr/local/clang8/bin/clang" \
CXX="/usr/local/clang8/bin/clang++" \
F77="/usr/local/gfortran/bin/gfortran" \
FC="/usr/local/gfortran/bin/gfortran" \
OBJC="clang" \
CFLAGS="-Wall -mtune=native -g -O2" \
CXXFLAGS="-Wall -mtune=native -g -O2" \
OBJCFLAGS="-Wall -mtune=native -g -O2 -fobjc-exceptions" \
F77FLAGS="-Wall -g -O2 -mtune=generic" \
FCFLAGS="$F77FLAGS" \
FLIBS="-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0
-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm" \
LDFLAGS="-L/usr/local/clang8/lib -L/usr/local/lib" \
DYLD_FALLBACK_LIBRARY_PATH="/usr/local/clang8/lib:/usr/local/lib" \
PKG_CONFIG_PATH="/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig"
\
JAVA_HOME="/System/Library/Frameworks/JavaVM.framework/Home" \
JAVA_CPPFLAGS="-I/System/Library/Frameworks/JavaVM.framework/Headers" \
JAVA_LD_LIBRARY_PATH="" \
JAVA_LIBS="-framework JavaVM" \
--enable-memory-profiling\
--x-includes=/opt/X11/include --x-libraries=/opt/X11/lib\
--with-blas="-framework Accelerate" | tee ../configure-${R_VERSION}
although I think we have moved back to Apple's clang for C etc compiler for
the CRAN version of R instead of Simon's clang8.
Best,
Kasper
On Tue, Sep 29, 2020 at 9:53 AM roy wrote:
> Hi Simon,
> Thanks for the info. I was totally unaware of ABI, vecLib, etc and that
> Apple has blas, lapack, etc. But after reading up on this and re-reading
> your email, I'm beginning to understand more about this.
>
> So, I would like to first checkout vecLib. From what you say, would I have
> to do something like the following?
>
> ./configure --enable-BLAS-shlib --with-blas="-lBLAS" ...
>
> Is this also possible with LAPACK?
>
> tx again.
> cheers, roy
>
>
> On Mon, Sep 28, 2020 at 3:01 PM Simon Urbanek >
> wrote:
>
> > Rollin,
> >
> > it has been several years since I last tested MKL, so take it with a
> grain
> > of salt, but in general you don't necessarily have to build R with MKL in
> > order to use it - you only need to use --enable-BLAS-shlib and link to
> any
> > ABI-compatible BLAS which can be vecLib as well. Then you can change the
> > link from vecLib to MKL in the BLAS stub. Note that we only need the C
> ABI,
> > there are wrappers vecLibg95f.* which re-map the F entry points to C
> entry
> > points as to avoid Fortran ABI issues thus you don't care about the
> > Fortran. However, historically, MKL has not been much more performant
> than
> > vecLib so it's unclear if it is worth the hassle. As with any accelerated
> > BLAS, note that this may have effects on results in R.
> >
> > Cheers,
> > Simon
> >
> >
> >
> > > On 28/09/2020, at 7:07 PM, rollin wrote:
> > >
> > > I wanted to build R from source on macos (10.15.5) so I could include
> > > Intel's MKL. So I first looked at building R from source without MKL.
> > >
> > > From the installation doc, I modified config.site to have the
> following:
> > >
> > > CC=clang
> > > OBJC=$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
> > > R-SIG-Mac@r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> >
>
> [[alternative HTML version deleted]]
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
--
Best,
Kasper
[[alternative HTML version deleted]]
___
R-SIG-Mac
Re: [R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS
In my understanding, almost all of the speed up comes from using an optimized BLAS. Optimizing LAPACK tend to have negligible impact on performance. At least that is my impression, although I won't say I'm an expert. Best, Kasper On Tue, Sep 29, 2020 at 9:53 AM roy 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 > > 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 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 > > > R-SIG-Mac@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > > > [[alternative HTML version deleted]] > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > -- Best, Kasper [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS
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 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 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 > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS
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 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=$CC > FC=/usr/local/bin/gfortran > CXX=clang++ > > > I then ran configuration via the command: > > ./configure -C --enable-R-shlib --enable-memory-profiling > --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib > PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig > > > And received the following information and error: > > checking if bzip2 version >= 1.0.6... no > checking whether bzip2 support suffices... configure: error: bzip2 library > and headers are required > > > By looking at the log, I saw a compiler error due to an implicit function. > I then made the following change in config.site: > > CFLAGS='-Wno-implicit-function-declaration -g -O2'' > > > And configure now ran without errors. > > However, when I looked at configuring to use MKL, I discovered that MKL on > macos does not support gnu fortran so, unless I purchase Intel's Fortran > compiler, it looks like I'm sol. > > Has anyone built R with MKL on macos (10.15)? In any event, I wanted to at > least note the issue and work around I encountered when building R on > macos with clang/xcode. > > [[alternative HTML version deleted]] > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Building R 4.0.2 from source via clang/xcode for MKL on macOS
I wanted to build R from source on macos (10.15.5) so I could include Intel's MKL. So I first looked at building R from source without MKL. >From the installation doc, I modified config.site to have the following: CC=clang OBJC=$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 R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
