Configuring compilers on Mac M1 (Big Sur, Monterey) for Rcpp and other tools

by

Background

Currently (2022-04-24), CRAN builds R 4.2 binaries for Apple silicon using Apple clang from Command Line Tools for Xcode 13.1 and using an experimental fork of GNU Fortran 12.

If you obtain R from CRAN (i.e., here), then you need to replicate CRAN’s compiler setup on your system before building R packages that contain C/C++/Fortran code from their sources (and before using Rcpp, etc.). This requirement ensures that your package builds are compatible with R itself.

A further complication is the fact that Apple clang doesn’t support OpenMP, so you need to do even more work to compile programs that make use of multithreading. You could circumvent the issue by building R itself and all R packages from sources with LLVM clang, which does support OpenMP, but that approach is onerous and “for experts only”.

There is another approach that has been tested by a few people, including Simon Urbanek, the maintainer of R for macOS. It is experimental and also “for experts only”, but it works on my machine and is much simpler than learning to build R yourself.

Instructions for obtaining a working toolchain

Warning: These come with no warranty and could break at any time. Some level of familiarity with C/C++/Fortran program compilation, Makefile syntax, and Unix shells is assumed. Everyone is encouraged to consult official documentation, which is more likely to be maintained than answers on SO. As usual, sudo at your own risk.

I will try to address compilers and OpenMP support at the same time. I am going to assume that you are starting from nothing. Feel free to skip steps you’ve already taken, though you might find a fresh start helpful.

I’ve tested these instructions on a machine running Big Sur, and at least one person has tested them on a machine running Monterey. I would be glad to hear from others.

  1. Download an R 4.2 binary from CRAN here and install. Be sure to select the binary built for Apple silicon.

  2. Run

    $ sudo xcode-select --install

    in Terminal to install the latest release version of Apple’s Command Line Tools for Xcode, which includes Apple clang. You can obtain earlier versions from your browser here. However, the version that you install should not be older than the one that CRAN used to build your R binary.

  3. Download the gfortran binary recommended here and install by unpacking to root:

    $ curl -LO https://mac.r-project.org/tools/gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz
$ sudo tar xvf gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C /
$ sudo ln -sfn $(xcrun --show-sdk-path) /opt/R/arm64/gfortran/SDK

    The last command updates a symlink inside of the gfortran installation so that it points to the SDK inside of your Command Line Tools installation.

  4. Download an OpenMP runtime suitable for your Apple clang version here and install by unpacking to root. You can query your Apple clang version with clang --version. For example, I have version 1300.0.29.3, so I did:

    $ curl -LO https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
$ sudo tar xvf openmp-12.0.1-darwin20-Release.tar.gz -C /

    After unpacking, you should find these files on your system:

    /usr/local/lib/libomp.dylib
/usr/local/include/ompt.h
/usr/local/include/omp.h
/usr/local/include/omp-tools.h

  5. Add the following lines to $(HOME)/.R/Makevars, creating the file if necessary.

    CPPFLAGS+=-I/usr/local/include -Xclang -fopenmp
LDFLAGS+=-L/usr/local/lib -lomp

FC=/opt/R/arm64/gfortran/bin/gfortran -mtune=native
FLIBS=-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm

  6. Run R and test that you can compile a program with OpenMP support. For example:

    if (!requireNamespace("RcppArmadillo", quietly = TRUE)) {
    install.packages("RcppArmadillo")
}
Rcpp::sourceCpp(code="
#include <RcppArmadillo.h>
#ifdef _OPENMP
# include <omp.h>
#endif

// [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::export]]
void omp_test()
{
#ifdef _OPENMP
    Rprintf("OpenMP threads available: %d\\n", omp_get_max_threads());
#else
    Rprintf("OpenMP not supported\\n");
#endif
}
")
omp_test()

    OpenMP threads available: 8

    If the C++ code fails to compile, or if it compiles without error but you get linker warnings or you find that OpenMP is not supported, then one of us has probably made a mistake. Please report any issues.

References

Everything is a bit scattered:

More Related Contents:

  1. Qt Creator – Project ERROR: Xcode not set up properly. You may need to confirm the license agreement by running /usr/bin/xcodebuild
  2. Relative Paths Not Working in Xcode C++
  3. Missing C++ header after updating OSX Command Line Tools 6.3
  4. C++ if statement/xcode [closed]
  5. C++ beginner here is it possible to call a function within another function?
  6. static variable link error [duplicate]
  7. Finding current executable’s path without /proc/self/exe
  8. Can’t compile a C program on a Mac after upgrading to Catalina 10.15
  9. Catalina C++: Using headers yield error: no member named ‘signbit’ in the global namespace
  10. using \ in a string as literal instead of an escape
  11. How can I compile and run C/C++ code in a Unix console or Mac terminal?
  12. Installing C++ Libraries on OS X
  13. How do you install Boost on MacOS?
  14. Determine Process Info Programmatically in Darwin/OSX
  15. Update GCC on OSX
  16. Simulating key press events in Mac OS X
  17. New to Xcode can’t open files in c++?
  18. linking with clang++ on OS X generates lots of symbol not found errors
  19. How to use Libraries
  20. How to compile C++ with C++11 support in Mac Terminal
  21. Clang C++ Cross Compiler – Generating Windows Executable from Mac OS X
  22. Conflict between dynamic linking priority in OSX?
  23. Broken c++ std libraries on macOS High Sierra 10.13
  24. Compile OpenMP programs with gcc compiler on OS X Yosemite
  25. OpenCV on Mac is not opening USB web camera
  26. “please check gdb is codesigned – see taskgated(8)” – How to get gdb installed with homebrew code signed?
  27. Undefined symbols for architecture x86_64 – Mavericks (Yosemite, El Capitan…)
  28. OSX equivalent of ShellExecute?
  29. How to use dylib in Mac OS X (C++)
  30. How can you compare two character strings statically at compile time

Leave a Comment