Merge pull request #162 from mabarnes/merge_fkpl_collisions-merge-master

Merge master branch into merge_fkpl_collisions
mabarnes · Nov 26, 2023 · c9a3766 · c9a3766
2 parents 6045a81 + b1d73e5
commit c9a3766
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diff --git a/.github/workflows/debug_checks.yml b/.github/workflows/debug_checks.yml
@@ -1,113 +1,26 @@
 # Based on example from https://github.com/julia-actions/julia-runtest
 name: Debug checks for correctness
 
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
 
 jobs:
-  # The commented out job would run all debug checks, but they are slow so it
-  # is better to run each type in a separate job so that the separate jobs can
-  # run at the same time
-  #debug-checks:
-  #  runs-on: ${{ matrix.os }}
-  #  strategy:
-  #    matrix:
-  #      # Only run on linux to save CI server cpu-hours
-  #      os: [ubuntu-latest]
-  #    fail-fast: false
-  #  timeout-minutes: 240
-
-  #  steps:
-  #    - uses: actions/checkout@v2
-  #    - uses: mpi4py/setup-mpi@v1
-  #      with:
-  #        mpi: 'openmpi'
-  #    - uses: actions/setup-python@v2
-  #    - uses: julia-actions/setup-julia@v1
-  #      with:
-  #        version: '1.8'
-  #        arch: x64
-  #    - uses: julia-actions/julia-buildpkg@v1
-  #      env:
-  #        # Use the system Python for PyCall - avoids library linking error on macOS
-  #        PYTHON: "${{ env.pythonLocation }}/bin/python"
-  #      name: Debug test
-  #      run: |
-  #        # Hard code the debug level so that we can run without using the
-  #        # `--compiled-modules=no` flag, which breaks Symbolics.jl at the
-  #        # moment.
-  #        sed -i -e "s/_debug_level = get_options.*/_debug_level = 2/" src/debugging.jl
-
-  #        pip3 install --user matplotlib
-  #        julia --project -e 'using MPIPreferences; MPIPreferences.use_system_binary()'
-  #        julia --project -e 'using Pkg; Pkg.build("MPI"; verbose=true)'
-
-  #        # Need to use openmpi so that the following arguments work:
-  #        # * `--mca rmaps_base_oversubscribe 1` allows oversubscription (more processes
-  #        #   than physical cores).
-  #        # * `--mca mpi_yield_when_idle 1` changes a setting to prevent excessively
-  #        #   terrible performance when oversubscribing.
-  #        ## Don't use --compiled-modules=no for now, as it currently breaks Symbolics.jl
-  #        #mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes --compiled-modules=no debug_test/runtests.jl --debug 3
-  #        mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes debug_test/runtests.jl --debug 3
-
-  debug-checks-sound-wave:
+  debug-checks:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         # Only run on linux to save CI server cpu-hours
         os: [ubuntu-latest]
       fail-fast: false
-    timeout-minutes: 240
+    timeout-minutes: 360
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: mpi4py/setup-mpi@v1
         with:
           mpi: 'openmpi'
-      - uses: actions/setup-python@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/setup-python@v4
         with:
-          version: '1.8'
-          arch: x64
-      - uses: julia-actions/julia-buildpkg@v1
-        env:
-          # Use the system Python for PyCall - avoids library linking error on macOS
-          PYTHON: "${{ env.pythonLocation }}/bin/python"
-      - name: Debug test sound-wave
-        run: |
-          # Hard code the debug level so that we can run without using the
-          # `--compiled-modules=no` flag, which breaks Symbolics.jl at the
-          # moment.
-          sed -i -e "s/_debug_level = get_options.*/_debug_level = 2/" src/debugging.jl
-
-          pip3 install --user matplotlib
-          julia --project -e 'using MPIPreferences; MPIPreferences.use_system_binary()'
-          julia --project -e 'using Pkg; Pkg.build("MPI"; verbose=true)'
-
-          # Need to use openmpi so that the following arguments work:
-          # * `--mca rmaps_base_oversubscribe 1` allows oversubscription (more processes
-          #   than physical cores).
-          # * `--mca mpi_yield_when_idle 1` changes a setting to prevent excessively
-          #   terrible performance when oversubscribing.
-          ## Don't use --compiled-modules=no for now, as it currently breaks Symbolics.jl
-          #mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes --compiled-modules=no debug_test/sound_wave_tests.jl --debug 2
-          mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes debug_test/sound_wave_tests.jl --debug 2
-
-  debug-checks-wall-bc:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        # Only run on linux to save CI server cpu-hours
-        os: [ubuntu-latest]
-      fail-fast: false
-    timeout-minutes: 240
-
-    steps:
-      - uses: actions/checkout@v2
-      - uses: mpi4py/setup-mpi@v1
-        with:
-          mpi: 'openmpi'
-      - uses: actions/setup-python@v2
+          python-version: '3.11'
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1.8'
@@ -116,7 +29,7 @@ jobs:
         env:
           # Use the system Python for PyCall - avoids library linking error on macOS
           PYTHON: "${{ env.pythonLocation }}/bin/python"
-      - name: Debug test wall-bc
+      - name: Debug test
         run: |
           # Hard code the debug level so that we can run without using the
           # `--compiled-modules=no` flag, which breaks Symbolics.jl at the
@@ -133,91 +46,5 @@ jobs:
           # * `--mca mpi_yield_when_idle 1` changes a setting to prevent excessively
           #   terrible performance when oversubscribing.
           ## Don't use --compiled-modules=no for now, as it currently breaks Symbolics.jl
-          #mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes --compiled-modules=no debug_test/wall_bc_tests.jl --debug 2
-          mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes debug_test/wall_bc_tests.jl --debug 2
-
-  debug-checks-harrisonthompson:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        # Only run on linux to save CI server cpu-hours
-        os: [ubuntu-latest]
-      fail-fast: false
-    timeout-minutes: 240
-
-    steps:
-      - uses: actions/checkout@v2
-      - uses: mpi4py/setup-mpi@v1
-        with:
-          mpi: 'openmpi'
-      - uses: actions/setup-python@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1.8'
-          arch: x64
-      - uses: julia-actions/julia-buildpkg@v1
-        env:
-          # Use the system Python for PyCall - avoids library linking error on macOS
-          PYTHON: "${{ env.pythonLocation }}/bin/python"
-      - name: Debug test Harrison-Thompson
-        run: |
-          # Hard code the debug level so that we can run without using the
-          # `--compiled-modules=no` flag, which breaks Symbolics.jl at the
-          # moment.
-          sed -i -e "s/_debug_level = get_options.*/_debug_level = 2/" src/debugging.jl
-
-          pip3 install --user matplotlib
-          julia --project -e 'using MPIPreferences; MPIPreferences.use_system_binary()'
-          julia --project -e 'using Pkg; Pkg.build("MPI"; verbose=true)'
-
-          # Need to use openmpi so that the following arguments work:
-          # * `--mca rmaps_base_oversubscribe 1` allows oversubscription (more processes
-          #   than physical cores).
-          # * `--mca mpi_yield_when_idle 1` changes a setting to prevent excessively
-          #   terrible performance when oversubscribing.
-          ## Don't use --compiled-modules=no for now, as it currently breaks Symbolics.jl
-          #mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes --compiled-modules=no debug_test/harrisonthompson.jl --debug 2
-          mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes debug_test/harrisonthompson.jl --debug 2
-
-  debug-checks-mms:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        # Only run on linux to save CI server cpu-hours
-        os: [ubuntu-latest]
-      fail-fast: false
-    timeout-minutes: 240
-
-    steps:
-      - uses: actions/checkout@v2
-      - uses: mpi4py/setup-mpi@v1
-        with:
-          mpi: 'openmpi'
-      - uses: actions/setup-python@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1.8'
-          arch: x64
-      - uses: julia-actions/julia-buildpkg@v1
-        env:
-          # Use the system Python for PyCall - avoids library linking error on macOS
-          PYTHON: "${{ env.pythonLocation }}/bin/python"
-      - name: Debug test MMS
-        run: |
-          # Hard code the debug level so that we can run without using the
-          # `--compiled-modules=no` flag, which breaks Symbolics.jl at the
-          # moment.
-          sed -i -e "s/_debug_level = get_options.*/_debug_level = 2/" src/debugging.jl
-
-          pip3 install --user matplotlib
-          julia --project -e 'using MPIPreferences; MPIPreferences.use_system_binary()'
-          julia --project -e 'using Pkg; Pkg.build("MPI"; verbose=true)'
-
-          # Need to use openmpi so that the following arguments work:
-          # * `--mca rmaps_base_oversubscribe 1` allows oversubscription (more processes
-          #   than physical cores).
-          # * `--mca mpi_yield_when_idle 1` changes a setting to prevent excessively
-          #   terrible performance when oversubscribing.
-          ## Don't use --compiled-modules=no for now, as it currently breaks Symbolics.jl
-          #mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes --compiled-modules=no debug_test/mms_tests.jl --debug 2
-          mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes debug_test/mms_tests.jl --debug 2
+          #mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes --compiled-modules=no debug_test/sound_wave_tests.jl --debug 2
+          mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project --check-bounds=yes debug_test/runtests.jl --debug 2
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -11,7 +11,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.8'

diff --git a/.github/workflows/documentation_cleanup.yml b/.github/workflows/documentation_cleanup.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
       - name: Delete preview and history + push changes

diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
@@ -1,7 +1,7 @@
 # Based on example from https://github.com/julia-actions/julia-runtest
 name: Check examples
 
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
 
 jobs:
   examples:
@@ -10,11 +10,13 @@ jobs:
       matrix:
         os: [ubuntu-latest, macOS-latest]
       fail-fast: false
-    timeout-minutes: 25
+    timeout-minutes: 35
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1.8'

diff --git a/.github/workflows/longtest.yml b/.github/workflows/longtest.yml
@@ -6,6 +6,7 @@ on:
   push:
     branches:
       - master
+  workflow_dispatch:
 
 jobs:
   test:
@@ -14,11 +15,13 @@ jobs:
       matrix:
         os: [ubuntu-latest, macOS-latest]
       fail-fast: false
-    timeout-minutes: 75
+    timeout-minutes: 90
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1.8'
@@ -33,5 +36,5 @@ jobs:
         #
       - run: |
           pip3 install --user matplotlib
-          julia --check-bounds=yes --color=yes --depwarn=yes --inline=yes --project=@. -e 'import Pkg; Pkg.test(; coverage = :true, test_args=["--long"])'
+          julia --check-bounds=yes --color=yes --depwarn=yes --project=@. -e 'import Pkg; Pkg.test(; test_args=["--long"])'
         shell: bash
diff --git a/.github/workflows/parallel_test.yml b/.github/workflows/parallel_test.yml
@@ -1,7 +1,7 @@
 # Run tests in parallel to check for bugs that only show up on multiple processes
 name: Run tests in parallel
 
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
 
 jobs:
   test:
@@ -12,23 +12,20 @@ jobs:
         include:
           - julia_version: '1.8'
       fail-fast: false
-    timeout-minutes: 90
+    timeout-minutes: 120
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: mpi4py/setup-mpi@v1
         with:
           mpi: 'openmpi'
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia_version }}
           arch: x64
-      # Install a specific Plots.jl version, because the job hangs on macOS with
-      # [email protected]
-      - name: Pin dependency versions
-        if: matrix.os == 'macOS-latest'
-        run: julia --project -e 'using Pkg; Pkg.add([PackageSpec(name="Plots", version="1.24.3")])'
       - uses: julia-actions/julia-buildpkg@v1
         env:
           # Use the system Python for PyCall - avoids library linking error on macOS
@@ -37,15 +34,14 @@ jobs:
           pip3 install --user matplotlib
           julia --project -e 'using MPIPreferences; MPIPreferences.use_system_binary()'
           julia --project -e 'using Pkg; Pkg.build("MPI"; verbose=true)'
-          julia -O3 --check-bounds=no precompile.jl --debug 1
           # Need to use openmpi so that the following arguments work:
           # * `--mca rmaps_base_oversubscribe 1` allows oversubscription (more processes
           #   than physical cores).
           # * `--mca mpi_yield_when_idle 1` changes a setting to prevent excessively
           #   terrible performance when oversubscribing.
-          mpiexec -np 3 --mca rmaps_base_oversubscribe 1 julia --project=@. -Jmoment_kinetics.so -O3 --check-bounds=no test/runtests.jl --debug 1
-          mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project=@. -Jmoment_kinetics.so -O3 --check-bounds=no test/runtests.jl --debug 1
-          mpiexec -np 2 --mca rmaps_base_oversubscribe 1 julia --project=@. -Jmoment_kinetics.so -O3 --check-bounds=no test/runtests.jl --debug 1 --long
+          mpiexec -np 3 --mca rmaps_base_oversubscribe 1 julia --project=@. -O3 --check-bounds=no test/runtests.jl --debug 1
+          mpiexec -np 4 --mca rmaps_base_oversubscribe 1 julia --project=@. -O3 --check-bounds=no test/runtests.jl --debug 1
+          mpiexec -np 2 --mca rmaps_base_oversubscribe 1 julia --project=@. -O3 --check-bounds=no test/runtests.jl --debug 1 --long
           # Note: MPI.jl's default implementation is mpich, which has a similar option
           # `--with-device=ch3:sock`, but that needs to be set when compiling mpich.
         shell: bash
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,7 +1,7 @@
 # Based on example from https://github.com/julia-actions/julia-runtest
 name: Run tests
 
-on: [push, pull_request]
+on: [push, pull_request, workflow_dispatch]
 
 jobs:
   test:
@@ -10,11 +10,13 @@ jobs:
       matrix:
         os: [ubuntu-latest, macOS-latest]
       fail-fast: false
-    timeout-minutes: 40
+    timeout-minutes: 50
 
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1.8'