update

.codecov.yaml

@@ -1,2 +1,7 @@
 ignore:
   - "**/pugi*"  # ignore pugixml
+coverage:
+  status:
+    project:
+      default:
+        threshold: 100%

.devcontainer/devcontainer.json

@@ -0,0 +1,13 @@
+{
+	"name": "Big (R+VTK)",
+	"image": "cfdgo/tclb:ubuntu-22.04-big",
+	"postCreateCommand": "make configure && ./configure --disable-cuda --enable-cpu-layout --with-openmp",
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"REditorSupport.r",
+				"CFD-GO.tclb-helper"
+			]
+		}
+	}
+}

.github/actions/install/action.yaml

@@ -48,13 +48,13 @@ inputs:
     default: false
   options:
     description: options for install script
-    default: "--group --retry 3 --retry-delay 5 --sudo"
+    default: "--group --retry 3 --retry-delay 5 --small --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: true
+    default: false
 runs:
   using: 'composite'
   steps:
@@ -130,20 +130,26 @@ runs:
       shell: bash
       name: "Installing CUDA"
       run: |
-        GPU="${{ inputs.cuda }}"
-        if test "$GPU" == "true"
+        VER="${{ inputs.cuda }}"
+        if test "$VER" == "true"
         then
-          GPU="11.7"
+          VER="11.7"
         fi
-        tools/install.sh ${{inputs.options}} cuda $GPU
-        CUDA_PATH=/usr/local/cuda-$GPU
+        tools/install.sh ${{inputs.options}} cuda $VER
+        CUDA_PATH=/usr/local/cuda-$VER
         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 ${{ inputs.hip }}
+      run: |
+        VER="${{ inputs.hip }}"
+        if test "$VER" == "true"
+        then
+          VER="5.4.1"
+        fi
+        tools/install.sh ${{inputs.options}} hip $VER
     - if: inputs.openmpi != 'false'
       name: "Installing OpenMPI"
       shell: bash

.github/actions/test/action.yaml

@@ -4,9 +4,13 @@ inputs:
   model:
     description: model to compile
     default: 'd2q9'
+  tests:
+    description: what tests to run
+    default: ''
+
 runs:
   using: 'composite'
   steps:
     - shell: bash
       name: Run tests
-      run: tools/tests.sh ${{ inputs.model }}
+      run: tools/tests.sh ${{ inputs.model }} ${{ inputs.tests }}

.github/workflows/cpu_test.yml

@@ -1,4 +1,4 @@
-name: TESTS_GCC
+name: CPU
 
 on: [ push, pull_request ]
 
@@ -8,7 +8,23 @@ 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_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_pf_velocity
+          - d3q27_cumulant_AVG_IB_SMAG
+          - d3q27_PSM_NEBB
     steps:
     - name: Git checkout
       uses: actions/checkout@v3

.github/workflows/gpu_comp.yml

@@ -1,4 +1,4 @@
-name: GPU
+name: CUDA
 
 on: [ push, pull_request ]
 
@@ -8,7 +8,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        model: [ d2q9, d2q9_bc, d3q27_cumulant, d3q27_cumulant_AVG_IB_SMAG]
+        model: 
+          - d2q9
+          - d2q9_bc
+          - d3q27_cumulant
+          - d3q27_cumulant_AVG_IB_SMAG
+          - d3q27_pf_velocity
+          - d3q27_PSM_NEBB
     steps:
     - name: Git checkout
       uses: actions/checkout@v3

.github/workflows/hip_comp.yml

@@ -8,7 +8,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        model: [ d2q9, d2q9_bc, d3q27_cumulant, d3q27_cumulant_AVG_IB_SMAG ]
+        model: 
+          - d2q9
+          - d2q9_bc
+          - d3q27_cumulant
+          - d3q27_cumulant_AVG_IB_SMAG
+          - d3q27_pf_velocity
+          - d3q27_PSM_NEBB
     steps:
     - name: Git checkout
       uses: actions/checkout@v3

.github/workflows/other_tests.yml

@@ -0,0 +1,46 @@
+name: TESTS
+
+on: [ push, pull_request ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        test: 
+          - solid
+    steps:
+    - name: Git checkout
+      uses: actions/checkout@v3
+      with:
+        submodules: true
+    - name: Install dependencies
+      uses: ./.github/actions/install
+      with:
+        essentials: true
+        r: false
+        rdep: false
+        cuda: false
+        hip: false
+        openmpi: false
+        lcov: true
+    - name: Compile
+      shell: bash
+      run: |
+        cd tests/${{ matrix.test }}
+        make ADD_FLAGS="-fprofile-arcs -ftest-coverage"
+    - name: Run
+      shell: bash
+      run: |
+        cd tests/${{ matrix.test }}
+        make run
+    - name: Gather coverage data
+      uses: ./.github/actions/coverage
+      id: coverage
+    - name: Send coverage data
+      uses: codecov/codecov-action@v3
+      if: steps.coverage.outputs.reports != ''
+      with:
+        files: ${{ steps.coverage.outputs.reports }}
+        flags: ${{ matrix.model }}

.github/workflows/rinside.yaml

@@ -0,0 +1,57 @@
+name: RInside
+
+on: [ push, pull_request ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        model:
+          - d2q9
+        precision:
+          - float
+          - double
+        arch:
+          - cpu
+          - cuda
+          - hip
+        include:
+          - precision: "double"
+            arch: "cpu"
+            test: true
+    steps:
+    - name: Git checkout
+      uses: actions/checkout@v3
+      with:
+        submodules: ${{ matrix.test }}
+    - name: Install dependencies
+      uses: ./.github/actions/install
+      with:
+        r: true
+        rdep: true
+        openmpi: true
+        rinside: true
+        reticulate: ${{ matrix.test }}
+        cuda: ${{ matrix.arch == 'cuda' }}
+        hip: ${{ matrix.arch == 'hip' }}
+    - name: Configure
+      uses: ./.github/actions/configure
+      with:
+        gpu: ${{ matrix.arch == 'cuda' }}
+        hip: ${{ matrix.arch == 'hip' }}
+        cuda_arch: sm_60
+        rinside: true
+        paranoid: true
+        precision: ${{ matrix.precision }}
+    - name: Compile
+      uses: ./.github/actions/compile
+      with:
+        model: ${{ matrix.model }}
+    - if: matrix.test
+      name: Run tests
+      uses: ./.github/actions/test
+      with:
+        model: ${{ matrix.model }}
+        tests: rinside

.github/workflows/storage_test.yml

@@ -8,10 +8,21 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        model: [d2q9]
-        precision: [float, double]
-        storage: ['same', 'half', 'half-shift', "float", "float-shift", 'double']
-        gpu: [true, false]
+        model:
+          - d2q9
+        precision:
+          - float
+          - double
+        storage: 
+          - 'same'
+          - 'half'
+          - 'half-shift'
+          - "float"
+          - "float-shift"
+          - 'double'
+        gpu:
+          - true
+          - false
         exclude:
           - gpu: false
             storage: 'half'

.gitignore

@@ -1,25 +1,49 @@
-*~
-makefile.main
-output*
-Running*.log
-Running*.time
-aux
-CLB
-*.cbp
-Snap*.dat
-/*.xml
+# files generated during compilation:
+/makefile.main
+/CLB/
 /config.*
 /configure
-src/test
-my/*
+
+# common temporary folders:
+aux/
+tmp/
+
+# common temporary files to ignore:
+*.cbp
 *.gcov
 *.gcda
 *.gcno
-wiki
-p
+*~
 *.pyc
+*.ipynb_checkpoint*
+
+# IDE related files:
+.idea/
+.vscode/
 .Rproj.user
+*.Rproj
+
+# file generated during runs:
+output/
+Snap*.dat
 /*.vtu
 /*.txt
-.idea/*
-*.ipynb_checkpoint*
+
+# files generated during tests:
+test-*/
+Running*.log
+Running*.time
+
+# cluster & overlay:
+/p
+/.tclb/
+
+# generated documentation files:
+/wiki
+/tools/.format/
+
+# tidy home directory: [discard in overlay]
+/*.xml
+/*.csv
+update.sh
+/.overlay*

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "TCLB_tests"]
-	path = tests
+	path = tests/external
 	url =  ../../CFD-GO/TCLB_tests.git