Merge pull request #1847 from MODFLOW-USGS/v6.5.0

Release 6.5.0

.build_rtd_docs/Doxyfile

@@ -37,7 +37,7 @@ PROJECT_NAME           = "MODFLOW 6"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = "version 6.5.0.dev0"
+PROJECT_NUMBER         = "version 6.5.0"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

.codespell.ignore

@@ -0,0 +1,19 @@
+alph
+wel
+nam
+gage
+drob
+delt
+lke
+ist
+inout
+ot
+initialx
+initialy
+initialz
+iterm
+dum
+shft
+lsat
+thi
+thckstrt

.gitattributes

@@ -18,3 +18,6 @@
 *.inc linguist-language=Fortran
 .build_rtd_docs/** linguist-documentation
 .doc/** linguist-documentation
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
+

.github/actions/build-par-win/action.yml

@@ -0,0 +1,20 @@
+name: Build parallel MF6 (Windows)
+description: Build parallel MODFLOW 6 on Windows
+runs:
+  using: "composite"
+  steps:
+
+    - name: Setup PETSc
+      uses: ./modflow6/.github/actions/build-petsc-win
+
+    - name: Build modflow6
+      shell: cmd
+      run: |
+        unix2dos -n "%GITHUB_WORKSPACE%\modflow6\.github\common\compile_modflow6.bat" "%TEMP%\compile_modflow6.bat"
+        "%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

.github/actions/build-petsc-win/action.yml

@@ -0,0 +1,81 @@
+name: Build PETSc (Windows)
+description: Build PETSc on Windows with Cygwin
+runs:
+  using: "composite"
+  steps:
+
+    - name: Convert line endings
+      shell: cmd
+      run: |
+        unix2dos -n "%GITHUB_WORKSPACE%\modflow6\.github\common\configure_petsc.sh" "%TEMP%\configure_petsc.sh"
+        unix2dos -n "%GITHUB_WORKSPACE%\modflow6\.github\common\compile_petsc.sh" "%TEMP%\compile_petsc.sh"
+
+    - 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: Setup oneAPI
+      uses: ./modflow6/.github/actions/setup-par-oneapi
+
+    - 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: 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
+
+    - name: Configure PETSc
+      if: steps.petsc-cache.outputs.cache-hit != 'true'
+      shell: cmd
+      run: |
+        "%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: |
+        "%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: Setup PETSC environment
+      shell: cmd
+      run: |
+        set PETSC_DIR=%GITHUB_WORKSPACE%\petsc
+        set 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%

.github/actions/setup-par-oneapi/action.yml

@@ -0,0 +1,48 @@
+name: Setup oneAPI for parallel MF6
+description: Setup oneAPI components for parallel MODFLOW 6
+runs:
+  using: "composite"
+  steps:
+
+    - name: Get date
+      id: get-date
+      shell: bash
+      run: echo "date=$(/bin/date -u "+%Y%m%d")" >> "$GITHUB_OUTPUT"
+
+    - name: Set oneAPI install dir
+      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 }}-${{ steps.get-date.outputs.date }}
+
+    - name: Install oneAPI BaseKit
+      shell: bash
+      if: steps.oneapi-cache.outputs.cache-hit != 'true'
+      run: |
+        url="https://registrationcenter-download.intel.com/akdlm/IRC_NAS/5cb30fb9-21e9-47e8-82da-a91e00191670/w_BaseKit_p_2024.0.1.45_offline.exe"
+        cmp="intel.oneapi.win.mkl.devel"
+        "$GITHUB_WORKSPACE/modflow6/.github/common/install_intel_windows.bat" $url $cmp
+        rm -rf $TEMP/webimage.exe
+        rm -rf $TEMP/webimage_extracted
+
+    - name: Install oneAPI HPCKit
+      shell: bash
+      if: steps.oneapi-cache.outputs.cache-hit != 'true'
+      run: |
+        url="https://registrationcenter-download.intel.com/akdlm/IRC_NAS/7a6db8a1-a8b9-4043-8e8e-ca54b56c34e4/w_HPCKit_p_2024.0.1.35_offline.exe"
+        cmp="intel.oneapi.win.cpp-dpcpp-common:intel.oneapi.win.ifort-compiler:intel.oneapi.win.mpi.devel"
+        "$GITHUB_WORKSPACE/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 }}

.github/actions/test-par-win/action.yml

@@ -0,0 +1,42 @@
+name: Test parallel MF6 (Windows)
+description: Build and test parallel MODFLOW 6 on Windows
+runs:
+  using: "composite"
+  steps:
+
+    - name: Build MF6 parallel
+      uses: ./modflow6/.github/actions/build-par-win
+
+    - name: Update flopy
+      working-directory: modflow6
+      shell: cmd
+      run: pixi run update-flopy
+
+    - name: Get executables
+      working-directory: modflow6/autotest
+      shell: cmd
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: pixi run get-exes
+
+    - name: Convert unix2dos
+      shell: cmd
+      run: |
+        unix2dos -n "%GITHUB_WORKSPACE%\modflow6\.github\common\test_modflow6.bat" "%TEMP%\test_modflow6.bat"
+
+    - name: Test programs
+      if: github.ref_name != 'master'
+      shell: cmd
+      env:
+        REPOS_PATH: ${{ github.workspace }}
+      run: |
+        "%ONEAPI_ROOT%\setvars.bat" intel64 vs2022 && "%TEMP%\test_modflow6.bat"
+
+    - name: Test programs
+      if: github.ref_name == 'master'
+      shell: cmd
+      env:
+        REPOS_PATH: ${{ github.workspace }}
+        MARKERS: not developmode
+      run: |
+        "%ONEAPI_ROOT%\setvars.bat" intel64 vs2022 && "%TEMP%\test_modflow6.bat"

.github/actions/test-par/action.yml

@@ -0,0 +1,82 @@
+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/lib/pkgconfig" >> $GITHUB_ENV
+        echo "$GITHUB_WORKSPACE/petsc/arch-darwin-gcc/bin" >> $GITHUB_PATH
+
+    - name: Configure PETSc
+      if: runner.os == 'Linux'
+      shell: bash
+      working-directory: petsc
+      run: |
+        sudo wget -P $GITHUB_WORKSPACE/petsc https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.2.tar.gz
+        sudo ./configure PETSC_ARCH=linux-gnu --download-fblaslapack --download-openmpi=$GITHUB_WORKSPACE/petsc/openmpi-5.0.2.tar.gz
+        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 --download-fblaslapack --download-openmpi --with-debugging=0
+        sudo make all
+
+    - name: Build modflow6
+      shell: bash
+      working-directory: modflow6
+      run: |
+        pixi run setup -Dparallel=true builddir
+        pixi run build builddir
+        pixi run test 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
+      working-directory: modflow6
+      run: pixi run update-flopy
+
+    - name: Get executables
+      shell: bash
+      working-directory: modflow6
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: pixi run get-exes
+
+    - name: Test programs
+      shell: bash
+      working-directory: modflow6
+      env:
+        REPOS_PATH: ${{ github.workspace }}
+      run: pixi run autotest --parallel -k "test_par"