edraizen/SingularityTorch:latest

$ singularity pull shub://edraizen/SingularityTorch:latest

Singularity Recipe

BootStrap: docker
From: nvidia/cuda:10.2-cudnn7-devel-ubuntu18.04

%post
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# this will install all necessary packages and prepare the container
    apt-get -y update
    apt-get -y upgrade



    # install other dependencies
    apt-get -y install --allow-downgrades --no-install-recommends \
        build-essential \
        dbus \
        wget \
        git \
        vim \
        nano \
        cmake \
        bzip2 \
        ca-certificates \
        libglib2.0-0 \
        libxext6 \
        libsm6 \
        libxrender1 \
        libboost-all-dev \
        gdb \
        libopenblas-dev

    echo "deb http://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1604/x86_64 /" > /etc/apt/sources.list.d/nvidia-ml.list

    apt-get -y install --allow-downgrades --no-install-recommends \
        libnccl2=2.7.8-1+cuda10.2\
        libnccl-dev=2.7.8-1+cuda10.2

    apt-get -y install software-properties-common
    add-apt-repository ppa:ubuntu-toolchain-r/test
    apt-get -y install g++-7
    #export CXX=gcc-7

    # Install the IB verbs
    apt-get install -y --no-install-recommends libibverbs*
    apt-get install -y --no-install-recommends ibverbs-utils librdmacm* infiniband-diags libmlx4* libmlx5* libnuma*

    rm /etc/machine-id
    dbus-uuidgen --ensure=/etc/machine-id

    export CUDA_HOME="/usr/local/cuda-10.2"
    export CPATH="$CUDA_HOME/include:$CPATH"
    export LD_LIBRARY_PATH="$CUDA_HOME/lib64:/opt/conda/lib:$LD_LIBRARY_PATH"
    export PATH="$CUDA_HOME/bin:$PATH"
    export PATH="/opt/conda/bin:$PATH"

    #required for LightGBM
    mkdir -p /etc/OpenCL/vendors && \
    echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd

    export BOOST_ROOT=/usr/local/boost

    wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
    /bin/bash ~/miniconda.sh -b -p /opt/conda
    rm ~/miniconda.sh

    . /opt/conda/etc/profile.d/conda.sh && conda activate && conda install -y python=3.7

    . /opt/conda/etc/profile.d/conda.sh && conda activate && conda install -c anaconda future conda-build numpy ninja pyyaml mkl mkl-include setuptools cmake cffi typing_extensions future six requests dataclasses #

    . /opt/conda/etc/profile.d/conda.sh && conda activate && conda install -c pytorch magma-cuda102


    #git clone https://github.com/pytorch/pytorch.git
    #cd pytorch
    #git checkout tags/v1.6.0
    #git submodule update --init --recursive
    
    #https://github.com/pytorch/pytorch/issues/13541 # -D_GLIBCXX_USE_CXX11_ABI=0
    #export TORCH_NVCC_FLAGS="-Xfatbin -compress-all"
    
    #echo 'set(TORCH_CXX_FLAGS "-D_GLIBCXX_USE_CXX11_ABI=0")' > no_abi.txt
    #cat no_abi.txt torch/CMakeLists.txt > torch/CMakeLists.txt.1
    #rm torch/CMakeLists.txt
    #mv torch/CMakeLists.txt.1 torch/CMakeLists.txt
    #rm no_abi.txt
    #sed -i 's/set(TORCH_CXX_FLAGS/#set(TORCH_CXX_FLAGS/g' cmake/TorchConfig.cmake.in
    #sed -i 's/@GLIBCXX_USE_CXX11_ABI@/0/g' cmake/TorchConfig.cmake.in
    
     #. /opt/conda/etc/profile.d/conda.sh && conda activate && TORCH_CUDA_ARCH_LIST="3.5 5.2 6.0 6.1" TORCH_NVCC_FLAGS="-Xfatbin -compress-all" \
    # CMAKE_PREFIX_PATH="$(dirname $(which conda))/../" \
    #MAX_JOBS=16 python setup.py install
    
    #cd /
    #. /opt/conda/etc/profile.d/conda.sh && conda activate && python -c "import torch; print('PYTORCH USING CXX11_ABI =', torch._C._GLIBCXX_USE_CXX11_ABI )"

    

    #IF NOT FROM SOURCE, UNOCMMENT
    . /opt/conda/etc/profile.d/conda.sh && conda activate && conda install numpy mkl-include pytorch=1.6.0 cudatoolkit=10.2 -c pytorch

    . /opt/conda/etc/profile.d/conda.sh && conda activate && conda install mkl-include cudatoolkit=10.2 -c pytorch


    #. /opt/conda/etc/profile.d/conda.sh && conda activate && pip install -U MinkowskiEngine
    git clone https://github.com/edraizen/MinkowskiEngine.git
    cd MinkowskiEngine
    make clean
    export CXX=gcc-7
    . /opt/conda/etc/profile.d/conda.sh && conda activate && python setup.py install --force_cuda --cuda_home=$CUDA_HOME

    # Install Open MPI
    apt-get install --reinstall openmpi-bin libopenmpi-dev
    export MPI_CXX=mpicc

    # Install Horovod, temporarily using CUDA stubs
    ldconfig $CUDA_HOME/targets/x86_64-linux/lib/stubs && \
    HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITHOUT_MXNET=1 HOROVOD_WITH_PYTORCH=1 pip install --no-cache-dir horovod && \
    ldconfig

    # Configure OpenMPI to run good defaults:
    #   --bind-to none --map-by slot --mca btl_tcp_if_exclude lo,docker0
    echo "hwloc_base_binding_policy = none" >> /usr/local/etc/openmpi-mca-params.conf && \
    echo "rmaps_base_mapping_policy = slot" >> /usr/local/etc/openmpi-mca-params.conf
    #echo "btl_tcp_if_exclude = lo,docker0" >> /usr/local/etc/openmpi-mca-params.conf

    # Install OpenSSH for MPI to communicate between containers
    apt-get install -y --no-install-recommends openssh-client openssh-server && \
        mkdir -p /var/run/sshd

    # Allow OpenSSH to talk to containers without asking for confirmation
    cat /etc/ssh/ssh_config | grep -v StrictHostKeyChecking > /etc/ssh/ssh_config.new && \
        echo "    StrictHostKeyChecking no" >> /etc/ssh/ssh_config.new && \
        mv /etc/ssh/ssh_config.new /etc/ssh/ssh_config

    # Set default NCCL parameters
    echo NCCL_DEBUG=INFO >> /etc/nccl.conf && \
    echo NCCL_SOCKET_IFNAME=^docker0 >> /etc/nccl.conf

    # install requirements for molmimic
    pip install dask[dataframe]
    pip install scikit-learn Biopython seaborn tqdm dask joblib torchnet tables fastparquet pyarrow
    . /opt/conda/etc/profile.d/conda.sh && conda activate && pip install --ignore-installed boto3 botocore awscli toil
     . /opt/conda/etc/profile.d/conda.sh && conda activate && pip install --ignore-installed freesasa==2.0.3.post7
    pip install tensorboardX
    #pip install pytorch-lightning
    pip install git+https://github.com/PytorchLightning/pytorch-lightning.git@master --upgrade
    pip install wandb

    # install ipython and kernel to create a new jupyter kernal
    pip install ipython ipykernel

    # install OpenCV
    pip install opencv-python

    #conda clean --index-cache --tarballs --packages --yes

%runscript
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# this text code will run whenever the container
# is called as an executable or with `singularity run`
exec python $@

%help
This container is backed by Anaconda version 4.4.0 and provides the Python 3.6 bindings for:
    * PyTorch 1.0
    * SparseConvNet
    * XGBoost
    * LightGBM
    * OpenCV
    * CUDA 9.0
    * CuDNN 7.0.5.15


%environment
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# This sets global environment variables for anything run within the container
    export CUDA_HOME="/usr/local/cuda-10.2"
    export CPATH="$CUDA_HOME/include:$CPATH"
    export LD_LIBRARY_PATH="$CUDA_HOME/lib64:/opt/conda/lib:$LD_LIBRARY_PATH"
    export PATH="$CUDA_HOME/bin:$PATH"

    export PATH="/opt/conda/bin:$PATH"
    unset CONDA_DEFAULT_ENV
    export ANACONDA_HOME=/opt/conda

    XGBOOSTROOT=/opt/xgboost
    export CPATH="$XGBOOSTROOT/include:$CPATH"
    export LD_LIBRARY_PATH="$XGBOOSTROOT/lib:$LD_LIBRARY_PATH"
    export PATH="$XGBOOSTROOT:$PATH"
    export PYTHONPATH=$XGBOOSTROOT/python-package:$PYTHONPATH

    LIGHTGBMROOT=/opt/LightGBM
    export CPATH="$LIGHTGBMROOT/include:$CPATH"
    export LD_LIBRARY_PATH="$LIGHTGBMROOT:$LD_LIBRARY_PATH"
    export PATH="$LIGHTGBMROOT:$PATH"
    export PYTHONPATH=$LIGHTGBMROOT/python-package:$PYTHONPATH

Collection

• Name: edraizen/SingularityTorch
• License: None

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