diff --git a/.github/workflows/sanitize.yml b/.github/workflows/sanitize.yml
index 3d6ee63de21e6cb67c2109789be9fe413b3d5d1c..1b40b7f0c20d9dabe20772c6623edeed3fc7410f 100644
--- a/.github/workflows/sanitize.yml
+++ b/.github/workflows/sanitize.yml
@@ -7,124 +7,46 @@ on:
jobs:
build:
name: "Sanitize"
- runs-on: ${{ matrix.os }}
+ runs-on: ubuntu-20.04
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"]
+ name: ["Sanitize"]
+ sanitizer: ["address", "undefined", "thread"]
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
+ CC: clang-10
+ CXX: clang++-10
+ ASAN_OPTIONS: detect_leaks=1
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
+ cmake-version: 3.19.x
- 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=${{ matrix.mpi }} -DARB_USE_BUNDLED_LIBS=ON
- make -j4 tests examples pyarb html
+ export SAN="-fsanitize=${{ matrix.sanitizer }} -fno-omit-frame-pointer"
+ cmake .. -DCMAKE_BUILD_TYPE=debug -DCMAKE_CXX_FLAGS="$SAN" -DCMAKE_C_FLAGS="$SAN" -DCMAKE_EXE_LINKER_FLAGS="$SAN" -DCMAKE_MODULE_LINKER_FLAGS="$SAN" -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DARB_VECTORIZE=${{ matrix.simd }} -DARB_WITH_MPI=OFF -DARB_USE_BUNDLED_LIBS=ON -DARB_WITH_PYTHON=ON -DPython3_EXECUTABLE=`which python`
+ make -j4 VERBOSE=1 tests examples pyarb
cd -
- name: Run unit tests
run: |
- build/bin/unit
+ build/bin/unit --gtest_filter=-*DeathTest
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 -v2
- - if: ${{ matrix.mpi == 'ON' }}
- name: Run python+MPI tests
- run: mpirun -n 4 -oversubscribe python python/test/unit_distributed/runner.py -v2
- - 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
- python python/example/single_cell_cable.py
+ - 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
diff --git a/example/dryrun/dryrun.cpp b/example/dryrun/dryrun.cpp
index 81773a97c143f771cb3ee30a428530cbceca35da..8a057d0972f9a00644212593f9d3fca69c85c74d 100644
--- a/example/dryrun/dryrun.cpp
+++ b/example/dryrun/dryrun.cpp
@@ -47,6 +47,7 @@ struct run_params {
double min_delay = 10;
double duration = 100;
cell_parameters cell;
+ bool defaulted = true;
};
void write_trace_json(const arb::trace_data<double>& trace);
@@ -146,15 +147,10 @@ int main(int argc, char** argv) {
#ifdef ARB_MPI_ENABLED
else {
ctx = arb::make_context(resources, MPI_COMM_WORLD);
- {
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- root = rank==0;
- }
+ if (params.defaulted) params.num_ranks = arb::num_ranks(ctx);
+ root = arb::rank(ctx)==0;
}
#endif
- assert(arb::num_ranks(ctx)==params.num_ranks);
-
#ifdef ARB_PROFILE_ENABLED
arb::profile::profiler_initialize(ctx);
@@ -165,10 +161,11 @@ int main(int argc, char** argv) {
std::cout << "gpu: " << (has_gpu(ctx)? "yes": "no") << "\n";
std::cout << "threads: " << num_threads(ctx) << "\n";
std::cout << "mpi: " << (has_mpi(ctx)? "yes": "no") << "\n";
- std::cout << "ranks: " << num_ranks(ctx) << "\n" << std::endl;
-
+ std::cout << "ranks: " << num_ranks(ctx) << "(" << params.num_ranks << ")\n" << std::endl;
std::cout << "run mode: " << distribution_type(ctx) << "\n";
+ assert(arb::num_ranks(ctx)==params.num_ranks);
+
arb::profile::meter_manager meters;
meters.start(ctx);
@@ -273,6 +270,9 @@ run_params read_options(int argc, char** argv) {
std::cout << "Using default parameters.\n";
return params;
}
+ else {
+ params.defaulted = false;
+ }
if (argc>2) {
throw std::runtime_error("More than one command line option is not permitted.");
}
diff --git a/test/unit/instrument_malloc.hpp b/test/unit/instrument_malloc.hpp
index 825d4df92bdb591c802e51cf45e9438cee744352..62efc835a4b18d15164ecb72fea134d3ca89a658 100644
--- a/test/unit/instrument_malloc.hpp
+++ b/test/unit/instrument_malloc.hpp
@@ -32,6 +32,9 @@
#if __has_feature(address_sanitizer)
#undef CAN_INSTRUMENT_MALLOC
#endif
+# if __has_feature(thread_sanitizer)
+#undef CAN_INSTRUMENT_MALLOC
+# endif
#endif
// This is how gcc tells us.
#if defined(__SANITIZE_ADDRESS__)