Use wider-compatible LLVM-OpenMP, bundle libgfortran dylibs for mac…

…OS wheels (pybamm-team#4092)

* Set `MACOSX_DEPLOYMENT_TARGET` for prerequisites

* Remove previously set environment variables

* Remove Homebrew libomp installations

* Ignore `pybamm-requires` OpenMP downloads

* Rework docs to add OpenMP instructions

* Download LLVM-OpenMP on macOS

* Remove unused compiler argument

* Fix rpath for libomp dylib at wheel repair

* Fix a failing link

* Revert "Fix rpath for libomp dylib at wheel repair"

This reverts commit 6fb8ef0.

* Fix RPATHs for SuiteSparse and libomp

* 11.1 for arm64 macOS and 11.0 for amd64 macOS

* Set up Fortran compiler via GHA

* Downgrade to gcc 12

* Try fix for macOS amd64 wheels first

* Build on macos-13 image instead

* Debug further, try building against 11.0

* And now build for macOS arm64

* Try building arm64 against 11.0

* Rename wheel from 11_1 to 11_0

* Cleanup and fix up commands

* Rename wheel in dest dir instead

* Cleanup plus references to SciPy license

.github/workflows/publish_pypi.yml

@@ -99,7 +99,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-12]
+        os: [ubuntu-latest, macos-13]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
@@ -109,15 +109,6 @@ jobs:
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
-      # sometimes gfortran cannot be found, so reinstall gcc just to be sure
-      - name: Install SuiteSparse and SUNDIALS on macOS
-        if: matrix.os == 'macos-12'
-        run: |
-          brew install graphviz libomp
-          brew reinstall gcc
-          python -m pip install cmake wget
-          python scripts/install_KLU_Sundials.py
-
       - name: Build wheels on Linux
         run: pipx run cibuildwheel --output-dir wheelhouse
         if: matrix.os == 'ubuntu-latest'
@@ -153,18 +144,57 @@ jobs:
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
-      - name: Install SuiteSparse and SUNDIALS on macOS
-        run: |
-          brew install graphviz libomp
-          brew reinstall gcc
-          python -m pip install cmake pipx
-          python scripts/install_KLU_Sundials.py
-
       - name: Build wheels on macOS arm64
-        run: python -m pipx run cibuildwheel --output-dir wheelhouse
+        run: |
+          python -m pip install cibuildwheel
+          python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
-          CIBW_REPAIR_WHEEL_COMMAND: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
+          MACOSX_DEPLOYMENT_TARGET: 11.0
+          # Sourced from
+          # License: BSD-3-Clause
+          # https://github.com/scipy/scipy/blob/f2d4775e7762fad984f8f0acd8227c725ff21630/tools/wheels/cibw_before_build_macos.sh#L23-L49
+          CIBW_BEFORE_ALL_MACOS: |
+            set -e -x
+
+            # download gfortran with proper macos minimum version (11.0)
+            curl -L https://github.com/isuruf/gcc/releases/download/gcc-11.3.0-2/gfortran-darwin-arm64-native.tar.gz -o gfortran.tar.gz
+
+            GFORTRAN_SHA256=$(shasum --algorithm 256 gfortran.tar.gz)
+            KNOWN_SHA256="84364eee32ba843d883fb8124867e2bf61a0cd73b6416d9897ceff7b85a24604  gfortran.tar.gz"
+            if [ "$GFORTRAN_SHA256" != "$KNOWN_SHA256" ]; then
+              echo "SHA256 mismatch for gfortran.tar.gz"
+              echo "expected: $KNOWN_SHA256"
+              echo "got: $GFORTRAN_SHA256"
+              exit 1
+            fi
+
+            mkdir -p gfortran_installed/
+            tar -xv -C gfortran_installed/ -f gfortran.tar.gz
+
+            export FC=$(pwd)/gfortran_installed/gfortran-darwin-arm64-native/bin/gfortran
+            export PATH=$(pwd)/gfortran_installed/gfortran-darwin-arm64-native/bin:$PATH
+
+            # link libgfortran.5.dylib, libgfortran.dylib, libquadmath.0.dylib, libquadmath.dylib, libgcc_s.1.1.dylib
+            # and place them in $HOME/.local/lib, and then change rpath
+            # note: libgcc_s.1.dylib not present for arm64, skip for now
+            # to $HOME/.local/lib
+
+            mkdir -p $HOME/.local/lib
+            lib_dir=$(pwd)/gfortran_installed/gfortran-darwin-arm64-native/lib
+            for lib in libgfortran.5.dylib libgfortran.dylib libquadmath.0.dylib libquadmath.dylib libgcc_s.1.1.dylib; do
+              cp $lib_dir/$lib $HOME/.local/lib/
+              install_name_tool -id $HOME/.local/lib/$lib $HOME/.local/lib/$lib
+            done
+
+            export SDKROOT=${SDKROOT:-$(xcrun --show-sdk-path)}
+
+            python -m pip install cmake wget
+            python scripts/install_KLU_Sundials.py
+          CIBW_BEFORE_BUILD_MACOS: python -m pip install --upgrade pip cmake casadi setuptools wheel delocate
+          # Use higher macOS target for now: https://github.com/casadi/casadi/issues/3698
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: |
+            delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel} --require-target-macos-version 11.1
+            for file in {dest_dir}/*.whl; do mv "$file" "${file//macosx_11_1/macosx_11_0}"; done
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for macOS arm64

.gitignore

@@ -137,3 +137,7 @@ results/
 
 # tests
 test_callback.log
+
+# openmp downloads
+install_KLU_Sundials/openmp-*
+install_KLU_Sundials/usr/

.lycheeignore

@@ -1,6 +1,7 @@
 # a list of links/files to be ignored by lychee link checker (see workflow file)
 https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v%7BSUITESPARSE_VERSION%7D.tar.gz
 https://github.com/LLNL/sundials/releases/download/v%7BSUNDIALS_VERSION%7D/sundials-%7BSUNDIALS_VERSION%7D.tar.gz
+https://mac.r-project.org/openmp/openmp-%7BOPENMP_VERSION%7D-darwin20-Release.tar.gz
 
 # Errors in docs/source/user_guide/getting_started.md
 file:///home/runner/work/PyBaMM/PyBaMM/docs/source/user_guide/api_docs

docs/source/user_guide/installation/install-from-source.rst

@@ -43,11 +43,11 @@ You can install the above with
 
 	Where ``X`` is the version sub-number.
 
-.. tab:: MacOS
+.. tab:: macOS
 
 	.. code:: bash
 
-		brew install python openblas gcc gfortran graphviz libomp cmake pandoc
+		brew install python openblas gcc gfortran graphviz cmake pandoc
 
 .. note::
 
@@ -82,8 +82,9 @@ If you are running windows, you can simply skip this section and jump to :ref:`p
 	  # in the PyBaMM/ directory
 	  nox -s pybamm-requires
 
-This will download, compile and install the SuiteSparse and SUNDIALS libraries.
-Both libraries are installed in ``~/.local``.
+This will download, compile and install the SuiteSparse and SUNDIALS (with OpenMP) libraries
+and the ``pybind11`` headers.
+SuiteSparse and SUNDIALS are installed in ``~/.local`` by default.
 
 For users requiring more control over the installation process, the ``pybamm-requires`` session supports additional command-line arguments:
 
@@ -110,7 +111,7 @@ If you'd rather do things yourself,
 
 1. Make sure you have CMake installed
 2. Compile and install SuiteSparse (PyBaMM only requires the ``KLU`` component).
-3. Compile and install SUNDIALS.
+3. Compile and install SUNDIALS with `OpenMP support <https://mac.r-project.org/openmp/>`_.
 4. Clone the pybind11 repository in the ``PyBaMM/`` directory (make sure the directory is named ``pybind11``).
 
 
@@ -315,12 +316,12 @@ source files to your current directory.
 ``ValueError: Integrator name ida does not exist``, or
 ``ValueError: Integrator name cvode does not exist``.
 
-**Solution:** This could mean that you have not installed
-``scikits.odes`` correctly, check the instructions given above and make
+**Solution:** This could mean that you have not linked to
+SUNDIALS correctly, check the instructions given above and make
 sure each command was successful.
 
 One possibility is that you have not set your ``LD_LIBRARY_PATH`` to
-point to the sundials library, type ``echo $LD_LIBRARY_PATH`` and make
+point to the SUNDIALS library, type ``echo $LD_LIBRARY_PATH`` and make
 sure one of the directories printed out corresponds to where the
 SUNDIALS libraries are located.
 

scripts/install_KLU_Sundials.py

@@ -7,18 +7,35 @@
 
 SUITESPARSE_VERSION = "6.0.3"
 SUNDIALS_VERSION = "6.5.0"
+
 SUITESPARSE_URL = f"https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v{SUITESPARSE_VERSION}.tar.gz"
 SUNDIALS_URL = f"https://github.com/LLNL/sundials/releases/download/v{SUNDIALS_VERSION}/sundials-{SUNDIALS_VERSION}.tar.gz"
+
 SUITESPARSE_CHECKSUM = (
     "7111b505c1207f6f4bd0be9740d0b2897e1146b845d73787df07901b4f5c1fb7"
 )
 SUNDIALS_CHECKSUM = "4e0b998dff292a2617e179609b539b511eb80836f5faacf800e688a886288502"
+
+# universal binaries for macOS 11.0 and later; sourced from https://mac.r-project.org/openmp/
+OPENMP_VERSION = "16.0.4"
+OPENMP_URL = (
+    f"https://mac.r-project.org/openmp/openmp-{OPENMP_VERSION}-darwin20-Release.tar.gz"
+)
+OPENMP_CHECKSUM = "a763f0bdc9115c4f4933accc81f514f3087d56d6528778f38419c2a0d2231972"
+
+
 DEFAULT_INSTALL_DIR = os.path.join(os.getenv("HOME"), ".local")
 
 
 def safe_remove_dir(path):
-    if os.path.exists(path):
-        shutil.rmtree(path)
+    """Remove a directory or file if it exists."""
+    try:
+        if os.path.isfile(path):
+            os.remove(path)
+        elif os.path.isdir(path):
+            shutil.rmtree(path)
+    except Exception as e:
+        print(f"Error while removing {path}: {e}")
 
 
 def install_suitesparse(download_dir):
@@ -44,11 +61,11 @@ def install_suitesparse(download_dir):
     env = os.environ.copy()
     for libdir in ["SuiteSparse_config", "AMD", "COLAMD", "BTF", "KLU"]:
         build_dir = os.path.join(suitesparse_src, libdir)
-        # We want to ensure that libsuitesparseconfig.dylib is not repeated in
-        # multiple paths at the time of wheel repair. Therefore, it should not be
-        # built with an RPATH since it is copied to the install prefix.
+        # Set an RPATH in order for libsuitesparseconfig.dylib to find libomp.dylib
         if libdir == "SuiteSparse_config":
-            env["CMAKE_OPTIONS"] = f"-DCMAKE_INSTALL_PREFIX={install_dir}"
+            env["CMAKE_OPTIONS"] = (
+                f"-DCMAKE_INSTALL_PREFIX={install_dir} -DCMAKE_INSTALL_RPATH={install_dir}/lib"
+            )
         else:
             # For AMD, COLAMD, BTF and KLU; do not set a BUILD RPATH but use an
             # INSTALL RPATH in order to ensure that the dynamic libraries are found
@@ -86,20 +103,9 @@ def install_sundials(download_dir, install_dir):
     # try to find OpenMP on mac
     if platform.system() == "Darwin":
         # flags to find OpenMP on mac
-        if platform.processor() == "arm":
-            OpenMP_C_FLAGS = (
-                "-Xpreprocessor -fopenmp -I/opt/homebrew/opt/libomp/include"
-            )
-            OpenMP_C_LIB_NAMES = "omp"
-            OpenMP_omp_LIBRARY = "/opt/homebrew/opt/libomp/lib/libomp.dylib"
-        elif platform.processor() == "i386":
-            OpenMP_C_FLAGS = "-Xpreprocessor -fopenmp -I/usr/local/opt/libomp/include"
-            OpenMP_C_LIB_NAMES = "omp"
-            OpenMP_omp_LIBRARY = "/usr/local/opt/libomp/lib/libomp.dylib"
-        else:
-            raise NotImplementedError(
-                f"Unsupported processor architecture: {platform.processor()}. Only 'arm' and 'i386' architectures are supported."
-            )
+        OpenMP_C_FLAGS = f"-Xpreprocessor -fopenmp -lomp -L{os.path.join(KLU_LIBRARY_DIR)} -I{os.path.join(KLU_INCLUDE_DIR)}"
+        OpenMP_C_LIB_NAMES = "omp"
+        OpenMP_omp_LIBRARY = os.path.join(KLU_LIBRARY_DIR, "libomp.dylib")
 
         cmake_args += [
             "-DOpenMP_C_FLAGS=" + OpenMP_C_FLAGS,
@@ -123,6 +129,47 @@ def install_sundials(download_dir, install_dir):
     subprocess.run(make_cmd, cwd=build_dir, check=True)
 
 
+# Relevant for macOS only because recent Xcode Clang versions do not include OpenMP headers.
+# Other compilers (e.g. GCC) include the OpenMP specification by default.
+def set_up_openmp(download_dir, install_dir):
+    print("-" * 10, "Extracting OpenMP archive", "-" * 40)
+
+    openmp_dir = f"openmp-{OPENMP_VERSION}"
+    openmp_src = os.path.join(download_dir, openmp_dir)
+
+    # extract OpenMP archive
+    with tarfile.open(
+        os.path.join(download_dir, f"{openmp_dir}-darwin20-Release.tar.gz")
+    ) as tar:
+        tar.extractall(openmp_src)
+
+    # create directories
+    os.makedirs(os.path.join(install_dir, "lib"), exist_ok=True)
+    os.makedirs(os.path.join(install_dir, "include"), exist_ok=True)
+
+    # copy files
+    shutil.copy(
+        os.path.join(openmp_src, "usr", "local", "lib", "libomp.dylib"),
+        os.path.join(install_dir, "lib"),
+    )
+    for file in os.listdir(os.path.join(openmp_src, "usr", "local", "include")):
+        shutil.copy(
+            os.path.join(openmp_src, "usr", "local", "include", file),
+            os.path.join(install_dir, "include"),
+        )
+
+    # fix rpath; for some reason the downloaded dylib has an absolute path
+    # to /usr/local/lib/, so use self-referential rpath
+    subprocess.check_call(
+        [
+            "install_name_tool",
+            "-id",
+            "@rpath/libomp.dylib",
+            f"{os.path.join(install_dir, 'lib', 'libomp.dylib')}",
+        ]
+    )
+
+
 def check_libraries_installed(install_dir):
     # Define the directories to check for SUNDIALS and SuiteSparse libraries
     lib_dirs = [install_dir]
@@ -170,7 +217,7 @@ def check_libraries_installed(install_dir):
         suitesparse_files = [file + ".dylib" for file in suitesparse_files]
     else:
         raise NotImplementedError(
-            f"Unsupported operating system: {platform.system()}. This script currently supports only Linux and macOS."
+            f"Unsupported operating system: {platform.system()}. This script supports only Linux and macOS."
         )
 
     suitesparse_lib_found = True
@@ -192,6 +239,16 @@ def check_libraries_installed(install_dir):
     return sundials_lib_found, suitesparse_lib_found
 
 
+def check_openmp_installed_on_macos(install_dir):
+    openmp_lib_found = isfile(join(install_dir, "lib", "libomp.dylib"))
+    openmp_headers_found = isfile(join(install_dir, "include", "omp.h"))
+    if not openmp_lib_found or not openmp_headers_found:
+        print("libomp.dylib or omp.h not found. Proceeding with OpenMP installation.")
+    else:
+        print(f"libomp.dylib and omp.h found in {install_dir}.")
+    return openmp_lib_found
+
+
 def calculate_sha256(file_path):
     sha256_hash = hashlib.sha256()
     with open(file_path, "rb") as f:
@@ -267,7 +324,7 @@ def parallel_download(urls, download_dir):
 
 # Get installation location
 parser = argparse.ArgumentParser(
-    description="Download, compile and install Sundials and SuiteSparse."
+    description="Download, compile and install SUNDIALS and SuiteSparse."
 )
 parser.add_argument(
     "--force",