Configure sanitizers in CMake, fix issues (#823)

* Use sanitizer helpers from hpc-coding-conventions.
* Integrate sanitizer-specific configuration into CMake
  configuration so less external magic is needed.
* Add ASan and UBSan jobs to the GitHub Actions CI.
  LSan is not currently enabled because of MPI.
* Add problem matchers to GitHub Actions CI so that
  compiler warnings and sanitizer issues are flagged.
* Drop two redundant macOS GitHub Actions CI jobs.
* Use ccache in GitHub Actions CI.
* Add UBSan exclusion file.
* Do not pass -undefined dynamic_lookup to vanilla Clang.
* Fix signed/unsigned comparison compiler warnings.
* Fix struct/class mismatch compiler warnings.
* stdindex2ptr: fix bugs when nrn_sav_rhs is too far away
  from _data in memory.
* Fix __restrict__ violation in sprintf.

Author: olupton

.github/problem-matchers/address.json

@@ -0,0 +1,15 @@
+
+{
+    "problemMatcher": [
+        {
+            "owner": "asan-problem-matcher",
+            "severity": "warning",
+            "pattern": [
+                {
+                    "regexp": "^.*AddressSanitizer: (.*)$",
+                    "message": 1
+                }
+            ]
+        }
+    ]
+}

.github/problem-matchers/gcc.json

@@ -0,0 +1,18 @@
+{
+    "__comment": "Taken from vscode-cpptools's Extension/package.json gcc rule",
+    "problemMatcher": [
+        {
+            "owner": "gcc-problem-matcher",
+            "pattern": [
+                {
+                    "regexp": "^\\.\\./(.*):(\\d+):(\\d+):\\s+(?:fatal\\s+)?(warning|error):\\s+(.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "column": 3,
+                    "severity": 4,
+                    "message": 5
+                }
+            ]
+        }
+    ]
+}

.github/problem-matchers/undefined.json

@@ -0,0 +1,20 @@
+{
+    "problemMatcher": [
+        {
+            "owner": "ubsan-problem-matcher",
+            "severity": "warning",
+            "pattern": [
+                {
+                    "regexp": "^.*\\/(src\\/.*):(\\d+):(\\d+): runtime error: (.*)$",
+                    "file": 1,
+                    "line": 2,
+                    "column": 3,
+                    "message": 4
+                },
+                {
+                    "regexp": "^.*UndefinedBehaviorSanitizer:.*$"
+                }
+            ]
+        }
+    ]
+}

.github/workflows/coreneuron-ci.yml

@@ -16,8 +16,8 @@ on:
 
 env:
   BUILD_TYPE: Release
-  DEVELOPER_DIR: /Applications/Xcode_11.3.1.app/Contents/Developer
   DEFAULT_PY_VERSION: 3.8
+  MACOSX_DEPLOYMENT_TARGET: 11.0
 
 jobs:
   ci:
@@ -26,22 +26,34 @@ jobs:
     name: ${{ matrix.os }} - ${{ toJson(matrix.config) }})
 
     env:
-      INSTALL_DIR: install
       SDK_ROOT: $(xcrun --sdk macosx --show-sdk-path)
 
     strategy:
       matrix:
-        os: [ ubuntu-20.04, macOS-10.15 ]
+        os: [ubuntu-20.04, macOS-11]
         config:
           # Defaults: CORENRN_ENABLE_MPI=ON
-          - {cmake_option: "-DCORENRN_ENABLE_MPI=ON -DCORENRN_ENABLE_DEBUG_CODE=ON", documentation: ON}
-          - {cmake_option: "-DCORENRN_ENABLE_MPI_DYNAMIC=ON"}
+          - {cmake_option: "-DCORENRN_ENABLE_MPI_DYNAMIC=ON", flag_warnings: ON}
           - {cmake_option: "-DCORENRN_ENABLE_MPI_DYNAMIC=ON -DCORENRN_ENABLE_SHARED=OFF"}
           - {cmake_option: "-DCORENRN_ENABLE_MPI=OFF"}
           - {use_nmodl: ON, py_version: 3.6.7}
           - {use_nmodl: ON}
           - {use_ispc: ON, py_version: 3.6.7}
-          - {gcc_version: 9}
+        include:
+          - os: ubuntu-20.04
+            config:
+              gcc_version: 10
+          - os: ubuntu-20.04
+            config:
+              cmake_option: -DCORENRN_ENABLE_DEBUG_CODE=ON
+              documentation: ON
+          - os: ubuntu-22.04
+            config:
+              sanitizer: address
+          - os: ubuntu-22.04
+            config:
+              flag_warnings: ON
+              sanitizer: undefined
       fail-fast: false
 
     steps:
@@ -50,29 +62,31 @@ jobs:
         if: startsWith(matrix.os, 'macOS')
         run: |
           brew update
-          brew install coreutils bison flex boost openmpi
+          brew install bison boost ccache coreutils flex ninja openmpi
+          echo /usr/local/opt/flex/bin:/usr/local/opt/bison/bin >> $GITHUB_PATH
         shell: bash
 
       - name: Install apt packages
         if: startsWith(matrix.os, 'ubuntu')
         run: |
-          sudo apt-get install doxygen bison flex libboost-all-dev libopenmpi-dev openmpi-bin python3-dev python3-pip libfl-dev
+          sudo apt-get install bison ccache doxygen flex libboost-all-dev \
+            libfl-dev libopenmpi-dev ninja-build openmpi-bin
         shell: bash
 
       - name: Install specific apt packages
         if: startsWith(matrix.os, 'ubuntu') && matrix.config.gcc_version
         run: |
-          sudo apt-get install g++-${GCC_VERSION}
+          sudo apt-get install gcc-${{matrix.config.gcc_version}}
+          echo CC="gcc-${{matrix.config.gcc_version}}" >> $GITHUB_ENV
+          echo CXX="g++-${{matrix.config.gcc_version}}" >> $GITHUB_ENV
         shell: bash
-        env:
-          GCC_VERSION: ${{ matrix.config.gcc_version }}
 
       - name: Set up Python3
         uses: actions/setup-python@v3
         with:
           python-version: ${{ env.PYTHON_VERSION }}
         env:
-          PYTHON_VERSION:  ${{ matrix.config.py_version || env.DEFAULT_PY_VERSION }}
+          PYTHON_VERSION: ${{matrix.config.py_version || env.DEFAULT_PY_VERSION}}
 
       - name: Install ISPC
         if: ${{ matrix.config.use_ispc == 'ON' }}
@@ -89,56 +103,116 @@ jobs:
           url="https://github.com/ispc/ispc/releases/download/${ispc_version}/ispc-${ispc_version}${ispc_version_suffix}-${url_os}.tar.gz";
           wget -O ispc.tar.gz $url;
           mkdir ispc && tar -xvzf ispc.tar.gz -C ispc --strip 1;
+
       - name: Install NMODL dependencies
         if: ${{ matrix.config.use_nmodl == 'ON' ||  matrix.config.use_ispc == 'ON' }}
         run: |
           python3 -m pip install --upgrade pip jinja2 pyyaml pytest sympy
 
       - uses: actions/checkout@v3
 
-      - name: Install Python3 documentation dependencies
-        if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.config.documentation == 'ON' }}
+      - name: Install documentation dependencies
+        if: ${{matrix.config.documentation == 'ON'}}
         working-directory: ${{runner.workspace}}/CoreNeuron
         run: |
+          sudo apt-get install doxygen
           python3 -m pip install --upgrade pip
           python3 -m pip install --upgrade -r docs/docs_requirements.txt
 
+      - name: Register compiler warning problem matcher
+        if: ${{matrix.config.flag_warnings == 'ON'}}
+        run: echo "::add-matcher::.github/problem-matchers/gcc.json"
+
+      - name: Register sanitizer problem matcher
+        if: ${{matrix.config.sanitizer}}
+        run: echo "::add-matcher::.github/problem-matchers/${{matrix.config.sanitizer}}.json"
+
+      - name: Hash config dictionary
+        run: |
+          cat << EOF > matrix.json
+          ${{toJSON(matrix.config)}}
+          EOF
+          echo matrix.config JSON:
+          cat matrix.json
+          echo -----
+
+      - name: Restore compiler cache
+        uses: pat-s/always-upload-cache@v3
+        with:
+          path: |
+            ${{runner.workspace}}/ccache
+          key: ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-${{github.sha}}
+          restore-keys: |
+            ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-
+            ${{matrix.os}}-${{hashfiles('matrix.json')}}-
+
       - name: Build and Test
         id: build-test
         shell: bash
         working-directory: ${{runner.workspace}}/CoreNeuron
         run:  |
-          if [ -n "$GCC_VERSION" ]; then
-              export CXX="g++-${GCC_VERSION}" CC="gcc-${GCC_VERSION}";
-          fi
-          
-          openmp=" -DCORENRN_ENABLE_OPENMP=ON"
+          cmake_args=(${{matrix.config.cmake_option}})
           if [[ "${{ startsWith(matrix.os, 'macOS') }}" = "true" ]]; then
-              export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH;
-              export CXX=g++;
-              export CC=gcc;
-              openmp=" -DCORENRN_ENABLE_OPENMP=OFF";
+              cmake_args+=(-DCORENRN_ENABLE_OPENMP=OFF)
+          else
+              cmake_args+=(-DCORENRN_ENABLE_OPENMP=ON)
+          fi
+
+          if [[ "${{matrix.config.flag_warnings}}" == "ON" ]]; then
+              cmake_args+=(-DCORENRN_EXTRA_CXX_FLAGS="-Wall")
+          fi
+
+          if [[ -n "${{matrix.config.sanitizer}}" ]]; then
+              CC=$(command -v clang-14)
+              CXX=$(command -v clang++-14)
+              symbolizer_path=$(realpath $(command -v llvm-symbolizer-14))
+              cmake_args+=(-DCMAKE_BUILD_TYPE=Custom \
+                           -DCMAKE_C_FLAGS="-O1 -g -Wno-writable-strings" \
+                           -DCMAKE_CXX_FLAGS="-O1 -g -Wno-writable-strings" \
+                           -DLLVM_SYMBOLIZER_PATH="${symbolizer_path}" \
+                           -DCORENRN_SANITIZERS=$(echo ${{matrix.config.sanitizer}} | sed -e 's/-/,/g'))
+          else
+              CC=${CC:-gcc}
+              CXX=${CXX:-g++}
           fi
           
           echo "------- Build, Test and Install -------"
           mkdir build && cd build
           if [[ "$USE_ISPC" == "ON" ]]; then
-              cmake ${openmp} -DCORENRN_ENABLE_ISPC=ON -DCMAKE_ISPC_COMPILER=${{runner.workspace}}/ispc/bin/ispc -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DPYTHON_EXECUTABLE=$(which python3) ..;
+              cmake_args+=(-DCORENRN_ENABLE_ISPC=ON -DCMAKE_ISPC_COMPILER=${{runner.workspace}}/ispc/bin/ispc)
           elif [[ "$USE_NMODL" == "ON" ]]; then
-              cmake ${openmp} -DCORENRN_ENABLE_NMODL=ON -DCORENRN_NMODL_FLAGS="sympy --analytic" -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DPYTHON_EXECUTABLE=$(which python3) ..;
-          else
-              cmake ${cmake_option} ${openmp} -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DPYTHON_EXECUTABLE=$(which python3) ..;
+              cmake_args+=(-DCORENRN_ENABLE_NMODL=ON "-DCORENRN_NMODL_FLAGS=sympy --analytic")
+          fi
+          cmake .. -G Ninja "${cmake_args[@]}" \
+            -DCMAKE_C_COMPILER="${CC}" \
+            -DCMAKE_C_COMPILER_LAUNCHER=ccache \
+            -DCMAKE_CXX_COMPILER="${CXX}" \
+            -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \
+            "-DCMAKE_INSTALL_PREFIX=${{runner.workspace}}/install" \
+            -DPYTHON_EXECUTABLE=$(command -v python3)
+          if ccache --version | grep -E '^ccache version 4\.(4|4\.1)$'
+          then
+            echo "------- Disable ccache direct mode -------"
+            # https://github.com/ccache/ccache/issues/935
+            export CCACHE_NODIRECT=1
           fi
-          make
-          ctest --output-on-failure
-          make install
+          ccache -z
+          # Older versions don't support -v (verbose)
+          ccache -vs 2>/dev/null || ccache -s
+          cmake --build . --parallel
+          ccache -vs 2>/dev/null || ccache -s
+          ctest -T Test --output-on-failure
+          cmake --build . --target install
         env:
-          cmake_option: ${{ matrix.config.cmake_option }}
-          USE_ISPC: ${{ matrix.config.use_ispc }}
-          USE_NMODL: ${{ matrix.config.use_nmodl }}
-          INSTALL_DIR: ${{ runner.workspace }}/install
-          GCC_VERSION: ${{ matrix.config.gcc_version }}
-          PYTHON_VERSION:  ${{ matrix.config.py_version || env.DEFAULT_PY_VERSION }}
+          CCACHE_BASEDIR: ${{runner.workspace}}/CoreNeuron
+          CCACHE_DIR: ${{runner.workspace}}/ccache
+          USE_ISPC: ${{matrix.config.use_ispc}}
+          USE_NMODL: ${{matrix.config.use_nmodl}}
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: ctest-results-${{hashfiles('matrix.json')}}-sanitizer
+          path: ${{runner.workspace}}/CoreNeuron/build/Testing/*/Test.xml
 
       # This step will set up an SSH connection on tmate.io for live debugging.
       # To enable it, you have to:
@@ -151,11 +225,10 @@ jobs:
       - name: Documentation
         if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.config.documentation == 'ON' }}
         id: documentation
-        working-directory: ${{runner.workspace}}/CoreNeuron
+        working-directory: ${{runner.workspace}}/CoreNeuron/build
         run: |
           echo "------- Build Doxygen Documentation -------";
-          pushd build;
-          make docs;
+          cmake --build . --target docs
           echo "-------- Disable jekyll --------";
           pushd docs;
           touch .nojekyll;

.sanitizers/undefined.supp

@@ -0,0 +1 @@
+unsigned-integer-overflow:_philox4x32bumpkey(r123array2x32)

CMake/AddCLI11Submodule.cmake

@@ -48,6 +48,12 @@ endif()
 # ~~~
 list(REMOVE_ITEM CORENRN_LINK_LIBS "Threads::Threads")
 
+string(JOIN " " CORENRN_COMMON_LDFLAGS ${CORENRN_EXTRA_LINK_FLAGS})
+if(CORENRN_SANITIZER_LIBRARY_DIR)
+  string(APPEND CORENRN_COMMON_LDFLAGS " -Wl,-rpath,${CORENRN_SANITIZER_LIBRARY_DIR}")
+endif()
+string(JOIN " " CORENRN_SANITIZER_ENABLE_ENVIRONMENT_STRING ${CORENRN_SANITIZER_ENABLE_ENVIRONMENT})
+
 # replicate CMake magic to transform system libs to -l<libname>
 foreach(link_lib ${CORENRN_LINK_LIBS})
   if(${link_lib} MATCHES "\-l.*")
@@ -82,7 +88,8 @@ string(
   ${CXX14_STD_FLAGS}
   ${NVHPC_ACC_COMP_FLAGS}
   ${NVHPC_CXX_INLINE_FLAGS}
-  ${CORENRN_COMPILE_DEF_FLAGS})
+  ${CORENRN_COMPILE_DEF_FLAGS}
+  ${CORENRN_EXTRA_MECH_CXX_FLAGS})
 
 # =============================================================================
 # nmodl/mod2c related options : TODO

CMake/MakefileBuildOptions.cmake

@@ -147,7 +147,7 @@ endforeach()
 # ===============================================================================
 # Allow undefined reference in shared library as mod files will be linked later
 # ===============================================================================
-if(CMAKE_CXX_COMPILER_ID MATCHES "Clang" OR ${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+if(CMAKE_CXX_COMPILER_ID MATCHES "AppleClang" OR ${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
   set(UNDEFINED_SYMBOLS_IGNORE_FLAG "-undefined dynamic_lookup")
   string(APPEND CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS " ${UNDEFINED_SYMBOLS_IGNORE_FLAG}")
   string(APPEND CMAKE_SHARED_LIBRARY_CREATE_C_FLAGS " ${UNDEFINED_SYMBOLS_IGNORE_FLAG}")