# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

ARG CUDA=11.1.1
FROM nvidia/cuda:${CUDA}-cudnn8-runtime-ubuntu18.04
# FROM directive resets ARGS, so we specify again (the value is retained if
# previously set).
ARG CUDA

# Use bash to support string substitution.
SHELL ["/bin/bash", "-o", "pipefail", "-c"]

RUN apt-get update \
    && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y \
        build-essential \
        cmake \
        cuda-command-line-tools-$(cut -f1,2 -d- <<< ${CUDA//./-}) \
        git \
        hmmer \
        kalign \
        tzdata \
        wget \
    && rm -rf /var/lib/apt/lists/* \
    && apt-get autoremove -y \
    && apt-get clean

# Compile HHsuite from source.
RUN git clone --branch v3.3.0 https://github.com/soedinglab/hh-suite.git /tmp/hh-suite \
    && mkdir /tmp/hh-suite/build \
    && pushd /tmp/hh-suite/build \
    && cmake -DHAVE_AVX2=1 -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \
    && make -j 4 && make install \
    && ln -s /opt/hhsuite/bin/* /usr/bin \
    && popd \
    && rm -rf /tmp/hh-suite

# Install Miniconda package manager.
RUN wget -q -P /tmp \
  https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
    && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
    && rm /tmp/Miniconda3-latest-Linux-x86_64.sh

# Install conda packages.
ENV PATH="/opt/conda/bin:$PATH"
RUN conda install -qy conda==4.13.0 \
    && conda install -y -c conda-forge \
      openmm=7.5.1 \
      cudatoolkit==${CUDA_VERSION} \
      pdbfixer \
      pip \
      python=3.8 \
      && conda clean --all --force-pkgs-dirs --yes

RUN git clone -b v2.3.0 --single-branch https://github.com/deepmind/alphafold.git /app/alphafold

RUN wget -q -P /app/alphafold/alphafold/common/ \
 https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt

# Install pip packages.
RUN pip3 install --upgrade pip --no-cache-dir \
    && pip3 install -r /app/alphafold/requirements.txt --no-cache-dir \
    && pip3 install --upgrade --no-cache-dir \
      jax==0.3.25 \
      jaxlib==0.3.25+cuda11.cudnn805 \
      -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

# Apply OpenMM patch.
WORKDIR /opt/conda/lib/python3.8/site-packages
RUN patch -p0 < /app/alphafold/docker/openmm.patch

# Add SETUID bit to the ldconfig binary so that non-root users can run it.
RUN chmod u+s /sbin/ldconfig.real

## SageMaker specific
RUN pip3 install sagemaker-training --upgrade --no-cache-dir
ENV PATH="/opt/ml/code:${PATH}"
# this environment variable is used by the SageMaker PyTorch container to determine our user code directory.
ENV SAGEMAKER_SUBMIT_DIRECTORY /opt/ml/code

## AWSCLI
RUN apt-get update && apt-get install --no-install-recommends -y unzip
RUN wget -q -P /opt/ https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip \
    && unzip /opt/awscli-exe-linux-x86_64.zip -d /opt/ \
    && /opt/aws/install