Simplify dockerfile

docker/Dockerfile

@@ -1,61 +1,31 @@
-FROM nvidia/cuda:10.1-cudnn7-devel-ubuntu18.04
-
-ENV CUDA_PATH /usr/local/cuda
-ENV CUDA_ROOT /usr/local/cuda/bin
-ENV LD_LIBRARY_PATH /usr/local/nvidia/lib64
+FROM pytorch/pytorch:1.9.0-cuda10.2-cudnn7-devel
 
 RUN apt-get -qq update
 # libsm6 and libxext6 are needed for cv2
-RUN apt-get update && apt-get install -y libxext6 libsm6 libxrender1 build-essential sudo \
+RUN apt-get update && apt-get install -y libxext6 libglib2.0-0 libsm6 build-essential sudo \
     libgl1-mesa-glx git wget rsync tmux nano dcmtk fftw3-dev liblapacke-dev libpng-dev libopenblas-dev jq && \
   rm -rf /var/lib/apt/lists/*
-RUN ldconfig
-
-# Make a user
-
-
-RUN adduser --disabled-password --gecos '' runner
-# RUN adduser runner sudo
-RUN echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
-ARG USER_ID
-ARG GROUP_ID
-RUN usermod -u ${USER_ID} runner
-RUN usermod -g ${GROUP_ID} runner
-USER runner
 
+RUN adduser --disabled-password --gecos '' ganslate_user
+USER ganslate_user
 
+# Setup apex for mixed precision
 WORKDIR /tmp
-RUN wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-RUN bash Miniconda3-latest-Linux-x86_64.sh -b
-
-ENV PATH "/home/runner/miniconda3/bin:$PATH:$CUDA_ROOT"
-
-# Setup python packages
-RUN conda update -n base conda -yq
-RUN conda install python=3.8
-RUN conda install numpy pyyaml mkl mkl-include setuptools cmake cffi typing boost
-RUN conda install pytorch torchvision cudatoolkit=10.1 -c pytorch
-RUN conda install scipy pandas scikit-learn scikit-image -yq
-RUN conda install cython tqdm jupyter sqlalchemy -yq
-
 RUN git clone https://github.com/NVIDIA/apex \
  && cd apex \
- && pip install -v --no-cache-dir --global-option="--cpp_ext" --global-option="--cuda_ext" ./ \
+ && pip install -v --disable-pip-version-check --no-cache-dir ./ \
  && cd ..
 
-RUN python -m pip install opencv-python simpleitk h5py -q
-RUN python -m pip install tb-nightly wandb -q
-RUN python -m pip install monai memcnn -q
-RUN python -m pip install omegaconf loguru -q
-
-
 USER root
-
-# Create folders for input and output
-RUN mkdir /ganslate && chmod 777 /ganslate
 RUN mkdir /data && chmod 777 /data
-USER runner
+USER ganslate_user
+
+WORKDIR /home/ganslate_user
+
+# Install the ganslate package #TODO: Replace with final package link
+RUN pip install --no-warn-script-location -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple ganslate==0.1.4
 
-WORKDIR /ganslate
+# Script are installed in ~/.local/bin, add it to PATH
+ENV PATH "~/.local/bin:$PATH"
 
-ENTRYPOINT $0 $@
+ENTRYPOINT /bin/bash