ci(parallel): add mf6 parallel test on windows (#1672)

* build petsc with ifort/cl from cygwin * factor out scripts for cygwin build steps * factor out actions for mf6 parallel testing * meson test serially to avoid errors on windows
MODFLOW-USGS · Mar 15, 2024 · c99aa8b · c99aa8b
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diff --git a/.github/actions/test-par-win/action.yml b/.github/actions/test-par-win/action.yml
@@ -0,0 +1,152 @@
+name: Test parallel MF6 (Windows)
+description: Build and test parallel MODFLOW 6 on Windows
+runs:
+  using: "composite"
+  steps:
+
+    - name: Convert line endings
+      shell: cmd
+      run: |
+        unix2dos -n "modflow6\.github\common\configure_petsc.sh" "%TEMP%\configure_petsc.sh"
+        unix2dos -n "modflow6\.github\common\compile_petsc.sh" "%TEMP%\compile_petsc.sh"
+        unix2dos -n "modflow6\.github\common\compile_modflow6.bat" "%TEMP%\compile_modflow6.bat"
+        unix2dos -n "modflow6\.github\common\test_modflow6.bat" "%TEMP%\test_modflow6.bat"
+
+    - name: Hide Strawberry programs
+      shell: bash
+      run: |
+        mkdir "$RUNNER_TEMP/strawberry"
+        mv /c/Strawberry/c/bin/gmake "$RUNNER_TEMP/strawberry/gmake"
+        mv /c/Strawberry/perl/bin/pkg-config "$RUNNER_TEMP/strawberry/pkg-config"
+        mv /c/Strawberry/perl/bin/pkg-config.bat "$RUNNER_TEMP/strawberry/pkg-config.bat"
+
+    - name: Get date
+      id: get-date
+      shell: bash
+      run: echo "date=$(/bin/date -u "+%Y%m%d")" >> "$GITHUB_OUTPUT"
+
+    - name: Set oneAPI install dir
+      id: oneapi-root
+      shell: bash
+      run: echo "ONEAPI_ROOT=C:\Program Files (x86)\Intel\oneAPI" >> "$GITHUB_ENV"
+
+    - name: Restore oneAPI cache
+      id: oneapi-cache
+      uses: actions/cache/restore@v3
+      with:
+        path: ${{ env.ONEAPI_ROOT }}
+        key: oneapi-${{ runner.os }}-${{ steps.get-date.outputs.date }}
+
+    - name: Install oneAPI BaseKit
+      shell: bash
+      if: steps.oneapi-cache.outputs.cache-hit != 'true'
+      run: |
+        url="https://registrationcenter-download.intel.com/akdlm/IRC_NAS/5cb30fb9-21e9-47e8-82da-a91e00191670/w_BaseKit_p_2024.0.1.45_offline.exe"
+        cmp="intel.oneapi.win.mkl.devel"
+        "modflow6/.github/common/install_intel_windows.bat" $url $cmp
+        rm -rf $TEMP/webimage.exe
+        rm -rf $TEMP/webimage_extracted
+
+    - name: Install oneAPI HPCKit
+      shell: bash
+      if: steps.oneapi-cache.outputs.cache-hit != 'true'
+      run: |
+        url="https://registrationcenter-download.intel.com/akdlm/IRC_NAS/7a6db8a1-a8b9-4043-8e8e-ca54b56c34e4/w_HPCKit_p_2024.0.1.35_offline.exe"
+        cmp="intel.oneapi.win.cpp-dpcpp-common:intel.oneapi.win.ifort-compiler:intel.oneapi.win.mpi.devel"
+        "modflow6/.github/common/install_intel_windows.bat" $url $cmp
+        rm -rf $TEMP/webimage.exe
+        rm -rf $TEMP/webimage_extracted
+
+    - name: Save oneAPI cache
+      if: steps.oneapi-cache.outputs.cache-hit != 'true'
+      uses: actions/cache/save@v3
+      with:
+        path: ${{ env.ONEAPI_ROOT }}
+        key: oneapi-${{ runner.os }}-${{ steps.get-date.outputs.date }}
+
+    - name: Restore PETSc cache
+      id: petsc-cache
+      uses: actions/cache/restore@v3
+      with:
+        path: petsc
+        key: petsc-${{ runner.os }}-${{ steps.get-date.outputs.date }}
+
+    - name: Configure environment
+      shell: bash
+      run: |
+        PETSC_DIR=$GITHUB_WORKSPACE/petsc
+        PETSC_ARCH=arch-mswin-c-opt
+        echo "PETSC_DIR=$PETSC_DIR" >> $GITHUB_ENV
+        echo "PETSC_ARCH=$PETSC_ARCH" >> $GITHUB_ENV
+        echo "$PETSC_DIR/$PETSC_ARCH/lib" >> $GITHUB_PATH
+
+    - name: Download PETSc
+      if: steps.petsc-cache.outputs.cache-hit != 'true'
+      shell: bash
+      run: |
+        curl https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-3.20.5.tar.gz -O -J
+        mkdir petsc
+        tar -xzf petsc-3.20.5.tar.gz -C petsc --strip-components=1
+
+    - name: Setup Cygwin
+      if: steps.petsc-cache.outputs.cache-hit != 'true'
+      uses: egor-tensin/setup-cygwin@v4
+      with:
+        packages: python3 make gcc-core gcc-g++ pkg-config
+
+    - name: Hide Cygwin linker
+      if: steps.petsc-cache.outputs.cache-hit != 'true'
+      shell: C:\tools\cygwin\bin\bash.exe --login --norc -eo pipefail -o igncr '{0}'
+      run: |
+        mv /usr/bin/link.exe /usr/bin/link-cygwin.exe
+        which link
+
+    - name: Configure PETSc
+      if: steps.petsc-cache.outputs.cache-hit != 'true'
+      shell: cmd
+      run: |
+        "${{ env.ONEAPI_ROOT }}\setvars.bat" intel64 vs2022 && "C:\tools\cygwin\bin\bash.exe" --login --norc -eo pipefail -o igncr "%TEMP%\configure_petsc.sh"
+
+    - name: Build PETSc
+      if: steps.petsc-cache.outputs.cache-hit != 'true'
+      shell: cmd
+      run: |
+        "${{ env.ONEAPI_ROOT }}\setvars.bat" intel64 vs2022 && "C:\tools\cygwin\bin\bash.exe" --login --norc -eo pipefail -o igncr "%TEMP%\compile_petsc.sh"
+
+    - name: Save PETSc cache
+      if: steps.petsc-cache.outputs.cache-hit != 'true'
+      uses: actions/cache/save@v3
+      with:
+        path: petsc
+        key: petsc-${{ runner.os }}-${{ steps.get-date.outputs.date }}
+
+    - name: Build modflow6
+      shell: cmd
+      run: |
+        "${{ env.ONEAPI_ROOT }}\setvars.bat" intel64 vs2022 && "%TEMP%\compile_modflow6.bat"
+
+    - name: Show Meson logs
+      if: failure()
+      shell: bash
+      working-directory: modflow6
+      run: cat builddir/meson-logs/meson-log.txt
+
+    - name: Update flopy
+      working-directory: modflow6/autotest
+      shell: cmd
+      run: micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 python update_flopy.py
+
+    - name: Get executables
+      working-directory: modflow6/autotest
+      shell: cmd
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 pytest -v --durations 0 get_exes.py
+
+    - name: Test programs
+      working-directory: modflow6/autotest
+      shell: cmd 
+      env:
+        REPOS_PATH: ${{ github.workspace }}
+      run: |
+        "${{ env.ONEAPI_ROOT }}\setvars.bat" intel64 vs2022 && "%TEMP%\test_modflow6.bat"
diff --git a/.github/actions/test-par/action.yml b/.github/actions/test-par/action.yml
@@ -0,0 +1,81 @@
+name: Test parallel MF6
+description: Build and test parallel MODFLOW 6
+runs:
+  using: "composite"
+  steps:
+
+    - name: Setup GNU Fortran
+      uses: fortran-lang/setup-fortran@v1
+      with:
+        compiler: gcc
+        version: 13
+
+    - name: Checkout PETSc
+      uses: actions/checkout@v4
+      with:
+        repository: petsc/petsc
+        path: petsc
+        ref: release
+
+    - name: Configure environment
+      if: runner.os == 'Linux'
+      shell: bash
+      run: |
+        echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/linux-gnu/lib/pkgconfig" >> $GITHUB_ENV
+        echo "$GITHUB_WORKSPACE/petsc/linux-gnu/bin" >> $GITHUB_PATH
+
+    - name: Configure environment
+      if: runner.os == 'macOS'
+      shell: bash
+      run: |
+        echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/lib/pkgconfig" >> $GITHUB_ENV
+        echo "$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/bin" >> $GITHUB_PATH
+
+    - name: Configure PETSc
+      if: runner.os == 'Linux'
+      shell: bash
+      working-directory: petsc
+      run: |
+        sudo ./configure PETSC_ARCH=linux-gnu --download-fblaslapack --download-openmpi
+        sudo make all
+
+    - name: Configure PETSc
+      if: runner.os == 'macOS'
+      shell: bash
+      working-directory: petsc
+      run: |
+        sudo ./configure PETSC_DIR="$GITHUB_WORKSPACE/petsc" PETSC_ARCH=arch-darwin-gcc-debug --download-fblaslapack --download-openmpi
+        sudo make all
+
+    - name: Build modflow6
+      shell: bash -l {0}
+      working-directory: modflow6
+      run: |
+        meson setup builddir -Ddebug=false -Dparallel=true --prefix=$(pwd) --libdir=bin
+        meson install -C builddir
+        meson test --verbose --no-rebuild -C builddir
+
+    - name: Show Meson logs
+      if: failure()
+      shell: bash
+      working-directory: modflow6
+      run: cat builddir/meson-logs/meson-log.txt
+
+    - name: Update flopy
+      shell: bash -l {0}
+      working-directory: modflow6/autotest
+      run: python update_flopy.py
+
+    - name: Get executables
+      shell: bash -l {0}
+      working-directory: modflow6/autotest
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: pytest -v --durations 0 get_exes.py
+
+    - name: Test programs
+      shell: bash -l {0}
+      working-directory: modflow6/autotest
+      env:
+        REPOS_PATH: ${{ github.workspace }}
+      run: pytest -v -n auto --parallel --durations 0 -k "test_par" --keep-failed .failed
diff --git a/.github/common/compile_modflow6.bat b/.github/common/compile_modflow6.bat
@@ -0,0 +1,5 @@
+set FC=ifort
+cd "%GITHUB_WORKSPACE%\modflow6"
+micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 meson setup builddir -Ddebug=false -Dparallel=true --prefix=%CD% --libdir=bin
+micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 meson install -C builddir
+micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 meson test --verbose --no-rebuild -C builddir
diff --git a/.github/common/compile_petsc.sh b/.github/common/compile_petsc.sh
@@ -0,0 +1,3 @@
+cd "$GITHUB_WORKSPACE/petsc"
+make all
+make check
diff --git a/.github/common/configure_petsc.sh b/.github/common/configure_petsc.sh
@@ -0,0 +1,12 @@
+cd "$GITHUB_WORKSPACE/petsc"
+./configure \
+    --with-debugging=0 \
+    --with-shared-libraries=1 \
+    --with-cc='cl' \
+    --with-fc='ifort' \
+    --with-cxx='cl' \
+    --with-blaslapack-lib='-L/cygdrive/c/PROGRA~2/Intel/oneAPI/mkl/latest/lib mkl_intel_lp64_dll.lib mkl_sequential_dll.lib mkl_core_dll.lib' \
+    --with-mpi-include='/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/include' \
+    --with-mpi-lib='/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/lib/impi.lib' \
+    --with-mpiexec='/cygdrive/c/PROGRA~2/Intel/oneAPI/mpi/latest/bin/mpiexec -localonly' \
+    --with-python-exec='/usr/bin/PYTHON~1.EXE'
diff --git a/.github/common/install_intel_windows.bat b/.github/common/install_intel_windows.bat
@@ -0,0 +1,8 @@
+@echo off
+
+:: download and unpack installer
+curl.exe --output %TEMP%\webimage.exe --url %1 --retry 5 --retry-delay 5
+start /b /wait %TEMP%\webimage.exe -s -x -f %TEMP%\webimage_extracted --log %TEMP%\extract.log
+
+:: run installer
+%TEMP%\webimage_extracted\bootstrapper.exe -s --action install --components=%2 --eula=accept -p=NEED_VS2017_INTEGRATION=0 -p=NEED_VS2019_INTEGRATION=0 -p=NEED_VS2022_INTEGRATION=1 --log-dir=%TEMP%
diff --git a/.github/common/test_modflow6.bat b/.github/common/test_modflow6.bat
@@ -0,0 +1,3 @@
+cd "%GITHUB_WORKSPACE%\modflow6\autotest"
+ldd ..\bin\mf6
+micromamba run -r "C:\Users\runneradmin\micromamba" -n modflow6 pytest -v -n auto --parallel -k "test_par" --durations 0 --keep-failed .failed