Merge branch 'master' into indiamai/new_def_integration

.github/workflows/build-mac.yml

@@ -0,0 +1,58 @@
+name: Install and test Firedrake (macOS)
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    # By default this workflow is run on the "opened", "synchronize" and
+    # "reopened" events. We add "labelled" so it will run if the PR is given a label.
+    types: [opened, synchronize, reopened, labeled]
+
+concurrency:
+  # Cancels jobs running if new commits are pushed
+  group: >
+    ${{ github.workflow }}-
+    ${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: Build Firedrake (macOS)
+    runs-on: [self-hosted, macOS]
+    # Only run this action if we are pushing to master or the PR is labelled "macOS"
+    if: ${{ (github.ref == 'refs/heads/master') || contains(github.event.pull_request.labels.*.name, 'macOS') }}
+    env:
+      FIREDRAKE_CI_TESTS: 1  # needed to symlink the checked out branch into the venv
+      OMP_NUM_THREADS: 1
+      OPENBLAS_NUM_THREADS: 1
+    steps:
+      - name: Add homebrew to PATH
+        # https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions#adding-a-system-path
+        run: echo "/opt/homebrew/bin" >> "$GITHUB_PATH"
+      - uses: actions/checkout@v4
+      - name: Pre-run cleanup
+        if: ${{ always() }}
+        run: |
+          cd ..
+          rm -rf firedrake_venv
+      - name: Install Python
+        run: brew install python python-setuptools
+      - name: Build Firedrake
+        run: |
+          cd ..
+          "$(brew --prefix)/bin/python3" \
+            firedrake/scripts/firedrake-install \
+            --venv-name firedrake_venv \
+            --disable-ssh \
+            || (cat firedrake-install.log && /bin/false)
+      - name: Run smoke tests
+        run: |
+          . ../firedrake_venv/bin/activate
+          python -m pytest -v tests/firedrake/regression/ -k "poisson_strong or stokes_mini or dg_advection"
+        timeout-minutes: 30
+      - name: Post-run cleanup
+        if: ${{ always() }}
+        run: |
+          cd ..
+          rm -rf firedrake_venv

.github/workflows/pip-mac.yml

@@ -0,0 +1,127 @@
+name: Pip install Firedrake (macOS)
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    # By default this workflow is run on the "opened", "synchronize" and
+    # "reopened" events. We add "labelled" so it will run if the PR is given a label.
+    types: [opened, synchronize, reopened, labeled]
+
+concurrency:
+  # Cancels jobs running if new commits are pushed
+  group: >
+    ${{ github.workflow }}-
+    ${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: "Build Firedrake using pip (macOS)"
+    runs-on: [self-hosted, macOS]
+    # Only run this action if we are pushing to master or the PR is labelled "macOS"
+    if: ${{ (github.ref == 'refs/heads/master') || contains(github.event.pull_request.labels.*.name, 'macOS') }}
+    env:
+      OMP_NUM_THREADS: 1
+      OPENBLAS_NUM_THREADS: 1
+    steps:
+      - name: Add homebrew to PATH
+        # https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/workflow-commands-for-github-actions#adding-a-system-path
+        run: echo "/opt/homebrew/bin" >> "$GITHUB_PATH"
+
+      - name: Install homebrew packages
+        run: brew install gcc autoconf pkg-config make automake cmake ninja libtool boost openblas python python-setuptools mpich
+
+      - name: Cleanup (pre)
+        if: ${{ always() }}
+        run: |
+          rm -rf pip_venv
+          "$(brew --prefix)/bin/python3" -m pip cache purge
+
+      - name: Create a virtual environment
+        run: |
+          "$(brew --prefix)/bin/python3" -m venv pip_venv
+          mkdir pip_venv/src
+
+      - name: Install PETSc
+        run: |
+          cd pip_venv/src
+          git clone https://github.com/firedrakeproject/petsc.git
+          cd petsc
+          ./configure PETSC_DIR="$PWD" PETSC_ARCH=default \
+            --with-shared-libraries=1 \
+            --with-mpi-dir=/opt/homebrew \
+            --with-zlib \
+            --download-bison \
+            --download-hdf5 \
+            --download-hwloc \
+            --download-hypre \
+            --download-metis \
+            --download-mumps \
+            --download-netcdf \
+            --download-pastix \
+            --download-pnetcdf \
+            --download-ptscotch \
+            --download-scalapack \
+            --download-suitesparse \
+            --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="$VIRTUAL_ENV" \
+            -DMPI_C_COMPILER=/opt/homebrew/bin/mpicc \
+            -DMPI_CXX_COMPILER=/opt/homebrew/bin/mpicxx \
+            -DMPI_Fortran_COMPILER=/opt/homebrew/bin/mpif90 \
+            -DCMAKE_Fortran_COMPILER=/opt/homebrew/bin/mpif90 \
+            -DMPIEXEC_EXECUTABLE=/opt/homebrew/bin/mpiexec
+          make
+          make install
+
+      - uses: actions/checkout@v4
+        with:
+          path: pip_venv/src/firedrake
+
+      - name: Pip install
+        run: |
+          export PETSC_DIR="$PWD/pip_venv/src/petsc"
+          export PETSC_ARCH=default
+          export HDF5_DIR="$PETSC_DIR/$PETSC_ARCH"
+          export HDF5_MPI=ON
+          export CC=/opt/homebrew/bin/mpicc
+          export CXX=/opt/homebrew/bin/mpicxx
+          export MPICC="$CC"
+          source pip_venv/bin/activate
+          cd pip_venv/src
+          python -m pip install \
+            --log=firedrake-install.log \
+            --no-binary h5py \
+            -v -e './firedrake[test]'
+
+      - name: Install CI-specific test dependencies
+        run: |
+          source pip_venv/bin/activate
+          python -m pip install -U pytest-timeout
+
+      - name: Run Firedrake smoke tests
+        run: |
+          source pip_venv/bin/activate
+          cd pip_venv/src/firedrake
+          python -m pytest --timeout=1800 -v tests/firedrake/regression \
+            -k "poisson_strong or stokes_mini or dg_advection"
+        timeout-minutes: 30
+
+      - name: Cleanup (post)
+        if: ${{ always() }}
+        run: |
+          rm -rf pip_venv
+          "$(brew --prefix)/bin/python3" -m pip cache purge

.github/workflows/pyop2.yml

@@ -1,14 +1,10 @@
-name: PyOP2
+name: Test PyOP2 and TSFC
 
-# Trigger the workflow on push or pull request,
-# but only for the master branch
 on:
   push:
     branches:
       - master
   pull_request:
-    branches:
-      - master
 
 jobs:
   test:
@@ -88,29 +84,40 @@ jobs:
           make
           make install
 
-      - name: Checkout PyOP2
+      - name: Checkout Firedrake
         uses: actions/checkout@v4
         with:
-          path: PyOP2
+          path: firedrake
 
       - name: Install PyOP2 dependencies
         shell: bash
-        working-directory: PyOP2
+        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: PyOP2
+        working-directory: firedrake
         run: |
           source ../venv/bin/activate
-          python -m pip install -v ".[test]"
+          export CC=mpicc
+          export HDF5_DIR="$PETSC_DIR/$PETSC_ARCH"
+          export HDF5_MPI=ON
+          python -m pip install --no-binary h5py -v ".[test]"
+
+      - name: Run TSFC tests
+        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 tests
+      - name: Run PyOP2 tests
         shell: bash
-        working-directory: PyOP2
+        working-directory: firedrake
         run: |
           source ../venv/bin/activate
           # Running parallel test cases separately works around a bug in pytest-mpi

AUTHORS.rst

@@ -90,6 +90,8 @@ Christopher Hawkes
 
 Miklós Homolya
 
+Joshua Hope-Collins...........<https://www.imperial.ac.uk/people/joshua.hope-collins13>
+
 Christian T. Jacobs
 
 Darko Janeković

CITATION.rst

@@ -12,7 +12,7 @@ If you publish results using Firedrake, we would be grateful if you would cite t
 
   @manual{FiredrakeUserManual,
     title        = {Firedrake User Manual},
-    author       = {David A. Ham and Paul H. J. Kelly and Lawrence Mitchell and Colin J. Cotter and Robert C. Kirby and Koki Sagiyama and Nacime Bouziani and Thomas J. Gregory and Jack Betteridge and Daniel R. Shapero and Reuben W. Nixon-Hill and Connor J. Ward and Patrick E. Farrell and Pablo D. Brubeck and India Marsden and Daiane I. Dolci and Sophia Vorderwuelbecke and Thomas H. Gibson and Miklós Homolya and Tianjiao Sun and Andrew T. T. McRae and Fabio Luporini and Alastair Gregory and Michael Lange and Simon W. Funke and Florian Rathgeber and Gheorghe-Teodor Bercea and Graham R. Markall},
+    author       = {David A. Ham and Paul H. J. Kelly and Lawrence Mitchell and Colin J. Cotter and Robert C. Kirby and Koki Sagiyama and Nacime Bouziani and Thomas J. Gregory and Jack Betteridge and Daniel R. Shapero and Reuben W. Nixon-Hill and Connor J. Ward and Patrick E. Farrell and Pablo D. Brubeck and India Marsden and Daiane I. Dolci and Joshua Hope-Collins and Sophia Vorderwuelbecke and Thomas H. Gibson and Miklós Homolya and Tianjiao Sun and Andrew T. T. McRae and Fabio Luporini and Alastair Gregory and Michael Lange and Simon W. Funke and Florian Rathgeber and Gheorghe-Teodor Bercea and Graham R. Markall},
     organization = {Imperial College London and University of Oxford and Baylor University and University of Washington},
     edition      = {First edition},
     year         = {2023},

Makefile

@@ -24,6 +24,8 @@ lint:
 	@python -m flake8 $(FLAKE8_FORMAT) pyop2
 	@echo "    Linting PyOP2 scripts"
 	@python -m flake8 $(FLAKE8_FORMAT) pyop2/scripts --filename=*
+	@echo "    Linting TSFC"
+	@python -m flake8 $(FLAKE8_FORMAT) tsfc
 
 actionlint:
 	@echo "    Pull latest actionlint image"

docker/Dockerfile.env

@@ -13,7 +13,7 @@ RUN apt-get update \
                  cmake gfortran git libopenblas-serial-dev \
                  libtool python3-dev python3-pip python3-tk python3-venv \
                  python3-requests zlib1g-dev libboost-dev sudo gmsh \
-                 bison flex ninja-build \
+                 bison flex ninja-build pkg-config \
                  libocct-ocaf-dev libocct-data-exchange-dev \
                  swig graphviz \
                  libcurl4-openssl-dev libxml2-dev \

docs/source/download.rst

@@ -135,6 +135,7 @@ they have the system dependencies:
 * zlib
 * flex, bison
 * Ninja
+* pkg-config
 
 Firedrake has been successfully installed on Windows 10 using the
 Windows Subsystem for Linux. There are more detailed instructions for
@@ -229,10 +230,10 @@ type::
 
 You should now be able to run ``firedrake-update``.
 
-Installing Firedrake with pip (experimental, Linux only)
+Installing Firedrake with pip (experimental)
 --------------------------------------------------------
 
-Firedrake has experimental support for installing using ``pip``, avoiding the need for the ``firedrake-install`` script. At present only Linux is tested using this install method.
+Firedrake has experimental support for installing using ``pip``, avoiding the need for the ``firedrake-install`` script.
 
 Requirements
 ~~~~~~~~~~~~

firedrake/assemble.py

@@ -469,8 +469,9 @@ def base_form_assembly_visitor(self, expr, tensor, *args):
                 return sum(weight * arg for weight, arg in zip(expr.weights(), args))
             elif all(isinstance(op, firedrake.Cofunction) for op in args):
                 V, = set(a.function_space() for a in args)
-                res = sum([w*op.dat for (op, w) in zip(args, expr.weights())])
-                return firedrake.Cofunction(V, res)
+                result = firedrake.Cofunction(V)
+                result.dat.maxpy(expr.weights(), [a.dat for a in args])
+                return result
             elif all(isinstance(op, ufl.Matrix) for op in args):
                 res = tensor.petscmat if tensor else PETSc.Mat()
                 is_set = False