From 199760b6cceaaf91b727f6f8985111649244a09f Mon Sep 17 00:00:00 2001
From: Marty Kandes <mkandes@sdsc.edu>
Date: Thu, 31 Dec 2020 16:10:23 -0800
Subject: [PATCH] Created new naked-singularity.sh helper script
Created the initial version of the new naked-singularity.sh helper
script. At present, the script only supports a first iteration of the
'install' command, which can be used to install Singularity from source
on a Linux system running either a CentOS or Ubuntu operating system.
---
README.md | 4 +-
log.sh | 55 ++++++++
naked-singularity.sh | 309 +++++++++++++++++++++++++++++++++++++++++++
3 files changed, 366 insertions(+), 2 deletions(-)
create mode 100644 log.sh
create mode 100755 naked-singularity.sh
diff --git a/README.md b/README.md
index 8539912..fe9fdc4 100644
--- a/README.md
+++ b/README.md
@@ -53,8 +53,8 @@ University of California, San Diego
## Version
-1.1.0
+1.2.3
## Last Updated
-Sunday, December 27th, 2020
+Thursday, December 31st, 2020
diff --git a/log.sh b/log.sh
new file mode 100644
index 0000000..24ac853
--- /dev/null
+++ b/log.sh
@@ -0,0 +1,55 @@
+#!/usr/bin/env bash
+# ======================================================================
+#
+# NAME
+#
+# log.sh
+#
+# DESCRIPTION
+#
+# A library of bash functions for writing formatted log messages to
+# standard output and standard error.
+#
+# USAGE
+#
+# If you would like to use this library in your bash script, then
+# source it at the beginning of your bash script.
+#
+# source log.sh
+#
+# Once the library has been sourced, you can call functions from the
+# library in your bash script.
+#
+# AUTHOR
+#
+# Marty Kandes, Ph.D.
+# Computational & Data Science Research Specialist
+# High-Performance Computing User Services Group
+# San Diego Supercomputer Center
+# University of California, San Diego
+#
+# LAST UPDATED
+#
+# Monday, December 28th, 2020
+#
+# ----------------------------------------------------------------------
+
+log::output() {
+
+ echo "${@}" >&1
+
+}
+
+log::error() {
+
+ echo "ERROR :: ${@}" >&2
+
+}
+
+log::warning() {
+
+ echo "WARNING :: ${@}" >&2
+
+}
+
+# ======================================================================
diff --git a/naked-singularity.sh b/naked-singularity.sh
new file mode 100755
index 0000000..2823202
--- /dev/null
+++ b/naked-singularity.sh
@@ -0,0 +1,309 @@
+#!/usr/bin/env bash
+# ======================================================================
+# NAME
+#
+# naked-singularity.sh
+#
+# DESCRIPTION
+#
+# A bash script to help users work with Singularity on their Linux
+# desktop, laptop, or virtual machine.
+#
+# USAGE
+#
+# Install Singularity from source.
+#
+# ./naked-singularity.sh install
+#
+# LAST UPDATED
+#
+# Thursday, December 31st, 2020
+#
+# ----------------------------------------------------------------------
+
+source log.sh
+
+# ----------------------------------------------------------------------
+# naked::install
+#
+# Install Singularity (from source).
+#
+# Globals:
+#
+# N/A
+#
+# Arguments:
+#
+# @
+#
+# Returns:
+#
+# True (0) if Singularity is installed sucessfully. False (1)
+# if the installation fails.
+#
+# ----------------------------------------------------------------------
+
+naked::install() {
+
+ local singularity_version='3.5.2'
+ local go_version='1.15.6'
+ local -i use_rpm=1
+
+ local os_release_id=''
+ local os_release_version_id=''
+
+ while (("${#}" > 0)); do
+ case "${1}" in
+ -g | --go )
+ go_version="${2}"
+ shift 2
+ ;;
+ -r | --rpm )
+ use_rpm=0
+ shift 1
+ ;;
+ -s | --singularity )
+ singularity_version="${2}"
+ shift 2
+ ;;
+ *)
+ log::error "Command-line option ${1} not recognized or not supported."
+ return 1
+ esac
+ done
+
+ log::output 'Checking if Singularity is already installed ...'
+ singularity --version > /dev/null 2>&1
+ if [[ "${?}" -eq 0 ]]; then
+ log:error "Singularity is installed: $(singularity --version)"
+ return 1
+ else
+ log::output 'Singularity is not installed.'
+ fi
+
+ log::output 'Parsing /etc/os-release to identify operating system ...'
+ if [[ -f '/etc/os-release' ]]; then
+
+ grep '^ID=' /etc/os-release > /dev/null 2>&1
+ if [[ "${?}" -eq 0 ]]; then
+ grep '^ID=' /etc/os-release | grep '"' > /dev/null 2>&1
+ if [[ "${?}" -eq 0 ]]; then
+ os_release_id="$(grep '^ID=' /etc/os-release | cut -d '"' -f 2)"
+ else
+ os_release_id="$(grep '^ID=' /etc/os-release | cut -d '=' -f 2)"
+ fi
+ log::output "Operating system identified as ${os_release_id}."
+ else
+ log::error '/etc/os-release does not contain ID parameter.'
+ return 1
+ fi
+
+ grep '^VERSION_ID=' /etc/os-release > /dev/null 2>&1
+ if [[ "${?}" -eq 0 ]]; then
+ grep '^VERSION_ID=' /etc/os-release | grep '"' > /dev/null 2>&1
+ if [[ "${?}" -eq 0 ]]; then
+ os_release_version_id="$(grep '^VERSION_ID=' /etc/os-release | cut -d '"' -f 2)"
+ else
+ os_release_version_id="$(grep '^VERSION_ID=' /etc/os-release | cut -d '=' -f 2)"
+ fi
+ log::output "Operating system version identified as ${os_release_version_id}."
+ else
+ log::error '/etc/os-release does not contain VERSION_ID parameter.'
+ return 1
+ fi
+
+ else
+
+ log::error '/etc/os-release does not exist.'
+ return 1
+
+ fi
+
+ if [[ "${os_release_id}" = 'centos' ]]; then
+
+ log::output 'Running yum update ...'
+ sudo yum -y update
+
+ log::output 'Installing Singularity dependencies ...'
+ sudo yum -y groupinstall 'Development Tools'
+ sudo yum -y install epel-release
+ sudo yum -y install openssl-devel
+ sudo yum -y install libuuid-devel
+ sudo yum -y install libseccomp-devel
+ sudo yum -y install wget
+ sudo yum -y install squashfs-tools
+ sudo yum -y install cryptsetup
+
+ elif [[ "${os_release_id}" = 'ubuntu' ]]; then
+
+ log::output 'Running apt-get update ...'
+ sudo apt-get -y update
+
+ log::output 'Installing Singularity dependencies ...'
+ sudo apt-get -y install build-essential
+ sudo apt-get -y install libssl-dev
+ sudo apt-get -y install uuid-dev
+ sudo apt-get -y install libgpgme-dev
+ sudo apt-get -y install squashfs-tools
+ sudo apt-get -y install libseccomp-dev
+ sudo apt-get -y install wget
+ sudo apt-get -y install pkg-config
+ sudo apt-get -y install git
+ sudo apt-get -y install cryptsetup-bin
+
+ else
+
+ log::error 'Operating system not recognized or not supported.'
+ return 1
+
+ fi
+
+ mkdir -p /tmp/go
+ cd /tmp/go
+
+ log::output 'Installing Go ...'
+ export CGO_ENABLED=0
+ wget https://dl.google.com/go/go1.4-bootstrap-20171003.tar.gz
+ tar -xf go1.4-bootstrap-20171003.tar.gz
+ mv go 1.4
+ cd 1.4/src
+ ./make.bash
+
+ export GOROOT_BOOTSTRAP='/tmp/go/1.4'
+
+ cd /tmp/go
+
+ export CGO_ENABLED=1
+ git clone https://go.googlesource.com/go "${go_version}"
+ cd "${go_version}"
+ git checkout "go${go_version}"
+ cd src
+ ./all.bash
+
+ export GOROOT="/tmp/go/${go_version}"
+ export PATH="${GOROOT}/bin:${PATH}"
+
+ cd /tmp
+
+ log::output 'Installing Singularity ...'
+ wget "https://github.com/hpcng/singularity/releases/download/v${singularity_version}/singularity-${singularity_version}.tar.gz"
+ tar -xf "singularity-${singularity_version}.tar.gz"
+ cd singularity
+ ./mconfig #--prefix=/opt/singularity
+ make -C ./builddir
+ sudo make -C ./builddir install
+
+ log::output 'Checking if Singularity was installed successully ...'
+ singularity --version
+ if [[ "${?}" -ne 0 ]]; then
+ log::error 'Singularity installation failed!'
+ return 1
+ fi
+
+ log::output 'Singularity was installed successfully!'
+
+ return 0
+
+}
+
+# ----------------------------------------------------------------------
+# naked::help
+#
+# Prints information on how to use this script to standard output.
+#
+# Globals:
+#
+# N/A
+#
+# Arguments:
+#
+# N/A
+#
+# Returns:
+#
+# True (0) always.
+#
+# ----------------------------------------------------------------------
+
+naked::help() {
+
+ log::output 'USAGE: naked-singularity.sh <command> [options] {value}'
+ log::output ''
+
+ return 0
+
+}
+
+# ----------------------------------------------------------------------
+# naked::main
+#
+# Controls the execution of the script.
+#
+# Globals:
+#
+# @
+#
+# Arguments:
+#
+# @
+#
+# Returns:
+#
+# True (0) if the script executes without issue. False (1) if the
+# script fails to executre properly.
+#
+# ----------------------------------------------------------------------
+
+naked::main() {
+
+ local naked_command=''
+
+ # If at least one command-line argument was provided by the user,
+ # then start parsing the command-line arguments. Otherwise, throw
+ # an error.
+ if (( "${#}" > 0 )); then
+
+ naked_command="${1}"
+ shift 1
+
+ if [[ "${naked_command}" = 'install' ]]; then
+
+ naked::install "${@}"
+ if [[ "${?}" -ne 0 ]]; then
+ log::error 'Failed to run install command.'
+ exit 1
+ fi
+
+ elif [[ "${naked_command}" = 'help' || \
+ "${naked_command}" = '-h' || \
+ "${naked_command}" = '--help' ]]; then
+
+ naked::help
+ if [[ "${?}" -ne 0 ]]; then
+ log::error 'Failed to run help command.'
+ exit 1
+ fi
+
+ else
+
+ log::error 'Command not recognized or not supported.'
+ exit 1
+
+ fi
+
+ else
+
+ log::error 'No command-line arguments were provided.'
+ exit 1
+
+ fi
+
+ exit 0
+
+}
+
+# ----------------------------------------------------------------------
+
+naked::main "${@}"
+
+# ======================================================================
--
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