Singularity

bootstrap:docker
From:nvidia/cuda:9.0-cudnn7-devel-centos7

%post

yum -y upgrade
yum -y install epel-release yum-plugin-priorities

# osg repo
yum -y install http://repo.opensciencegrid.org/osg/3.4/osg-3.4-el7-release-latest.rpm

# pegasus repo
echo -e "# Pegasus\n[Pegasus]\nname=Pegasus\nbaseurl=http://download.pegasus.isi.edu/wms/download/rhel/7/\$basearch/\ngpgcheck=0\nenabled=1\npriority=50" >/etc/yum.repos.d/pegasus.repo

# well rounded basic system to support a wide range of user jobs
yum -y groups mark convert
yum -y grouplist
yum -y groupinstall "Compatibility Libraries" \
                    "Development Tools" \
                    "Scientific Support"


yum -y install \
	redhat-lsb \
	bc \
	binutils \
	binutils-devel \
	coreutils \
	curl \
	fontconfig \
	gcc \
	gcc-c++ \
	gcc-gfortran \
	git \
	glew-devel \
	glib2-devel \
	glib-devel \
	graphviz \
	gsl-devel \
        gtk3 \
	java-1.8.0-openjdk \
	java-1.8.0-openjdk-devel \
        libcurl \
	libgfortran \
	libGLU \
	libgomp \
	libicu \
	libquadmath \
	libtool \
	libtool-ltdl \
	libtool-ltdl-devel \
	libX11-devel \
	libXaw-devel \
	libXext-devel \
	libXft-devel \
	libxml2 \
	libxml2-devel \
	libXmu-devel \
	libXpm \
	libXpm-devel \
	libXt \
	mesa-libGL-devel \
	openssh \
	openssh-server \
	openssl \
        openssl-devel \
	osg-wn-client \
	p7zip \
	p7zip-plugins \
	python-devel \
	redhat-lsb-core \
	rsync \
        stashcache-client \
	subversion \
	tcl-devel \
	tcsh \
	time \
	tk-devel \
	wget \
	which

# osg
yum -y install osg-ca-certs osg-wn-client
rm -f /etc/grid-security/certificates/*.r0

# htcondor - include so we can chirp
yum -y install condor

# pegasus
yum -y install pegasus

# Cleaning caches to reduce size of image
yum clean all

# required directories
for MNTPOINT in \
    /cvmfs \
    /hadoop \
    /hdfs \
    /lizard \
    /mnt/hadoop \
    /mnt/hdfs \
    /xenon \
    /spt \
    /stash2 \
    /srv \
    /scratch \
    /data \
    /project \
; do \
    mkdir -p $MNTPOINT ; \
done

# make sure we have a way to bind host provided libraries
# see https://github.com/singularityware/singularity/issues/611
mkdir -p /host-libs /etc/OpenCL/vendors

##############################################
# Install TensorFlow, Keras, etc. with Python

#curl -O https://bootstrap.pypa.io/2.6/get-pip.py && \
curl -O https://bootstrap.pypa.io/get-pip.py
python get-pip.py
rm get-pip.py
    
#pip --no-cache-dir install \
#            h5py \
#            ipykernel \
#            jupyter \
#            matplotlib \
#            numpy \
#            pandas \
#            Pillow \
#            scipy \
#            sklearn
    
#$PYTHON -m ipykernel.kernelspec
    
echo "/usr/local/cuda/lib64/" >/etc/ld.so.conf.d/cuda.conf
echo "/usr/local/cuda/extras/CUPTI/lib64/" >>/etc/ld.so.conf.d/cuda.conf

# Create an empty location for nvidia-smi
touch /usr/bin/nvidia-smi

# Install TensorFlow GPU version
pip install --upgrade https://storage.googleapis.com/tensorflow/linux/gpu/tensorflow_gpu-1.12.0-cp27-none-linux_x86_64.whl
    
# keras
pip install --upgrade keras
    

#############################
# now do the same for python3
    
#curl -O https://bootstrap.pypa.io/get-pip.py && \
#        python3 get-pip.py && \
#        rm get-pip.py
#    
#pip3 --no-cache-dir install \
#            h5py \
#            ipykernel \
#            jupyter \
#            matplotlib \
#            numpy \
#            pandas \
#            Pillow \
#            scipy \
#            sklearn
#    
#python3 -m ipykernel.kernelspec
#    
# Install TensorFlow GPU version
#pip3 uninstall tensorflow-gpu || true
#pip3 install --upgrade tensorflow-gpu==1.12
#    
# keras
#pip3 install --upgrade keras




# build info
echo "Timestamp:" `date --utc` | tee /image-build-info.txt