Feature/kokkos

.github/workflows/ci.yml

@@ -1,8 +1,8 @@
 name: CI
 
-on: 
+on:
   push:
-    branches: 
+    branches:
       - '**' # Push events on all branches
     paths-ignore:
       - '.github/workflows/init.yml'
@@ -12,17 +12,23 @@ on:
 jobs:
 
   build_docs:
-    runs-on: ubuntu-22.04
+    runs-on: self-ubuntu-22.04
     name: Build, Install, Package documentation
     if: "!contains(github.event.head_commit.message, 'docs skip')"
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install credentials
       run: echo https://$GITHUB_OAUTH:@github.com > $HOME/.git-credentials
       env:
         GITHUB_OAUTH: ${{ secrets.CR_PAT_WORKFLOW }}
     - name: Build
       run: |
+        if [ -f /data/cemosis/spack/share/spack/setup-env.sh ]; then
+          source /data/cemosis/spack/share/spack/setup-env.sh
+          spack env activate feelpp
+        else
+          echo "Spack environment setup script not found."
+        fi
         npm install
         npm run antora
       working-directory: docs
@@ -40,29 +46,30 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'code skip')"
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         lfs: true
         recursive: true
-    - 
-      name: Build 
+    -
+      name: Build
       run: |
+        spack env activate feelpp-openmpi4-kokkos
         cmake --preset default
         cmake --build --preset default
-    - 
-      name: Check 
+    -
+      name: Check
       run: |
          echo "not yet enabled, need to add tests"
 #        ctest --preset default
       env:
-        OMPI_ALLOW_RUN_AS_ROOT: 1 
+        OMPI_ALLOW_RUN_AS_ROOT: 1
         OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
-    - 
+    -
       name: Package
       run: |
         cmake --build --preset default -t package
     - name: Upload Artifact
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         # Artifact name
         name: parallel-programming-artifacts
@@ -89,8 +96,8 @@ jobs:
       with:
         lfs: true
         submodules: 'recursive'
-    - name: Download 
-      uses: actions/download-artifact@v3
+    - name: Download
+      uses: actions/download-artifact@v4
       with:
         # Artifact name
         name: parallel-programming-artifacts
@@ -113,20 +120,20 @@ jobs:
     -
       name: Set up Docker Buildx
       uses: docker/setup-buildx-action@v2
-    - 
+    -
       name: Login to GitHub Container Registry
       uses: docker/login-action@v2
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
         password: ${{ secrets.CR_PAT }}
-    - 
+    -
       name: Build container image
       uses: docker/build-push-action@v4
-      with: 
+      with:
         context: artifacts
         push: ${{ github.event_name != 'pull_request' }}
         tags: ${{ steps.meta.outputs.tags }}
         labels: ${{ steps.meta.outputs.labels }}
         file: ./Dockerfile
-        
+

.gitignore

@@ -44,3 +44,10 @@ jupyter/
 auto-save-list
 tramp
 .\#*
+_minted*
+*.aux
+*.log
+*.synctex.gz
+*.fls
+/cpp/
+/cpp.old/

.vscode/settings.json

@@ -1,4 +1,108 @@
 {
     "C_Cpp.default.configurationProvider": "vector-of-bool.cmake-tools",
-    "cmake.buildDirectory": "${workspaceFolder}/build-${variant:buildType}"
+    "cmake.buildDirectory": "${workspaceFolder}/build-${variant:buildType}",
+    "files.associations": {
+        "*.json": "jsonc",
+        "*.dat": "csv (whitespace)",
+        "*.pgf": "tex",
+        "*.pdf_tex": "tex",
+        ".py.in": "Python",
+        "*.tikz": "tex",
+        "*.slurm": "shellscript",
+        "cctype": "cpp",
+        "clocale": "cpp",
+        "cmath": "cpp",
+        "csetjmp": "cpp",
+        "csignal": "cpp",
+        "cstdarg": "cpp",
+        "cstddef": "cpp",
+        "cstdio": "cpp",
+        "cstdlib": "cpp",
+        "cstring": "cpp",
+        "ctime": "cpp",
+        "cwchar": "cpp",
+        "cwctype": "cpp",
+        "any": "cpp",
+        "array": "cpp",
+        "atomic": "cpp",
+        "hash_map": "cpp",
+        "strstream": "cpp",
+        "barrier": "cpp",
+        "bit": "cpp",
+        "*.tcc": "cpp",
+        "bitset": "cpp",
+        "cfenv": "cpp",
+        "charconv": "cpp",
+        "chrono": "cpp",
+        "cinttypes": "cpp",
+        "codecvt": "cpp",
+        "compare": "cpp",
+        "complex": "cpp",
+        "concepts": "cpp",
+        "condition_variable": "cpp",
+        "coroutine": "cpp",
+        "cstdint": "cpp",
+        "cuchar": "cpp",
+        "deque": "cpp",
+        "forward_list": "cpp",
+        "list": "cpp",
+        "map": "cpp",
+        "set": "cpp",
+        "string": "cpp",
+        "unordered_map": "cpp",
+        "unordered_set": "cpp",
+        "vector": "cpp",
+        "exception": "cpp",
+        "algorithm": "cpp",
+        "functional": "cpp",
+        "iterator": "cpp",
+        "memory": "cpp",
+        "memory_resource": "cpp",
+        "numeric": "cpp",
+        "optional": "cpp",
+        "random": "cpp",
+        "ratio": "cpp",
+        "regex": "cpp",
+        "source_location": "cpp",
+        "string_view": "cpp",
+        "system_error": "cpp",
+        "tuple": "cpp",
+        "type_traits": "cpp",
+        "utility": "cpp",
+        "hash_set": "cpp",
+        "slist": "cpp",
+        "fstream": "cpp",
+        "future": "cpp",
+        "initializer_list": "cpp",
+        "iomanip": "cpp",
+        "iosfwd": "cpp",
+        "iostream": "cpp",
+        "istream": "cpp",
+        "latch": "cpp",
+        "limits": "cpp",
+        "mutex": "cpp",
+        "new": "cpp",
+        "numbers": "cpp",
+        "ostream": "cpp",
+        "ranges": "cpp",
+        "scoped_allocator": "cpp",
+        "semaphore": "cpp",
+        "shared_mutex": "cpp",
+        "span": "cpp",
+        "sstream": "cpp",
+        "stdexcept": "cpp",
+        "stop_token": "cpp",
+        "streambuf": "cpp",
+        "syncstream": "cpp",
+        "thread": "cpp",
+        "typeindex": "cpp",
+        "typeinfo": "cpp",
+        "valarray": "cpp",
+        "variant": "cpp",
+        "expected": "cpp",
+        "spanstream": "cpp",
+        "stacktrace": "cpp",
+        "format": "cpp",
+        "__nullptr": "cpp"
+    }
 }

course-parallel-programming.code-workspace

@@ -0,0 +1,7 @@
+{
+	"folders": [
+		{
+			"path": "."
+		}
+	]
+}

docs/CMakeLists.txt

@@ -8,8 +8,8 @@ if ( NPM_EXECUTABLE )
 
 add_custom_command(OUTPUT "${ANTORA_OUTPUT_DIR}" ALL
     COMMENT "Building documentation... "
-    COMMAND "${npm}" install 
-    COMMAND "${npm}" run antora 
+    COMMAND "${npm}" install
+    COMMAND "${npm}" run antora
     WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
 )
 if ( NOT TARGET doc )
@@ -21,4 +21,6 @@ endif()
 install(DIRECTORY "${ANTORA_OUTPUT_DIR}/" DESTINATION ${APPLICATION_DOC_DIR} OPTIONAL)
 else()
     message(STATUS "npm is not installed, can use antora ")
-endif()
+endif()
+
+add_subdirectory( modules/kokkos/examples/src )

docs/antora.yml

@@ -27,7 +27,7 @@ ext:
         base: modules/ROOT/attachments/
     - run:
         command: |
-          ./generate-jupyter.sh docs/modules/exos
+          ./generate-jupyter.sh docs/modules
       scan:
         dir: jupyter/exos/
         files: '**/*.ipynb'

docs/modules/ROOT/pages/CUDA_Coding.adoc

@@ -2,7 +2,7 @@
 
 image::CUDA_Logo.png[Img401,50,50,role="left"]
 
-* Compiling a program for CUDA 
+* Compiling a program for CUDA
 *** For example, to compile MyProg.cu you would use a command like
 *** nvcc -o MyProg MyProg.cu
 

docs/modules/ROOT/pages/HEAT_Coding.adoc

@@ -2,11 +2,9 @@
 
 
 
-.Heat equation in 2D
-[.examp]
-****
+== Heat equation in 2D
 
-* Theory
+=== Theory
 
 Heat (or diffusion) equation is a partial differential equation that describes the variation of temperature in a given region over time
 
@@ -42,17 +40,17 @@ u^{m+1}(i,j) = u^m(i,j) + \Delta t \alpha \nabla^2 u^m(i,j)
 
 Note: The algorithm is stable only when
 
+[stem]
+++++
 \begin{align*}
 \Delta t < \frac{1}{2 \alpha} \frac{(\Delta x \Delta y)^2}{(\Delta x)^2 (\Delta y)^2}
 \end{align*}
+++++
 
-****
 
 
+== Code
 
-.Code
-[.examp]
-****
 The solver carries out the time development of the 2D heat equation over the number of time steps provided by the user. The default geometry is a flat
 rectangle (with grid size provided by the user), but other shapes may be used via input files. The program will produce an image (PNG) of the temperature field after every 100 iterations.
 
@@ -74,18 +72,10 @@ include::ROOT:example$src/Heat_Equation_ParallelPrograming_Comparison/MPI_OpenMP
 ----
 include::ROOT:example$src/Heat_Equation_ParallelPrograming_Comparison/Cuda/core_cuda.cu[indent=0]
 ----
-****
 
-.*Performance*
 ****
+.*Performance*
 ADD SOME RESULTS
 ****
 
-
-
-
-
-
-
-...
-
+...

docs/modules/ROOT/pages/HIP_Coding.adoc

@@ -67,7 +67,6 @@ include::ROOT:example$src/HIP/Matrix_Summation/03_matrix_summation_GPU_2D2D_2D1D
 
 
 
-****
 .*Profiling Performance*
 ****
 ADD SOME RESULTS