diff options
Diffstat (limited to 'project')
| -rwxr-xr-x | project | 291 |
1 files changed, 291 insertions, 0 deletions
@@ -0,0 +1,291 @@ +#!/bin/bash +# +# High-level script to manage the project. +# Run `./project --help' for a description of how to use it. +# +# Copyright (C) 2019 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# +# This script is free software: you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the +# Free Software Foundation, either version 3 of the License, or (at your +# option) any later version. +# +# This script is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +# Public License for more details. See <http://www.gnu.org/licenses/>. + + +# Basic settings +# -------------- +# Stop the script if there are any errors. +set -e + +# Default option values +jobs=0 # 0 is for the default for the `configure.sh' script. +group= +debug= +host_cc=0 +operation= +build_dir= +input_dir= +make_targets= +software_dir= +existing_conf=0 +scriptname="./project" +minmapsize=10000000000 + + + + + +# Parse the options +# ----------------- +# +# Separate command-line arguments from options. Then put the option value +# into the respective variable. +# +# Each option has two lines because we want to process both these formats: +# `--name=value' and `--name value'. The former (with `=') is a single +# command-line argument, so we just need to shift the counter by one. The +# latter (without `=') is two arguments, so we'll need two shifts. +# +# Note on the case strings: for every option, we need three lines: one when +# the option name and value are separate. Another when there is an equal +# between them, and finally one where the value is immediately after the +# short-format. This exact order is important. Otherwise, there will be a +# conflict between them. + +print_help() { + # Print the output. + cat <<EOF +Usage: $scriptname configure [OPTIONS] + $scriptname make [OPTIONS] + +Top-level script to manage the reproducible project. The high-level +operation is defined by the (mandatory) second argument: + + configure - Configure project for this machine (e.g., build software). + make - Run the project (do analysis and build outputs). + +RECOMMENDATION: If this is the first time you are configuring this +template, please don't use the options and let the script explain each +parameter in full detail by simply running './project configure'. + +With the options below you can modify the default behavior. + +Configure options: + -b, --build-dir=STR Top directory to build the project in. + -e, --existing-conf Use (possibly existing) local configuration. + --host-cc Use host system's C compiler, don't build GCC. + -i, --input-dir=STR Directory containing input datasets (optional). + -m, --minmapsize=INT [Gnuastro] Minimum number of bytes to use RAM. + -s, --software-dir=STR Directory containing necessary software tarballs. + +Configure and Make options: + -g, --group=STR Build and run with write permissions for a group. + -j, --jobs=INT Number of threads to build/run the software. + -?, --help Print this help list. + +Make options: + -d, --debug=FLAGS Print various types of debugging information. + +Mandatory or optional arguments to long options are also mandatory or optional +for any corresponding short options. + +Reproducible paper template: https://gitlab.com/makhlaghi/reproducible-paper + +Report bugs to mohammad@akhlaghi.org +EOF +} + +on_off_option_error() { + if [ "x$2" = x ]; then + echo "$scriptname: '$1' doesn't take any values." + else + echo "$scriptname: '$1' (or '$2') doesn't take any values." + fi + exit 1 +} + +check_v() { + if [ x"$2" = x ]; then + echo "$scriptname: option '$1' requires an argument." + echo "Try '$scriptname --help' for more information." + exit 1; + fi +} + +func_operation_set() { + if [ x$operation = x ]; then + operation=$1 + else + echo "Only one operation ('configure' or 'make') may be given." + exit 1 + fi +} + +while [[ $# -gt 0 ]] +do + case $1 in + # Main operation. + configure) func_operation_set $1; shift;; + make) func_operation_set $1; shift;; + + + # Configure options: + -b|--builddir) build_dir="$2"; check_v "$1" "$build_dir"; shift;shift;; + -b=*|--build-dir=*) build_dir="${1#*=}"; check_v "$1" "$build_dir"; shift;; + -b*) build_dir=$(echo "$1" | sed -e's/-b//'); check_v "$1" "$build_dir"; shift;; + -e|--existing-conf) existing_conf=1; shift;; + -e*|--existing-conf=*) on_off_option_error --existing-conf -e;; + --host-cc) host_cc=1; shift;; + --host-cc=*) on_off_option_error --host-cc;; + -i|--inputdir) input_dir="$2"; check_v "$1" "$input_dir"; shift;shift;; + -i=*|--inputdir=*) input_dir="${1#*=}"; check_v "$1" "$input_dir"; shift;; + -i*) input_dir=$(echo "$1" | sed -e's/-i//'); check_v "$1" "$input_dir"; shift;; + -m|--minmapsize) minmapsize="$2"; check_v "$1" "$minmapsize"; shift;shift;; + -m=*|--minmapsize=*) minmapsize="${1#*=}"; check_v "$1" "$minmapsize"; shift;; + -m*) minmapsize=$(echo "$1" | sed -e's/-m//'); check_v "$1" "$minmapsize"; shift;; + -s|--software-dir) software_dir="$2"; check_v "$1" "$software_dir"; shift;shift;; + -s=*|--software-dir=*) software_dir="${1#*=}"; check_v "$1" "$software_dir"; shift;; + -s*) software_dir=$(echo "$1" | sed -e's/-s//'); check_v "$1" "$software_dir"; shift;; + + # Configure and Make options: + -g|--group) group="$2"; check_v group "$group"; shift;shift;; + -g=*|--group=*) group="${1#*=}"; check_v group "$group"; shift;; + -g*) group=$(echo "$1" | sed -e's/-g//'); check_v group "$group"; shift;; + -j|--jobs) jobs="$2"; check_v jobs "$jobs"; shift;shift;; + -j=*|--jobs=*) jobs="${1#*=}"; check_v jobs "$jobs"; shift;; + -j*) jobs=$(echo "$1" | sed -e's/-j//'); check_v jobs "$jobs"; shift;; + -'?'|--help) print_help; exit 0;; + -'?'*|--help=*) on_off_option_error --help -?;; + + # Make options (note that Make's `debug' can take values, but when called + # without any value, it is like giving it a value of `a'): + -d|--debug) if [ x"$2" = x ]; then debug=a; shift; + else debug="$2"; check_v debug "$debug"; shift;shift; fi;; + -d=*|--debug=*) debug="${1#*=}"; check_v debug "$debug"; shift;; + -d*) debug=$(echo "$1" | sed -e's/-d//'); check_v debug "$debug"; shift;; + + # Unrecognized option: + -*) echo "$scriptname: unknown option '$1'"; exit 1;; + + # Not an option, an argument (so its a Make target). + *) make_targets="$make_targets $1"; shift;; + esac +done + + + + + +# Basic group settings +# -------------------- +if ! [ x$group = x ]; then + + # Check if group is usable. + if ! sg "$group" "echo test &> /dev/null" &> /dev/null; then + echo "$scriptname: '$group' is not a usable group name on this system."; + echo "(TIP: you can use the 'groups' command to see your groups)" + exit 1 + fi + + # Set the group option for running Make. + gopt="reproducible_paper_group_name=$group" +fi + + + + + +# Do requested operation +# ---------------------- +perms="u+r,u+w,g+r,g+w,o-r,o-w,o-x" +configscript=./reproduce/software/bash/configure.sh +case $operation in + + # Build the project's software. + configure) + + # Variables to pass to the configuration script. + export jobs=$jobs + export host_cc=$host_cc + export build_dir=$build_dir + export input_dir=$input_dir + export scriptname=$scriptname + export minmapsize=$minmapsize + export software_dir=$software_dir + export existing_conf=$existing_conf + export reproducible_paper_group_name=$group + + # Run the configuration script + if [ x"$group" = x ]; then + $configscript + else + # Set the group and permission flags. + sg "$group" "umask $perms && $configscript" + + # Set the group writing permission for everything in the + # installed software directory. The common build process sets + # the writing permissions of the installed programs/libraries + # to `755'. So group members can't write over a file. This + # creates problems when another group member wants to update + # the software for example. We thus need to manually add the + # group writing flag to all installed software files. + echo "Enabling group writing permission on all installed software..." + .local/bin/chmod -R g+w .local/; + fi + ;; + + # Run the project + make) + + # Make sure the configure script has been completed properly + # (`configuration-done.txt' exists). + if ! [ -f .build/software/configuration-done.txt ]; then + cat <<EOF + +The project isn't configured for this system, or the configuration wasn't +successful. To configure the project, please use this command: + + '$ ./project configure' + +(TIP: if you have already ran this command once, run it with '-e' to use +the previous configuration, run with '--help' for more info) + +EOF + exit 1 + fi + + # Get the full address of the build directory: + bdir=`.local/bin/realpath .build` + + + # Remove all existing environment variables (with `env -i') and + # only use some pre-defined environment variables, then build the + # project. + envmake=".local/bin/env -i HOME= sys-rm=$(which rm) $gopt" + envmake="$envmake .local/bin/make -f reproduce/analysis/make/top.mk" + if ! [ x"$debug" = x ]; then envmake="$envmake --debug=$debug"; fi + + # Set the number of jobs. Note that for the `configure.sh' script + # the default value has to be 0, so the default is the maximum + # number of threads. But here, the default value is 1. + if ! [ x"$jobs" = x0 ]; then envmake="$envmake -j$jobs"; fi + + # Run the project + if [ x"$group" = x ]; then + $envmake $make_targets + else + # Set the group and permission flags. + sg "$group" "umask $perms && $envmake $make_targets" + fi + ;; + + # Operation not specified. + *) + echo "No operation defined (you can give 'configure' or 'make')." + exit 1 + ;; +esac |