Update main branch (#136)

* Update CI versions and behavior

* Refactor timings, due to:
FEniCS/dolfinx#3487
FEniCS/dolfinx#3488

* API changes from:  FEniCS/dolfinx#3500

* Fix demo

* Install boost

* Set tag

* Only check docker on release branch

* Fixes for refernece value size

* More timing fixes

* Another round of timing changes

* Remove last old timing instance

.github/workflows/build_docs.yml

@@ -5,11 +5,11 @@ on:
   workflow_call:
   pull_request:
     branches:
-      - main
+      - release
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     container: ghcr.io/fenics/dolfinx/dev-env:current-mpich
     env:
       # Directory that will be published on github pages
@@ -18,9 +18,16 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          ref: release
+
+      - name: Install libbost for backwards compatibility
+        run: |
+          apt-get update
+          apt-get install -y libboost-dev libboost-timer-dev
 
       - name: Install DOLFINx
-        uses: jorgensd/actions/install-dolfinx@v0.3
+        uses: jorgensd/actions/install-dolfinx@v0.4
         with:
           dolfinx: v0.9.0
           ufl: 2024.2.0

.github/workflows/docker.yml

@@ -5,7 +5,6 @@ on:
   pull_request:
     branches:
       - release
-      - main
 
   workflow_dispatch:
 

.github/workflows/sonarcloud.yml

@@ -67,7 +67,7 @@ jobs:
           echo "$HOME/.sonar/build-wrapper-linux-x86" >> $GITHUB_PATH
 
       - name: Install DOLFINx
-        uses: jorgensd/actions/install-dolfinx@v0.3
+        uses: jorgensd/actions/install-dolfinx@v0.4
         with:
           petsc_arch: ${PETSC_ARCH}
           dolfinx: main

.github/workflows/test_mpc.yml

@@ -14,7 +14,7 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/dolfinx:stable
+    container: ghcr.io/fenics/dolfinx/dolfinx:nightly
 
     strategy:
       matrix:
@@ -37,10 +37,10 @@ jobs:
         #   - CC: clang
         #     CXX: c++
     env:
-      DOLFINX_BRANCH: v0.9.0
-      BASIX_BRANCH: v0.9.0
-      UFL_BRANCH: 2024.2.0
-      FFCX_BRANCH: v0.9.0
+      DOLFINX_BRANCH: main
+      BASIX_BRANCH: main
+      UFL_BRANCH: main
+      FFCX_BRANCH: main
 
       CC: ${{ matrix.CC }}
       CXX: ${{ matrix.CXX }}
@@ -88,7 +88,7 @@ jobs:
           python3 -m pip install --no-build-isolation  --no-cache-dir --no-binary=h5py h5py
 
       - name: Install DOLFINx
-        uses: jorgensd/actions/install-dolfinx@v0.3
+        uses: jorgensd/actions/install-dolfinx@v0.4
         with:
           dolfinx: ${{ env.DOLFINX_BRANCH }}
           ufl: ${{ env.UFL_BRANCH }}

cpp/PeriodicConstraint.h

@@ -65,7 +65,7 @@ dolfinx_mpc::mpc_data<T> _create_periodic_condition(
       parents_glob[i] = parents_glob[i] * bs + parent_rems[i];
     return parents_glob;
   };
-  if (const std::size_t value_size = V.value_size() / V.element()->block_size();
+  if (const std::size_t value_size = V.element()->reference_value_size();
       value_size > 1)
     throw std::runtime_error(
         "Periodic conditions for vector valued spaces are not "

cpp/mpc_helpers.h

@@ -231,10 +231,7 @@ create_extended_functionspace(const dolfinx::fem::FunctionSpace<U>& V,
       old_dofmap.element_dof_layout(), new_index_map, old_dofmap.bs(),
       std::move(flattened_dofmap), old_dofmap.bs());
 
-  return dolfinx::fem::FunctionSpace(
-      V.mesh(), element, new_dofmap,
-      dolfinx::fem::compute_value_shape(element, V.mesh()->topology()->dim(),
-                                        V.mesh()->geometry().dim()));
+  return dolfinx::fem::FunctionSpace(V.mesh(), element, new_dofmap);
 }
 
 } // namespace dolfinx_mpc

cpp/utils.h

@@ -1007,8 +1007,7 @@ evaluate_basis_functions(const dolfinx::fem::FunctionSpace<U>& V,
   auto element = V.element();
   assert(element);
   const int bs_element = element->block_size();
-  const std::size_t reference_value_size
-      = element->reference_value_size() / bs_element;
+  const std::size_t reference_value_size = element->reference_value_size();
 
   // If the space has sub elements, concatenate the evaluations on the
   // sub elements
@@ -1026,7 +1025,7 @@ evaluate_basis_functions(const dolfinx::fem::FunctionSpace<U>& V,
 
   assert(basis_shape[2]
          == std::size_t(element->space_dimension() / bs_element));
-  assert(basis_shape[3] == std::size_t(V.value_size() / bs_element));
+  assert(basis_shape[3] == std::size_t(element->reference_value_size()));
   std::array<std::size_t, 3> reference_shape
       = {basis_shape[1], basis_shape[2], basis_shape[3]};
   std::vector<U> output_basis(std::reduce(

python/benchmarks/bench_contact_3D.py

@@ -19,7 +19,7 @@
 import numpy as np
 from basix.ufl import element
 from dolfinx import default_real_type, default_scalar_type
-from dolfinx.common import Timer, TimingType, list_timings, timing
+from dolfinx.common import Timer, list_timings, timing
 from dolfinx.cpp.mesh import entities_to_geometry
 from dolfinx.fem import (
     Constant,
@@ -297,7 +297,7 @@ def sigma(v):
     apply_lifting(b, [bilinear_form], [bcs], mpc)
     b.ghostUpdate(addv=PETSc.InsertMode.ADD_VALUES, mode=PETSc.ScatterMode.REVERSE)  # type: ignore
     set_bc(b, bcs)
-    list_timings(MPI.COMM_WORLD, [TimingType.wall])
+    list_timings(MPI.COMM_WORLD)
 
     # Solve Linear problem
     opts = PETSc.Options()  # type: ignore
@@ -365,13 +365,13 @@ def sigma(v):
         for op in operations:
             op_timing = timing(f"{num_dofs}: {op}")
             num_calls = op_timing[0]
-            wall_time = op_timing[1]
+            wall_time = op_timing[1].total_seconds()
             avg_time = comm.allreduce(wall_time, op=MPI.SUM) / comm.size
             min_time = comm.allreduce(wall_time, op=MPI.MIN)
             max_time = comm.allreduce(wall_time, op=MPI.MAX)
             if comm.rank == 0:
                 print(op, num_calls, avg_time, min_time, max_time, file=results_file)
-        list_timings(MPI.COMM_WORLD, [TimingType.wall])
+        list_timings(MPI.COMM_WORLD)
     b.destroy()
     solver.destroy()
 

python/benchmarks/bench_elasticity.py

@@ -17,7 +17,7 @@
 import h5py
 import numpy as np
 from dolfinx import default_real_type, default_scalar_type
-from dolfinx.common import Timer, TimingType, list_timings
+from dolfinx.common import Timer, list_timings
 from dolfinx.fem import (
     Constant,
     Function,
@@ -157,7 +157,7 @@ def l2b(li):
         solver.solve(b, uh)
         uh.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)  # type: ignore
         mpc.backsubstitution(uh)
-        solver_time = timer.elapsed()
+        solver_time = timer.elapsed().total_seconds()
 
     it = solver.getIterationNumber()
     if kspview:
@@ -176,7 +176,7 @@ def l2b(li):
         d_set = out_hdf5.get("num_dofs")
         d_set[r_lvl] = num_dofs
         d_set = out_hdf5.get("solve_time")
-        d_set[r_lvl, MPI.COMM_WORLD.rank] = solver_time[0]
+        d_set[r_lvl, MPI.COMM_WORLD.rank] = solver_time
     if xdmf:
         # Write solution to file
         u_h = Function(mpc.function_space)
@@ -223,5 +223,5 @@ def l2b(li):
         log_info(f"Run {i} in progress")
         bench_elasticity_one(r_lvl=i, out_hdf5=h5f, xdmf=args.xdmf, boomeramg=args.boomeramg, kspview=args.kspview)
         if args.timings and i == N - 1:
-            list_timings(MPI.COMM_WORLD, [TimingType.wall])
+            list_timings(MPI.COMM_WORLD)
     h5f.close()

python/benchmarks/bench_elasticity_edge.py

@@ -16,7 +16,7 @@
 import h5py
 import numpy as np
 from dolfinx import default_real_type, default_scalar_type
-from dolfinx.common import Timer, TimingType, list_timings
+from dolfinx.common import Timer, list_timings
 from dolfinx.fem import (
     Constant,
     Function,
@@ -190,7 +190,7 @@ def sigma(v):
         solver.solve(b, uh.x.petsc_vec)
         uh.x.scatter_forward()
         mpc.backsubstitution(uh)
-        solver_time = timer.elapsed()
+        solver_time = timer.elapsed().total_seconds()
     if kspview:
         solver.view()
 
@@ -206,7 +206,7 @@ def sigma(v):
         d_set = out_hdf5.get("num_slaves")
         d_set[r_lvl, MPI.COMM_WORLD.rank] = mpc.num_local_slaves
         d_set = out_hdf5.get("solve_time")
-        d_set[r_lvl, MPI.COMM_WORLD.rank] = solver_time[0]
+        d_set[r_lvl, MPI.COMM_WORLD.rank] = solver_time
     if info:
         log_info(f"Lvl: {r_lvl}, Its: {it}, max Mem: {mem}, dim(V): {num_dofs}")
 
@@ -278,5 +278,5 @@ def sigma(v):
         )
 
         if args.timings and i == N - 1:
-            list_timings(MPI.COMM_WORLD, [TimingType.wall])
+            list_timings(MPI.COMM_WORLD)
     h5f.close()

python/benchmarks/bench_periodic.py

@@ -21,7 +21,7 @@
 import h5py
 import numpy as np
 from dolfinx import default_scalar_type
-from dolfinx.common import Timer, TimingType, list_timings
+from dolfinx.common import Timer, list_timings
 from dolfinx.fem import Function, dirichletbc, form, functionspace, locate_dofs_geometrical
 from dolfinx.fem.petsc import set_bc
 from dolfinx.io import XDMFFile
@@ -148,7 +148,7 @@ def periodic_relation(x):
         uh.x.scatter_forward()
         mpc.backsubstitution(uh)
 
-        solver_time = timer.elapsed()
+        solver_time = timer.elapsed().total_seconds()
         if kspview:
             solver.view()
 
@@ -163,7 +163,7 @@ def periodic_relation(x):
         d_set = out_hdf5.get("num_slaves")
         d_set[r_lvl, MPI.COMM_WORLD.rank] = mpc.num_local_slaves
         d_set = out_hdf5.get("solve_time")
-        d_set[r_lvl, MPI.COMM_WORLD.rank] = solver_time[0]
+        d_set[r_lvl, MPI.COMM_WORLD.rank] = solver_time
 
     if MPI.COMM_WORLD.rank == 0:
         print(f"Rlvl {r_lvl}, Iterations {it}")
@@ -241,5 +241,5 @@ def periodic_relation(x):
 
         # List_timings
         if args.timings and i == N - 1:
-            list_timings(MPI.COMM_WORLD, [TimingType.wall])
+            list_timings(MPI.COMM_WORLD)
     h5f.close()

python/benchmarks/ref_elasticity.py

@@ -18,7 +18,7 @@
 import h5py
 import numpy as np
 from dolfinx import default_real_type, default_scalar_type
-from dolfinx.common import Timer, TimingType, list_timings
+from dolfinx.common import Timer, list_timings
 from dolfinx.fem import (
     Constant,
     Function,
@@ -257,5 +257,5 @@ def sigma(v):
             degree=args.degree,
         )
         if args.timings and i == N - 1:
-            list_timings(MPI.COMM_WORLD, [TimingType.wall])
+            list_timings(MPI.COMM_WORLD)
     h5f.close()

python/benchmarks/ref_periodic.py

@@ -27,7 +27,7 @@
 import h5py
 import numpy as np
 from dolfinx import default_scalar_type
-from dolfinx.common import Timer, TimingType, list_timings
+from dolfinx.common import Timer, list_timings
 from dolfinx.fem import Function, dirichletbc, form, functionspace, locate_dofs_geometrical
 from dolfinx.fem.petsc import apply_lifting, assemble_matrix, assemble_vector, set_bc
 from dolfinx.io import XDMFFile
@@ -219,5 +219,5 @@ def dirichletboundary(x):
         )
 
         if args.timings and i == N - 1:
-            list_timings(MPI.COMM_WORLD, [TimingType.wall])
+            list_timings(MPI.COMM_WORLD)
     h5f.close()

python/demos/demo_contact_2D.py

@@ -23,7 +23,7 @@
 import numpy as np
 import scipy.sparse.linalg
 from dolfinx import default_real_type, default_scalar_type
-from dolfinx.common import Timer, TimingType, list_timings
+from dolfinx.common import Timer, list_timings
 from dolfinx.fem import Constant, dirichletbc, form, functionspace, locate_dofs_geometrical
 from dolfinx.fem.petsc import apply_lifting, assemble_matrix, assemble_vector, set_bc
 from dolfinx.io import XDMFFile
@@ -263,4 +263,4 @@ def left_corner(x):
 
     outfile.close()
     if args.timing:
-        list_timings(MPI.COMM_WORLD, [TimingType.wall])
+        list_timings(MPI.COMM_WORLD)

python/demos/demo_contact_3D.py

@@ -19,7 +19,7 @@
 import numpy as np
 import scipy.sparse.linalg
 from dolfinx import default_real_type, default_scalar_type
-from dolfinx.common import Timer, TimingType, list_timings
+from dolfinx.common import Timer, list_timings
 from dolfinx.io import XDMFFile
 from dolfinx.mesh import CellType
 from ufl import Identity, TestFunction, TrialFunction, dx, grad, inner, sym, tr
@@ -232,7 +232,7 @@ def sigma(v):
             uh_numpy = K @ d
             assert np.allclose(uh_numpy, u_mpc)
 
-    list_timings(mesh.comm, [TimingType.wall])
+    list_timings(mesh.comm)
     b.destroy()
     L_org.destroy()
     solver.destroy()
@@ -298,4 +298,4 @@ def sigma(v):
 
     log_info("Simulation finished")
     if args.timing:
-        list_timings(MPI.COMM_WORLD, [TimingType.wall])
+        list_timings(MPI.COMM_WORLD)

python/demos/demo_periodic3d_topological.py

@@ -25,7 +25,7 @@
 import numpy as np
 import scipy.sparse.linalg
 from dolfinx import default_scalar_type
-from dolfinx.common import Timer, TimingType, list_timings
+from dolfinx.common import Timer, list_timings
 from dolfinx.io import VTXWriter
 from dolfinx.mesh import CellType, create_unit_cube, locate_entities_boundary, meshtags
 from numpy.typing import NDArray
@@ -185,4 +185,4 @@ def periodic_relation(x):
 if __name__ == "__main__":
     for celltype in [CellType.hexahedron, CellType.tetrahedron]:
         demo_periodic3D(celltype)
-    list_timings(MPI.COMM_WORLD, [TimingType.wall])
+    list_timings(MPI.COMM_WORLD)

python/demos/demo_periodic_geometrical.py

@@ -22,7 +22,7 @@
 import numpy as np
 import scipy.sparse.linalg
 from dolfinx import default_scalar_type
-from dolfinx.common import Timer, TimingType, list_timings
+from dolfinx.common import Timer, list_timings
 from dolfinx.io import XDMFFile
 from dolfinx.mesh import create_unit_square, locate_entities_boundary
 from ufl import (
@@ -185,5 +185,5 @@ def periodic_relation(x):
         # Back substitution to full solution vector
         uh_numpy = K.astype(scipy_dtype) @ d.astype(scipy_dtype)
         assert np.allclose(uh_numpy.astype(u_mpc.dtype), u_mpc, atol=float(tol))
-list_timings(MPI.COMM_WORLD, [TimingType.wall])
+list_timings(MPI.COMM_WORLD)
 L_org.destroy()

python/demos/demo_stokes.py

@@ -329,4 +329,4 @@ def T(u: Expr, p: Expr, mu: Expr):
 # ## Timings
 # Finally, we list the execution time of various operations used in the demo
 
-common.list_timings(MPI.COMM_WORLD, [common.TimingType.wall])
+common.list_timings(MPI.COMM_WORLD)

python/demos/demo_stokes_nest.py

@@ -362,4 +362,4 @@ def T(u: Expr, p: Expr, mu: Expr):
 Uh.destroy()
 ksp.destroy()
 # -------------------- List timings --------------------------
-dolfinx.common.list_timings(MPI.COMM_WORLD, [dolfinx.common.TimingType.wall])
+dolfinx.common.list_timings(MPI.COMM_WORLD)

python/tests/test_cube_contact.py

@@ -19,7 +19,7 @@
 import scipy.sparse.linalg
 import ufl
 from dolfinx import default_scalar_type
-from dolfinx.common import Timer, TimingType, list_timings
+from dolfinx.common import Timer, list_timings
 from dolfinx.io import gmshio
 
 import dolfinx_mpc
@@ -301,4 +301,4 @@ def sigma(v):
     b.destroy()
     solver.destroy()
 
-    list_timings(comm, [TimingType.wall])
+    list_timings(comm)