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Ci/sanitize (#1521)
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Add clang sanitizer passes to GH CI.
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@thorstenhater
thorstenhater authored Jul 23, 2021
1 parent cb36a7c commit 7ddefe6
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122 changes: 22 additions & 100 deletions .github/workflows/sanitize.yml
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Expand Up @@ -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
18 changes: 9 additions & 9 deletions example/dryrun/dryrun.cpp
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Expand Up @@ -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);
Expand Down Expand Up @@ -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);
Expand All @@ -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);

Expand Down Expand Up @@ -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.");
}
Expand Down
3 changes: 3 additions & 0 deletions test/unit/instrument_malloc.hpp
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Expand Up @@ -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__)
Expand Down

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