Gpunufft2.0 #495
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| name: CI | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| workflow_dispatch: | |
| env: | |
| PYTHON_VERSION: "3.10" | |
| BART_VERSION: "0.8.00" | |
| ref_backend: "finufft" | |
| jobs: | |
| linter-check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Python ${{ env.PYTHON_VERSION }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: pip | |
| - name: Install Python deps | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -e .[test,dev] | |
| - name: Black Check | |
| shell: bash | |
| run: black . --diff --color --check | |
| - name: ruff Check | |
| shell: bash | |
| run: ruff src | |
| test-cpu: | |
| runs-on: ubuntu-latest | |
| needs: linter-check | |
| strategy: | |
| matrix: | |
| backend: [finufft, pynfft, pynufft, bart, sigpy] | |
| exclude: | |
| - backend: bart | |
| - backend: pynfft | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: pip | |
| - name: Install Dependencies | |
| shell: bash | |
| run: | | |
| python --version | |
| - name: Install Python Deps | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -e .[test] | |
| - name: Install pynfft | |
| if: ${{ matrix.backend == 'pynfft' || env.ref_backend == 'pynfft' }} | |
| shell: bash | |
| run: | | |
| sudo apt install -y libnfft3-dev | |
| python -m pip install pynfft2 "cython<3.0.0" | |
| - name: Install pynufft | |
| if: ${{ matrix.backend == 'pynufft' || env.ref_backend == 'pynufft' }} | |
| run: python -m pip install pynufft | |
| - name: Install finufft | |
| if: ${{ matrix.backend == 'finufft' || env.ref_backend == 'finufft'}} | |
| shell: bash | |
| run: python -m pip install finufft | |
| - name: Install Sigpy | |
| if: ${{ matrix.backend == 'sigpy' || env.ref_backend == 'sigpy'}} | |
| shell: bash | |
| run: python -m pip install sigpy | |
| - name: Install BART | |
| if: ${{ matrix.backend == 'bart' || env.ref_backend == 'bart'}} | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE | |
| sudo apt-get install make gcc libfftw3-dev liblapacke-dev libpng-dev libopenblas-dev | |
| wget https://github.com/mrirecon/bart/archive/v${{ env.BART_VERSION }}.tar.gz | |
| tar xzvf v${{ env.BART_VERSION }}.tar.gz | |
| cd bart-${{ env.BART_VERSION }} | |
| make | |
| echo $PWD >> $GITHUB_PATH | |
| - name: Run Tests | |
| shell: bash | |
| run: | | |
| export COVERAGE_FILE=coverage_${{ matrix.backend }} | |
| pytest --backend ${{ matrix.backend }} --ref ${{ env.ref_backend }} --cov --disable-pytest-warnings --cov-branch --cov-report=term | |
| - name: Upload coverage | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage_data | |
| path: coverage_${{ matrix.backend}} | |
| test-gpu: | |
| runs-on: GPU | |
| needs: linter-check | |
| strategy: | |
| matrix: | |
| backend: [gpunufft, cufinufft] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install mri-nufft and finufft | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE | |
| python --version | |
| python -m venv venv | |
| source $RUNNER_WORKSPACE/venv/bin/activate | |
| pip install --upgrade pip wheel | |
| pip install -e mri-nufft[test] | |
| pip install finufft | |
| - name: Install Experimental cufinufft | |
| if: ${{ matrix.backend == 'cufinufft' }} | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE | |
| rm -rf finufft | |
| git clone https://github.com/flatironinstitute/finufft | |
| cd finufft && mkdir build && cd build | |
| export PATH=/usr/local/cuda-11.8/bin:$PATH | |
| export CUDA_PATH=/usr/local/cuda-11.8 | |
| export LD_LIBRARY_PATH=/usr/local/cuda-11.8/lib64:$LD_LIBRARY_PATH | |
| export CUDA_BIN_PATH=/usr/local/cuda-11.8 | |
| cmake -DFINUFFT_USE_CUDA=1 ../ && cmake --build . && cp libcufinufft.so ../python/cufinufft/. | |
| # enter venv | |
| source $RUNNER_WORKSPACE/venv/bin/activate | |
| pip install cupy-cuda11x | |
| cd $RUNNER_WORKSPACE/finufft/python/cufinufft | |
| python setup.py develop | |
| # FIXME: This is hardcoded | |
| cp libcufinufft.so cufinufftc.cpython-310-x86_64-linux-gnu.so | |
| cd $RUNNER_WORKSPACE | |
| - name: Install gpuNUFFT | |
| if: ${{ matrix.backend == 'gpunufft' }} | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE | |
| rm -rf gpuNUFFT | |
| git clone https://github.com/chaithyagr/gpuNUFFT | |
| cd gpuNUFFT | |
| export PATH=/usr/local/cuda-11.8/bin:$PATH | |
| export CUDA_PATH=/usr/local/cuda-11.8 | |
| export LD_LIBRARY_PATH=/usr/local/cuda-11.8/lib64:$LD_LIBRARY_PATH | |
| export CUDA_BIN_PATH=/usr/local/cuda-11.8 | |
| source $RUNNER_WORKSPACE/venv/bin/activate | |
| python setup.py install | |
| pip install cupy-cuda11x | |
| - name: Run Tests | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE/mri-nufft | |
| source $RUNNER_WORKSPACE/venv/bin/activate | |
| export COVERAGE_FILE=coverage_${{ matrix.backend }} | |
| python -m pytest --ref ${{ env.ref_backend }} --backend ${{ matrix.backend }} --disable-pytest-warnings --cov --cov-branch --cov-report=term | |
| - name: Upload coverage | |
| if: success() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage_data | |
| path: coverage_${{ matrix.backend }} | |
| - name: Cleanup | |
| if: always() | |
| shell: bash | |
| run: | | |
| cd $RUNNER_WORKSPACE | |
| ls -al | |
| rm -rf finufft | |
| rm -rf gpuNUFFT | |
| rm -rf venv | |
| test-examples: | |
| runs-on: ubuntu-latest | |
| needs: linter-check | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: pip | |
| - name: Install Python deps | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -e .[test,dev] | |
| python -m pip install finufft pooch brainweb-dl | |
| - name: Run examples | |
| shell: bash | |
| run: | | |
| export COVERAGE_FILE=coverage_plots | |
| pytest examples --cov --cov-branch --cov-report=term | |
| - name: Upload coverage | |
| if: success() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: coverage_data | |
| path: coverage_plots | |
| coverage: | |
| runs-on: ubuntu-latest | |
| needs: [test-cpu, test-gpu, test-examples] | |
| if: ${{ always() }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Collect Coverages | |
| uses: actions/download-artifact@v2 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| cache: pip | |
| - name: add the coverage tool | |
| shell: bash | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install coverage[toml] | |
| python -m pip install -e . | |
| - name: Combine coverage | |
| run: coverage combine -a coverage_data/* | |
| - name: Reports | |
| run: | | |
| coverage xml | |
| coverage report |