Merge branch 'master' into pbrubeck/fix/restricted-cofunction

.github/workflows/build-mac.yml

@@ -50,6 +50,9 @@ jobs:
         run: |
           . ../firedrake_venv/bin/activate
           python -m pytest -v tests/firedrake/regression/ -k "poisson_strong or stokes_mini or dg_advection"
+          # also test for 'problem libraries' (spatialindex and libsupermesh)
+          python -m pytest -v tests/firedrake/regression/test_locate_cell.py
+          python -m pytest -v tests/firedrake/supermesh/test_assemble_mixed_mass_matrix.py
         timeout-minutes: 30
       - name: Post-run cleanup
         if: ${{ always() }}

.github/workflows/build.yml

@@ -66,6 +66,7 @@ jobs:
             --mpicxx="$MPICH_DIR"/mpicxx \
             --mpif90="$MPICH_DIR"/mpif90 \
             --mpiexec="$MPICH_DIR"/mpiexec \
+            --mpihome="$MPICH_DIR"/.. \
             --venv-name firedrake_venv \
             --no-package-manager \
             --disable-ssh \

.github/workflows/pip-mac.yml

@@ -68,25 +68,6 @@ jobs:
             --download-superlu_dist
           make
 
-      - name: Install libsupermesh
-        run: |
-          source pip_venv/bin/activate
-          python -m pip install 'rtree>=1.2'
-          cd pip_venv/src
-          git clone https://github.com/firedrakeproject/libsupermesh.git
-          mkdir -p libsupermesh/build
-          cd libsupermesh/build
-          cmake .. \
-            -DBUILD_SHARED_LIBS=ON \
-            -DCMAKE_INSTALL_PREFIX="$VIRTUAL_ENV" \
-            -DMPI_C_COMPILER=/opt/homebrew/bin/mpicc \
-            -DMPI_CXX_COMPILER=/opt/homebrew/bin/mpicxx \
-            -DMPI_Fortran_COMPILER=/opt/homebrew/bin/mpif90 \
-            -DCMAKE_Fortran_COMPILER=/opt/homebrew/bin/mpif90 \
-            -DMPIEXEC_EXECUTABLE=/opt/homebrew/bin/mpiexec
-          make
-          make install
-
       - uses: actions/checkout@v4
         with:
           path: pip_venv/src/firedrake
@@ -118,6 +99,9 @@ jobs:
           cd pip_venv/src/firedrake
           python -m pytest --timeout=1800 -v tests/firedrake/regression \
             -k "poisson_strong or stokes_mini or dg_advection"
+          # also test for 'problem libraries' (spatialindex and libsupermesh)
+          python -m pytest -v tests/firedrake/regression/test_locate_cell.py
+          python -m pytest -v tests/firedrake/supermesh/test_assemble_mixed_mass_matrix.py
         timeout-minutes: 30
 
       - name: Cleanup (post)

.github/workflows/pip.yml

@@ -56,25 +56,6 @@ jobs:
         with:
           path: src/firedrake
 
-      - name: Install libsupermesh
-        run: |
-          source pip_venv/bin/activate
-          python -m pip install 'rtree>=1.2'
-          cd pip_venv/src
-          git clone https://github.com/firedrakeproject/libsupermesh.git
-          mkdir -p libsupermesh/build
-          cd libsupermesh/build
-          cmake .. \
-            -DBUILD_SHARED_LIBS=ON \
-            -DCMAKE_INSTALL_PREFIX="$VIRTUAL_ENV" \
-            -DMPI_C_COMPILER="$MPICH_DIR/mpicc" \
-            -DMPI_CXX_COMPILER="$MPICH_DIR/mpicxx" \
-            -DMPI_Fortran_COMPILER="$MPICH_DIR/mpif90" \
-            -DCMAKE_Fortran_COMPILER="$MPICH_DIR/mpif90" \
-            -DMPIEXEC_EXECUTABLE="$MPICH_DIR/mpiexec"
-          make
-          make install
-
       - name: Pip install
         run: |
           source pip_venv/bin/activate

.github/workflows/pyop2.yml

@@ -35,17 +35,6 @@ jobs:
         id: setup-python
         with:
           python-version: ${{ matrix.python-version }}
-          # By default setup-python pollutes the environment in such a way that virtual
-          # environments cannot be used. This prevents us from building libsupermesh because
-          # it relies on having rtree installed into a venv.
-          # https://github.com/actions/setup-python/issues/851
-          # https://github.com/actions/setup-python/blob/main/docs/advanced-usage.md#using-update-environment-flag
-          update-environment: false
-
-      - name: Create virtual environment
-        shell: bash
-        run: |
-          ${{ steps.setup-python.outputs.python-path }} -m venv venv
 
       - name: Clone PETSc
         uses: actions/checkout@v4
@@ -65,25 +54,6 @@ jobs:
             --with-fortran-bindings=0
           make
 
-      - name: Install libsupermesh
-        shell: bash
-        run: |
-          source venv/bin/activate
-          python -m pip install 'rtree>=1.2'
-          git clone https://github.com/firedrakeproject/libsupermesh.git
-          mkdir -p libsupermesh/build
-          cd libsupermesh/build
-          cmake .. \
-            -DBUILD_SHARED_LIBS=ON \
-            -DCMAKE_INSTALL_PREFIX="$VIRTUAL_ENV" \
-            -DMPI_C_COMPILER=mpicc \
-            -DMPI_CXX_COMPILER=mpicxx \
-            -DMPI_Fortran_COMPILER=mpif90 \
-            -DCMAKE_Fortran_COMPILER=mpif90 \
-            -DMPIEXEC_EXECUTABLE=mpiexec
-          make
-          make install
-
       - name: Checkout Firedrake
         uses: actions/checkout@v4
         with:
@@ -93,15 +63,13 @@ jobs:
         shell: bash
         working-directory: firedrake
         run: |
-          source ../venv/bin/activate
           python -m pip install -U pip
           python -m pip install -U pytest-timeout
 
       - name: Install PyOP2
         shell: bash
         working-directory: firedrake
         run: |
-          source ../venv/bin/activate
           export CC=mpicc
           export HDF5_DIR="$PETSC_DIR/$PETSC_ARCH"
           export HDF5_MPI=ON
@@ -111,15 +79,13 @@ jobs:
         shell: bash
         working-directory: firedrake
         run: |
-          source ../venv/bin/activate
           pytest --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/tsfc
         timeout-minutes: 10
 
       - name: Run PyOP2 tests
         shell: bash
         working-directory: firedrake
         run: |
-          source ../venv/bin/activate
           pytest -m "not parallel" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/pyop2
           mpiexec -n 2 --oversubscribe pytest -m "parallel[2]" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/pyop2
           mpiexec -n 3 --oversubscribe pytest -m "parallel[3]" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/pyop2

docker/Dockerfile.complex

@@ -18,5 +18,6 @@ RUN bash -c "python3 firedrake-install \
     --mpicxx=$MPICH_DIR/mpicxx \
     --mpif90=$MPICH_DIR/mpif90 \
     --mpiexec=$MPICH_DIR/mpiexec \
+    --mpihome=$MPICH_DIR/.. \
     --slepc \
     --documentation-dependencies"

docker/Dockerfile.vanilla

@@ -16,4 +16,5 @@ RUN bash -c "python3 firedrake-install \
     --mpicc=$MPICH_DIR/mpicc \
     --mpicxx=$MPICH_DIR/mpicxx \
     --mpif90=$MPICH_DIR/mpif90 \
-    --mpiexec=$MPICH_DIR/mpiexec"
+    --mpiexec=$MPICH_DIR/mpiexec \
+    --mpihome=$MPICH_DIR/.."

docs/source/download.rst

@@ -241,7 +241,6 @@ Requirements
 * An activated virtual environment.
 * All the system requirements listed in :ref:`system-requirements`.
 * A Firedrake-compatible PETSc installation (using our `fork of PETSc <https://github.com/firedrakeproject/petsc.git>`_). The set of flags passed to PETSc can be retrieved by passing the command ``--show-petsc-configure-options`` to ``firedrake-install``.
-* `libsupermesh <https://github.com/firedrakeproject/libsupermesh.git>`_ to be installed inside the virtual environment (see `here <https://github.com/firedrakeproject/firedrake/blob/master/.github/workflows/pip.yml>`_ for an example of how to do this).
 *  The following environment variables to be set:
 
   * ``PETSC_DIR`` and ``PETSC_ARCH`` to point to the correct location for the PETSc installation.

docs/source/parallelism.rst

@@ -45,11 +45,12 @@ firedrake installer to use it, by running:
 
 .. code-block:: shell
 
-   python3 firedrake-install --mpiexec=mpiexec --mpicc=mpicc --mpicxx=mpicxx --mpif90=mpif90
+   python3 firedrake-install --mpiexec=mpiexec --mpicc=mpicc --mpicxx=mpicxx --mpif90=mpif90 --mpihome mpihome
 
 where ``mpiexec``, ``mpicc``, ``mpicxx``, and ``mpif90`` are the
 commands to run an MPI job and to compile C, C++, and Fortran 90 code,
-respectively.
+respectively. ``mpihome`` is an extra variable that must point to the
+root directory of the MPI installation (e.g. ``/usr`` or ``/opt/mpich``).
 
 Printing in parallel
 ====================

firedrake/supermeshing.py

@@ -1,7 +1,8 @@
 # Code for projections and other fun stuff involving supermeshes.
 import firedrake
 import ctypes
-import sys
+import pathlib
+import libsupermesh
 from firedrake.cython.supermeshimpl import assemble_mixed_mass_matrix as ammm, intersection_finder
 from firedrake.mg.utils import get_level
 from firedrake.petsc import PETSc
@@ -428,7 +429,8 @@ def likely(cell_A):
         "complex_mode": 1 if complex_mode else 0
     }
 
-    dirs = get_petsc_dir() + (sys.prefix, )
+    libsupermesh_dir = pathlib.Path(libsupermesh.get_include()).parent.absolute()
+    dirs = get_petsc_dir() + (libsupermesh_dir,)
     includes = ["-I%s/include" % d for d in dirs]
     libs = ["-L%s/lib" % d for d in dirs]
     libs = libs + ["-Wl,-rpath,%s/lib" % d for d in dirs] + ["-lpetsc", "-lsupermesh"]

pyproject.toml

@@ -38,6 +38,7 @@ dependencies = [
   "fenics-fiat @ git+https://github.com/firedrakeproject/fiat.git",
   "pyadjoint-ad @ git+https://github.com/dolfin-adjoint/pyadjoint.git",
   "loopy @ git+https://github.com/firedrakeproject/loopy.git@main",
+  "libsupermesh @ git+https://github.com/firedrakeproject/libsupermesh.git",
 ]
 classifiers = [
   "Development Status :: 5 - Production/Stable",
@@ -98,6 +99,7 @@ requires = [
   "mpi4py; python_version < '3.13'",
   "petsc4py",
   "rtree>=1.2",
+  "libsupermesh @ git+https://github.com/firedrakeproject/libsupermesh.git",
 ]
 build-backend = "setuptools.build_meta"
 

requirements-git.txt

@@ -4,3 +4,4 @@ git+https://github.com/dolfin-adjoint/pyadjoint.git#egg=pyadjoint-ad
 git+https://github.com/firedrakeproject/loopy.git@main#egg=loopy
 git+https://github.com/firedrakeproject/pytest-mpi.git@main#egg=pytest-mpi
 git+https://github.com/firedrakeproject/petsc.git@firedrake#egg=petsc
+git+https://github.com/firedrakeproject/libsupermesh.git#egg=libsupermesh

scripts/firedrake-install

@@ -76,7 +76,7 @@ class FiredrakeConfiguration(dict):
                     self["options"][o] = args.__dict__[o]
 
     _persistent_options = ["package_manager",
-                           "minimal_petsc", "mpicc", "mpicxx", "mpif90", "mpiexec", "disable_ssh",
+                           "minimal_petsc", "mpicc", "mpicxx", "mpif90", "mpiexec", "mpihome", "disable_ssh",
                            "honour_petsc_dir", "with_parmetis",
                            "slepc", "packages", "honour_pythonpath",
                            "opencascade", "torch", "jax",
@@ -306,6 +306,9 @@ honoured.""",
     parser.add_argument("--mpiexec", type=str,
                         action="store", default=None,
                         help="MPI launcher. If not set, MPICH will be downloaded and used.")
+    parser.add_argument("--mpihome", type=str,
+                        action="store", default=None,
+                        help="Location of MPI files. If not set, MPICH will be downloaded and used.")
     parser.add_argument("--mpi4py-version", help="Specify an exact version of mpi4py to install")
     parser.add_argument("--show-petsc-configure-options", action="store_true",
                         help="Print out the configure options passed to PETSc and exit")
@@ -339,9 +342,9 @@ honoured.""",
     args = parser.parse_args()
 
     # If the user has set any MPI info, they must set them all
-    if args.mpicc or args.mpicxx or args.mpif90 or args.mpiexec:
-        if not (args.mpicc and args.mpicxx and args.mpif90 and args.mpiexec):
-            log.error("If you set any MPI information, you must set all of {mpicc, mpicxx, mpif90, mpiexec}.")
+    if args.mpicc or args.mpicxx or args.mpif90 or args.mpiexec or args.mpihome:
+        if not (args.mpicc and args.mpicxx and args.mpif90 and args.mpiexec and args.mpihome):
+            log.error("If you set any MPI information, you must set all of {mpicc, mpicxx, mpif90, mpiexec, mpihome}.")
             sys.exit(1)
 
     if args.package_branch:
@@ -1252,36 +1255,6 @@ def build_and_install_h5py():
         log.info("No need to rebuild h5py")
 
 
-def build_and_install_libsupermesh(cc, cxx, f90, mpiexec):
-    log.info("Installing libsupermesh")
-    url = "git+https://github.com/firedrakeproject/libsupermesh.git"
-    if os.path.exists("libsupermesh"):
-        changed = git_update("libsupermesh", url)
-    else:
-        git_clone(url)
-        changed = True
-    if changed:
-        with directory("libsupermesh"):
-            check_call(["git", "reset", "--hard"])
-            check_call(["git", "clean", "-f", "-x", "-d"])
-            check_call(["mkdir", "-p", "build"])
-            with directory("build"):
-                cmd = [
-                    "cmake", "..", "-DBUILD_SHARED_LIBS=ON",
-                    "-DCMAKE_INSTALL_PREFIX=" + firedrake_env,
-                    "-DMPI_C_COMPILER=" + cc,
-                    "-DMPI_CXX_COMPILER=" + cxx,
-                    "-DMPI_Fortran_COMPILER=" + f90,
-                    "-DCMAKE_Fortran_COMPILER=" + f90,
-                    "-DMPIEXEC_EXECUTABLE=" + mpiexec,
-                ]
-                check_call(cmd)
-                check_call(["make"])
-                check_call(["make", "install"])
-    else:
-        log.info("No need to rebuild libsupermesh")
-
-
 def build_and_install_pythonocc():
     log.info("Installing pythonocc-core")
     url = "git+https://github.com/tpaviot/pythonocc-core.git@595b0a4e8e60e8d6011bea0cdb54ac878efcfcd2"
@@ -1420,7 +1393,7 @@ if args.rebuild_script:
     sys.exit(0)
 
 
-def create_compiler_env(cc, cxx, f90):
+def create_compiler_env(cc, cxx, f90, mpihome):
     env = dict()
     if cc:
         env["MPICC"] = cc
@@ -1439,8 +1412,10 @@ def create_compiler_env(cc, cxx, f90):
         env["CXX"] = cxx
     if f90:
         env["MPIF90"] = f90
-        env["MPI_C_COMPILER"] = f90
+        env["MPI_Fortran_COMPILER"] = f90
         env["F90"] = f90
+    if mpihome:
+        env["MPI_HOME"] = mpihome
 
     return env
 
@@ -1688,6 +1663,8 @@ run_pip(["install", "-U", "hatch"])
 run_pip(["install", "-U", "editables"])
 run_pip(["install", "-U", "pip"])
 run_pip(["install", "-U", "wheel"])
+run_pip(["install", "-U", "scikit-build-core"])
+run_pip(["install", "-U", "rtree>=1.2"])
 
 # Extra numpy dependendencies, see
 # https://github.com/numpy/numpy/blob/main/pyproject.toml
@@ -1733,7 +1710,18 @@ cc = options["mpicc"]
 cxx = options["mpicxx"]
 f90 = options["mpif90"]
 mpiexec = options["mpiexec"]
-compiler_env = create_compiler_env(cc, cxx, f90)
+try:
+    mpihome = options["mpihome"]
+except KeyError:
+    if cc:
+        try:
+            mpihome = os.environ["MPI_HOME"]
+        except KeyError:
+            raise InstallError("MPI compilers specified but mpihome is missing from "
+                               "configuration. Please set MPI_HOME to continue.")
+    else:
+        mpihome = None
+compiler_env = create_compiler_env(cc, cxx, f90, mpihome)
 os.chdir(firedrake_env)
 
 # Dict to store BLAS and OPENBLAS environment variables
@@ -1830,7 +1818,8 @@ if mode == "install":
         cxx = os.path.join(compilerbin, "mpicxx")
         f90 = os.path.join(compilerbin, "mpif90")
         mpiexec = os.path.join(compilerbin, "mpiexec")
-        compiler_env = create_compiler_env(cc, cxx, f90)
+        mpihome = os.path.join(compilerbin, "..")
+        compiler_env = create_compiler_env(cc, cxx, f90, mpihome)
 
     # Make sure that we link against the right MPI and PETSc shared libraries
     link_env = {
@@ -1877,9 +1866,6 @@ if mode == "install":
                 install(p+"/")
             sys.path.append(os.getcwd() + "/" + p)
 
-    with environment(**compiler_env):
-        build_and_install_libsupermesh(cc, cxx, f90, mpiexec)
-
     with pipargs("--no-deps"), environment(**compiler_env, **link_env):
         install("firedrake/")
 
@@ -1986,7 +1972,8 @@ else:
             cxx = os.path.join(compilerbin, "mpicxx")
             f90 = os.path.join(compilerbin, "mpif90")
             mpiexec = os.path.join(compilerbin, "mpiexec")
-            compiler_env = create_compiler_env(cc, cxx, f90)
+            mpihome = os.path.join(compilerbin, "..")
+            compiler_env = create_compiler_env(cc, cxx, f90, mpihome)
 
     # Make sure that we link against the right MPI and PETSc shared libraries
     link_env = {
@@ -2059,9 +2046,6 @@ Please consider updating your PETSc manually.
             else:
                 install(p+"/")
 
-        with environment(**compiler_env):
-            build_and_install_libsupermesh(cc, cxx, f90, mpiexec)
-
         with pipargs("--no-deps"), environment(**compiler_env, **link_env):
             install("firedrake/")