NEKO v0.8.0

.github/workflows/citation.yml

@@ -0,0 +1,20 @@
+on:
+#  push:
+#    paths:
+#      - CITATION.cff
+  workflow_dispatch:
+
+name: CITATION.cff
+jobs:
+  Validate-CITATION-cff:
+    runs-on: ubuntu-latest
+    name: Validate CITATION.cff
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Validate CITATION.cff
+        uses: dieghernan/cff-validator@v3

.github/workflows/develop.yml

@@ -1,38 +1,54 @@
 name: develop
 
-# Controls when the action will run. 
+# Controls when the action will run.
 on:
   pull_request:
      branches: [develop,release/*]
+     types:
+       - opened
+       - synchronize
+       - reopened
+       - ready_for_review
   workflow_dispatch:
-  
+
 jobs:
+  is_draft:
+    name: Check if PR is a draft
+    if: github.event.pull_request.draft == true
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if PR is a draft
+        run: echo "This PR is a draft"
+
   linting:
       name: "Flint"
+      if: github.event.pull_request.draft != true
       runs-on: ubuntu-20.04
       steps:
         - name: Setup env.
           run: |
             sudo apt-get update && sudo apt-get install -yq python3-dev python3-pip python3-tk
             pip install nobvisual==0.2.0 flinter==0.4.0
         - name: Checkout
-          uses: actions/checkout@v3
+          uses: actions/checkout@v4
           with:
             fetch-depth: 1
         - name: Lint
           run: |
             flint score src/ -d 10 -r flinter_rc.yml | tee flint.txt
             score=$(awk '$1==0{print $3}' flint.txt)
-            if (( $(echo "$score < 8.13" |bc -l) )) ; then
+            if (( $(echo "$score < 8.06" |bc -l) )) ; then
               exit 1
             fi
         - name: Archive linter report
-          uses: actions/upload-artifact@v3
+          uses: actions/upload-artifact@v4
           with:
             name: flint-report
             path: flint.txt
             retention-days: 5
   GNU:
+    if: github.event.pull_request.draft != true
     needs: linting
     runs-on: ${{matrix.os}}
     strategy:
@@ -58,7 +74,7 @@ jobs:
         include:
         - os: ubuntu-20.04
           setup-env: |
-            sudo apt-get update && sudo apt-get install -y openmpi-bin libopenmpi-dev autoconf automake autotools-dev libopenblas-dev make git m4 python3  cmake-curses-gui 
+            sudo apt-get update && sudo apt-get install -y openmpi-bin libopenmpi-dev autoconf automake autotools-dev libopenblas-dev make git m4 python3  cmake-curses-gui
         - os: macos-13
           setup-env: export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 && brew install openmpi && brew install automake && brew install gcc@11 && brew install gcc@12
     env:
@@ -74,7 +90,7 @@ jobs:
         run: ${{ matrix.setup-env }}
       - name: Cache pFUnit
         id: cache-pfunit
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/pkg/pfunit
           key: pfunit-${{ runner.os }}-${{ matrix.os }}-${{ matrix.compiler }}
@@ -96,14 +112,14 @@ jobs:
           +         error stop '*** Encountered 1 or more failures/errors during testing. ***'
            #endif
                  end if
-           
+
           _ACEOF
           git apply pfunit_error_stop.patch && mkdir b && cd b
           cmake -DCMAKE_INSTALL_PREFIX=${HOME}/pkg/pfunit ..
           make -j$(nproc) && make install && cd ../../
       - name: Cache json-fortran
         id: cache-json-fortran
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/pkg/json-fortran
           key: json-fortran-${{ runner.os }}-${{ matrix.os }}-${{ matrix.compiler }}
@@ -121,36 +137,36 @@ jobs:
           echo "PKG_CONFIG_PATH=${PKG_CONFIG_PATH}:${HOME}/pkg/json-fortran/lib/pkgconfig/" >> $GITHUB_ENV
           echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/pkg/json-fortran/lib/" >> $GITHUB_ENV
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
       - name: Build (CPU backend)
         if: matrix.backend == 'cpu'
         run: |
           echo $PKG_CONFIG_PATH
-          ./regen.sh 
+          ./regen.sh
           ./configure FC=${FC} FCFLAGS="-O2 -pedantic -std=f2008"  --with-pfunit=${HOME}/pkg/pfunit/PFUNIT-4.4 --enable-real=${RP}
           make -j$(nproc)
-      - name: Build (CUDA backend)        
+      - name: Build (CUDA backend)
         if: matrix.backend == 'cuda'
         run: |
           sudo apt-get install -y nvidia-cuda-toolkit
-          ./regen.sh 
+          ./regen.sh
           ./configure FC=${FC} FCFLAGS="-O2 -pedantic -std=f2008"  --enable-real=${RP} --with-cuda=/usr
           make -j$(nproc)
-      - name: Build (HIP backend)        
+      - name: Build (HIP backend)
         if: matrix.backend == 'HIP'
         run: |
           wget -q -O - https://repo.radeon.com/rocm/rocm.gpg.key | sudo apt-key add -
           echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/debian/ ubuntu main' | sudo tee /etc/apt/sources.list.d/rocm.list
           sudo apt-get update && sudo apt-get install -y rocm-dev
-          ./regen.sh 
-          ./configure FC=${FC} FCFLAGS="-O2 -pedantic -std=f2008" HIP_HIPCC_FLAGS="-O2 -fPIE" --enable-real=${RP} --with-hip=/opt/rocm-6.0.0
+          ./regen.sh
+          ./configure FC=${FC} FCFLAGS="-O2 -pedantic -std=f2008" HIP_HIPCC_FLAGS="-O2 -fPIE" --enable-real=${RP} --with-hip=/opt/rocm-6.1.2
           make -j$(nproc)
       - name: Build (OpenCL backend)
         if: matrix.backend == 'opencl'
         run: |
-          ./regen.sh 
+          ./regen.sh
           ./configure FC=${FC} FCFLAGS="-O2 -pedantic -std=f2008"  --enable-real=${RP} --with-opencl
           make -j$(nproc)
       - name: Check
@@ -190,7 +206,7 @@ jobs:
           mkdir releng
           tar xf neko-*.tar.gz -C releng
           cd releng/neko-*
-          ./configure FC=${FC} FCFLAGS="-fPIE" --enable-real=${RP} HIP_HIPCC_FLAGS="-O2 -fPIE" --with-hip=/opt/rocm-6.0.0
+          ./configure FC=${FC} FCFLAGS="-fPIE" --enable-real=${RP} HIP_HIPCC_FLAGS="-O2 -fPIE" --with-hip=/opt/rocm-6.1.2
           make -j $(nproc)
       - name: Dist (OpenCL backend)
         if: matrix.backend == 'opencl'
@@ -201,8 +217,9 @@ jobs:
           cd releng/neko-*
           ./configure FC=${FC} --enable-real=${RP} --with-opencl
           make -j $(nproc)
-    
+
   Intel:
+    if: github.event.pull_request.draft != true
     needs: linting
     runs-on: ${{matrix.os}}
     strategy:
@@ -218,7 +235,8 @@ jobs:
             wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null && echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list && sudo apt-get update -y && sudo apt install -y --no-install-recommends intel-oneapi-compiler-fortran intel-oneapi-mpi intel-oneapi-mpi-devel intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
             source /opt/intel/oneapi/setvars.sh
             sudo apt install -y autoconf automake autotools-dev libopenblas-dev make git m4 python3 ca-certificates cmake
-            export PATH=/opt/intel/oneapi/compiler/2024.0/bin:${PATH}
+            INTEL_PATH=$(find /opt/intel/oneapi/compiler/ -name "${FC}" -type f | xargs dirname)
+            export PATH=$INTEL_PATH:${PATH}
             printenv >> $GITHUB_ENV
     env:
       CC: icc
@@ -230,7 +248,7 @@ jobs:
         run: ${{ matrix.setup-env }}
       - name: Cache json-fortran
         id: cache-json-fortran
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/pkg/json-fortran
           key: json-fortran-${{ runner.os }}-${{ matrix.os }}-${{ matrix.compiler }}
@@ -248,16 +266,17 @@ jobs:
           echo "PKG_CONFIG_PATH=${PKG_CONFIG_PATH}:${HOME}/pkg/json-fortran/lib/pkgconfig/" >> $GITHUB_ENV
           echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/pkg/json-fortran/lib/" >> $GITHUB_ENV
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
       - name: Build
         run: |
           echo $PKG_CONFIG_PATH
           ./regen.sh
-          ./configure FC=${FC} CC=${CC} MPIFC"=mpiifort -fc=${FC}" --enable-real=${RP} 
+          ./configure FC=${FC} CC=${CC} MPIFC"=mpiifort -fc=${FC}" --enable-real=${RP}
           make FCFLAGS="-O2 -stand f08 -warn errors `pkg-config --cflags json-fortran`" -j$(nproc)
   NVIDIA:
+    if: github.event.pull_request.draft != true
     needs: linting
     runs-on: ${{matrix.os}}
     strategy:
@@ -269,7 +288,7 @@ jobs:
         precision: [dp]
         include:
         - os: ubuntu-20.04
-          setup-env: sudo apt-get update && sudo apt-get install -y autoconf automake autotools-dev make git m4 libopenblas-dev && curl https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg && echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list && sudo apt-get update -y && sudo apt-get install -y nvhpc-23-7 &&  NVARCH=`uname -s`_`uname -m`; export NVARCH && NVCOMPILERS=/opt/nvidia/hpc_sdk; export NVCOMPILERS && PATH=$NVCOMPILERS/$NVARCH/23.7/compilers/bin:$PATH; export PATH &&  export PATH=$NVCOMPILERS/$NVARCH/23.7/comm_libs/mpi/bin:$PATH && printenv >> $GITHUB_ENV
+          setup-env: sudo apt-get update && sudo apt-get install -y autoconf automake autotools-dev make git m4 libopenblas-dev && curl https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg && echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list && sudo apt-get update -y && sudo apt-get install -y nvhpc-24-3 &&  NVARCH=`uname -s`_`uname -m`; export NVARCH && NVCOMPILERS=/opt/nvidia/hpc_sdk; export NVCOMPILERS && PATH=$NVCOMPILERS/$NVARCH/24.3/compilers/bin:$PATH; export PATH &&  export PATH=$NVCOMPILERS/$NVARCH/24.3/comm_libs/mpi/bin:$PATH && printenv >> $GITHUB_ENV
     env:
       CC: gcc
       FC: ${{ matrix.compiler }}
@@ -285,7 +304,7 @@ jobs:
         run: ${{ matrix.setup-env }}
       - name: Cache json-fortran
         id: cache-json-fortran
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/pkg/json-fortran
           key: json-fortran-${{ runner.os }}-${{ matrix.os }}-${{ matrix.compiler }}
@@ -303,7 +322,7 @@ jobs:
           echo "PKG_CONFIG_PATH=${PKG_CONFIG_PATH}:${HOME}/pkg/json-fortran/lib/pkgconfig/" >> $GITHUB_ENV
           echo "LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/pkg/json-fortran/lib/" >> $GITHUB_ENV
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
       - name: Build (CPU backend)
@@ -318,9 +337,32 @@ jobs:
         run: |
           git apply patches/nvhpc_bge.patch
           ./regen.sh
-          ./configure FC=${FC} FCFLAGS="-O3" --enable-real=${RP} --with-cuda=/opt/nvidia/hpc_sdk/Linux_x86_64/23.7/cuda/
+          ./configure FC=${FC} FCFLAGS="-O3" --enable-real=${RP} --with-cuda=/opt/nvidia/hpc_sdk/Linux_x86_64/24.3/cuda/
           make
+      - name: Dist (CPU backend)
+        if: matrix.backend == 'cpu'
+        run: |
+          git stash
+          make dist
+          mkdir releng
+          tar xf neko-*.tar.gz -C releng
+          cd releng/neko-*
+          patch -u src/common/signal.f90 -i patches/nvhpc_bge.patch
+          ./configure FC=${FC} FCFLAGS="-O3" --enable-real=${RP}
+          make -j $(nproc)
+      - name: Dist (CUDA backend)
+        if: matrix.backend == 'cuda'
+        run: |
+          git stash
+          make dist
+          mkdir releng
+          tar xf neko-*.tar.gz -C releng
+          cd releng/neko-*
+          patch -u src/common/signal.f90 -i patches/nvhpc_bge.patch
+          ./configure FC=${FC} FCFLAGS="-O3" --enable-real=${RP} --with-cuda=/opt/nvidia/hpc_sdk/Linux_x86_64/24.3/cuda/
+          make -j $(nproc)
   ReFrame:
+    if: github.event.pull_request.draft != true
     needs: GNU
     runs-on: ubuntu-20.04
     strategy:
@@ -340,10 +382,10 @@ jobs:
       - name: Setup env.
         run: |
           sudo apt-get update && sudo apt-get install -y openmpi-bin libopenmpi-dev autoconf automake autotools-dev libopenblas-dev make git m4 python3
-          pip install reframe-hpc 
+          pip install reframe-hpc
       - name: Cache json-fortran
         id: cache-json-fortran
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/pkg/json-fortran
           key: json-fortran-${{ runner.os }}-${{ matrix.os }}-${{ matrix.compiler }}
@@ -364,7 +406,7 @@ jobs:
         run: |
           reframe --detect-host-topology
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
       - name: Regression tests

.github/workflows/docsdev.yml

@@ -3,11 +3,13 @@ name: Documentation (develop)
 on:
   schedule:
     # * is a special character in YAML so you have to quote this string
-    - cron:  '55 19 * * *'
+    - cron:  '30 03 * * *'
 #  workflow_dispatch:
-  
+
 jobs:
   build-dev-documentation:
+    # This workflow runs only on the official repository.
+    if: github.repository == 'ExtremeFLOW/neko'
     runs-on: ubuntu-latest
 
     steps:
@@ -28,7 +30,7 @@ jobs:
         ./regen.sh
         ./configure FC=${FC}
         make html
-    
+
     # Deploy the HTML documentation to GitHub Pages
     - name: GH Pages Deployment
       uses: peaceiris/actions-gh-pages@v3

.github/workflows/documentation.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Setup env.
       run: |
         sudo apt-get update && sudo apt-get install -y git openmpi-bin libopenmpi-dev autoconf automake autotools-dev libopenblas-dev make git m4 python3 doxygen fonts-freefont-ttf graphviz
@@ -30,13 +30,13 @@ jobs:
 
     # Deploy the HTML documentation to GitHub Pages
     - name: GH Pages Deployment
-      uses: peaceiris/actions-gh-pages@v3
+      uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./doc/html/
         allow_empty_commit: false
         force_orphan: false
         publish_branch: gh-pages
-        destination_dir: docs
+        destination_dir: docs/release
         keep_files: false
         enable_jekyll: true

.github/workflows/formatter.yml

@@ -0,0 +1,31 @@
+name: Formatting
+
+# Controls when the action will run.
+on:
+#  pull_request:
+#     branches: [develop,release/*,master]
+  workflow_dispatch:
+
+jobs:
+  formatting:
+      name: "Formatter (findent)"
+      description: "Check if the code is formatted according to the rules"
+      runs-on: ubuntu-20.04
+      steps:
+        - name: Setup env.
+          run: |
+            sudo apt-get update && sudo apt-get install -yq python3-dev python3-pip python3-tk
+            pip install findent
+        - name: Checkout
+          uses: actions/checkout@v3
+          with:
+            fetch-depth: 1
+        - name: Check Format
+          run: |
+            export FINDENT_FLAGS="-i2 -d3 -f3 -s3 -w3 -t3 -j3 -k- -Rr -c3"
+            find src/ -name "*.f90" -exec bash -c 'findent < {} > {}.tmp; mv -f {}.tmp {}' \;
+            if [ "$(git diff --exit-code)" != 0 ]; then
+              >&2 echo "Formatting rules violated"
+              git diff --exit-code
+              exit 1
+            fi