Supercomputing

.github/actions/pip_installation/action.yml

@@ -14,8 +14,18 @@ runs:
     - name: Install dependencies
       shell: bash
       run: |
-              export CC="mpicc" HDF5_MPI="ON"
-              python -m pip install -r requirements.txt
-              python -m pip install numba
-              python -m pip install pythran
-
+        export CC="mpicc" HDF5_MPI="ON"
+        python -m pip install -r requirements.txt
+        python -m pip install numba
+        python -m pip install pythran
+    - uses: actions/checkout@v5
+      with:
+        repository: EmilyBourne/hptt
+        path: hptt
+    - name: Install hptt
+      shell: bash
+      run: |
+        cd hptt
+        make -j
+        cd pythonAPI
+        python -m pip install .

.github/actions/selalib_installation/action.yml

@@ -0,0 +1,16 @@
+name: 'SeLaLib installation'
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/checkout@v5
+      with:
+        repository: selalib/selalib
+        path: selalib
+    - name: Compile SeLaLib
+      shell: bash
+      run: |
+        cd selalib
+        cmake -B build .
+        cmake --build build -j 4 -t sll_splines
+

.github/workflows/testing.yml

@@ -11,7 +11,6 @@ on:
       - 'mpi_tester.py'
 
   pull_request:
-    branches: [ main ]
     types:
       - opened
       - synchronize
@@ -28,49 +27,51 @@ on:
 
 jobs:
 
-  Coverage:
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-            python-version: '3.10'
-      - name: Install dependencies
-        uses: ./.github/actions/linux_install
-      - name: Cache pip
-        uses: actions/cache@v3
-        with:
-          # This path is specific to Ubuntu
-          path: ~/.cache/pip
-          # Look to see if there is a cache hit for the corresponding requirements file
-          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-            ${{ runner.os }}-
-      - name: Install python dependencies
-        uses: ./.github/actions/pip_installation
-      - name: Coverage install
-        uses: ./.github/actions/coverage_install
-      - name: Unit tests
-        run: |
-          coverage run -p --source=pygyro -m pytest pygyro -m "serial and not long" --short
-          make
-          coverage run -p --source=pygyro -m pytest pygyro -m serial
-          mpirun -n 1 coverage run -p mpi_tester.py pygyro -m parallel --mpisub
-          mpirun -n 4 --oversubscribe coverage run -p mpi_tester.py pygyro -m parallel --mpisub
-          mpirun -n 6 --oversubscribe coverage run -p mpi_tester.py pygyro -m parallel --mpisub
-      - name: Collect coverage information
-        continue-on-error: True
-        uses: ./.github/actions/coverage_collection
-      - name: Run codacy-coverage-reporter
-        uses: codacy/codacy-coverage-reporter-action@master
-        continue-on-error: True
-        with:
-          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
-          coverage-reports: current_coverage.xml
+    #Coverage:
+
+    #  runs-on: ubuntu-latest
+
+    #  steps:
+    #    - uses: actions/checkout@v3
+    #    - name: Set up Python
+    #      uses: actions/setup-python@v4
+    #      with:
+    #          python-version: '3.10'
+    #    - name: Install dependencies
+    #      uses: ./.github/actions/linux_install
+    #    - name: Install SeLaLib
+    #      uses: ./.github/actions/selalib_installation
+    #    - name: Cache pip
+    #      uses: actions/cache@v3
+    #      with:
+    #        # This path is specific to Ubuntu
+    #        path: ~/.cache/pip
+    #        # Look to see if there is a cache hit for the corresponding requirements file
+    #        key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+    #        restore-keys: |
+    #          ${{ runner.os }}-pip-
+    #          ${{ runner.os }}-
+    #    - name: Install python dependencies
+    #      uses: ./.github/actions/pip_installation
+    #    - name: Coverage install
+    #      uses: ./.github/actions/coverage_install
+    #    - name: Unit tests
+    #      run: |
+    #        coverage run -p --source=pygyro -m pytest pygyro -m "serial and not long" --short
+    #        make
+    #        coverage run -p --source=pygyro -m pytest pygyro -m serial
+    #        mpirun -n 1 coverage run -p mpi_tester.py pygyro -m parallel --mpisub
+    #        mpirun -n 4 --oversubscribe coverage run -p mpi_tester.py pygyro -m parallel --mpisub
+    #        mpirun -n 6 --oversubscribe coverage run -p mpi_tester.py pygyro -m parallel --mpisub
+    #    - name: Collect coverage information
+    #      continue-on-error: True
+    #      uses: ./.github/actions/coverage_collection
+    #    - name: Run codacy-coverage-reporter
+    #      uses: codacy/codacy-coverage-reporter-action@master
+    #      continue-on-error: True
+    #      with:
+    #        project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+    #        coverage-reports: current_coverage.xml
 
   Pyccel_Fortran:
 
@@ -84,6 +85,8 @@ jobs:
             python-version: '3.10'
       - name: Install dependencies
         uses: ./.github/actions/linux_install
+      - name: Install SeLaLib
+        uses: ./.github/actions/selalib_installation
       - name: Cache pip
         uses: actions/cache@v3
         env:
@@ -99,86 +102,86 @@ jobs:
       - name: Unit tests
         uses: ./.github/actions/pytest_run
 
-  Pyccel_C:
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-            python-version: '3.10'
-      - name: Install dependencies
-        uses: ./.github/actions/linux_install
-      - name: Cache pip
-        uses: actions/cache@v3
-        env:
-          cache-name: cache-pip
-        with:
-          path: ~/.local
-          key: ${{runner.os }}-build-${{ env.cache-name }}
-      - name: Install python dependencies
-        uses: ./.github/actions/pip_installation
-      - name: Make with pyccel
-        run: |
-          make LANGUAGE=c pycc
-      - name: Unit tests
-        uses: ./.github/actions/pytest_run
-
-  Numba:
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-            python-version: '3.10'
-      - name: Install dependencies
-        uses: ./.github/actions/linux_install
-      - name: Cache pip
-        uses: actions/cache@v3
-        env:
-          cache-name: cache-pip
-        with:
-          path: ~/.local
-          key: ${{runner.os }}-build-${{ env.cache-name }}
-      - name: Install python dependencies
-        uses: ./.github/actions/pip_installation
-      - name: Make with numba
-        run: |
-          make ACC=numba numba
-      - name: Unit tests
-        uses: ./.github/actions/pytest_run
-
-  Pythran:
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-            python-version: '3.10'
-      - name: Install dependencies
-        uses: ./.github/actions/linux_install
-      - name: Cache pip
-        uses: actions/cache@v3
-        env:
-          cache-name: cache-pip
-        with:
-          path: ~/.local
-          key: ${{runner.os }}-build-${{ env.cache-name }}
-      - name: Install python dependencies
-        uses: ./.github/actions/pip_installation
-      - name: Make with pyccel
-        run: |
-          make ACC=pythran pythran
-      - name: Unit tests
-        uses: ./.github/actions/pytest_run
+  #Pyccel_C:
+
+  #  runs-on: ubuntu-latest
+
+  #  steps:
+  #    - uses: actions/checkout@v3
+  #    - name: Set up Python
+  #      uses: actions/setup-python@v4
+  #      with:
+  #          python-version: '3.10'
+  #    - name: Install dependencies
+  #      uses: ./.github/actions/linux_install
+  #    - name: Cache pip
+  #      uses: actions/cache@v3
+  #      env:
+  #        cache-name: cache-pip
+  #      with:
+  #        path: ~/.local
+  #        key: ${{runner.os }}-build-${{ env.cache-name }}
+  #    - name: Install python dependencies
+  #      uses: ./.github/actions/pip_installation
+  #    - name: Make with pyccel
+  #      run: |
+  #        make LANGUAGE=c pycc
+  #    - name: Unit tests
+  #      uses: ./.github/actions/pytest_run
+
+  #Numba:
+
+  #  runs-on: ubuntu-latest
+
+  #  steps:
+  #    - uses: actions/checkout@v3
+  #    - name: Set up Python
+  #      uses: actions/setup-python@v4
+  #      with:
+  #          python-version: '3.10'
+  #    - name: Install dependencies
+  #      uses: ./.github/actions/linux_install
+  #    - name: Cache pip
+  #      uses: actions/cache@v3
+  #      env:
+  #        cache-name: cache-pip
+  #      with:
+  #        path: ~/.local
+  #        key: ${{runner.os }}-build-${{ env.cache-name }}
+  #    - name: Install python dependencies
+  #      uses: ./.github/actions/pip_installation
+  #    - name: Make with numba
+  #      run: |
+  #        make ACC=numba numba
+  #    - name: Unit tests
+  #      uses: ./.github/actions/pytest_run
+
+  #Pythran:
+
+  #  runs-on: ubuntu-latest
+
+  #  steps:
+  #    - uses: actions/checkout@v3
+  #    - name: Set up Python
+  #      uses: actions/setup-python@v4
+  #      with:
+  #          python-version: '3.10'
+  #    - name: Install dependencies
+  #      uses: ./.github/actions/linux_install
+  #    - name: Cache pip
+  #      uses: actions/cache@v3
+  #      env:
+  #        cache-name: cache-pip
+  #      with:
+  #        path: ~/.local
+  #        key: ${{runner.os }}-build-${{ env.cache-name }}
+  #    - name: Install python dependencies
+  #      uses: ./.github/actions/pip_installation
+  #    - name: Make with pyccel
+  #      run: |
+  #        make ACC=pythran pythran
+  #    - name: Unit tests
+  #      uses: ./.github/actions/pytest_run
 
   Pep8:
 
@@ -195,15 +198,15 @@ jobs:
             python -m pip install autopep8
       - name: Check for pep changes
         run: |
-            if [[ $(autopep8 -r --diff pygyro/) ]]
+            if [[ $(autopep8 --ignore=E265,E226,E24,W50,W690 -r --diff pygyro/) ]]
             then
-              echo "Please run 'autopep8 -ir pygyro/' to clean up formatting"
-              autopep8 -r --diff pygyro/
+              echo "Please run 'autopep8 --ignore=E265,E226,E24,W50,W690 -ir pygyro/' to clean up formatting"
+              autopep8 --ignore=E265,E226,E24,W50,W690 -r --diff pygyro/
               exit 1
             fi
-            if [[ $(autopep8 -r --diff plotting/) ]]
+            if [[ $(autopep8 --ignore=E265,E226,E24,W50,W690 -r --diff plotting/) ]]
             then
-              echo "Please run 'autopep8 -ir plotting/' to clean up formatting"
-              autopep8 -r --diff plotting/
+              echo "Please run 'autopep8 --ignore=E265,E226,E24,W50,W690 -ir plotting/' to clean up formatting"
+              autopep8 --ignore=E265,E226,E24,W50,W690 -r --diff plotting/
               exit 1
             fi

Makefile

@@ -42,7 +42,7 @@ SO_EXT := $(shell $(PYTHON) -c "import sysconfig; print(sysconfig.get_config_var
 
 ifeq ($(ACC), pycc)
 	TOOL := pyccel
-	TOOL_FLAGS := --compiler-family=$(COMP) --flags ' $(FC_FLAGS)' --language=$(LANGUAGE)
+	TOOL_FLAGS := --compiler-family=$(COMP) --flags ' $(FC_FLAGS)' --language=$(LANGUAGE) --openmp
 	NAME_PREFIX := 
 else
 	ifeq ($(ACC), numba)