feat(ci): refactor linux CI

* Use nice container feature of github actions
* Remove automated builds for CUDA 8 and 9

.github/workflows/build.yml

@@ -4,41 +4,25 @@ on: [push]
 
 jobs:
 
-  LinuxCuda8:
+  LinuxCuda:
     runs-on: ubuntu-latest
+    container: stitchem/stitchem:latest
     steps:
     - uses: actions/checkout@v1
     - name: CMake
-      run: docker build . --file docker/ci-cuda.dockerfile --tag stitchem-cuda8:latest --build-arg version=8
+      run: mkdir ../build && cd ../build && cmake -DCMAKE_BUILD_TYPE=Release -DRTMP_NVENC=OFF -DCUDA_TARGET_ARCH="50" -DGPU_BACKEND_CUDA=ON -DGPU_BACKEND_OPENCL=OFF -DDISABLE_OPENCL_SPIR=ON -G Ninja ../stitchEm
     - name: Build
-      run: docker run stitchem-cuda8:latest
-
-  LinuxCuda9:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v1
-    - name: CMake
-      run: docker build . --file docker/ci-cuda.dockerfile --tag stitchem-cuda9:latest --build-arg version=9
-    - name: Build
-      run: docker run stitchem-cuda9:latest
-
-  LinuxCuda10:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v1
-    - name: CMake
-      run: docker build . --file docker/ci-cuda.dockerfile --tag stitchem-cuda10:latest --build-arg version=10
-    - name: Build
-      run: docker run stitchem-cuda10:latest
+      run: cd ../build && ninja
 
   LinuxOpenCL:
     runs-on: ubuntu-latest
+    container: stitchem/stitchem:latest
     steps:
     - uses: actions/checkout@v1
     - name: CMake
-      run: docker build . --file docker/ci-opencl.dockerfile --tag stitchem-opencl:latest
+      run: mkdir ../build && cd ../build && cmake -DCMAKE_BUILD_TYPE=Release -DGPU_BACKEND_CUDA=OFF -DGPU_BACKEND_OPENCL=ON -DDISABLE_OPENCL_SPIR=ON -G Ninja ../stitchEm
     - name: Build
-      run: docker run stitchem-opencl:latest
+      run: cd ../build && ninja
 
   MacOpenCL:
     runs-on: macos-latest

docker/README.md

 # How does it work?
 
-To avoid rebuilding an entire docker container at each build, we use base images for each cuda version (currently 8.0, 9.2 and 10.1). Those images are built locally and pushed to [dockerhub](https://hub.docker.com/u/stitchem). Then, the travis CI builds the ci image (that depends on the base images), adds the stitchEm sources and builds the applications.
+To cache apt dependency, and avoid installing them all at each CI build, we use this docker image.
 
-# Modifying the images
-
-## Modifying base image (base.dockerfile)
-
-* Push your changes, create PR and merge it in master
-* Ask for the rights to https://hub.docker.com/r/stitchem/stitchem-base
-* Build the image locally: `docker build --tag stitchem/stitchem-base:latest --file docker/base.dockerfile .`
-* Push the image: `docker push stitchem/stitchem-base:latest`
-* Do the next section for x in 8, 9, 10
-
-## Modifying base_cuda_x (base_cuda_x.dockerfile)
-
-* Push your changes, create PR and merge it in master
-* Ask for the rights to https://hub.docker.com/r/stitchem/stitchem-base-cudax
-* Build the image locally: `docker build --tag stitchem/stitchem-base-cudax:latest --file docker/base_cuda_x.dockerfile .`
-* Push the image: `docker push stitchem/stitchem-base-cudax:latest`
-
-## Modifying CI image (ci.dockerfile)
-
-* Push your changes, create PR and merge it in master
-* You're all set
+You need rights to [dockerhub](https://hub.docker.com/u/stitchem).
+```
+docker build --tag stitchem/stitchem:latest --file docker/stitchem.dockerfile .
+docker push stitchem/stitchem:latest
+```

docker/base_cuda_10.dockerfile

-FROM stitchem/stitchem-base:latest
-
-ENV CUDA=10.2.89-1
-ENV CUDA_APT=10-2
-ENV CUDA_SHORT=10.2
-ENV CUDA_INSTALLER=cuda-repo-ubuntu1804_${CUDA}_amd64.deb
-ENV NV_LIB=libnvidia-compute-418
-
-RUN wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/${CUDA_INSTALLER}
-RUN dpkg -i ${CUDA_INSTALLER}
-RUN apt update -qq && apt install -y \
-  cuda-compiler-${CUDA_APT} \
-  cuda-cudart-dev-${CUDA_APT} \
-  cuda-cufft-dev-${CUDA_APT} \
-  cuda-nvml-dev-${CUDA_APT} \
-  ${NV_LIB}
-
-ENV CUDA_HOME=/usr/local/cuda-${CUDA_SHORT}
-ENV PATH=${PATH}:${CUDA_HOME}/bin
-ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${CUDA_HOME}/lib64

docker/base_cuda_8.dockerfile

-FROM stitchem/stitchem-base:latest
-
-ENV CUDA=8.0.61-1
-ENV CUDA_APT=8-0
-ENV CUDA_SHORT=8.0
-ENV CUDA_INSTALLER=cuda-repo-ubuntu1604_${CUDA}_amd64.deb
-ENV NV_DRIVER=nvidia-418
-
-RUN apt update && apt install -y gcc-5 g++-5
-ENV CC=gcc-5
-ENV CXX=g++-5
-
-RUN wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/${CUDA_INSTALLER}
-RUN dpkg -i ${CUDA_INSTALLER}
-RUN apt update -qq && apt install -y \
-  cuda-core-${CUDA_APT} \
-  cuda-cudart-dev-${CUDA_APT} \
-  cuda-cufft-dev-${CUDA_APT} \
-  cuda-nvml-dev-${CUDA_APT}
-RUN mkdir /usr/lib/nvidia
-RUN apt install -y -o Dpkg::Options::="--force-overwrite" \
-  ${NV_DRIVER}
-
-
-ENV CUDA_HOME=/usr/local/cuda-${CUDA_SHORT}
-ENV PATH=${PATH}:${CUDA_HOME}/bin
-ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${CUDA_HOME}/lib64

docker/base_cuda_9.dockerfile

-FROM stitchem/stitchem-base:latest
-
-ENV CUDA=9.2.148-1
-ENV CUDA_APT=9-2
-ENV CUDA_SHORT=9.2
-ENV CUDA_INSTALLER=cuda-repo-ubuntu1604_${CUDA}_amd64.deb
-ENV NV_DRIVER=nvidia-410
-
-RUN wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/${CUDA_INSTALLER}
-RUN dpkg -i ${CUDA_INSTALLER}
-RUN apt update -qq && apt install -y \
-  cuda-core-${CUDA_APT} \
-  cuda-cudart-dev-${CUDA_APT} \
-  cuda-cufft-dev-${CUDA_APT} \
-  cuda-nvml-dev-${CUDA_APT}
-RUN mkdir /usr/lib/nvidia
-RUN apt install -y -o Dpkg::Options::="--force-overwrite" \
-  ${NV_DRIVER}
-
-ENV CUDA_HOME=/usr/local/cuda-${CUDA_SHORT}
-ENV PATH=${PATH}:${CUDA_HOME}/bin
-ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${CUDA_HOME}/lib64

docker/ci-cuda.dockerfile

-ARG version
-FROM stitchem/stitchem-base-cuda${version}:latest
-
-ADD . stitchEm
-WORKDIR stitchEm
-RUN echo ${CUDA_SHORT} > cuda.version
-WORKDIR build
-RUN cmake -DCMAKE_BUILD_TYPE=Release -DRTMP_NVENC=OFF -DCUDA_TARGET_ARCH="50" -DGPU_BACKEND_CUDA=ON -DGPU_BACKEND_OPENCL=OFF -DDISABLE_OPENCL_SPIR=ON -G Ninja ..
-CMD ninja

docker/ci-opencl.dockerfile

-ARG version
-FROM stitchem/stitchem-base:latest
-
-ADD . stitchEm
-WORKDIR stitchEm
-WORKDIR build
-RUN cmake -DCMAKE_BUILD_TYPE=Release -DGPU_BACKEND_CUDA=OFF -DGPU_BACKEND_OPENCL=ON -DDISABLE_OPENCL_SPIR=ON -G Ninja ..
-CMD ninja

docker/base.dockerfile → docker/stitchem.dockerfile

@@ -37,3 +37,20 @@ RUN pip install cmake
 RUN wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
 RUN apt-key add 7fa2af80.pub
 RUN apt clean
+
+ENV CUDA=10.2.89-1
+ENV CUDA_APT=10-2
+ENV CUDA_SHORT=10.2
+ENV CUDA_INSTALLER=cuda-repo-ubuntu1804_${CUDA}_amd64.deb
+RUN wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/${CUDA_INSTALLER}
+RUN apt install ./${CUDA_INSTALLER}
+RUN apt update -qq && apt install -y \
+  cuda-compiler-${CUDA_APT} \
+  cuda-cudart-dev-${CUDA_APT} \
+  cuda-cufft-dev-${CUDA_APT} \
+  cuda-nvml-dev-${CUDA_APT} \
+  ${NV_LIB}
+
+ENV CUDA_HOME=/usr/local/cuda-${CUDA_SHORT}
+ENV PATH=${PATH}:${CUDA_HOME}/bin
+ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${CUDA_HOME}/lib64