Reorganize (#67)

* add musica c test * add temp directory for the review * make musica fortran shared lib * musica fortran working version for the intel compilers * clean up musica * clean up musica-fortran * reorganizing the cmake files, using MUSICA prefix * renaming directory * investingating cross-compiler library usage * things build and link, but segfault happens * trying a different interface * sigh... * c null char * intent * intent * printing things * calling the constructor... * differnt constructor * syntax * removing prints * comment out prints * trying raw pointer * uhhhh.... * return type * trying to make the interface smaller * fixing type * adding pointer * correcting thing * wish I could read * removing import * yes, i do * commenting out print * pass by value * thing * removing value * uncommenting thing * trying a thing * adding it back * adding invalid * new interface * adding failure test * trying to fix paths * more paths * thing * reordering includes, giving up on trying to remove installed directories * updating tuv branch * going back to that version * smaller interface * getting the test to work * moving fortran things to the fortran side * removing musica_core, updating tuvx branch * removing old tuvx git stuff * what is happening * including tuvx that can be built with gcc 13 * different actions * more actions * not looking for fortran stuff when we don't need it * installing dependencies * removing unused dependency * trying to set compiler * wait maybe it was right * fix clang linking bad c++ version * trying to add multiple clang versions on ubuntu * removing duplicate build * removing unused header * correcting build * seeing if 13 and 14 work * not specifying clang version * adding readme ci badges * updating doi badge * only installing micm_core.F90 * removing json fortran deps * better openmp find interface * huh, another seg fault * trying a thing * undoing one thing, keeping a thing * okay so it needs it * trying different standard library * that didn't work * adding gcc test to github * commenting out writes * pointer assignment * yeah, pointer assignment * removing reference to json fortran in module * adding module message * adding fortran install instructions * some changes * verbose * actual verbose * something different * trying to remove a thing * trying different ubuntu version * trying a different thing * maybe here * maybe this * trying a different interface * trying to pass the pointer by value * passing by value * catching a bad allocation * comments * updating install stuff * windows builds? * adding c compiler for clang * adding nvhpc dockerfile * Update src/component_versions.c Co-authored-by: Matt Dawson <[email protected]> * including memcheck build * removing gfortran dependencies for builds that don't need them --------- Co-authored-by: Jiwon Gim <[email protected]> Co-authored-by: Matt Dawson <[email protected]>
NCAR · Mar 14, 2024 · 66176ba · 66176ba
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diff --git a/.dockerignore b/.dockerignore
@@ -2,13 +2,13 @@
 *
 
 # add things to copy
+!.git/
+!.gitmodules
 !CMakeLists.txt
-!musica/
-!musica-fortran/
-!docs/
 !cmake/
+!configs
+!docs/
+!fortran/
+!include/
 !lib/
-!src/
-!test/
-!.gitmodules
-!.git/
+!src/
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -0,0 +1,56 @@
+name: Docker
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  docker-build-and-test:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    name: Build and Test - ${{ matrix.dockerfile }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        dockerfile:
+          - Dockerfile
+          - Dockerfile.memcheck
+          - Dockerfile.fortran-intel
+          - Dockerfile.fortran-gcc
+          - Dockerfile.fortran-nvhpc
+          - Dockerfile.openmp
+          - Dockerfile.mpi
+          - Dockerfile.mpi_openmp
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          submodules: recursive
+
+      - name: Delete huge unnecessary tools folder
+        run: rm -rf /opt/hostedtoolcache
+
+      - name: Build Docker image
+        run: docker build -t tuvx -f docker/${{ matrix.dockerfile }} .
+
+      - name: Run tests in container
+        if: matrix.dockerfile != 'Dockerfile.coverage'
+        run: docker run --name test-container -t tuvx bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
+
+      - name: Run coverage tests in container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker run --name test-container -t tuvx bash -c 'make coverage ARGS="--rerun-failed --output-on-failure -j8"'
+
+      - name: Copy coverage from container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker cp test-container:build/coverage.info .
+
+      - name: Upload coverage report
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.info
diff --git a/.github/workflows/mac.yml b/.github/workflows/mac.yml
@@ -0,0 +1,63 @@
+name: Mac
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  c_cxx:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        compiler:
+          - { cpp: g++-11, c: gcc-11}
+          - { cpp: g++-12, c: gcc-12}
+          - { cpp: g++-13, c: gcc-13}
+          - { cpp: clang++, c: clang}
+        build_type: [Debug, Release]
+    env:
+      CC: ${{ matrix.compiler.c }}
+      CXX: ${{ matrix.compiler.cpp }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
+  fortran:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        gcc_version: [11, 12, 13]
+        build_type: [Debug, Release]
+    env:
+      FC: gfortran-${{ matrix.gcc_version }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install dependencies
+        run: brew install netcdf netcdf-fortran
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
+
+      - name: Build
+        run: cmake --build build --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
@@ -0,0 +1,65 @@
+name: Ubuntu
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref || github.run_id }}
+  cancel-in-progress: true
+
+jobs:
+  c_cxx:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        compiler:
+          - { cpp: g++-11, c: gcc-11}
+          - { cpp: g++-12, c: gcc-12}
+          - { cpp: g++-13, c: gcc-13}
+          - { cpp: clang++, c: clang}
+        build_type: [Debug, Release]
+    env:
+      CC: ${{ matrix.compiler.c }}
+      CXX: ${{ matrix.compiler.cpp }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}
+
+      - name: Build
+        run: cmake --build build --verbose
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10
+  fortran:
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        gcc_version: [11, 12, 13]
+        build_type: [Debug, Release]
+    env:
+      FC: gfortran-${{ matrix.gcc_version }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libnetcdf-dev netcdf-bin libnetcdff-dev
+
+      - name: Run Cmake 
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
+
+      - name: Build
+        run: cmake --build build --parallel 10
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C ${{ matrix.build_type }} --rerun-failed --output-on-failure . --verbose -j 10