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Singularity.ExplainAI
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Singularity.ExplainAI
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Bootstrap: docker
From: tensorflow/tensorflow:1.13.1-gpu-py3
# adapted from: https://github.com/marcc-hpc/tensorflow
%environment
# use bash as default shell
SHELL=/bin/bash
export SHELL
export HDF5_USE_FILE_LOCKING='FALSE'
%setup
# runs on host
# the path to the image is $SINGULARITY_ROOTFS
%post
# post-setup script
# load environment variables
. /environment
# use bash as default shell
echo 'SHELL=/bin/bash' >> /environment
# make environment file executable
chmod +x /environment
# default mount paths
mkdir /scratch
# fix this issue: https://github.com/singularityware/singularity/issues/1182#issuecomment-381796545
touch /usr/bin/nvidia-smi
apt-get update && apt-get -y install locales
locale-gen en_US.UTF-8
apt-get install -y git wget
apt-get clean
apt-get install -y --no-install-recommends \
python3 \
python3-tk \
python3-pip \
python3-scipy
# scikit, scipy
#apt-get install -y python3-scipy
#apt-get install python3-pip
pip3 install scipy scikit-learn scikit-image
# PIL (pillow for python 3)
#python3-dev python3-pip python3-tk cmake
pip3 install Pillow
pip3 install matplotlib
pip3 install -e git+https://github.com/marcoancona/DeepExplain.git#egg=deepexplain
# SimpleITK
pip3 install simpleitk
#comet
pip3 install comet_ml
#pandas
pip3 install pandas