Merge pull request #39 from finsberg/codspeed

Run problem 1,2 and 3 as benchmark to monitor performance

Author: finsberg

.cspell_dict.txt

@@ -11,12 +11,14 @@ deviatoric
 dirichletbc
 dofs
 dolfinx
+endo
 fenics
 fenicsx
 fenicsx_pulse
 ffun
 finsberg
 functionspace
+geodir
 gradu
 Guccione
 Holzapfel

.github/workflows/codspeed.yml

@@ -0,0 +1,35 @@
+name: codspeed-benchmarks
+
+on:
+  push:
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+jobs:
+  benchmarks:
+    runs-on: ubuntu-22.04
+    container:
+      image: ghcr.io/fenics/dolfinx/dolfinx:v0.8.0
+      options: --privileged
+    env:
+      DEB_PYTHON_INSTALL_LAYOUT: deb_system
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install package needed by codspeed
+        run: apt-get update && apt-get install -y curl lsb-release
+
+      - name: Install package
+        run: python3 -m pip install -e .[benchmark]
+
+      - name : Install codspeed
+        run: curl -fsSL https://github.com/CodSpeedHQ/runner/releases/download/v2.4.2/codspeed-runner-installer.sh | bash -s
+
+      - name: Fix git owner
+        run: git config --global --add safe.directory "*"
+
+      - name: Run benchmarks
+        run: |
+          $HOME/.cargo/bin/codspeed-runner --token ${{ secrets.CODSPEED_TOKEN }} "python3 -m pytest tests/ --codspeed"

.github/workflows/test_package_coverage.yml

@@ -20,7 +20,7 @@ jobs:
         run: python3 -m pip install .[test]
 
       - name: Run tests
-        run: python3 -m pytest -v
+        run: python3 -m pytest -m "not benchmark"
 
       - name: Extract Coverage
         run: |

pyproject.toml

@@ -33,6 +33,10 @@ docs = [
    "trame-vuetify",
    "ipywidgets",
 ]
+benchmark = [
+    "pytest-codspeed",
+    "fenicsx_pulse[test]",
+]
 
 all = [
    "fenicsx_pulse[test]",
@@ -46,7 +50,7 @@ addopts = [
    "--cov-report=html",
    "--cov-report=xml",
    "--cov-report=term-missing",
-   "-v"
+   "-v",
 ]
 testpaths = [
     "tests"

tests/test_benchmarks.py

@@ -0,0 +1,89 @@
+from mpi4py import MPI
+
+import dolfinx
+import fenicsx_pulse
+import numpy as np
+import pytest
+from dolfinx import log
+
+
+@pytest.mark.benchmark
+def test_problem1():
+    L = 10.0
+    W = 1.0
+    mesh = dolfinx.mesh.create_box(
+        MPI.COMM_WORLD,
+        [[0.0, 0.0, 0.0], [L, W, W]],
+        [30, 3, 3],
+        dolfinx.mesh.CellType.hexahedron,
+    )
+
+    left = 1
+    bottom = 2
+    boundaries = [
+        fenicsx_pulse.Marker(
+            name="left",
+            marker=left,
+            dim=2,
+            locator=lambda x: np.isclose(x[0], 0),
+        ),
+        fenicsx_pulse.Marker(
+            name="bottom",
+            marker=bottom,
+            dim=2,
+            locator=lambda x: np.isclose(x[2], 0),
+        ),
+    ]
+
+    geo = fenicsx_pulse.Geometry(
+        mesh=mesh,
+        boundaries=boundaries,
+        metadata={"quadrature_degree": 4},
+    )
+
+    material_params = {
+        "C": dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(2.0)),
+        "bf": dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(8.0)),
+        "bt": dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(2.0)),
+        "bfs": dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(4.0)),
+    }
+    f0 = dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type((1.0, 0.0, 0.0)))
+    s0 = dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type((0.0, 1.0, 0.0)))
+    n0 = dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type((0.0, 0.0, 1.0)))
+    material = fenicsx_pulse.Guccione(f0=f0, s0=s0, n0=n0, **material_params)
+
+    active_model = fenicsx_pulse.active_model.Passive()
+    comp_model = fenicsx_pulse.Incompressible()
+
+    model = fenicsx_pulse.CardiacModel(
+        material=material,
+        active=active_model,
+        compressibility=comp_model,
+    )
+
+    def dirichlet_bc(
+        state_space: dolfinx.fem.FunctionSpace,
+    ) -> list[dolfinx.fem.bcs.DirichletBC]:
+        V, _ = state_space.sub(0).collapse()
+        facets = geo.facet_tags.find(left)  # Specify the marker used on the boundary
+        mesh.topology.create_connectivity(mesh.topology.dim - 1, mesh.topology.dim)
+        dofs = dolfinx.fem.locate_dofs_topological((state_space.sub(0), V), 2, facets)
+        u_fixed = dolfinx.fem.Function(V)
+        u_fixed.x.array[:] = 0.0
+        return [dolfinx.fem.dirichletbc(u_fixed, dofs, state_space.sub(0))]
+
+    traction = dolfinx.fem.Constant(mesh, dolfinx.default_scalar_type(0.0))
+    neumann = fenicsx_pulse.NeumannBC(traction=traction, marker=bottom)
+    bcs = fenicsx_pulse.BoundaryConditions(dirichlet=(dirichlet_bc,), neumann=(neumann,))
+    problem = fenicsx_pulse.MechanicsProblemMixed(model=model, geometry=geo, bcs=bcs)
+
+    log.set_log_level(log.LogLevel.INFO)
+
+    for t in [0.0, 0.001, 0.002, 0.003, 0.004]:
+        print(f"Solving problem for traction={t}")
+        traction.value = t
+        problem.solve()
+
+    # Now let us turn off the logging again
+
+    log.set_log_level(log.LogLevel.WARNING)