From c63a5afe710c539c2cfea139b5cb73061164fdc8 Mon Sep 17 00:00:00 2001
From: thorstenhater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 10 May 2021 12:09:39 +0200
Subject: [PATCH] Add Clang's Leak, Thread, Memory, and Address Sanitizers.
(#1501)
* Add a GH workflow to build and run Arbor tests and examples with Clang sanitizers.
* Fix some uninitialized struct members; missing `override` qualifiers.
---
.github/workflows/sanitize.yml | 129 +++++++++++++++++++++++++++++++++
modcc/printer/cexpr_emit.hpp | 4 +-
test/unit/test_simulation.cpp | 4 +-
3 files changed, 133 insertions(+), 4 deletions(-)
create mode 100644 .github/workflows/sanitize.yml
diff --git a/.github/workflows/sanitize.yml b/.github/workflows/sanitize.yml
new file mode 100644
index 00000000..1c36ae74
--- /dev/null
+++ b/.github/workflows/sanitize.yml
@@ -0,0 +1,129 @@
+name: Sanitize
+
+on:
+ pull_request:
+ branches: [ master ]
+
+jobs:
+ build:
+ name: "Sanitize"
+ runs-on: ${{ matrix.os }}
+ strategy:
+ fail-fast: false
+ matrix:
+ name: ["Linux Clang -fsanitize ${{ matrix.sanitizer }}"]
+ os: ["ubuntu-20.04"]
+ cc: ["clang-10"]
+ cxx: ["clang++-10"]
+ py: ["3.9"]
+ cmake: ["3.19.x"]
+ mpi: ["ON"]
+ simd: ["ON", "OFF"]
+ sanitizer: ["address", "leak", "undefined", "memory", "thread"]
+ env:
+ CC: ${{ matrix.cc }}
+ CXX: ${{ matrix.cxx }}
+ # We set PYTHONPATH instead of installing arbor to avoid distribution/OS specific behaviour.
+ PYTHONPATH: ${{ github.workspace }}/build/python
+ steps:
+ - name: Set up cmake
+ uses: jwlawson/actions-setup-cmake@v1.7
+ with:
+ cmake-version: ${{ matrix.cmake }}
+ - name: Set up Python
+ uses: actions/setup-python@v2
+ with:
+ python-version: ${{ matrix.py }}
+ - name: OpenMPI cache
+ uses: actions/cache@v2
+ id: cache-ompi
+ with:
+ path: ~/openmpi-4.0.2
+ key: ${{ matrix.os }}-openmpi-4.0.2-${{ matrix.cxx }}
+ - name: Build OpenMPI
+ if: ${{ steps.cache-ompi.outputs.cache-hit != 'true' }}
+ run: |
+ echo cache-hit='${{ steps.cache-ompi.outputs.cache-hit }}'
+ cd ~
+ wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.2.tar.gz
+ tar -xvf ./openmpi-4.0.2.tar.gz
+ cd openmpi-4.0.2
+ ./configure --disable-mpi-fortran
+ make -j4
+ - name: Install OpenMPI
+ run: |
+ echo "Going to install ompi"
+ cd ~
+ cd openmpi-4.0.2
+ sudo make install
+ cd -
+ - name: Update shared library cache
+ if: ${{ startsWith(matrix.os, 'ubuntu') }}
+ run: sudo ldconfig
+ - name: Install Python packages
+ run: pip install numpy sphinx svgwrite sphinx-rtd-theme mpi4py pandas seaborn
+ - name: Clone w/ submodules
+ uses: actions/checkout@v2
+ with:
+ submodules: recursive
+ - name: Check config
+ run: |
+ $CC --version
+ $CXX --version
+ python --version
+ mpic++ --show
+ mpicc --show
+ echo $PYTHONPATH
+ - name: Build arbor
+ run: |
+ mkdir build
+ cd build
+ cmake .. -DCMAKE_BUILD_TYPE=debug -DCMAKE_CXX_FLAGS="-fsanitize=${{ matrix.sanitizer }} -fno-omit-frame-pointer" -DCMAKE_C_FLAGS="-fsanitize=${{ matrix.sanitizer }} -fno-omit-frame-pointer" -DCMAKE_EXE_LINKER_FLAGS="-fsanitize=${{ matrix.sanitizer }}" -DCMAKE_MODULE/_LINKER_FLAGS="-fsanitize=${{ matrix.sanitizer }}" -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DARB_WITH_PYTHON=ON -DARB_VECTORIZE=${{ matrix.simd }} -DPython3_EXECUTABLE=`which python` -DARB_WITH_MPI=${{ matrix.mpi }} -DARB_USE_BUNDLED_LIBS=ON
+ make -j4 tests examples pyarb html
+ cd -
+ - name: Run unit tests
+ run: |
+ build/bin/unit
+ build/bin/unit-modcc
+ - if: ${{ matrix.mpi == 'ON' }}
+ name: Run MPI tests
+ run: mpirun -n 4 -oversubscribe build/bin/unit-mpi
+ - if: ${{ matrix.mpi == 'OFF' }}
+ name: Run examples
+ run: |
+ build/bin/bench
+ build/bin/brunel
+ build/bin/dryrun
+ build/bin/gap_junctions
+ build/bin/generators
+ build/bin/lfp
+ build/bin/probe-demo v
+ build/bin/ring
+ build/bin/single-cell
+ - if: ${{ matrix.mpi == 'ON' }}
+ name: Run examples with MPI
+ run: |
+ mpirun -n 4 -oversubscribe build/bin/bench
+ mpirun -n 4 -oversubscribe build/bin/brunel
+ mpirun -n 4 -oversubscribe build/bin/dryrun
+ mpirun -n 4 -oversubscribe build/bin/gap_junctions
+ mpirun -n 4 -oversubscribe build/bin/generators
+ mpirun -n 4 -oversubscribe build/bin/lfp
+ mpirun -n 4 -oversubscribe build/bin/probe-demo v
+ mpirun -n 4 -oversubscribe build/bin/ring
+ mpirun -n 4 -oversubscribe build/bin/single-cell
+ - name: Run python tests
+ run: python python/test/unit/runner.py
+ - if: ${{ matrix.mpi == 'ON' }}
+ name: Run python+MPI tests
+ run: mpirun -n 4 -oversubscribe python python/test/unit_distributed/runner.py
+ - name: Run Python examples
+ run: |
+ python python/example/network_ring.py
+ python python/example/single_cell_model.py
+ python python/example/single_cell_recipe.py
+ python python/example/single_cell_stdp.py
+ python python/example/brunel.py -n 400 -m 100 -e 20 -p 0.1 -w 1.2 -d 1 -g 0.5 -l 5 -t 100 -s 1 -G 50 -S 123
+ python python/example/single_cell_swc.py python/example/single_cell_detailed.swc
+ python python/example/single_cell_detailed.py python/example/single_cell_detailed.swc
+ python python/example/single_cell_detailed_recipe.py python/example/single_cell_detailed.swc
diff --git a/modcc/printer/cexpr_emit.hpp b/modcc/printer/cexpr_emit.hpp
index f17cbf56..9a2c3dbc 100644
--- a/modcc/printer/cexpr_emit.hpp
+++ b/modcc/printer/cexpr_emit.hpp
@@ -60,8 +60,8 @@ public:
protected:
static std::unordered_set<std::string> mask_names_;
- bool processing_true_;
- bool is_indirect_;
+ bool processing_true_ = false;
+ bool is_indirect_ = false;
std::string current_mask_, current_mask_bar_, input_mask_;
std::unordered_set<std::string> scalars_;
Visitor* fallback_;
diff --git a/test/unit/test_simulation.cpp b/test/unit/test_simulation.cpp
index 88d39b72..04c41ab4 100644
--- a/test/unit/test_simulation.cpp
+++ b/test/unit/test_simulation.cpp
@@ -92,7 +92,7 @@ struct lif_chain: public recipe {
return lif;
}
- std::vector<cell_connection> connections_on(cell_gid_type target) const {
+ std::vector<cell_connection> connections_on(cell_gid_type target) const override {
if (target) {
return {cell_connection({target-1, 0}, 0, weight_, delay_)};
}
@@ -101,7 +101,7 @@ struct lif_chain: public recipe {
}
}
- std::vector<event_generator> event_generators(cell_gid_type target) const {
+ std::vector<event_generator> event_generators(cell_gid_type target) const override {
if (target) {
return {};
}
--
GitLab