Merge master

.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

@@ -27,25 +27,14 @@ jobs:
         shell: bash
         run: |
           sudo apt update
-          sudo apt install build-essential mpich libmpich-dev \
+          sudo apt install build-essential libopenmpi-dev \
             libblas-dev liblapack-dev gfortran libhwloc-dev libfabric-dev
 
       - name: Set correct Python version
         uses: actions/setup-python@v5
         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
@@ -111,16 +79,14 @@ 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
-          # Running parallel test cases separately works around a bug in pytest-mpi
-          pytest -k "not parallel" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/pyop2
-          mpiexec -n 3 pytest -k "parallel[3]" --tb=native --timeout=480 --timeout-method=thread -o faulthandler_timeout=540 -v tests/pyop2
+          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
         timeout-minutes: 10

AUTHORS.rst

@@ -172,5 +172,7 @@ Florian Wechsung..............<https://florianwechsung.github.io>
 
 Yian Zeng
 
+Umberto Zerbinati.............<https://www.uzerbinati.eu>
+
 Fangyi Zhou
 

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.env

@@ -67,9 +67,14 @@ RUN bash -c 'cd petsc; \
         --download-suitesparse \
         --download-superlu_dist \
         PETSC_ARCH=packages; \
-        mv packages/include/petscconf.h packages/include/old_petscconf.nope;'
+        mv packages/include/petscconf.h packages/include/old_petscconf.nope; \
+        rm -rf /home/firedrake/petsc/**/externalpackages; \
+        rm -rf /home/firedrake/petsc/src/docs; \
+        rm -f /home/firedrake/petsc/src/**/tutorials/output/*; \
+        rm -f /home/firedrake/petsc/src/**/tests/output/*'
 # Don't run make here, we only want MPICH and HWLOC
 # It is also necessary to move `petscconf.h` so packages isn't treated like a working PETSc
+# Cleaned up unnecessary files
 
 # Build default Firedrake PETSc
 RUN bash -c 'export PACKAGES=/home/firedrake/petsc/packages; \
@@ -149,12 +154,6 @@ RUN bash -c 'export PETSC_DIR=/home/firedrake/petsc; \
     ./configure; \
     make SLEPC_DIR=/home/firedrake/slepc PETSC_DIR=/home/firedrake/petsc PETSC_ARCH=complex;'
 
-# Clean up unnecessary files
-RUN rm -rf /home/firedrake/petsc/**/externalpackages \
-    && rm -rf /home/firedrake/petsc/src/docs \
-    && rm -f /home/firedrake/petsc/src/**/tutorials/output/* \
-    && rm -f /home/firedrake/petsc/src/**/tests/output/*
-
 # Set some useful environment variables
 ENV PETSC_DIR /home/firedrake/petsc
 ENV SLEPC_DIR /home/firedrake/slepc

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/element_list.py

@@ -1,6 +1,6 @@
 from finat.ufl.elementlist import ufl_elements
 # ~ from ufl.finiteelement.elementlist import ufl_elements
-from tsfc.finatinterface import supported_elements
+from finat.element_factory import supported_elements
 import csv
 
 shape_names = {

docs/source/events.rst

@@ -8,10 +8,18 @@
 Firedrake events
 ----------------
 
+Firedrake USA'25
+~~~~~~~~~~~~~~~~
+
+The ninth Firedrake user and developer workshop will be held 28 February
+and 1 March 2025 at Baylor University in Texas, USA.  For more information
+see :doc:`the workshop page <firedrake_usa_25>`.
+
+
 Firedrake '24
 ~~~~~~~~~~~~~
 
-The eighth Firedrake user and developer workshop will be held
+The eighth Firedrake user and developer workshop was held
 between 16-18 September 2024 at the University of Oxford. For more
 information see :doc:`the workshop page <firedrake_24>`.
 

docs/source/firedrake_usa_20.rst

@@ -60,9 +60,7 @@ Organising Committee
   University of Washington.
 * `David Ham <https://www.imperial.ac.uk/people/david.ham>`_, Imperial
   College London.
-* `Lawrence Mitchell
-  <https://www.dur.ac.uk/computer.science/staff/profile/?id=17243>`_,
-  Durham University.
+* Lawrence Mitchell, Durham University.
 
 
 Further details

docs/source/firedrake_usa_25.rst

@@ -0,0 +1,97 @@
+:orphan: true
+
+.. title:: Firedrake USA '25
+
+.. image:: images/baylor.jpg
+   :alt: Baylor University
+   :width: 100%
+   :align: center
+
+Firedrake USA'25
+----------------
+
+The ninth Firedrake user and developer workshop will be held at 
+`Baylor University 
+<https://math.artsandsciences.baylor.edu>`__ from 28 February-1 March 2025.
+
+The workshop will be an opportunity for Firedrake users and developers
+to discuss the latest developments in the
+project, anticipated future developments, and how Firedrake can be used
+in the numerical solution of partial differential equations. The event
+will provide Firedrake users with the opportunity to interact directly
+with developers and with other users.
+
+The conference will begin with a tutorial session on the morning of 28 February and end on the evening of 1 March. 
+
+
+Conference venue
+----------------
+
+The conference will take place in the Bill Daniel Student Center in Room 202 in the heart of the Baylor campus.  A `campus map <https://map.baylor.edu/>`__ is available online, and both Apple Maps and Google Maps accurately locate the Bill Daniel Student Center.  
+
+
+Accommodation
+-------------
+
+We have reserved a block of hotel rooms at SpringHill Suites Waco, about a 15 minute walk from the Bill Daniel Student Center.  Follow `this link <https://www.marriott.com/event-reservations/reservation-link.mi?id=1734040121673&key=GRP&guestreslink2=true&app=resvlink/>`__ to hold your room.  The group rate is only available until 20 January 2025.
+
+
+Conference dinner
+-----------------
+
+The conference dinner will be held Friday night at the Baylor Club in McLane Stadium.  The dinner is included with the registration fee.
+
+
+Registration
+------------
+
+Registration will be open soon.
+
+The registration fees are as follows:
+
+.. list-table::
+   :widths: 25 50
+   :header-rows: 0
+
+   * - Student:
+     - $50
+   * - Non-student:
+     - $200
+
+The `SIAM Texas-Louisiana Section <https://www.siam.org/get-involved/connect-with-a-community/sections/siam-texas-louisiana-section/>`__ is providing some support for students currently attending universities in Texas or Louisiana to attend.
+Conference registration is coming soon.
+
+
+
+Abstract submission
+-------------------
+
+Abstracts can be submitted `via EasyChair <https://easychair.org/conferences/?conf=firedrakeusa25>`__.
+
+
+
+Support
+-------
+
+The conference has been kindly supported by the SIAM TX-LA Section and EPSRC.
+
+
+Travel to Waco
+--------------
+
+* By air:  Waco has a small airport.  There is daily service between Waco and Dallas/Fort Worth International Airport via American Airlines.  
+
+* By ground:  We are less than two hours by car from the Dallas and Austin airports, and just under three hours from Bush Intercontinental Airport in Houston.  Additionally, Waco is reachable by bus services such as Greyhound and FlixBus.
+
+* Parking on campus:  Baylor has plenty of visitor parking for your personal or rental vehicle, but consult `these instructions <https://dps.web.baylor.edu/parking-transportation/visitors>`__ and make sure to `register your vehicle <https://dps.web.baylor.edu/parking-transportation/visitors/visitor-parking-permit>`__.
+
+
+
+Organising committee
+--------------------
+
+* `Robert Kirby <https://sites.baylor.edu/robert_kirby/>`__, Baylor University
+* `David Ham <https://profiles.imperial.ac.uk/david.ham>`__, Imperial College London
+
+
+

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
 ====================