Merge pull request #434 from CFD-GO/develop

Version 6.6
CFD-GO · May 15, 2023 · 5cdc2df · 5cdc2df
2 parents 1bbefc0 + 916dbc8
commit 5cdc2df
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diff --git a/.codecov.yaml b/.codecov.yaml
@@ -1,2 +1,7 @@
 ignore:
   - "**/pugi*"  # ignore pugixml
+coverage:
+  status:
+    project:
+      default:
+        threshold: 100%
diff --git a/.github/actions/compile/action.yaml b/.github/actions/compile/action.yaml
@@ -9,4 +9,5 @@ runs:
   steps:
     - shell: bash
       id: compile
+      name: "Compile"
       run: make ${{ inputs.model }}
diff --git a/.github/actions/configure/action.yaml b/.github/actions/configure/action.yaml
@@ -2,28 +2,34 @@ name: 'TCLB Test'
 description: 'This action tests TCLB'
 inputs:
   gpu:
-    description: compile a GPU version
+    description: compile a CUDA version
     default: false
   cuda_arch:
     description: CUDA arch (sm_) to use
-    default: 'sm_50'
+    default: ''
+  hip:
+    description: compile a HIP version
+    default: false
   precision:
     description: compute precision to use
     default: 'double'
+  storage:
+    description: the storage type to use
+    default: 'same'
   rinside:
-    description: compute precision to use
+    description: use RInside
     default: false
   marklines:
-    description: compute precision to use
+    description: make RT add line references for nicer error messages
     default: true
   coverage:
-    description: compute precision to use
+    description: compile with coverage support
     default: false
   paranoid:
-    description: compute precision to use
+    description: compile in paranoid mode, with all compile checks turned on
     default: true
   python:
-    description: compute precision to use
+    description: compile with python support
     default: false
   options:
     description: other configure options
@@ -32,20 +38,35 @@ runs:
   using: 'composite'
   steps:
     - shell: bash
-      id: compile
+      id: configure
+      name: "Running configure"
       run: |
         make configure
         CONFOPT=""
         case "${{ inputs.gpu }}" in
-          true) CONFOPT="$CONFOPT --enable-cuda --with-cuda-arch=${{ inputs.cuda_arch }}" ;;
+          true) CONFOPT="$CONFOPT --enable-cuda"
+                if test "${{ inputs.cuda_arch }}"
+                then
+                  CONFOPT="$CONFOPT --with-cuda-arch=${{ inputs.cuda_arch }}"
+                fi;;
           false) CONFOPT="$CONFOPT --disable-cuda" ;;
           *) echo "Wrong 'gpu' input in configure action"; exit -1
         esac
+        case "${{ inputs.hip }}" in
+          true) CONFOPT="$CONFOPT --enable-hip" ;;
+          false) CONFOPT="$CONFOPT" ;;
+          *) echo "Wrong 'hip' input in configure action"; exit -1
+        esac
         case "${{ inputs.precision }}" in
           double) CONFOPT="$CONFOPT --enable-double" ;;
           float) CONFOPT="$CONFOPT --disable-double" ;;
           *) echo "Wrong 'precision' input in configure action"; exit -1
         esac
+        case "${{ inputs.storage }}" in
+          half|half-shift|float|float-shift|double) CONFOPT="$CONFOPT --with-storage=${{ inputs.storage }}" ;;
+          same) ;;
+          *) echo "Wrong 'storage' input in configure action"; exit -1
+        esac
         case "${{ inputs.rinside }}" in
           true) CONFOPT="$CONFOPT --enable-rinside" ;;
           false) CONFOPT="$CONFOPT --disable-rinside" ;;

diff --git a/.github/actions/coverage/action.yaml b/.github/actions/coverage/action.yaml
@@ -8,6 +8,7 @@ runs:
   using: 'composite'
   steps:
     - shell: bash
+      name: "Gathering coverage data"
       id: gather
       run: |
         lcov --capture --directory . --output-file coverage.info

diff --git a/.github/actions/install/action.yaml b/.github/actions/install/action.yaml
@@ -22,6 +22,9 @@ inputs:
   cuda:
     description: install cuda
     default: false
+  hip:
+    description: install hip
+    default: false
   openmpi:
     description: install openmpi
     default: true
@@ -43,53 +46,146 @@ inputs:
   tapenade:
     description: install tapenade
     default: false
+  options:
+    description: options for install script
+    default: "--group --retry 3 --retry-delay 5 --sudo"
+  cache:
+    description: use github cache to store apt packages and r packages
+    default: false
+  bestapt:
+    description: select the best APT before installing stuff
+    default: false
 runs:
   using: 'composite'
   steps:
+    - if: inputs.bestapt != 'false'
+      shell: bash
+      run: |
+        sudo gem install apt-spy2
+        sudo apt-spy2 fix --commit
+    - if: inputs.cache != 'false'
+      shell: bash
+      id: keys
+      run: |
+        echo "apt"               >tmp.inp.apt
+        echo "${{ runner.os }}" >>tmp.inp.apt
+        echo "rpack"             >tmp.inp.r
+        echo "${{ runner.os }}" >>tmp.inp.r
+        test "${{ inputs.essentials }}" != "false" && echo "ess"                     >>tmp.inp.apt
+        test "${{ inputs.r }}"          != "false" && echo "r"                       >>tmp.inp.apt
+        test "${{ inputs.rdep }}"       != "false" && echo "rdep"                    >>tmp.inp.r
+        test "${{ inputs.rpython }}"    != "false" && echo "rpython"                 >>tmp.inp.r
+        test "${{ inputs.reticulate }}" != "false" && echo "reticulate"              >>tmp.inp.r
+        test "${{ inputs.rinside }}"    != "false" && echo "rinside"                 >>tmp.inp.r
+        test "${{ inputs.cuda }}"       != "false" && echo "cuda ${{ inputs.cuda }}" >>tmp.inp.apt
+        test "${{ inputs.hip }}"        != "false" && echo "hip ${{ inputs.hip }}"   >>tmp.inp.apt
+        test "${{ inputs.openmpi }}"    != "false" && echo "openmpi"                 >>tmp.inp.apt
+        test "${{ inputs.lcov }}"       != "false" && echo "lcov"                    >>tmp.inp.apt
+        test "${{ inputs.python-dev }}" != "false" && echo "pydev"                   >>tmp.inp.apt
+        echo "aptkey=$(echo $(cat tmp.inp.apt) | sed 's/ /-/g')" >>$GITHUB_OUTPUT
+        echo "rkey=$(echo $(cat tmp.inp.r) | sed 's/ /-/g')" >>$GITHUB_OUTPUT
+    - if: inputs.cache != 'false'
+      uses: actions/cache/restore@v3
+      with:
+        path: cache_apt/
+        key: ${{ steps.keys.outputs.aptkey }}
+        restore-keys: ${{ steps.keys.outputs.aptkey }}-
+    - if: inputs.cache != 'false'
+      shell: bash
+      run: test -d "cache_apt" && sudo mv cache_apt/*.deb /var/cache/apt/archives/ || true
     - if: inputs.essentials != 'false'
+      name: "Installing essentials"
       shell: bash
-      run: tools/install.sh --sudo essentials
+      run: tools/install.sh ${{inputs.options}} essentials
     - if: inputs.r != 'false'
+      name: "Installing R"
+      id: r
       shell: bash
-      run: tools/install.sh --sudo r
+      run: |
+        tools/install.sh ${{inputs.options}} r
+        echo "rlibpath=$(R --slave -e 'cat(path.expand(Sys.getenv("R_LIBS_USER")));')" >>$GITHUB_OUTPUT
+    - if: inputs.cache != 'false' && inputs.r != 'false'
+      uses: actions/cache/restore@v3
+      with:
+        path: ${{ steps.r.outputs.rlibpath }}/
+        key: ${{ steps.keys.outputs.rkey }}
+        restore-keys: ${{ steps.keys.outputs.rkey }}-
     - if: inputs.rdep != 'false'
+      name: "Installing R packages"
       shell: bash
-      run: tools/install.sh --sudo rdep
+      run: tools/install.sh ${{inputs.options}} rdep
     - if: inputs.rpython != 'false'
+      name: "Installing R package: rPython"
       shell: bash
-      run: tools/install.sh --sudo rpython
+      run: tools/install.sh ${{inputs.options}} rpython
     - if: inputs.reticulate != 'false'
+      name: "Installing R package: Reticulate"
       shell: bash
-      run: tools/install.sh --sudo reticulate
+      run: tools/install.sh ${{inputs.options}} reticulate
     - if: inputs.rinside != 'false'
+      name: "Installing R package: rInside"
       shell: bash
-      run: tools/install.sh --sudo rinside
+      run: tools/install.sh ${{inputs.options}} rinside
     - if: inputs.cuda != 'false'
       shell: bash
+      name: "Installing CUDA"
       run: |
-        tools/install.sh --sudo cuda ${{ inputs.cuda }}
-        CUDA_PATH=/usr/local/cuda-${{ inputs.cuda }}
+        GPU="${{ inputs.cuda }}"
+        if test "$GPU" == "true"
+        then
+          GPU="11.7"
+        fi
+        tools/install.sh ${{inputs.options}} cuda $GPU
+        CUDA_PATH=/usr/local/cuda-$GPU
         echo "$CUDA_PATH/bin" >>$GITHUB_PATH
         echo "LD_LIBRARY_PATH=$CUDA_PATH/lib64:$LD_LIBRARY_PATH" >>$GITHUB_ENV
         echo "CUDA_PATH=$CUDA_PATH" >>$GITHUB_OUTPUT
+    - if: inputs.hip != 'false'
+      name: "Installing ROCm/HIP"
+      shell: bash
+      run: tools/install.sh ${{inputs.options}} hip ${{ inputs.hip }}
     - if: inputs.openmpi != 'false'
+      name: "Installing OpenMPI"
       shell: bash
-      run: tools/install.sh --sudo openmpi
+      run: tools/install.sh ${{inputs.options}} openmpi
     - if: inputs.lcov != 'false'
+      name: "Installing lcov"
       shell: bash
-      run: tools/install.sh --sudo lcov
+      run: tools/install.sh ${{inputs.options}} lcov
     - if: inputs.submodules != 'false'
+      name: "Fetching git submodules"
       shell: bash
-      run: tools/install.sh --sudo submodules
+      run: tools/install.sh ${{inputs.options}} submodules
     - if: inputs.gitdep != 'false'
+      name: "Fetching git dep's (see tools/install.sh)"
       shell: bash
-      run: tools/install.sh --sudo gitdep
+      run: tools/install.sh ${{inputs.options}} gitdep
     - if: inputs.python-dev != 'false'
+      name: "Installing Python headers/libraries"
       shell: bash
-      run: tools/install.sh --sudo python-dev
+      run: tools/install.sh ${{inputs.options}} python-dev
     - if: inputs.module != 'false'
+      name: "Installing module"
       shell: bash
-      run: tools/install.sh --sudo module
+      run: tools/install.sh ${{inputs.options}} module
     - if: inputs.tapenade != 'false'
+      name: "Installing Tapenade"
+      shell: bash
+      run: tools/install.sh ${{inputs.options}} tapenade
+    - if: inputs.cache != 'false'
       shell: bash
-      run: tools/install.sh --sudo tapenade
+      id: hashes
+      run: |
+        mkdir -p cache_apt/ && sudo mv /var/cache/apt/archives/*.deb cache_apt/
+        echo "apthash=$(sha256sum cache_apt/*.deb | sha256sum | cut -c 1-15)" >>$GITHUB_OUTPUT
+        echo "rhash=$(cat ${{ steps.r.outputs.rlibpath }}/**/DESCRIPTION | grep -v '^Built' | sha256sum | cut -c 1-15)" >>$GITHUB_OUTPUT
+    - if: inputs.cache != 'false' && inputs.r != 'false'
+      uses: actions/cache/save@v3
+      with:
+        path: ${{ steps.r.outputs.rlibpath }}/
+        key: ${{ steps.keys.outputs.rkey }}-${{ steps.hashes.outputs.rhash }}
+    - if: inputs.cache != 'false'
+      uses: actions/cache/save@v3
+      with:
+        path: cache_apt/
+        key: ${{ steps.keys.outputs.aptkey }}-${{ steps.hashes.outputs.apthash }}
diff --git a/.github/actions/test/action.yaml b/.github/actions/test/action.yaml
@@ -8,4 +8,5 @@ runs:
   using: 'composite'
   steps:
     - shell: bash
+      name: Run tests
       run: tools/tests.sh ${{ inputs.model }}
diff --git a/.github/workflows/gpu_comp.yml b/.github/workflows/gpu_comp.yml
@@ -1,4 +1,4 @@
-name: GPU
+name: CUDA
 
 on: [ push, pull_request ]
 
@@ -8,7 +8,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        model: [d2q9_npe_guo, d2q9_bc, d2q9, d2q9_SRT, d2q9_thin_film, d3q19, d3q19_les, d3q19_heat, d2q9_kuper, d2q9_pf, d2q9_pf_fd, d3q27, d3q27_cumulant, d3q27_cumulant_AVG_IB_SMAG]
+        model: [ d2q9, d2q9_bc, d3q27_cumulant, d3q27_cumulant_AVG_IB_SMAG]
     steps:
     - name: Git checkout
       uses: actions/checkout@v3
@@ -26,7 +26,6 @@ jobs:
       uses: ./.github/actions/configure
       with:
         gpu: true
-        cuda_arch: sm_60
         paranoid: true
     - name: Compile
       uses: ./.github/actions/compile

diff --git a/.github/workflows/hip_comp.yml b/.github/workflows/hip_comp.yml
@@ -0,0 +1,33 @@
+name: HIP
+
+on: [ push, pull_request ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        model: [ d2q9, d2q9_bc, d3q27_cumulant, d3q27_cumulant_AVG_IB_SMAG ]
+    steps:
+    - name: Git checkout
+      uses: actions/checkout@v3
+      with:
+        submodules: true
+    - name: Install dependencies
+      uses: ./.github/actions/install
+      with:
+        r: true
+        rdep: true
+        openmpi: true
+        rinside: true
+        hip: 5.4.1
+    - name: Configure
+      uses: ./.github/actions/configure
+      with:
+        hip: true
+        paranoid: true
+    - name: Compile
+      uses: ./.github/actions/compile
+      with:
+        model: ${{ matrix.model }}
diff --git a/.github/workflows/storage_test.yml b/.github/workflows/storage_test.yml
@@ -0,0 +1,44 @@
+name: Storage
+
+on: [ push, pull_request ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        model: [d2q9]
+        precision: [float, double]
+        storage: ['same', 'half', 'half-shift', "float", "float-shift", 'double']
+        gpu: [true, false]
+        exclude:
+          - gpu: false
+            storage: 'half'
+          - gpu: false
+            storage: 'half-shift'
+          - precision: 'float'
+            storage: 'double'
+    steps:
+    - name: Git checkout
+      uses: actions/checkout@v3
+    - name: Install dependencies
+      uses: ./.github/actions/install
+      with:
+        r: true
+        rdep: true
+        openmpi: true
+        rinside: true
+        cuda: ${{ matrix.gpu }}
+    - name: Configure
+      uses: ./.github/actions/configure
+      with:
+        gpu: ${{ matrix.gpu }}
+        cuda_arch: sm_60
+        paranoid: true
+        precision: ${{ matrix.precision }}
+        storage: ${{ matrix.storage }}
+    - name: Compile
+      uses: ./.github/actions/compile
+      with:
+        model: ${{ matrix.model }}