testing deepcsr

.github/workflows/docker-image.yml

@@ -15,11 +15,11 @@ jobs:
  steps:
  - uses: actions/checkout@v3
  - name: Build the Docker image
- run: docker build . --file Dockerfile --tag hvgazula/test_image
+ run: docker build . --file Dockerfile --tag hvgazula/deepcsr
 
  # Push the Docker image to Docker Hub (only if the PR is merged)
  - name: Push Docker image
 # if: github.event.pull_request.merged == true
  run: |
  docker login -u ${{ secrets.DOCKER_USERNAME }} -p ${{ secrets.DOCKER_PASSWORD }}
- docker push hvgazula/test_image
+ docker push hvgazula/deepcsr

Dockerfile

@@ -1,4 +1,58 @@
-# Basic nginx dockerfile starting with Ubuntu 20.04
-FROM ubuntu:20.04
-RUN apt-get -y update
-RUN apt-get -y install nginx
+FROM nvidia/cuda:11.3.1-cudnn8-devel-ubuntu20.04 
+ENV LANG=C.UTF-8
+ENV LC_ALL=C.UTF-8
+ENV PATH=/opt/miniconda3/bin:$PATH
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
+ENV PYTHONIOENCODING=UTF-8
+ENV PIPENV_VENV_IN_PROJECT=1
+ENV JCC_JDK=/usr/lib/jvm/java-8-openjdk-amd64
+RUN USE_CUDA=1
+RUN CUDA_VERSION=11.3.1
+RUN CUDNN_VERSION=8
+RUN LINUX_DISTRO=ubuntu
+RUN DISTRO_VERSION=20.04
+RUN TORCH_CUDA_ARCH_LIST="7.0 7.5 8.0 8.6"
+RUN rm -f /etc/apt/apt.conf.d/docker-clean; \
+echo 'Binary::apt::APT::Keep-Downloaded-Packages "true";' \
+> /etc/apt/apt.conf.d/keep-cache
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata && apt-get install -y --no-install-recommends \
+build-essential \
+ca-certificates \
+ccache \
+curl \
+git \
+wget \
+cmake \
+openjdk-8-jdk \
+libaio-dev && \
+apt-get install -y --no-install-recommends llvm-10 lldb-10 llvm-10-dev libllvm10 llvm-10-runtime
+RUN rm -rf /var/lib/apt/lists/*
+ENV PYTHON_VERSION=3.8
+ENV CONDA_URL=https://repo.anaconda.com/miniconda/Miniconda3-py38_4.10.3-Linux-x86_64.sh
+RUN curl -fsSL -v -o ~/miniconda.sh -O ${CONDA_URL} && \
+chmod +x ~/miniconda.sh && \
+~/miniconda.sh -b -p /opt/miniconda3 
+
+WORKDIR /app
+COPY requirements.yml .
+COPY CBSI.tar.gz .
+RUN tar -xf CBSI.tar.gz
+RUN mkdir niftyreg-build
+ENV CMAKE_BUILD_TYPE=Release
+WORKDIR /app/niftyreg-build
+RUN cmake ../niftyreg-CBSI
+RUN make
+RUN make install
+WORKDIR /app
+RUN conda env create -f requirements.yml
+SHELL ["conda", "run", "-n", "deepcsr", "/bin/bash", "-c"]
+RUN git clone https://github.com/neuroneural/DeepCSR-fork.git
+WORKDIR /app/DeepCSR-fork/docker/nighres
+RUN git checkout tags/docker1
+RUN ./build.sh
+RUN python3 -m pip install .
+RUN apt-get clean
+RUN pip cache purge
+RUN conda clean -a
+ENTRYPOINT ["/bin/bash", "-l", "-c"]