Add feature maps (fmaps) mode for sliding-kernel feature extraction #470
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| name: Build CUDA 11 Wheels | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| force_prereqs: | |
| description: 'Force rebuild prereqs (ignore cache)' | |
| type: boolean | |
| default: false | |
| pull_request: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.sha }} | |
| cancel-in-progress: true | |
| permissions: | |
| actions: write | |
| contents: read | |
| jobs: | |
| build_prereqs: | |
| name: Build prereqs for CUDA 11 | |
| runs-on: ubuntu-22.04 | |
| continue-on-error: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| name: Check out | |
| - name: Compute cache key | |
| id: cache-key | |
| run: echo "key=prereqs-cuda11-ubuntu-22.04-${{ hashFiles('ci-utils/install_prereq_linux.sh', 'ci-utils/install_prereq_win.bat', 'ci-utils/validate_prereqs.sh') }}" >> "$GITHUB_OUTPUT" | |
| - name: Delete prereq cache (force rebuild) | |
| if: inputs.force_prereqs == true | |
| continue-on-error: true | |
| env: | |
| GH_TOKEN: ${{ github.token }} | |
| run: | | |
| gh actions-cache delete "${{ steps.cache-key.outputs.key }}" \ | |
| -R ${{ github.repository }} --confirm || true | |
| - name: Restore cached prereqs | |
| id: cache | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: prereqs.tar.gz | |
| key: ${{ steps.cache-key.outputs.key }} | |
| - name: Build prereqs (Linux) | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: | | |
| docker run --rm \ | |
| -v "${{ github.workspace }}:/work" \ | |
| -w /work \ | |
| quay.io/pypa/manylinux2014_x86_64:latest \ | |
| bash -c " | |
| sed -i s/mirror.centos.org/vault.centos.org/g /etc/yum.repos.d/*.repo && | |
| sed -i s/^#.*baseurl=http/baseurl=http/g /etc/yum.repos.d/*.repo && | |
| sed -i s/^mirrorlist=http/#mirrorlist=http/g /etc/yum.repos.d/*.repo && | |
| yum install -y llvm libevent-devel openssl-devel && | |
| bash ci-utils/install_prereq_linux.sh --build_arrow yes | |
| " | |
| - name: Validate prereqs | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash | |
| run: bash ci-utils/validate_prereqs.sh | |
| - name: Compress prereqs | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: tar -czf prereqs.tar.gz local_install | |
| - name: Save prereqs cache | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: prereqs.tar.gz | |
| key: ${{ steps.cache-key.outputs.key }} | |
| - name: Upload prereqs | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: prereqs-cuda11-ubuntu-22.04 | |
| path: prereqs.tar.gz | |
| retention-days: 1 | |
| build_wheels: | |
| name: Build wheels on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| needs: build_prereqs | |
| continue-on-error: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-22.04] | |
| cibw_archs: ["auto64"] | |
| cibw_build: ["cp310", "cp311", "cp312", "cp313"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| name: Check out | |
| with: | |
| submodules: recursive | |
| - name: Download prereqs | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: prereqs-cuda11-ubuntu-22.04 | |
| path: . | |
| - name: Extract prereqs | |
| run: tar -xzf prereqs.tar.gz | |
| - name: Free disk space on Linux host | |
| if: runner.os == 'Linux' | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| large-packages: true | |
| docker-images: false | |
| swap-storage: true | |
| tool-cache: false | |
| - name: Prune Docker (pre-build) | |
| run: | | |
| docker system prune -af || true | |
| docker builder prune -af || true | |
| - uses: actions/setup-python@v4 | |
| name: Install Python | |
| with: | |
| python-version: '3.11' | |
| - name: Install cibuildwheel | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install cibuildwheel==3.0.0 delvewheel wheel | |
| - name: Building wheels on Linux | |
| run: | | |
| python -m cibuildwheel --output-dir dist | |
| env: | |
| CIBW_BUILD: ${{ matrix.cibw_build }}-* | |
| CIBW_SKIP: "*musllinux*" | |
| CIBW_BUILD_VERBOSITY: 3 | |
| CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014 | |
| CIBW_BEFORE_ALL_LINUX: sed -i s/mirror.centos.org/vault.centos.org/g /etc/yum.repos.d/*.repo && | |
| sed -i s/^#.*baseurl=http/baseurl=http/g /etc/yum.repos.d/*.repo && | |
| sed -i s/^mirrorlist=http/#mirrorlist=http/g /etc/yum.repos.d/*.repo && | |
| yum install -y llvm libevent-devel openssl-devel && | |
| bash ci-utils/install_cuda_yum.sh 11 && | |
| mkdir -p /tmp/nyxus_bld && | |
| cp -a local_install /tmp/nyxus_bld | |
| CIBW_ENVIRONMENT_LINUX: LD_LIBRARY_PATH="/tmp/nyxus_bld/local_install/lib:/tmp/nyxus_bld/local_install/lib64:/usr/local/cuda/targets/x86_64-linux/lib:$LD_LIBRARY_PATH" CPATH="/usr/local/cuda/targets/x86_64-linux/include:$CPATH" PATH="/usr/local/cuda/bin:$PATH" NYXUS_DEP_DIR="/tmp/nyxus_bld/local_install" CXXFLAGS="-I /usr/local/cuda/include" CMAKE_ARGS="-DUSEGPU=ON -DCMAKE_CUDA_COMPILER=/usr/local/cuda/bin/nvcc -DCMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES=/usr/local/cuda/include" NYXUS_GPU_WHEEL="ON" PIP_ONLY_BINARY=":all:" | |
| CIBW_REPAIR_WHEEL_COMMAND_LINUX: "auditwheel repair --exclude=libcufft.so --exclude=libcufft.so.10 --exclude=libcufft.so.10.4.2.109 --exclude=libcudart.so --exclude=libcudart.so.11.0 --exclude=libcudart.so.11.3.109 -w {dest_dir} {wheel}" | |
| CIBW_ARCHS: ${{ matrix.cibw_archs }} | |
| CIBW_TEST_REQUIRES: numpy pandas pyarrow pytest bfio | |
| CIBW_TEST_REQUIRES_LINUX: pandas pyarrow pytest bfio | |
| CIBW_TEST_COMMAND: python -m pip check | |
| - name: Upload Artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: nyxus-cuda11-wheels-${{ matrix.os }}-${{ matrix.cibw_archs }}-${{ matrix.cibw_build }} | |
| path: dist/*.whl | |
| retention-days: 1 |