Containers/tut.sf at master · timkphd/Containers · GitHub

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Bootstrap: docker
From: ubuntu:latest

%post
    apt-get -y update
    apt-get -y install wget
    apt-get -y install curl
    apt-get -y libcurl4-openssl-dev
    apt-get -y install gawk
    apt-get -y install git
    apt-get -y install apt-transport-https
# Next lines require to download Intel Python
    #wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
    #apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2019.PUB
    #wget https://apt.repos.intel.com/setup/intelproducts.list -O /etc/apt/sources.list.d/intelproducts.list
    apt-get -y update
# This prevents some questions being asked
    export DEBIAN_FRONTEND=noninteractive
    apt-get install dialog
date
# Intalling Fortran also gives us C.
    apt install -y gfortran
# Installing g++ make installing openmpi easier
    apt install -y g++
    apt install -y make
date

apt install -y python3
apt install -y pip

oldcd=`pwd`

mkdir -p /opt/install
cd /opt/install

wget https://bootstrap.pypa.io/get-pip.py
#python3 get-pip.py

cd $oldcd


# Build openmpi
# This will, at best be slow over network and most likely
# will only work for a single node.
# We need ssh for this to work.

apt install -y openssh-server
apt install -y openssh-client

apt install -y openmpi-bin

export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
export PATH=/usr/local/bin:$PATH

which mpicc


# Install editors
  apt install -y nano
  apt install -y vim

# lpr might be needed by enscript
  apt install -y lpr

# The next two lines install a perl module needed
# by the backup app installed below.
   apt install -y cpanminus
   cpan install Term::ANSIColor

# Install Rrrrrrrr
# 08/04/19
apt-get -y install software-properties-common
apt update
apt install -y r-base


# Install Rmpi
mkdir -p /opt/install/rlibs
cd /opt/install
wget https://cran.r-project.org/src/contrib/Rmpi_0.6-9.1.tar.gz
#R CMD INSTALL -l /opt/install/rlibs --configure-args=" \
#--with-Rmpi-include='/usr/local/include' \
#--with-Rmpi-libpath='/usr/local/lib' \
#--with-mpi='/usr/local' \
#--with-Rmpi-type='OPENMPI' " \

# Install rest of tutorial stuff
cd /opt/install
cat > bonk.R << EOF
install.packages("ggplot2", lib="/opt/install/rlibs", repos="http://cran.r-project.org")
install.packages("ggmap", lib="/opt/install/rlibs", repos="http://cran.r-project.org")
install.packages("maps", lib="/opt/install/rlibs", repos="http://cran.r-project.org")
install.packages("mapdata", lib="/opt/install/rlibs", repos="http://cran.r-project.org")
install.packages("dplyr", lib="/opt/install/rlibs", repos="http://cran.r-project.org")
install.packages("doParallel", lib="/opt/install/rlibs", repos="http://cran.r-project.org")
install.packages("gplots", lib="/opt/install/rlibs", repos="http://cran.r-project.org")
install.packages("foreach", lib="/opt/install/rlibs", repos="http://cran.r-project.org")
install.packages("tictoc", lib="/opt/install/rlibs", repos="http://cran.r-project.org")
install.packages("stringr", lib="/opt/install/rlibs", repos="http://cran.r-project.org")
EOF

Rscript bonk.R

export CFLAGS="-std=c99"
pip install mpi4py
unset CFLAGS


# Get the rest of Tim's examples:
    mkdir -p /opt/examples/tims
    cd /opt/examples/tims
    git clone https://github.com/timkphd/examples

date
%environment
    export LC_ALL=C
# Python order is important if you want both 3 and 2
# because there is "python" under intelpython3 that is
# actually python3
    export PATH=/opt/install:$PATH
    export PATH=/opt/examples:$PATH
    export PATH=/usr/local/bin:$PATH
    export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
    export export R_LIBS=/opt/install/rlibs/

%labels
    Author thkphd