add CI (#25)

* add CI * point to pytorch install * fix vars * fix vars again * create symlink * sudo * add mesa * Retry * make sure we only use conda-forge * pin pytorch * try other env config for ubuntu * try other way for cuda * try cmake_args * patch envs with versions * export CUDA_PATH too? * add nvcc metapkg * restraint nvcc too * link to stubs * make CUDA required (temporarily) * debug libcuda.so * symlink libcuda stub * fix symlink * try luck with library paths * try cmake_prefix_path * fix python paths * try different env vars * try like this instead * use extra_compile_flags * summarize skipped tests too * Clean up a bit * update readme * try pocl for tests * debug opencl platforms * more debugging * pytorch >= 1.7 * fix typo * explicit pytorch gpu * rename jobs * workaround with custom flag * alternative attempt * do not use cmake_args * is it opencl's fault? * is it openmm? * openmm _on linux_ * remove nvidia's opencl * try pocl again * force pytorch gpu * build opencl again * fix pytorch req * plugin info * try ld_library_path * add python tests too * fix ld path * fix pytest call * export ld for python tests too
openmm · Feb 2, 2021 · 51615eb · 51615eb
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -0,0 +1,150 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - "master"
+  pull_request:
+    branches:
+      - "master"
+  schedule:
+    # Nightly tests run on master by default:
+    #   Scheduled workflows run on the latest commit on the default or base branch.
+    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+    - cron: "0 0 * * *"
+
+
+jobs:
+  unix:
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.name }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: Linux CPU CUDA 10.0 Python 3.6
+            python-version: "3.6"
+            os: ubuntu-latest
+            gcc-version: "9"
+            cuda-version: "10.0"
+            cdt-name: cos6  # cuda 11+ requires cos7
+            CMAKE_FLAGS: |
+              -DNN_BUILD_CUDA_LIB=ON \
+              -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
+              -DEXTRA_COMPILE_FLAGS="-L/usr/local/cuda/lib64/stubs -Wl,-rpath,/usr/local/cuda/lib64/stubs -Wl,-rpath-link,/usr/local/cuda/lib64/stubs"
+
+          - name: MacOS Intel CPU Python 3.9
+            python-version: "3.9"
+            os: macos-latest
+            cuda-version: ""
+            CMAKE_FLAGS: ""
+
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: "Patch conda env (if needed)"
+        if: startsWith(matrix.os, 'ubuntu')
+        run: |
+          sed -i -e "s/@CDT_NAME@/${{ matrix.cdt-name }}/g" \
+                 -e "s/@GCC_VERSION@/${{ matrix.gcc-version }}.*/g" \
+                 -e "s/@CUDATOOLKIT_VERSION@/${{ matrix.cuda-version }}.*/g" \
+                 devtools/conda-envs/build-${{ matrix.os }}.yml
+
+      - uses: conda-incubator/setup-miniconda@v2
+        name: "Prepare base dependencies"
+        with:
+          python-version: ${{ matrix.python-version }}
+          activate-environment: build
+          environment-file: devtools/conda-envs/build-${{ matrix.os }}.yml
+          auto-activate-base: false
+          channels: conda-forge
+
+      - name: "Install CUDA on Ubuntu (if needed)"
+        if: matrix.cuda-version != ''
+        env:
+          CUDA_VERSION: ${{ matrix.cuda-version }}
+        run: source devtools/scripts/install_cuda.sh
+
+      - name: "Set SDK on MacOS (if needed)"
+        if: startsWith(matrix.os, 'macos')
+        run: source devtools/scripts/install_macos_sdk.sh
+
+      - name: "Conda info"
+        shell: bash -l {0}
+        run: |
+          conda info -a
+          conda list
+
+      - name: "Configure build with CMake"
+        shell: bash -l {0}
+        run: |
+          mkdir build
+          cd build
+
+          SHLIB_EXT=".so"
+          if [[ ${{ matrix.os }} == macos-* ]]; then
+            SHLIB_EXT=".dylib"
+          fi
+
+          cmake .. \
+            -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX} \
+            -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DOPENMM_DIR=${CONDA_PREFIX} \
+            -DPYTORCH_DIR=${CONDA_PREFIX}/lib/python${{ matrix.python-version }}/site-packages/torch \
+            -DTorch_DIR=${CONDA_PREFIX}/lib/python${{ matrix.python-version }}/site-packages/torch/share/cmake/Torch \
+            -DNN_BUILD_OPENCL_LIB=ON \
+            -DOPENCL_INCLUDE_DIR=${CONDA_PREFIX}/include \
+            -DOPENCL_LIBRARY=${CONDA_PREFIX}/lib/libOpenCL${SHLIB_EXT} \
+            ${{ matrix.CMAKE_FLAGS }}
+
+      - name: "Build"
+        shell: bash -l {0}
+        run: |
+          cd build
+          make -j2 install
+          make -j2 PythonInstall
+
+      - name: "Plugin information"
+        shell: bash -l {0}
+        run: |
+          export LD_LIBRARY_PATH="${CONDA_PREFIX}/lib/python${{ matrix.python-version }}/site-packages/torch/lib:${LD_LIBRARY_PATH}"
+          python -c "import simtk.openmm as mm; print('---Loaded---', *mm.pluginLoadedLibNames, '---Failed---', *mm.Platform.getPluginLoadFailures(), sep='\n')"
+
+      - name: "Test C++"
+        shell: bash -l {0}
+        run: |
+          export LD_LIBRARY_PATH="${CONDA_PREFIX}/lib/python${{ matrix.python-version }}/site-packages/torch/lib:${LD_LIBRARY_PATH}"
+          cd build
+          set +e
+          summary=""
+          exitcode=0
+          for f in Test*; do
+            echo "::group::$f"
+            summary+="\n${f}: "
+            if [[ $f == *Cuda* ]]; then
+              echo "Skipping $f..."
+              summary+="Skipped"
+              echo "::endgroup::"
+              continue
+            fi
+            echo "Running $f..."
+            ./${f}
+            thisexitcode=$?
+            if [[ $thisexitcode == 0 ]]; then summary+="OK"; else summary+="FAILED"; fi
+            ((exitcode+=$thisexitcode))
+            echo "::endgroup::"
+          done
+          echo "-------"
+          echo "Summary"
+          echo "-------"
+          echo -e "${summary}"
+          exit $exitcode
+
+      - name: "Test Python"
+        shell: bash -l {0}
+        run: |
+          export LD_LIBRARY_PATH="${CONDA_PREFIX}/lib/python${{ matrix.python-version }}/site-packages/torch/lib:${LD_LIBRARY_PATH}"
+          cd python/tests
+          python -m pytest -v Test*
diff --git a/README.md b/README.md
@@ -1,3 +1,7 @@
+[![GH Actions Status](https://github.com/openmm/openmm-torch/workflows/CI/badge.svg)](https://github.com/openmm/openmm-torch/actions?query=branch%3Amaster+workflow%3ACI)
+[![Conda](https://img.shields.io/conda/v/conda-forge/openmm-torch.svg)](https://anaconda.org/conda-forge/openmm-torch)
+[![Anaconda Cloud Badge](https://anaconda.org/conda-forge/openmm-torch/badges/downloads.svg)](https://anaconda.org/conda-forge/openmm-torch)
+
 OpenMM PyTorch Plugin
 =====================
 

diff --git a/devtools/conda-envs/build-macos-latest.yml b/devtools/conda-envs/build-macos-latest.yml
@@ -0,0 +1,18 @@
+name: build
+channels:
+- conda-forge
+dependencies:
+# build
+- cmake
+- make
+- compilers
+# host
+- python
+- pip
+- swig
+- openmm
+- pytorch-cpu >=1.7
+- khronos-opencl-icd-loader
+- pocl
+# test
+- pytest
diff --git a/devtools/conda-envs/build-ubuntu-latest.yml b/devtools/conda-envs/build-ubuntu-latest.yml
@@ -0,0 +1,27 @@
+name: build
+channels:
+- conda-forge
+dependencies:
+# build
+- cmake
+- make
+- gcc_linux-64 @GCC_VERSION@
+- gxx_linux-64 @GCC_VERSION@
+- nvcc_linux-64 @CUDATOOLKIT_VERSION@
+- libx11-common-@CDT_NAME@-x86_64
+- libx11-@CDT_NAME@-x86_64
+- mesa-dri-drivers-@CDT_NAME@-x86_64
+- mesa-dri1-drivers-@CDT_NAME@-x86_64
+- mesa-libgl-@CDT_NAME@-x86_64
+- mesa-libgl-devel-@CDT_NAME@-x86_64
+# host
+- python
+- pip
+- swig
+- openmm
+- pytorch >=1.7 cuda*
+- ocl-icd
+- cudatoolkit @CUDATOOLKIT_VERSION@
+- pocl
+# test
+- pytest
diff --git a/devtools/scripts/install_cuda.sh b/devtools/scripts/install_cuda.sh
@@ -0,0 +1,47 @@
+# This script install CUDA on Ubuntu-based systemws
+# It uses the Nvidia repos for Ubuntu 18.04, which as of Dec 2020
+# includes packages for CUDA 10.0, 10.1, 10.2, 11.0, 11.1, 11.2
+# Future versions might require an updated repo (maybe Ubuntu 20)
+# It expects a $CUDA_VERSION environment variable set to major.minor (e.g. 10.0)
+
+set -euxo pipefail
+
+# Enable retrying
+echo 'APT::Acquire::Retries "5";' | sudo tee /etc/apt/apt.conf.d/80-retries
+
+sudo wget --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 --tries 5 \
+    -O /etc/apt/preferences.d/cuda-repository-pin-600 \
+    https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
+sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
+sudo add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
+sudo apt-get update -qq
+
+CUDA_APT=${CUDA_VERSION/./-}
+## cufft changed package names in CUDA 11
+if [[ ${CUDA_VERSION} == 10.* ]]; then CUFFT="cuda-cufft"; else CUFFT="libcufft"; fi
+sudo apt-get install -y \
+    libgl1-mesa-dev cuda-compiler-${CUDA_APT} \
+    cuda-drivers cuda-driver-dev-${CUDA_APT} \
+    cuda-cudart-${CUDA_APT} cuda-cudart-dev-${CUDA_APT} \
+    ${CUFFT}-${CUDA_APT} ${CUFFT}-dev-${CUDA_APT} \
+    cuda-nvprof-${CUDA_APT} tree
+sudo apt-get clean
+
+if [[ ! -d /usr/local/cuda ]]; then
+    sudo ln -s /usr/local/cuda-${CUDA_VERSION} /usr/local/cuda
+fi
+
+if [[ -f /usr/local/cuda-${CUDA_VERSION}/lib64/stubs/libcuda.so ]]; then
+    sudo ln -s /usr/local/cuda-${CUDA_VERSION}/lib64/stubs/libcuda.so /usr/local/cuda-${CUDA_VERSION}/lib64/stubs/libcuda.so.1
+fi
+
+# Remove Nvidia's OpenCL
+sudo rm -rf /usr/local/cuda-${CUDA_VERSION}/lib64/libOpenCL.* /usr/local/cuda-${CUDA_VERSION}/include/CL /etc/OpenCL/vendors/nvidia.icd
+
+export CUDA_HOME="/usr/local/cuda"
+export CUDA_PATH="/usr/local/cuda"
+export PATH="${CUDA_HOME}/bin:${PATH}"
+
+echo "CUDA_HOME=${CUDA_HOME}" >> ${GITHUB_ENV}
+echo "CUDA_PATH=${CUDA_PATH}" >> ${GITHUB_ENV}
+echo "PATH=${PATH}" >> ${GITHUB_ENV}
diff --git a/devtools/scripts/install_macos_sdk.sh b/devtools/scripts/install_macos_sdk.sh
@@ -0,0 +1,31 @@
+# Install an older MacOS SDK
+# This should guarantee OpenMM builds with extended compatibility across MacOS versions
+# Adapted from conda-forge-ci-setup scripts:
+# * https://github.com/conda-forge/conda-forge-ci-setup-feedstock/blob/dde296e/recipe/run_conda_forge_build_setup_osx
+# * https://github.com/conda-forge/conda-forge-ci-setup-feedstock/blob/dde296e/recipe/download_osx_sdk.sh
+#
+# Some possible updates might involve upgrading the download link to future MacOS releases (10.15 to something else),
+# depending on the version provided by the CI
+
+OSX_SDK_DIR="$(xcode-select -p)/Platforms/MacOSX.platform/Developer/SDKs"
+export MACOSX_DEPLOYMENT_TARGET=10.9
+export MACOSX_SDK_VERSION=10.9
+
+export CMAKE_OSX_SYSROOT="${OSX_SDK_DIR}/MacOSX${MACOSX_SDK_VERSION}.sdk"
+
+if [[ ! -d ${CMAKE_OSX_SYSROOT}} ]]; then
+    echo "Downloading ${MACOSX_SDK_VERSION} sdk"
+    curl -L -O --connect-timeout 5 --max-time 10 --retry 5  --retry-delay 0 --retry-max-time 40 --retry-connrefused --retry-all-errors \
+        https://github.com/phracker/MacOSX-SDKs/releases/download/10.15/MacOSX${MACOSX_SDK_VERSION}.sdk.tar.xz
+    tar -xf MacOSX${MACOSX_SDK_VERSION}.sdk.tar.xz -C "$(dirname ${CMAKE_OSX_SYSROOT})"
+fi
+
+if [[ "$MACOSX_DEPLOYMENT_TARGET" == 10.* ]]; then
+# set minimum sdk version to our target
+plutil -replace MinimumSDKVersion -string ${MACOSX_SDK_VERSION} $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist
+plutil -replace DTSDKName -string macosx${MACOSX_SDK_VERSION}internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist
+fi
+
+echo "MACOSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET}" >> ${GITHUB_ENV}
+echo "CMAKE_OSX_SYSROOT=${MACOSX_DEPLOYMENT_TARGET}" >> ${GITHUB_ENV}
+echo "CMAKE_OSX_SYSROOT=${CMAKE_OSX_SYSROOT}" >> ${GITHUB_ENV}
diff --git a/platforms/cuda/CMakeLists.txt b/platforms/cuda/CMakeLists.txt
@@ -64,7 +64,7 @@ TARGET_LINK_LIBRARIES(${SHARED_TARGET} OpenMMCUDA)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${NN_LIBRARY_NAME})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES
     COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY ${EXTRA_COMPILE_FLAGS}"
-    LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    LINK_FLAGS "${EXTRA_COMPILE_FLAGS} ${EXTRA_LINK_FLAGS_CUDA}")
 IF (APPLE)
     SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "-F/Library/Frameworks -framework CUDA ${EXTRA_COMPILE_FLAGS}")
 ENDIF (APPLE)