DO NOT SQUASH Merge release

.github/actions/install/action.yml

@@ -154,6 +154,7 @@ runs:
           EXTRA_PIP_FLAGS='--no-build-isolation'
         elif [ ${{ inputs.base_ref }} = 'release' ]; then
           EXTRA_PIP_FLAGS=''
+          export PIP_BUILD_CONSTRAINT=constraints.txt
         else
           echo "Unrecognised 'base_ref' input: '${{ inputs.base_ref }}"
           exit 1

AUTHORS.rst

@@ -58,6 +58,8 @@ Ed Bueler
 
 Henrik Buesing
 
+Anastasia Chanbour
+
 Justin Chang
 
 Cyrus Cheng

docs/Makefile

@@ -103,7 +103,7 @@ copy_notebooks:
 source/element_list.csv: source/element_list.py
 	cd source; python3 element_list.py
 
-source/team.rst: source/team2.py
+source/team.rst: source/team2.py source/team.ini
 	cd source; python3 team2.py; mv AUTHORS.rst ../..
 
 source/apt_deps.txt:

docs/source/firedrake_19.rst

@@ -58,8 +58,8 @@ presenters.
 * Colin Cotter: `Time (integrator) parallel exponential integration
   and phase-averaging for geophysical fluid dynamics
   <_static/firedrake19-slides/cotter.pdf>`__
-* Matt Knepley: `Understanding multivariate computation using the
-  Kolmogorov superposition theorem <https://cse.buffalo.edu/~knepley/presentations/PresFiredrake2019.pdf>`_
+* Matt Knepley: Understanding multivariate computation using the
+  Kolmogorov superposition theorem
 * Lawrence Mitchell: `PCPATCH: topological construction of multigrid
   relaxation methods <_static/firedrake19-slides/mitchell.pdf>`__
 * Joe Wallwork: `Anisotropic goal-oriented mesh adaptation in

docs/source/team.ini

@@ -50,6 +50,7 @@ Daiane I. Dolci:
 Joshua Hope-Collins: https://www.imperial.ac.uk/people/joshua.hope-collins13
 Umberto Zerbinati: https://www.uzerbinati.eu
 Leo Collins:
+Anastasia Chanbour:
 
 [inactive-team]
 Lawrence Mitchell: https://www.wence.uk/

firedrake/assemble.py

@@ -1074,7 +1074,14 @@ def parloops(self, tensor):
         if hasattr(self, "_parloops"):
             for (lknl, _), parloop in zip(self.local_kernels, self._parloops):
                 data = self._as_pyop2_type(tensor, lknl.indices)
-                parloop.arguments[0].data = data
+                if isinstance(data, op2.Global):
+                    # In parloops we swap out globals with private ones so
+                    # increments don't double add. The right attribute to swap
+                    # out here is therefore reduced_globals instead of arguments.
+                    tmp = parloop.arguments[0].data
+                    parloop.reduced_globals[tmp] = op2.GlobalParloopArg(data)
+                else:
+                    parloop.arguments[0].data = data
 
         else:
             # Make parloops for one concrete output tensor and cache them.

firedrake/supermeshing.py

@@ -4,6 +4,7 @@
 import pathlib
 import libsupermesh
 import petsctools
+import rtree
 
 from firedrake.cython.supermeshimpl import assemble_mixed_mass_matrix as ammm, intersection_finder
 from firedrake.mg.utils import get_level
@@ -462,9 +463,14 @@ def likely(cell_A):
 
     libsupermesh_dir = pathlib.Path(libsupermesh.get_include()).parent.absolute()
     dirs = petsctools.get_petsc_dirs() + (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"]
+    includes = [f"-I{d}/include" for d in dirs]
+    libs = [
+        *[f"-L{d}/lib" for d in dirs],
+        *[f"-Wl,-rpath,{d}/lib" for d in dirs],
+        "-lpetsc",
+        "-lsupermesh",
+        str(pathlib.Path(rtree.core.rt._name).absolute()),  # libspatialindex.so
+    ]
     dll = load(
         supermesh_kernel_str, "c",
         cppargs=includes,

pyproject.toml

@@ -27,7 +27,8 @@ dependencies = [
   "h5py>3.12.1",
   "firedrake-rtree>=2026.2.0",
   "immutabledict",
-  "libsupermesh>=2026.0",
+  # TODO RELEASE
+  "libsupermesh @ git+https://github.com/firedrakeproject/libsupermesh.git@main",
   "loopy>2024.1",
   "numpy",
   "packaging",
@@ -41,6 +42,7 @@ dependencies = [
   "pycparser",
   "pytools[siphash]",
   "requests",
+  "rtree",
   "scipy",
   "sympy",
   "islpy<2026.2",
@@ -159,7 +161,8 @@ docker = [  # Used in firedrake-vanilla container
 requires = [
   "Cython>=3.0",
   "firedrake-rtree>=2026.2.0",
-  "libsupermesh>=2026.0",
+  # TODO RELEASE
+  "libsupermesh @ git+https://github.com/firedrakeproject/libsupermesh.git@main",
   "mpi4py>3; python_version >= '3.13'",
   "mpi4py; python_version < '3.13'",
   "numpy",
@@ -169,6 +172,7 @@ requires = [
   "pkgconfig",
   "pybind11",
   "setuptools>=77.0.3",
+  "rtree",
 ]
 build-backend = "setuptools.build_meta"
 

requirements-build.txt

@@ -1,14 +1,16 @@
 # Core build dependencies (adapted from pyproject.toml)
 Cython>=3.0
 firedrake-rtree>=2026.2.0
-libsupermesh>=2026.0
+# TODO RELEASE
+libsupermesh @ git+https://github.com/firedrakeproject/libsupermesh.git@main
 mpi4py>3; python_version >= '3.13'
 mpi4py; python_version < '3.13'
 numpy
 pkgconfig
 petsctools
 pybind11
 setuptools>=77.0.3
+rtree
 
 # Transitive build dependencies
 hatchling

setup.py

@@ -10,6 +10,7 @@
 
 import libsupermesh
 import firedrake_rtree
+import rtree
 import numpy as np
 import pybind11
 import petsctools
@@ -138,6 +139,19 @@ def __getitem__(self, key):
     ],
 )
 
+# libspatialindex
+# example:
+# gcc -I/rtree/include
+# gcc /rtree.libs/libspatialindex.so -Wl,-rpath,$ORIGIN/../../Rtree.libs
+libspatialindex_so = Path(rtree.core.rt._name).absolute()
+spatialindex_ = ExternalDependency(
+    include_dirs=[rtree.finder.get_include()],
+    extra_link_args=[str(libspatialindex_so)],
+    runtime_library_dirs=[
+        os.path.join(dir, "Rtree.libs") for dir in sitepackage_dirs
+    ],
+)
+
 # libsupermesh
 # example:
 # gcc -Ipath/to/libsupermesh/include
@@ -205,7 +219,7 @@ def extensions():
         name="firedrake.cython.supermeshimpl",
         language="c",
         sources=[os.path.join("firedrake", "cython", "supermeshimpl.pyx")],
-        **(mpi_ + petsc_ + numpy_ + libsupermesh_)
+        **(mpi_ + petsc_ + numpy_ + libsupermesh_ + spatialindex_)
     ))
     # pyop2/sparsity.pyx: petsc, numpy,
     cython_list.append(Extension(

tests/firedrake/regression/test_real_space.py

@@ -1,4 +1,5 @@
 import pytest
+import pytest_mpi
 import numpy as np
 
 from firedrake import *
@@ -428,3 +429,22 @@ def test_real_space_hex():
     assert np.allclose(val.dat.data_ro, [2.])
     val = assemble(inner(r, TestFunction(DG)) * dx)
     assert np.allclose(val.dat.data, [1., 1.])
+
+
+@pytest.mark.parallel
+def test_real_space_repeated_assembly():
+    """Test that repeated assembly of the same form works in parallel.
+
+    This test is of particular importance to the Real space because Real
+    functions are globals and this can lead to problems with halo
+    increments.
+
+    """
+    mesh = UnitSquareMesh(3, 3)
+    R = FunctionSpace(mesh, "R", 0)
+    q = TestFunction(R)
+
+    form = q*dx + q*ds  # area + perimeter of the unit square = 1 + 4 = 5
+    for i in range(3):
+        x = assemble(form)
+        pytest_mpi.parallel_assert(np.isclose(x.dat.data_ro.item(), 5))