Tommi Mäklin

Postdoctoral researcher | University of Helsinki

Cross-compiling C++ binaries for macOS arm64 and x86_64

Published December 12, 2023

there’s an example script for cross-compiling at the end

Installing software made by other people is one of the several annoying and time-consuming tasks I have to deal with as a bioinformatician. Luckily tools like conda have become much more widespread than they were when I started my career in 2016 but the prebuilt binary remains my go-to choice due to it’s simplicity - provided that one is made available by the maintainers.

Personally I try to provide binaries for my own tools, but cross-compiling for macOS has become a major annoyance after my first (and last if I have a say in the matter) macOS laptop died a while ago. Apple’s transition to the arm64 architecture made the situation worse since maintaining macOS binaries would now require two laptops.

Prebuilding binaries for other Linux distros is easy in a Docker container

For my prebuilt Linux x86_64 C++ binaries, I have been using the Holy Build Box for a few years to create executables that run on different distros without problems. Holy Build Box accomplishes this by compiling the binaries in a Docker container that contains a minimal and the oldest possible Linux install that supports whatever C++ standard you happen to be interested in using. I originally came across this approach in a blog post by Páll Melsted. You can find an example of the wrapper scripts I use on GitHub.

Unfortunately a Holy Build Box style container for macOS builds did not really at the time I created by build scripts, so I was relegated to compiling the binaries on the hardware I had at the time and hoping that they run on other people’s macs. This obviously didn’t work anymore with the arm64 and x86_64 architecture mismatch and although cross-compiling from x86_64 macs to arm64 ones might be possible I just decided to drop support altogether and instruct people to install my tools for mac from bioconda.

Cross-compiling for macOS from a Linux environment

Recently, I discovered the macOS Cross Compiler project by Jerred Shepherd which provides exactly what Holy Build Box project does - a Docker container that sets up an environment where building results in binaries that run on mac under the target architecture. This is great.

Setting up the macOS cross compiler is a bit of work but the result seems to do exactly what I want and calling it is very similar to how I had set up the Linux binaries. I currently use the macOS Cross Compiler to build binaries for mSWEEP, which are detailed below.

Example: compiling mSWEEP for macOS arm64 and x86_64

My workflow consists of two scripts: sets up the compiler toolchain for the target architecture and calls the script inside a Docker container:

## Wrapper for calling the build script `` inside the
## macoss-cross-compiler docker container. 
# Arguments
## 1: version number to build (checked out from the git source tree)
## 2: architecture (one of x86-64,arm64)

set -eo pipefail

if [[ -z $VER ]]; then
  echo "Error: specify version as argument 1"

if [[ -z $ARCH ]]; then
  echo "Error: specify architecture (one of x86-64,arm64) as argument 2"

set -ux

cp ../$2-toolchain.cmake ./

docker run \
  -v `pwd`:/io \
  --rm \
  -it \ \
  /bin/bash /io/ $1 $2

rm $2-toolchain.cmake

In the script above the $ARCH-toolchain.cmake file defines cmake environment variables that point to the compiler toolchain that’s needed. Have a look at the .cmake files in tmaklin/biobins for an example.

The second script,, is specific to the project I’m building and defines how the source should be compiled and which files are included in the release tarball. For mSWEEP, this consists of

## Build script for cross-compiling mSWEEP for macOS x86-64 or arm64.
## Call this from `` unless you know what you're doing.

set -exo pipefail

if [[ -z $VER ]]; then
  echo "Error: specify version"

if [[ -z $ARCH ]]; then
  echo "Error: specify architecture (one of x86-64,arm64)"

apt update
apt install -y cmake git libomp5 libomp-dev

# Extract and enter source
mkdir /io/tmp && cd /io/tmp
git clone
## git checkout v${VER}
git checkout cross-compilation-compatibility

# compile x86_64
mkdir build
cd build
if [ "$ARCH" = "x86-64" ]; then
    cmake -DCMAKE_TOOLCHAIN_FILE="/io/$ARCH-toolchain.cmake" \
          -DCMAKE_C_FLAGS="-march=$ARCH -mtune=generic -m64 -fPIC -fPIE" \
          -DCMAKE_CXX_FLAGS="-march=$ARCH -mtune=generic -m64 -fPIC -fPIE" \
          -DBZIP2_LIBRARIES="/osxcross/SDK/MacOSX13.0.sdk/usr/lib/libbz2.tbd" -DBZIP2_INCLUDE_DIR="/osxcross/SDK/MacOSX13.0.sdk/usr/include" \
          -DZLIB_LIBRARY="/osxcross/SDK/MacOSX13.0.sdk/usr/lib/libz.tbd" -DZLIB_INCLUDE_DIR="/osxcross/SDK/MacOSX13.0.sdk/usr/include" \
          -DCMAKE_BUILD_WITH_FLTO=0  ..
elif [ "$ARCH" = "arm64" ]; then
    cmake -DCMAKE_TOOLCHAIN_FILE="/io/$ARCH-toolchain.cmake" \
          -DCMAKE_C_FLAGS="-arch $ARCH -mtune=generic -m64 -fPIC -fPIE" \
          -DCMAKE_CXX_FLAGS="-arch $ARCH -mtune=generic -m64 -fPIC -fPIE" \
          -DBZIP2_LIBRARIES="/osxcross/SDK/MacOSX13.0.sdk/usr/lib/libbz2.tbd" -DBZIP2_INCLUDE_DIR="/osxcross/SDK/MacOSX13.0.sdk/usr/include" \
          -DZLIB_LIBRARY="/osxcross/SDK/MacOSX13.0.sdk/usr/lib/libz.tbd" -DZLIB_INCLUDE_DIR="/osxcross/SDK/MacOSX13.0.sdk/usr/include" \
          -DCMAKE_BUILD_WITH_FLTO=0  ..
make VERBOSE=1 -j

## gather the stuff to distribute
target=$(echo $target | sed 's/x86-64/x86_64/g')
mkdir $path
cp ../build/bin/mSWEEP $path/
cp ../ $path/
cp ../ $path/
cp ../LICENSE $path/
cd /io/tmp
tar -zcvf $target.tar.gz $target
mv $target.tar.gz /io/
cd /io/
rm -rf tmp cache

In the end we have the mSWEEP_macos-$ARCH-v${VER} tarball containing the prebuilt binary. Neat!