Merge remote-tracking branch 'upstream/master' into benchmarking

.github/SECURITY.md

@@ -0,0 +1,9 @@
+# Security Policy
+
+## Supported Versions
+
+Only the latest `master` git branch can be expected to include fixes for security issues.
+
+## Reporting a Vulnerability
+
+Please email <[email protected]> with security issues.

.github/workflows/docker.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Login to Docker Hub
       uses: docker/login-action@v2

.github/workflows/docs.yml

@@ -18,13 +18,14 @@ jobs:
       cancel-in-progress: true
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     # We build doxygen from source because of
     # https://github.com/doxygen/doxygen/issues/9016
     - name: Build Doxygen
       run:  |
-        sudo apt install cmake ninja-build graphviz graphviz
+        sudo apt update -y
+        sudo apt install -y cmake ninja-build graphviz graphviz
         git clone https://github.com/doxygen/doxygen.git ../doxygen
         cmake -S ../doxygen -B ../doxygen/build -G Ninja
         sudo ninja -C ../doxygen/build install
@@ -35,6 +36,22 @@ jobs:
         cmake -S . -B build -G Ninja --install-prefix=$(pwd)/build/install -D MFC_DOCUMENTATION=ON
         ninja -C build install
 
+    # From here https://github.com/cicirello/generate-sitemap
+    - name: Generate the sitemap
+      id: sitemap
+      uses: cicirello/generate-sitemap@v1
+      with:
+        base-url-path: https://mflowcode.github.io/
+        path-to-root: build/install/docs/mfc
+        include-pdf: false
+        sitemap-format: txt
+
+    - name: Output stats
+      run: |
+        echo "sitemap-path = ${{ steps.sitemap.outputs.sitemap-path }}"
+        echo "url-count = ${{ steps.sitemap.outputs.url-count }}"
+        echo "excluded-count = ${{ steps.sitemap.outputs.excluded-count }}"
+
     - name: Publish Documentation
       run:  |
         set +e

.github/workflows/lint.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Lint the toolchain
       run: ./mfc.sh lint

.github/workflows/pretty.yml

@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Check formatting
       run: |
-        ./mfc.sh format
+        ./mfc.sh format -j $(nproc)
         git diff --exit-code

.github/workflows/spelling.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Spell Check
       uses: crate-ci/typos@master

.github/workflows/test.yml

@@ -33,7 +33,7 @@ jobs:
     runs-on: ${{ matrix.os }}-latest
     steps:
       - name: Clone
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup MacOS
         if:   matrix.os == 'macos'
@@ -46,10 +46,7 @@ jobs:
       - name: (MacOS) Build OpenMPI
         if:   matrix.os == 'macos' && matrix.mpi == 'mpi'
         run: |
-          echo "OMPI_FC=gfortran-13" >> $GITHUB_ENV
-          echo "OMPI_CXX=g++-13"     >> $GITHUB_ENV
-          echo "OMPI_MPICC=gcc-13"   >> $GITHUB_ENV
-          HOMEBREW_MAKE_JOBS=$(nproc) brew install --cc=gcc-13 --verbose --build-from-source open-mpi
+          brew install mpich
 
       - name: Setup Ubuntu
         if:   matrix.os == 'ubuntu' && matrix.intel == false
@@ -60,7 +57,8 @@ jobs:
       - name: Setup Ubuntu (Intel)
         if:   matrix.os == 'ubuntu' && matrix.intel == true
         run: |
-          sudo apt install tar wget make cmake python3 python3-dev
+          sudo apt update -y
+          sudo apt install -y tar wget make cmake python3 python3-dev
           wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
           sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
           rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
@@ -95,7 +93,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Clone
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Test
       run:  sudo ./mfc.sh docker ./mfc.sh test -j $(nproc) -a

.gitignore

@@ -73,3 +73,9 @@ benchmarks/*.jpg
 benchmarks/*.png
 
 *.mod
+
+# Video Files
+*.mp4
+*.mov
+*.mkv
+*.avi

.vscode/settings.json

@@ -11,7 +11,8 @@
 
     "cmake.configureOnOpen": false,
 
+    "python.defaultInterpreterPath": "${workspaceFolder}/build/venv/bin/python3",
+
     "fortran.preferredCase":       "lowercase",
     "fortran.linter.includePaths": [ "${workspacefolder}/src/**" ],
-    "fortran.linter.fypp.enabled": true
 }

CMakeLists.txt

@@ -112,7 +112,8 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
             -fcheck=all,no-array-temps 
             -fbacktrace
             -fimplicit-none
-        )
+            #-ffpe-trap=invalid,zero,denormal,overflow
+	)
     endif()
 
     if (CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER 10)
@@ -153,11 +154,20 @@ elseif ((CMAKE_Fortran_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_Fortran_COMPILER_
         add_compile_options(
             $<$<COMPILE_LANGUAGE:Fortran:-minline>
         )
+    elseif (CMAKE_BUILD_TYPE STREQUAL "Debug")
+        add_compile_options(
+            $<$<COMPILE_LANGUAGE:Fortran:-O0>
+        )
     endif()
-    
+
     if (CMAKE_BUILD_TYPE STREQUAL "Debug")
         add_compile_options(-C -g -O0 -traceback -Mchkptr -Mchkstk -Minform=inform -Mbounds)
     endif()
+
+    if (DEFINED ENV{MFC_CUDA_CC})
+        string(REGEX MATCHALL "[0-9]+" MFC_CUDA_CC $ENV{MFC_CUDA_CC})
+        message(STATUS "Found $MFC_CUDA_CC specified. GPU code will be generated for ${MFC_CUDA_CC}.")
+    endif()
 endif()
 
 if (CMAKE_BUILD_TYPE STREQUAL "Release")
@@ -395,13 +405,19 @@ function(MFC_SETUP_TARGET)
                 target_compile_definitions(${ARGS_TARGET} PRIVATE MFC_cuTENSOR)
             endif()
 
-            if     (CMAKE_BUILD_TYPE STREQUAL "Release")
+            foreach (cc ${MFC_CUDA_CC})
                 target_compile_options(${ARGS_TARGET}
-                    PRIVATE -gpu=keep,ptxinfo,lineinfo
+                    PRIVATE -gpu=cc${cc}
                 )
-            elseif (CMAKE_BUILD_TYPE STREQUAL "Debug")
+            endforeach()
+
+            target_compile_options(${ARGS_TARGET}
+                PRIVATE -gpu=keep,ptxinfo,lineinfo
+            )
+
+            if (CMAKE_BUILD_TYPE STREQUAL "Debug")
                 target_compile_options(${ARGS_TARGET}
-                    PRIVATE -gpu=keep,ptxinfo,lineinfo,autocompare,debug -O0
+                    PRIVATE -gpu=autocompare,debug
                 )
             endif()
         endif()
@@ -470,8 +486,12 @@ if (MFC_DOCUMENTATION)
 
     macro(GEN_DOCS target name)
         set(DOXYGEN_PROJECT_NAME     "\"${name}\"")
-        set(DOXYGEN_INPUT            "\"${CMAKE_CURRENT_SOURCE_DIR}/src/${target}\"\
-                                     \"${CMAKE_CURRENT_SOURCE_DIR}/docs/${target}\"")
+        set(DOXYGEN_INPUT            "\"${CMAKE_CURRENT_SOURCE_DIR}/docs/${target}\"")
+
+        foreach (f90 ${${target}_SRCs})
+            set(DOXYGEN_INPUT "${DOXYGEN_INPUT} \"${f90}\"")
+        endforeach()
+
         set(DOXYGEN_HTML_HEADER      "\"${CMAKE_CURRENT_SOURCE_DIR}/docs/header.html\"")
         set(DOXYGEN_HTML_FOOTER      "\"${CMAKE_CURRENT_SOURCE_DIR}/docs/footer.html\"")
         set(DOXYGEN_HTML_OUTPUT      "\"${CMAKE_CURRENT_BINARY_DIR}/${target}\"")
@@ -547,6 +567,9 @@ if (MFC_DOCUMENTATION)
     install(DIRECTORY   "${CMAKE_CURRENT_SOURCE_DIR}/docs/res"
             DESTINATION "docs/mfc")
 
+    install(FILES       "${CMAKE_CURRENT_SOURCE_DIR}/docs/robots.txt"
+            DESTINATION "docs/mfc")
+
     install(FILES       "${CMAKE_CURRENT_SOURCE_DIR}/docs/index.html"
             DESTINATION "docs/mfc")
 endif()