Revert "Use wider-compatible LLVM-OpenMP, bundle libgfortran dylibs…

… for macOS wheels (pybamm-team#4092)" (pybamm-team#4109) This reverts commit becb1a4.
js1tr3 · Aug 12, 2024 · 98b45ab · 98b45ab
1 parent c5012ba
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diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
@@ -100,7 +100,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-13]
+        os: [ubuntu-latest, macos-12]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
@@ -110,6 +110,15 @@ 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'
@@ -145,57 +154,18 @@ jobs:
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
-      - name: Build wheels on macOS arm64
+      - name: Install SuiteSparse and SUNDIALS on macOS
         run: |
-          python -m pip install cibuildwheel
-          python -m cibuildwheel --output-dir wheelhouse
-        env:
-          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
+          brew install graphviz libomp
+          brew reinstall gcc
+          python -m pip install cmake pipx
+          python scripts/install_KLU_Sundials.py
 
-            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
+      - name: Build wheels on macOS arm64
+        run: python -m pipx run 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}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for macOS arm64

diff --git a/.gitignore b/.gitignore
@@ -137,7 +137,3 @@ results/
 
 # tests
 test_callback.log
-
-# openmp downloads
-install_KLU_Sundials/openmp-*
-install_KLU_Sundials/usr/
diff --git a/.lycheeignore b/.lycheeignore
@@ -1,7 +1,6 @@
 # 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

diff --git a/docs/source/user_guide/installation/install-from-source.rst b/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 cmake pandoc
+		brew install python openblas gcc gfortran graphviz libomp cmake pandoc
 
 .. note::
 
@@ -82,9 +82,8 @@ 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 (with OpenMP) libraries
-and the ``pybind11`` headers.
-SuiteSparse and SUNDIALS are installed in ``~/.local`` by default.
+This will download, compile and install the SuiteSparse and SUNDIALS libraries.
+Both libraries are installed in ``~/.local``.
 
 For users requiring more control over the installation process, the ``pybamm-requires`` session supports additional command-line arguments:
 
@@ -111,7 +110,7 @@ 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 with `OpenMP support <https://mac.r-project.org/openmp/>`_.
+3. Compile and install SUNDIALS.
 4. Clone the pybind11 repository in the ``PyBaMM/`` directory (make sure the directory is named ``pybind11``).
 
 
@@ -316,12 +315,12 @@ 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 linked to
-SUNDIALS correctly, check the instructions given above and make
+**Solution:** This could mean that you have not installed
+``scikits.odes`` 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.
 

diff --git a/scripts/install_KLU_Sundials.py b/scripts/install_KLU_Sundials.py
@@ -7,35 +7,18 @@
 
 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):
-    """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}")
+    if os.path.exists(path):
+        shutil.rmtree(path)
 
 
 def install_suitesparse(download_dir):
@@ -61,11 +44,11 @@ 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)
-        # Set an RPATH in order for libsuitesparseconfig.dylib to find libomp.dylib
+        # 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.
         if libdir == "SuiteSparse_config":
-            env["CMAKE_OPTIONS"] = (
-                f"-DCMAKE_INSTALL_PREFIX={install_dir} -DCMAKE_INSTALL_RPATH={install_dir}/lib"
-            )
+            env["CMAKE_OPTIONS"] = f"-DCMAKE_INSTALL_PREFIX={install_dir}"
         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
@@ -103,9 +86,20 @@ def install_sundials(download_dir, install_dir):
     # try to find OpenMP on mac
     if platform.system() == "Darwin":
         # flags to find OpenMP on mac
-        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")
+        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."
+            )
 
         cmake_args += [
             "-DOpenMP_C_FLAGS=" + OpenMP_C_FLAGS,
@@ -129,47 +123,6 @@ 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]
@@ -217,7 +170,7 @@ 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 supports only Linux and macOS."
+            f"Unsupported operating system: {platform.system()}. This script currently supports only Linux and macOS."
         )
 
     suitesparse_lib_found = True
@@ -239,16 +192,6 @@ 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:
@@ -324,7 +267,7 @@ 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",