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naked-singularity.sh
naked-singularity.sh 14.00 KiB
# ======================================================================
#
# NAME
#
# naked-singularity.sh
#
# DESCRIPTION
#
# A bash script to help users create Singularity containers from the
# definition (or recipe) files available in the naked-singularity
# repository.
#
# USAGE
#
# 1. Install Singularity on your local desktop, laptop, or virtual
# machine.
#
# ./naked-singularity.sh install
#
# 2. Build a simple Ubuntu Singularity container for Comet at SDSC.
#
# ./naked-singularity.sh build -s comet -a ubuntu -d ubuntu.def
#
# 3. Uninstall Singularity from your local desktop, laptop, or
# virtual machine.
#
# ./naked-singularity.sh uninstall
#
# LAST UPDATED
#
# Tuesday, November 6th, 2018
#
# ----------------------------------------------------------------------
naked_out() {
echo "naked-singularity: ${@}" >&1
}
naked_err() {
echo "naked-singularity: ERROR :: ${@}" >&2
}
naked_warn() {
echo "naked-singularity: WARNING :: ${@}" >&2
}
naked_build() {
local path_to_definition_file="${naked_dir}/definition-files"
local path_to_image="${naked_dir}/images"
local system=''
local application=''
local definition_file=''
local image=''
local -i image_size='-1'
local writable='false'
local force_overwrite='false'
naked_out "Read in all command-line options for 'build' command ..."
while (( "${#}" > 0 )); do
naked_out "Read in command-line option '${1}' with input value '${2}' ... "
case "${1}" in
-s | --system )
system="${2}"
shift 2
;;
-a | --application )
application="${2}"
shift 2
;;
-d | --definition-file )
definition_file="${2}"
shift 2
;;
-i | --image )
image="${2}"
shift 2
;;
-z | --image-size )
image_size="${2}"
shift 2
;;
-w | --writable )
writable='true'
shift 1
;;
-f | --force-overwrite )
force_overwrite='true'
shift 1
;;
*)
naked_err "Command-line option ${1} not recognized or not supported."
return 1
esac
done
naked_out "All command-line options for 'build' command have been read ... "
naked_out 'Check if DEFINITION FILE is exists ...'
if [[ -z "${system}" ]]; then
naked_err 'No SYSTEM name was provided.'
naked_err 'Use the -s (or --system) command-line option to specify the name of the target SYSTEM.'
naked_err 'Listing all SYSTEMs to choose from ...'
echo "ls ${path_to_definition_file}"
echo "$(ls "${path_to_definition_file}")"
return 1
fi
path_to_definition_file+="/${system}"
if [[ ! -d "${path_to_definition_file}" ]]; then
naked_err "${path_to_definition_file} does not exist."
naked_err 'Use the -s (or --system) command-line option to specify the name of the target SYSTEM.'
naked_err 'Listing all SYSTEMs to choose from ...'
echo "ls ${path_to_definition_file%/${system}}"
echo "$(ls "${path_to_definition_file%/${system}}")"
return 1
fi
if [[ -z "${application}" ]]; then
naked_err 'No APPLICATION name was provided.'
naked_err 'Use the -a (or --application) command-line option to specify the name of the APPLICATION to be run on the target SYSTEM.'
naked_err 'Listing all APPLICATIONs to choose from ...'
echo "ls ${path_to_definition_file}"
echo "$(ls "${path_to_definition_file}")"
return 1
fi
path_to_definition_file+="/${application}"
if [[ ! -d "${path_to_definition_file}" ]]; then
naked_err "${path_to_definition_file} does not exist."
naked_err 'Use the -a (or --application) command-line option to specify the name of the APPLICATION to be run on the target SYSTEM.'
naked_err 'Listing all APPLICATIONs to choose from ...'
echo "ls ${path_to_definition_file%/${application}}"
echo "$(ls "${path_to_definition_file%/${application}}")"
return 1
fi
if [[ -z "${definition_file}" ]]; then
naked_err 'No DEFINITION FILE was provided.'
naked_err 'Use the -d (or --definition-file) command-line option to specify the name of the DEFINITION FILE.'
naked_err 'Listing all DEFINITION FILEs to choose from ...'
echo "ls ${path_to_definition_file}"
echo "$(ls "${path_to_definition_file}")"
return 1
fi
path_to_definition_file+="/${definition_file}"
if [[ ! -f "${path_to_definition_file}" ]]; then
naked_err "${path_to_definition_file} does not exist."
naked_err 'Use the -d (or --definition-file) command-line option to specify the name of the DEFINITION FILE.'
naked_err 'Listing all DEFINITION FILEs to choose from ...'
echo "ls ${path_to_definition_file%/${definition_file}}"
echo "$(ls "${path_to_definition_file%/${definition_file}}")"
return 1
fi
naked_out "DEFINITION FILE exists ... ${path_to_definition_file}"
naked_out 'Check if IMAGE exists ...'
if [[ -z "${image}" ]]; then
naked_warn 'WARNING :: No IMAGE name was provided.'
naked_warn 'Use the -i (or --image) command-line option to specify the name of the IMAGE.'
image="$(echo "${definition_file}" | sed 's/.def//')"
if [[ "${writable}" = 'true' ]]; then
image+='.img'
else
image+='.simg'
fi
naked_out "Setting IMAGE name ... ${image}"
fi
path_to_image+="/${system}"
path_to_image+="/${application}"
path_to_image+="/${image}"
if [[ ! -f "${path_to_image}" ]]; then
naked_out "${path_to_image} does not exist yet ..."
naked_out "Prepare to build a new Singularity IMAGE from ${path_to_definition_file} ..."
naked_out 'Make parent directories to accomodate new IMAGE if they do not exist already ...'
echo "mkdir -p $(dirname ${path_to_image})"
mkdir -p "$(dirname "${path_to_image}")"
if [[ "${writable}" = 'true' ]]; then
naked_out "Build new $(basename "${path_to_image}") as a writable ext3 Singularity IMAGE ..."
if (( "${image_size}" <= 0 )); then
naked_warn 'WARNING :: IMAGE_SIZE is less than or equal to zero.'
naked_warn 'IMAGE_SIZE is the size of the IMAGE in integer-valued units of MiB.'
naked_warn 'Attempting to set IMAGE SIZE from DEFINITION FILE ...'
grep 'SINGULARITY_IMAGE_SIZE' "${path_to_definition_file}"
if [[ "${?}" -ne 0 ]]; then
naked_err 'SINGULARITY_IMAGE_SIZE not found in DEFINITION FILE ... '
return 1
else
naked_out 'Setting IMAGE_SIZE equal to SINGULARITY_IMAGE_SIZE ... '
image_size="$(grep 'SINGULARITY_IMAGE_SIZE' "${path_to_definition_file}" | \
sed s'/ SINGULARITY_IMAGE_SIZE //')"
fi
fi
naked_out 'Creating writable ext3 Singularity IMAGE now ...'
echo "singularity image.create --size ${image_size} ${path_to_image}"
singularity image.create --size "${image_size}" "${path_to_image}"
naked_out 'IMAGE created ...'
naked_out 'Starting build now ...'
echo "sudo singularity build --writable ${path_to_image} ${path_to_definition_file}"
sudo singularity build --writable "${path_to_image}" "${path_to_definition_file}"
else
naked_out "Build $(basename "${path_to_image}") as a read-only squashfs Singularity IMAGE ..."
naked_out 'Starting build now ...'
echo "sudo singularity build ${path_to_image} ${path_to_definition_file}"
sudo singularity build "${path_to_image}" "${path_to_definition_file}"
fi
else
naked_err "${path_to_image} already exists ..."
naked_err 'Cannot overwrite existing IMAGE ...'
return 1
fi
naked_out 'Build complete.'
return 0
}
naked_inspect() {
echo 'run singularity inspect command ... '
}
naked_install() {
local operating_system='ubuntu'
local prefix='/usr/local'
local version='2.6.1'
naked_out "Read in all command-line options of the 'install' command ..."
while (( "${#}" > 0 )); do
naked_out "Read in command-line option '${1}' with input value '${2}' ... "
case "${1}" in
-o | --os )
operating_system="${2,,}"
shift 2
;;
-p | --prefix )
prefix="${2}"
shift 2
;;
-v | --version )
version="${2}"
shift 2
;;
*)
naked_err "Command-line option ${1} not recognized or not supported."
return 1
esac
done
naked_out "All command-line options for 'install' command have been read ... "
naked_out 'Checking if Singularity is already installed on this system ...'
echo 'singularity --version'
singularity --version
if [[ "${?}" -eq 0 ]]; then
naked_err 'Singularity is already installed on this system!'
naked_err 'Please uninstall the existing version of Singularity prior to installing a new version.'
return 1
fi
naked_out 'Singularity is not yet installed on this system ...'
if [[ "${operating_system}" = 'centos' ]]; then
naked_out 'Running update ...'
echo 'sudo yum -y update'
sudo yum -y update
naked_out 'Installing Singularity dependencies ...'
echo "sudo yum groupinstall -y 'Development Tools'"
sudo yum groupinstall -y 'Development Tools'
echo 'sudo yum install -y libarchive-devel'
sudo yum install -y libarchive-devel
elif [[ "${operating_system}" = 'ubuntu' ]]; then
naked_out 'Running update ...'
echo 'sudo apt-get -y update'
sudo apt-get -y update
naked_out 'Installing Singularity dependencies ...'
echo 'sudo apt-get -y install python'
sudo apt-get -y install python
echo 'sudo apt-get -y install dh-autoreconf'
sudo apt-get -y install dh-autoreconf
echo 'sudo apt-get -y install build-essential'
sudo apt-get -y install build-essential
echo 'sudo apt-get -y install libarchive-dev'
sudo apt-get -y install libarchive-dev
echo 'sudo apt-get -y install debootstrap'
sudo apt-get -y install debootstrap
echo 'sudo apt-get -y install squashfs-tools'
sudo apt-get -y install squashfs-tools
else
naked_err 'Operating system not recognized or not supported.'
return 1
fi
naked_out 'Downloading Singularity source code...'
echo "wget https://github.com/singularityware/singularity/releases/download/${version}/singularity-${version}.tar.gz"
wget "https://github.com/singularityware/singularity/releases/download/${version}/singularity-${version}.tar.gz"
naked_out 'Extracting Singularity source code...'
echo "tar -xzvf singularity-${version}.tar.gz"
tar -xzvf singularity-${version}.tar.gz
naked_out 'Configuring Singularity ...'
echo "cd singularity-${version}"
cd "singularity-${version}"
echo "./configure --prefix=${prefix}"
./configure --prefix="${prefix}"
naked_out 'Compiling Singularity ...'
echo 'make'
make
naked_out 'Installing Singularity ...'
echo 'sudo make install'
sudo make install
naked_out 'Checking if Singularity was installed successully ...'
singularity --version
if [[ "${?}" -ne 0 ]]; then
naked_err 'Singularity was NOT installed successfully ...'
return 1
fi
naked_out 'Singularity was installed successfully!'
naked_out 'Cleaning up ...'
cd ../
rm -rf "singularity-${version}.tar.gz"
rm -rf "singularity-${version}"
return 0
}
naked_shell() {
echo 'run singularity shell command ... '
}
naked_uninstall() {
local prefix='/usr/local'
naked_out "Read in all command-line options of the 'uninstall' command ..."
while (( "${#}" > 0 )); do
naked_out "Read in command-line option '${1}' with input value '${2}' ... "
case "${1}" in
-p | --prefix )
prefix="${2}"
shift 2
;;
*)
naked_err "Command-line option ${1} not recognized or not supported."
return 1
esac
done
naked_out "All command-line options for 'uninstall' command have been read ... "
naked_out 'Checking if Singularity is installed ...'
echo 'singularity --version'
singularity --version
if [[ "${?}" -ne 0 ]]; then
naked_err 'Singularity is not installed on this system.'
return 1
fi
naked_out 'Uninstalling Singularity ...'
sudo rm -rf "${prefix}/libexec/singularity"
sudo rm -rf "${prefix}/etc/singularity"
sudo rm -rf "${prefix}/include/singularity"
sudo rm -rf "${prefix}/lib/singularity"
sudo rm -rf "${prefix}/var/lib/singularity"
sudo rm "${prefix}/bin/singularity"
sudo rm "${prefix}/bin/run-singularity"
sudo rm "${prefix}/etc/bash_completion.d/singularity"
sudo rm "${prefix}/man/man1/singularity.1"
naked_out 'Checking if Singularity was uninstalled successfully ...'
which singularity
if [[ "${?}" -eq 0 ]]; then
naked_err 'Singularity was NOT uninstalled!'
return 1
fi
naked_out 'Singularity was uninstalled successfully!'
return 0
}
naked_upload() {
echo 'Upload image to users HOME directory on target system ...'
}
naked_verify() {
echo 'Verify checksums of definition file and image match ... '
}
main() {
local naked_command=''
local naked_dir="${PWD}"
if (( "${#}" > 0 )); then # at least one command-line arguments was
# provided. The first argument is expected to be main command issued
# by the user. Read in that command and then determine if it is a
# valid command.
naked_command="${1}"
shift 1
if [[ "${naked_command}" = 'build' ]]; then
naked_build "${@}"
if [[ "${?}" -ne 0 ]]; then
exit 1
fi
elif [[ "${naked_command}" = 'install' ]]; then
naked_install "${@}"
if [[ "${?}" -ne 0 ]]; then
exit 1
fi
elif [[ "${naked_command}" = 'uninstall' ]]; then
naked_uninstall "${@}"
if [[ "${?}" -ne 0 ]]; then
exit 1
fi
elif [[ "${naked_command}" = 'help' || \
"${naked_command}" = '-h' || \
"${naked_command}" = '--help' ]]; then # return help.
echo "USAGE: naked-singularity.sh <command> [options] {values}"
echo ""
echo "Finish writing help later ... ."
else
naked_err 'Command not recognized or not supported.'
exit 1
fi
else
naked_err 'No command-line arguments were provided.'
exit 1
fi
exit 0
}
main "${@}"
# ======================================================================