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Commit 6872f3d0 authored by Michael Blaschek's avatar Michael Blaschek :bicyclist:
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restructured repo, gitlab ci

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definition-files/MPI/Singularity.ubuntu-18.04-OMPI-gcc → definition-files/Singularity.ubuntu.18.04.ompi.gcc
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......@@ -2,7 +2,7 @@ Bootstrap: library
From: mblaschek/imgw/ubuntu:18.04
%files
definition-files/MPI/mpitest.c /opt
./src/mpitest.c /opt
%environment
export OMPI_DIR=/opt/ompi
......
.gitlabci/build.sh → definition-files/build.sh 100644 → 100755
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definition-files/imgw 0 → 100644
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#!/bin/bash
# By MB
# IMGW introduction on the container environment
cat <<EOF
IMGW - Institut für Meteorologie und Geophysik
Universität Wien
Österreich
Department of Meteorology and Geophysics
Welcome inside a IMGW container!
Please try the following
EOF
\ No newline at end of file
definition-files/runscript 100644 → 100755
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File mode changed from 100644 to 100755
definition-files/MPI/mpitest.c → definition-files/src/mpitest.c
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install-singularity.sh deleted 100755 → 0
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#!/usr/bin/env bash
# ======================================================================
# NAME
#
# install-singularity.sh
#
# DESCRIPTION
#
# A bash shell utility to help you work with Singularity (and the
# definition files within the monkey-singularity repository) on your
# Linux desktop, laptop, or virtual machine.
#
# USAGE
#
# Install Singularity from source.
#
# ./install-singularity.sh install
#
# LAST UPDATED
#
# Thursday, Nov 18th, 2021
# Based on MKandas naked-singularity
#
# ----------------------------------------------------------------------
source log.sh
# ----------------------------------------------------------------------
# monkey::install
#
# Installs Singularity from source [or via rpm].
#
# Globals:
#
# N/A
#
# Arguments:
#
# @
#
# Returns:
#
# True (0) if Singularity is installed sucessfully.
# False (1) if the installation of Singularity fails.
#
# ----------------------------------------------------------------------
monkey::install() {
local singularity_version='3.5.3'
local go_version='1.15.6'
local use_rpm='false'
local rpm_repo='epel'
local os_release_id=''
local os_release_version_id=''
while (("${#}" > 0)); do
case "${1}" in
-s | --singularity )
singularity_version="${2}"
shift 2
;;
-g | --go )
go_version="${2}"
shift 2
;;
-r | --rpm )
use_rpm='true'
shift 1
;;
-e | --enable-repo )
rpm_repo="${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 ...'
yum -y update
log::output 'Installing Singularity dependencies ...'
yum -y groupinstall 'Development Tools'
yum -y install epel-release
yum -y install openssl-devel
yum -y install libuuid-devel
yum -y install libseccomp-devel
yum -y install wget
yum -y install squashfs-tools
yum -y install cryptsetup
yum -y install debootstrap
elif [[ "${os_release_id}" = 'ubuntu' ]]; then
log::output 'Running apt-get update ...'
apt-get -y update
log::output 'Installing Singularity dependencies ...'
apt-get -y install build-essential
apt-get -y install libssl-dev
apt-get -y install uuid-dev
apt-get -y install libgpgme-dev
apt-get -y install squashfs-tools
apt-get -y install libseccomp-dev
apt-get -y install wget
apt-get -y install pkg-config
apt-get -y install git
apt-get -y install cryptsetup-bin
apt-get -y install debootstrap
apt-get -y install yum-utils
# https://github.com/hpcng/singularity/issues/241
echo '%_var /var' > ~/.rpmmacros
echo '%_dbpath %{_var}/lib/rpm' >> ~/.rpmmacros
else
log::error 'Operating system not recognized or not supported.'
return 1
fi
if [[ "${os_release_id}" = 'centos' && "${use_rpm}" = 'true' ]]; then
log::output 'Installing Singularity ...'
yum -y install --enablerepo="${rpm_repo}" singularity-"${singularity_version}"
else # build and install singularity from source
mkdir -p /tmp/go
cd /tmp/go
log::output 'Installing Go ...'
export CGO_ENABLED=0
wget https://dl.google.com/go/go1.4-bootstrap-20171003.tar.gz
tar -xf go1.4-bootstrap-20171003.tar.gz
mv go 1.4
cd 1.4/src
./make.bash
export GOROOT_BOOTSTRAP='/tmp/go/1.4'
cd /tmp/go
export CGO_ENABLED=1
git clone https://go.googlesource.com/go "${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 <- include prefix as used-defined option?
make -C ./builddir
make -C ./builddir install
fi
# Prepend the path of the install directory of Singularity to PATH
# because not all secure_paths in /etc/sudoers may include it. If it
# is not included as one of the secure_paths by default, then the
# final install test below will fail erroneously, even when
# Singularity has been installed successfully.
#
# https://unix.stackexchange.com/questions/8646/why-are-path-variables-different-when-running-via-sudo-and-su
export PATH="/usr/local/bin:${PATH}"
log::output 'Checking if Singularity was installed successully ...'
singularity --version
if [[ "${?}" -ne 0 ]]; then
log::error 'Singularity installation failed!'
return 1
fi
log::output 'Singularity was installed successfully!'
return 0
}
# ----------------------------------------------------------------------
# monkey::uninstall
#
# Removes an existing source [or rpm-based] installation of Singularity.
#
# Globals:
#
# N/A
#
# Arguments:
#
# @
#
# Returns:
#
# True (0) if Singularity is uninstalled and removed sucessfully.
# False (1) if the removal of Singularity fails.
#
# ----------------------------------------------------------------------
monkey::uninstall() {
local singularity_prefix='/usr/local'
local use_rpm='false'
local os_release_id=''
local os_release_version_id=''
while (("${#}" > 0)); do
case "${1}" in
-p | --prefix )
singularity_prefix="${2}"
shift 2
;;
-r | --rpm )
use_rpm='true'
shift 1
;;
*)
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::output "Singularity is installed: $(singularity --version)"
else
log::error 'Singularity is not installed.'
return 1
fi
log::output 'Parsing /etc/os-release to identify operating system ...'
if [[ -f '/etc/os-release' ]]; then
grep '^ID=' /etc/os-release > /dev/null 2>&1
if [[ "${?}" -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 ${os_release_version_id}."
else
log::error '/etc/os-release does not contain VERSION_ID parameter.'
return 1
fi
else
log::error '/etc/os-release does not exist.'
return 1
fi
log::output 'Uninstalling Singularity ...'
if [[ "${os_release_id}" = 'centos' && "${use_rpm}" = 'true' ]]; then
yum -y remove singularity
else # remove source-based install
rm -rf "${singularity_prefix}/libexec/singularity"
rm -rf "${singularity_prefix}/var/singularity"
rm -rf "${singularity_prefix}/etc/singularity"
rm -rf "${singularity_prefix}/bin/singularity"
rm -rf "${singularity_prefix}/bin/run-singularity"
rm -rf "${singularity_prefix}/etc/bash_completion.d/singularity"
fi
log::output 'Checking if Singularity was uninstalled successfully ...'
which singularity
if [[ "${?}" -eq 0 ]]; then
log::error 'Singularity was NOT uninstalled!'
return 1
fi
log::output 'Singularity was uninstalled successfully!'
return 0
}
# ----------------------------------------------------------------------
# monkey::help
#
# Prints information on how to use this script to standard output.
#
# Globals:
#
# N/A
#
# Arguments:
#
# N/A
#
# Returns:
#
# True (0) always.
#
# ----------------------------------------------------------------------
monkey::help() {
log::output 'USAGE: install-singularity.sh <command> [options] {value}'
log::output ''
return 0
}
# ----------------------------------------------------------------------
# monkey::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.
#
# ----------------------------------------------------------------------
monkey::main() {
local monkey_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 (( "${#}" > 0 )); then
monkey_command="${1}"
shift 1
if [[ "${monkey_command}" = 'install' ]]; then
monkey::install "${@}"
if [[ "${?}" -ne 0 ]]; then
log::error 'Failed to run install command.'
exit 1
fi
elif [[ "${monkey_command}" = 'uninstall' ]]; then
monkey::uninstall "${@}"
if [[ "${?}" -ne 0 ]]; then
log::error 'Failed to run uninstall command.'
exit 1
fi
elif [[ "${monkey_command}" = 'help' || \
"${monkey_command}" = '-h' || \
"${monkey_command}" = '--help' ]]; then
monkey::help
if [[ "${?}" -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
}
# ----------------------------------------------------------------------
monkey::main "${@}"
# ======================================================================
log.sh deleted 100644 → 0
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#!/usr/bin/env bash
# ======================================================================
#
# NAME
#
# log.sh
#
# DESCRIPTION
#
# A library of bash functions for writing formatted log messages to
# standard output and standard error.
#
# USAGE
#
# If you would like to use this library in your bash script, then
# source it at the beginning of your bash script.
#
# source log.sh
#
# Once the library has been sourced, you can call functions from the
# library in your bash script.
#
# AUTHOR
#
# Marty Kandes, Ph.D.
# Computational & Data Science Research Specialist
# High-Performance Computing User Services Group
# San Diego Supercomputer Center
# University of California, San Diego
#
# LAST UPDATED
#
# Monday, December 28th, 2020
#
# ----------------------------------------------------------------------
log::output() {
echo "${@}" >&1
}
log::error() {
echo "ERROR :: ${@}" >&2
}
log::warning() {
echo "WARNING :: ${@}" >&2
}
# ======================================================================
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