Merge pull request #34 from raimis/ci

CI for NNPOps

Author: Raimondas Galvelis

.github/workflows/ci.yml

@@ -0,0 +1,68 @@
+name: CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        include:
+          - cuda: 10.2.89
+            gcc: 8.5.0
+            nvcc: 10.2
+            python: 3.8
+            pytorch: 1.7.1
+          - cuda: 11.2.2
+            gcc: 10.3.0
+            nvcc: 11.2
+            python: 3.9
+            pytorch: 1.8.0 # Cannot test with PyTorch 1.9, because of https://github.com/aiqm/torchani/issues/598
+
+    steps:
+    - name: Check out
+      uses: actions/checkout@v2
+
+    - name: Install CUDA Toolkit
+      uses: Jimver/cuda-toolkit@v0.2.4
+      with:
+        cuda: ${{ matrix.cuda }}
+
+    - name: Install Miniconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: ""
+        auto-activate-base: true
+        miniforge-variant: Miniforge3
+
+    - name: Install dependencies
+      shell: bash -l {0}
+      run: |
+        sed -i -e "/cudatoolkit/c\  - cudatoolkit ${{ matrix.cuda }}" \
+               -e "/gxx_linux-64/c\  - gxx_linux-64 ${{ matrix.gcc }}" \
+               -e "/nvcc_linux-64/c\  - nvcc_linux-64 ${{ matrix.nvcc }}" \
+               -e "/python/c\  - python ${{ matrix.python }}" \
+               -e "/pytorch-gpu/c\  - pytorch-gpu ${{ matrix.pytorch }}" \
+               environment.yml
+        conda env create -n nnpops -f environment.yml
+
+    - name: Configure, compile, and install
+      shell: bash -l {0}
+      run: |
+        conda activate nnpops
+        mkdir build && cd build
+        cmake .. \
+              -DTorch_DIR=$CONDA_PREFIX/lib/python${{ matrix.python }}/site-packages/torch/share/cmake/Torch \
+              -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX
+        make install
+
+    - name: Test
+      shell: bash -l {0}
+      run: |
+        conda activate nnpops
+        cd build
+        ctest --verbose --exclude-regex TestCuda

CMakeLists.txt

@@ -29,8 +29,8 @@ foreach(TEST_PATH ${TEST_PATHS})
     add_test(${TEST_NAME} ${TEST_NAME})
 endforeach()
 
-add_test(TestSymmetryFunctions pytest ${CMAKE_SOURCE_DIR}/src/pytorch/TestSymmetryFunctions.py)
-add_test(TestBatchedNN pytest ${CMAKE_SOURCE_DIR}/src/pytorch/TestBatchedNN.py)
+add_test(TestBatchedNN         pytest -v ${CMAKE_SOURCE_DIR}/src/pytorch/TestBatchedNN.py)
+add_test(TestSymmetryFunctions pytest -v ${CMAKE_SOURCE_DIR}/src/pytorch/TestSymmetryFunctions.py)
 
 install(TARGETS ${LIBRARY} DESTINATION ${Python_SITEARCH}/${NAME})
 install(FILES src/pytorch/__init__.py

README.md

@@ -59,7 +59,7 @@ $ make install
 
 - Run the tests
 ```bash
-$ ctest
+$ ctest --verbose
 ```
 
 ## Usage

environment.yml

@@ -2,10 +2,11 @@ channels:
   - conda-forge
 dependencies:
   - cmake
-  - gxx_linux-64 <=10
+  - cudatoolkit 11.2.2
+  - gxx_linux-64 10.3.0
   - make
   - mdtraj
-  - nvcc_linux-64
+  - nvcc_linux-64 11.2
   - torchani 2.2
   - pytest
   - python 3.9

src/pytorch/TestBatchedNN.py

@@ -38,6 +38,9 @@ def test_import():
 @pytest.mark.parametrize('molFile', ['1hvj', '1hvk', '2iuz', '3hkw', '3hky', '3lka', '3o99'])
 def test_compare_with_native(deviceString, molFile):
 
+    if deviceString == 'cuda' and not torch.cuda.is_available():
+        pytest.skip('CUDA is not available')
+
     from NNPOps.BatchedNN import TorchANIBatchedNN
 
     device = torch.device(deviceString)
@@ -70,6 +73,9 @@ def test_compare_with_native(deviceString, molFile):
 @pytest.mark.parametrize('molFile', ['1hvj', '1hvk', '2iuz', '3hkw', '3hky', '3lka', '3o99'])
 def test_model_serialization(deviceString, molFile):
 
+    if deviceString == 'cuda' and not torch.cuda.is_available():
+        pytest.skip('CUDA is not available')
+
     from NNPOps.BatchedNN import TorchANIBatchedNN
 
     device = torch.device(deviceString)

src/pytorch/TestSymmetryFunctions.py

@@ -38,6 +38,9 @@ def test_import():
 @pytest.mark.parametrize('molFile', ['1hvj', '1hvk', '2iuz', '3hkw', '3hky', '3lka', '3o99'])
 def test_compare_with_native(deviceString, molFile):
 
+    if deviceString == 'cuda' and not torch.cuda.is_available():
+        pytest.skip('CUDA is not available')
+
     from NNPOps.SymmetryFunctions import TorchANISymmetryFunctions
 
     device = torch.device(deviceString)
@@ -70,6 +73,9 @@ def test_compare_with_native(deviceString, molFile):
 @pytest.mark.parametrize('molFile', ['1hvj', '1hvk', '2iuz', '3hkw', '3hky', '3lka', '3o99'])
 def test_model_serialization(deviceString, molFile):
 
+    if deviceString == 'cuda' and not torch.cuda.is_available():
+        pytest.skip('CUDA is not available')
+
     from NNPOps.SymmetryFunctions import TorchANISymmetryFunctions
 
     device = torch.device(deviceString)