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Diffstat (limited to 'reproduce/software/bash')
| -rwxr-xr-x | reproduce/software/bash/configure.sh | 1224 |
1 files changed, 1224 insertions, 0 deletions
diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh new file mode 100755 index 0000000..65b728e --- /dev/null +++ b/reproduce/software/bash/configure.sh @@ -0,0 +1,1224 @@ +#! /bin/bash +# +# Necessary preparations/configurations for the reproducible project. +# +# Copyright (C) 2018-2019 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. +# +# A copy of the GNU General Public License is available at +# <http://www.gnu.org/licenses/>. + + +# Script settings +# --------------- +# Stop the script if there are any errors. +set -e + + + + + +# Internal directories +# -------------------- +# +# These are defined to help make this script more readable. +topdir=$(pwd) +optionaldir="/optional/path" +adir=reproduce/analysis/config +cdir=reproduce/software/config + +sbdir=$cdir/installation + +pconf=$sbdir/LOCAL.mk +ptconf=$sbdir/LOCAL_tmp.mk +poconf=$sbdir/LOCAL_old.mk +depverfile=$cdir/installation/versions.mk +# --------- Delete for no Gnuastro --------- +glconf=$cdir/gnuastro/gnuastro-local.conf +# ------------------------------------------ + + + + + +# Notice for top of generated files +# --------------------------------- +# +# In case someone opens the files output from the configuration scripts in +# a text editor and wants to edit them, it is important to let them know +# that their changes are not going to be permenant. +function create_file_with_notice() { + if echo "# IMPORTANT: file can be RE-WRITTEN after './project configure'" > "$1" + then + echo "#" >> "$1" + echo "# This file was created during configuration" >> "$1" + echo "# ('./project configure'). Therefore, it is not under" >> "$1" + echo "# version control and any manual changes to it will be" >> "$1" + echo "# over-written if the project re-configured." >> "$1" + echo "#" >> "$1" + else + echo; echo "Can't write to $1"; echo; + exit 1 + fi +} + + + + + +# Get absolute address +# -------------------- +# +# Since the build directory will go into a symbolic link, we want it to be +# an absolute address. With this function we can make sure of that. +function absolute_dir() { + if stat "$1" 1> /dev/null; then + echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")" + else + exit 1; + fi +} + + + + + +# Inform the user +# --------------- +# +# Print some basic information so the user gets a feeling of what is going +# on and is prepared on what will happen next. +cat <<EOF + +----------------------------- +Project's local configuration +----------------------------- + +Local configuration includes things like top-level directories, or +processing steps. It is STRONGLY recommended to read the comments, and set +the best values for your system (where necessary). + +EOF + + + + + +# What to do with possibly existing configuration file +# ---------------------------------------------------- +# +# `LOCAL.mk' is the top-most local configuration for the project. If it +# already exists when this script is run, we'll make a copy of it as backup +# (for example the user might have ran `./project configure' by mistake). +printnotice=yes +rewritepconfig=yes +rewritegconfig=yes +if [ -f $pconf ] || [ -f $glconf ]; then + if [ $existing_conf = 1 ]; then + printnotice=no + if [ -f $pconf ]; then rewritepconfig=no; fi + if [ -f $glconf ]; then rewritegconfig=no; fi + fi +fi + + + + +# Make sure the group permissions satisfy the previous configuration (if it +# exists and we don't want to re-write it). +if [ $rewritepconfig = no ]; then + oldgroupname=$(awk '/GROUP-NAME/ {print $3; exit 0}' $pconf) + if [ "x$oldgroupname" = "x$reproducible_paper_group_name" ]; then + just_a_place_holder_to_avoid_not_equal_test=1; + else + echo "-----------------------------" + echo "!!!!!!!! ERROR !!!!!!!!" + echo "-----------------------------" + if [ "x$oldgroupname" = x ]; then + status="NOT configured for groups" + confcommand="./project configure" + else + status="configured for '$oldgroupname' group" + confcommand="./project configure --group=$oldgroupname" + fi + echo "Project was previously $status!" + echo "Either enable re-write of this configuration file," + echo "or re-run this configuration like this:" + echo + echo " $confcommand"; echo + exit 1 + fi +fi + + + + + +# Identify the downloader tool +# ---------------------------- +# +# After this script finishes, we will have both Wget and cURL for +# downloading any necessary dataset during the processing. However, to +# complete the configuration, we may also need to download the source code +# of some necessary software packages (including the downloaders). So we +# need to check the host's available tool for downloading at this step. +if [ $rewritepconfig = yes ]; then + if type wget > /dev/null 2>/dev/null; then + name=$(which wget) + + # By default Wget keeps the remote file's timestamp, so we'll have + # to disable it manually. + downloader="$name --no-use-server-timestamps -O"; + elif type curl > /dev/null 2>/dev/null; then + name=$(which curl) + + # - cURL doesn't keep the remote file's timestamp by default. + # - With the `-L' option, we tell cURL to follow redirects. + downloader="$name -L -o" + else + cat <<EOF + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +Couldn't find GNU Wget, or cURL on this system. These programs are used for +downloading necessary programs and data if they aren't already present (in +directories that you can specify with this configure script). Therefore if +the necessary files are not present, the project will crash. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + downloader="no-downloader-found" + fi; +fi + + + + + +# Build directory +# --------------- +if [ $rewritepconfig = yes ]; then + cat <<EOF + +=============== +Build directory +=============== + +The project's "source" (this directory) and "build" directories are treated +separately. This greatly helps in managing the many intermediate files that +are created during the build. The intermediate build files don't need to be +archived or backed up: you can always re-build them with the contents of +the source directory. The build directory also needs a relatively large +amount of free space (atleast serveral Giga-bytes), while the source +directory (all plain text) will usually be a mega-byte or less. + +'.build' (a symbolic link to the build directory) will also be created +during this configuration. It can help encourage you to set the actual +build directory in a very different address from this one (one that can be +deleted and has large volume), while having easy access to it from here. + +EOF + bdir= + junkname=pure-junk-974adfkj38 + while [ x$bdir == x ] + do + # Ask the user (if not already set on the command-line). + if [ x"$build_dir" = x ]; then + read -p"Please enter the top build directory: " build_dir + fi + + # If it exists, see if we can write in it. If not, try making it. + if [ -d $build_dir ]; then + if mkdir $build_dir/$junkname 2> /dev/null; then + bdir=$(absolute_dir $build_dir) + echo " -- Build directory: '$bdir'" + rm -rf $build_dir/$junkname + else + echo " -- Can't write in '$build_dir'" + fi + else + if mkdir $build_dir 2> /dev/null; then + bdir=$(absolute_dir $build_dir) + echo " -- Build directory set to (the newly created): '$bdir'" + else + echo " -- Can't create '$build_dir'" + fi + fi + + # Reset `build_dir' to blank, so it continues asking when the + # previous value wasn't usable. + build_dir= + done +fi + + + + + +# Input directory +# --------------- +if [ x"$input_dir" = x ]; then + indir=$optionaldir +else + indir=$input_dir +fi +wfpc2name=$(awk '!/^#/ && $1=="WFPC2IMAGE" {print $3}' $adir/INPUTS.mk) +wfpc2md5=$(awk '!/^#/ && $1=="WFPC2MD5" {print $3}' $adir/INPUTS.mk) +wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE" {print $3}' $adir/INPUTS.mk) +wfpc2url=$(awk '!/^#/ && $1=="WFPC2URL" {print $3}' $adir/INPUTS.mk) +if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then + cat <<EOF + +---------------------------------- +(OPTIONAL) Input dataset directory +---------------------------------- + +This project needs the dataset(s) listed below. If you already have them, +please specify the directory hosting them on this system. If you don't, +they will be downloaded automatically. Each file is shown with its total +volume and its 128-bit MD5 checksum in parenthesis. + + $wfpc2name ($wfpc2size, $wfpc2md5): + A 100x100 Hubble Space Telescope WFPC II image used in the FITS + standard webpage as a demonstration of this file format. + URL: $wfpc2url/$wfpc2name + +NOTE I: This directory, or the datasets above, are optional. If it doesn't +exist, the files will be downloaded in the build directory and used. + +NOTE II: This directory (if given) will only be read, nothing will be +written into it, so no writing permissions are necessary. + +TIP: If you have these files in multiple directories on your system and +don't want to download them or make duplicates, you can create symbolic +links to them and put those symbolic links in the given top-level +directory. + +EOF + read -p"(OPTIONAL) Input datasets directory ($indir): " inindir + if [ x$inindir != x ]; then + indir=$inindir + echo " -- Using '$indir'" + fi +fi + + + + + +# Dependency tarball directory +# ---------------------------- +if [ x"$software_dir" = x ]; then + ddir=$optionaldir +else + ddir=$software_dir +fi +if [ $rewritepconfig = yes ] && [ x"$software_dir" = x ]; then + cat <<EOF + +--------------------------------------- +(OPTIONAL) Software tarball directory +--------------------------------------- + +To ensure an identical build environment, the project will use its own +build of the programs it needs. Therefore the tarball of the relevant +programs are necessary. If a tarball isn't present in the specified +directory, *IT WILL BE DOWNLOADED* automatically. + +If you don't specify any directory here, or it doesn't contain the tarball +of a dependency, it is necessary to have an internet connection. The +project will download the tarballs it needs automatically. + +EOF + read -p"(OPTIONAL) Directory of dependency tarballs ($ddir): " tmpddir + if [ x"$tmpddir" != x ]; then + ddir=$tmpddir + echo " -- Using '$ddir'" + fi +fi + + + + + +# Write the parameters into the local configuration file. +if [ $rewritepconfig = yes ]; then + + # Add commented notice. + create_file_with_notice $pconf + + # Write the values. + sed -e's|@bdir[@]|'"$bdir"'|' \ + -e's|@indir[@]|'"$indir"'|' \ + -e's|@ddir[@]|'"$ddir"'|' \ + -e's|@downloader[@]|'"$downloader"'|' \ + -e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \ + $pconf.in >> $pconf +else + # Read the values from existing configuration file. + inbdir=$(awk '$1=="BDIR" {print $3}' $pconf) + + # Read the software directory. + ddir=$(awk '$1=="DEPENDENCIES-DIR" {print $3}' $pconf) + + # The downloader command may contain multiple elements, so we'll just + # change the (in memory) first and second tokens to empty space and + # write the full line (the original file is unchanged). + downloader=$(awk '$1=="DOWNLOADER" {$1=""; $2=""; print $0}' $pconf) + + # Make sure all necessary variables have a value + err=0 + verr=0 + novalue="" + if [ x"$inbdir" = x ]; then novalue="BDIR, "; fi + if [ x"$downloader" = x ]; then novalue="$novalue"DOWNLOADER; fi + if [ x"$novalue" != x ]; then verr=1; err=1; fi + + # Make sure `bdir' is an absolute path and it exists. + berr=0 + ierr=0 + bdir=$(absolute_dir $inbdir) + + if ! [ -d $bdir ]; then if ! mkdir $bdir; then berr=1; err=1; fi; fi + if [ $err = 1 ]; then + cat <<EOF + +################################################################# +######## ERORR reading existing configuration file ############ +################################################################# +EOF + if [ $verr = 1 ]; then + cat <<EOF + +These variables have no value: $novalue. +EOF + fi + if [ $berr = 1 ]; then + cat <<EOF + +Couldn't create the build directory '$bdir' (value to 'BDIR') in +'$pconf'. +EOF + fi + + cat <<EOF + +Please run the configure script again (accepting to re-write existing +configuration file) so all the values can be filled and checked. +################################################################# +EOF + fi +fi + + + + + +# --------- Delete for no Gnuastro --------- +# Get the version of Gnuastro that must be used. +gversion=$(awk '$1=="gnuastro-version" {print $NF}' $depverfile) + +# Gnuastro's local configuration settings +if [ $rewritegconfig = yes ]; then + create_file_with_notice $glconf + echo "# Minimum number of bytes to use HDD/SSD instead of RAM." >> $glconf + echo " minmapsize $minmapsize" >> $glconf + echo >> $glconf + echo "# Version of Gnuastro that must be used." >> $glconf + echo " onlyversion $gversion" >> $glconf +else + ingversion=$(awk '$1=="onlyversion" {print $NF}' $glconf) + if [ x$ingversion != x$gversion ]; then + cat <<EOF +______________________________________________________ +!!!!!!!!!!!!!!!!!!CONFIGURATION ERROR!!!!!!!!!!!!!!!!! + +Gnuastro's version in '$glconf' ($ingversion) doesn't match the tarball +version that this project was designed to use in '$depverfile' +($gversion). Please re-run after removing the former file: + + $ rm $glconf + $ ./project configure + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + exit 1 + fi +fi +# ------------------------------------------ + + + + + +# Delete final configuration target +# --------------------------------- +# +# We only want to start running the project later if this script has +# completed successfully. To make sure it hasn't crashed in the middle +# (without the user noticing), in the end of this script we make a file and +# we'll delete it here (at the start). Therefore if the script crashed in +# the middle that file won't exist. +sdir=$bdir/software +finaltarget=$sdir/configuration-done.txt +if ! [ -d $sdir ]; then mkdir $sdir; fi +rm -f $finaltarget + + + + + +# Project's top-level directories +# ------------------------------- +# +# These directories are possibly needed by many steps of process, so to +# avoid too many directory dependencies throughout the software and +# analysis Makefiles (thus making them hard to read), we are just building +# them here +# Software tarballs +tardir=$sdir/tarballs +if ! [ -d $tardir ]; then mkdir $tardir; fi + +# Installed software +instdir=$sdir/installed +if ! [ -d $instdir ]; then mkdir $instdir; fi + +# To record software versions and citation. +verdir=$instdir/version-info +if ! [ -d $verdir ]; then mkdir $verdir; fi + +# Program and library versions and citation. +ibidir=$verdir/proglib +if ! [ -d $ibidir ]; then mkdir $ibidir; fi + +# Python module versions and citation. +ipydir=$verdir/python +if ! [ -d $ipydir ]; then mkdir $ipydir; fi + +# Used software BibTeX entries. +ictdir=$verdir/cite +if ! [ -d $ictdir ]; then mkdir $ictdir; fi + +# TeXLive versions. +itidir=$verdir/tex +if ! [ -d $itidir ]; then mkdir $itidir; fi + +# Top-level LaTeX. +texdir=$bdir/tex +if ! [ -d $texdir ]; then mkdir $texdir; fi + +# LaTeX macros. +mtexdir=$texdir/macros +if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi + + +# TeX build directory. If built in a group scenario, the TeX build +# directory must be separate for each member (so they can work on their +# relevant parts of the paper without conflicting with each other). +if [ "x$reproducible_paper_group_name" = x ]; then + texbdir=$texdir/build +else + user=$(whoami) + texbdir=$texdir/build-$user +fi +if ! [ -d $texbdir ]; then mkdir $texbdir; fi + +# TiKZ (for building figures within LaTeX). +tikzdir=$texbdir/tikz +if ! [ -d $tikzdir ]; then mkdir $tikzdir; fi + + +# Set the symbolic links for easy access to the top project build +# directories. Note that these are put in each user's source/cloned +# directory, not in the build directory (which can be shared between many +# users and thus may already exist). +# +# Note: if we don't delete them first, it can happen that an extra link +# will be created in each directory that points to its parent. So to be +# safe, we are deleting all the links on each re-configure of the project. +rm -f .build .local tex/build tex/tikz .gnuastro +ln -s $bdir .build +ln -s $instdir .local +ln -s $texdir tex/build +ln -s $tikzdir tex/tikz +# --------- Delete for no Gnuastro --------- +ln -s $topdir/reproduce/software/config/gnuastro .gnuastro +# ------------------------------------------ + + +# Temporary software un-packing/build directory: if the host has the +# standard `/dev/shm' mounting-point, we'll do it in shared memory (on the +# RAM), to avoid harming/over-using the HDDs/SSDs. The RAM of most systems +# today (>8GB) is large enough for the parallel building of the software. +# +# For the name of the directory under `/dev/shm' (for this project), we'll +# use the names of the two parent directories to the current/running +# directory, separated by a `-' instead of `/'. We'll then appended that +# with the user's name (in case multiple users may be working on similar +# project names). Maybe later, we can use something like `mktemp' to add +# random characters to this name and make it unique to every run (even for +# a single user). +tmpblddir=$sdir/build-tmp +rm -rf $tmpblddir/* $tmpblddir # If its a link, we need to empty its + # contents first, then itself. + +# Set the top-level shared memory location. +if [ -d /dev/shm ]; then shmdir=/dev/shm +else shmdir="" +fi + +# If a shared memory mounted directory exists and there is enough space +# there (in RAM), build a temporary directory for this project. +needed_space=2000000 +if [ x"$shmdir" != x ]; then + available_space=$(df $shmdir | awk 'NR==2{print $4}') + if [ $available_space -gt $needed_space ]; then + dirname=$(pwd | sed -e's/\// /g' \ + | awk '{l=NF-1; printf("%s-%s",$l, $NF)}') + tbshmdir=$shmdir/"$dirname"-$(whoami) + if ! [ -d $tbshmdir ]; then mkdir $tbshmdir; fi + fi +else + tbshmdir="" +fi + +# If a shared memory directory was created set `build-tmp' to be a +# symbolic link to it. Otherwise, just build the temporary build +# directory under the project build directory. +if [ x$tbshmdir = x ]; then mkdir $tmpblddir; +else ln -s $tbshmdir $tmpblddir; +fi + + + + + +# Check for C/C++ compilers +# ------------------------- +# +# To build the software, we'll need some basic tools (the compilers in +# particular) to be present. +hascc=0; +if type cc > /dev/null 2>/dev/null; then + if type c++ > /dev/null 2>/dev/null; then hascc=1; fi +else + if type gcc > /dev/null 2>/dev/null; then + if type g++ > /dev/null 2>/dev/null; then hascc=1; fi + else + if type clang > /dev/null 2>/dev/null; then + if type clang++ > /dev/null 2>/dev/null; then hascc=1; fi + fi + fi +fi +if [ $hascc = 0 ]; then + cat <<EOF +______________________________________________________ +!!!!!!! C/C++ Compiler NOT FOUND !!!!!!! + +To build the project's software, the host system needs to have basic C and +C++ compilers. The executables that were checked are 'cc', 'gcc' and +'clang' for a C compiler, and 'c++', 'g++' and 'clang++' for a C++ +compiler. If you have a relevant compiler that is not checked, please get +in touch with us (with the form below) so we add it: + + https://savannah.nongnu.org/support/?func=additem&group=reproduce +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + exit 1 +fi + + + + + +# See if the C compiler can build static libraries +# ------------------------------------------------ + +# We are manually only working with shared libraries: because some +# high-level programs like Wget and cURL need dynamic linking and if we +# build the libraries statically, our own builds will be ignored and these +# programs will go and find their necessary libraries on the host system. +# +# Another good advantage of shared libraries is that we can actually use +# the shared library tool of the system (`ldd' with GNU C Library) and see +# exactly where each linked library comes from. But in static building, +# unless you follow the build closely, its not easy to see if the source of +# the library came from the system or our build. +static_build=no + +#oprog=$sdir/static-test +#cprog=$sdir/static-test.c +#echo "#include <stdio.h>" > $cprog +#echo "int main(void) {return 0;}" >> $cprog +#if [ x$CC = x ]; then CC=gcc; fi; +#if $CC $cprog -o$oprog -static &> /dev/null; then +# export static_build="yes" +#else +# export static_build="no" +#fi +#rm -f $oprog $cprog +#if [ $printnotice = yes ] && [ $static_build = "no" ]; then +# cat <<EOF +#_________________________________________________________________________ +#!!!!!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!! +# +#Your system's C compiler ('$CC') doesn't support building static +#libraries. Therefore the dependencies will be built dynamically. This means +#that they will depend more strongly on changes/updates in the host +#system. For high-level applications (like most research projects in natural +#sciences), this shouldn't be a significant problem. +# +#But generally, for reproducibility, its better to build static libraries +#and programs. For more on their difference (and generally an introduction +#on linking), please see the link below: +# +#https://www.gnu.org/software/gnuastro/manual/html_node/Linking.html +# +#If you have other compilers on your system, you can select a different +#compiler by setting the 'CC' environment variable before running +#'./project configure'. +# +#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +# +#EOF +# sleep 5 +#fi + + + + + +# See if the linker accepts -Wl,-rpath-link +# ----------------------------------------- +# +# `-rpath-link' is used to write the information of the linked shared +# library into the shared object (library or program). But some versions of +# LLVM's linker don't accept it an can cause problems. +oprog=$sdir/rpath-test +cprog=$sdir/rpath-test.c +echo "#include <stdio.h>" > $cprog +echo "int main(void) {return 0;}" >> $cprog +if [ x$CC = x ]; then CC=gcc; fi; +if $CC $cprog -o$oprog -Wl,-rpath-link &> /dev/null; then + export rpath_command="-Wl,-rpath-link=$instdir/lib" +else + export rpath_command="" +fi +rm -f $oprog $cprog + + + + + +# See if we need the dynamic-linker (-ldl) +# ---------------------------------------- +# +# Some programs (like Wget) need dynamic loading (using `libdl'). On +# GNU/Linux systems, we'll need the `-ldl' flag to link such programs. But +# Mac OS doesn't need any explicit linking. So we'll check here to see if +# it is present (thus necessary) or not. +oprog=$sdir/ldl-test +cprog=$sdir/ldl-test.c +cat > $cprog <<EOF +#include <stdio.h> +#include <dlfcn.h> +int +main(void) { + void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY); + return 0; +} +EOF +if gcc $cprog -o$oprog &> /dev/null; then needs_ldl=no; else needs_ldl=yes; fi +rm -f $oprog $cprog + + + + + +# inform the user that the build process is starting +# ------------------------------------------------- +if [ $printnotice = yes ]; then + tsec=10 + cat <<EOF + +------------------------- +Building dependencies ... +------------------------- + +Necessary dependency programs and libraries will be built in $tsec sec. + +NOTE: the built software will NOT BE INSTALLED on your system (no root +access is required). They are only for local usage by this project. They +will be installed in: + + $sdir/installed + +EOF + sleep $tsec +fi + + + + + +# If we are on a Mac OS system +# ---------------------------- +# +# For the time being, we'll use the existance of `otool' to see if we are +# on a Mac OS system or not. Some tools (for example OpenSSL) need to know +# this. +# +# On Mac OS, the building of GCC crashes sometimes while building libiberty +# with CLang's `g++'. Until we find a solution, we'll just use the host's C +# compiler. +if type otool > /dev/null 2>/dev/null; then + host_cc=1 + on_mac_os=yes +else + on_mac_os=no +fi + + + + + +# Build `flock' +# ------------- +# +# Flock (or file-lock) is a unique program that is necessary to serialize +# the (generally parallel) processing of make when necessary. GNU/Linux +# machines have it as part of their `util-linux' programs. But to be +# consistent in non-GNU/Linux systems, we will be using our own build. +# +# The reason that `flock' is sepecial is that we need it to serialize the +# download process of the software tarballs. +flockversion=$(awk '/flock-version/{print $3}' $depverfile) +flocktar=flock-$flockversion.tar.gz +flockurl=http://github.com/discoteq/flock/releases/download/v$flockversion/ + +# Prepare/download the tarball. +if ! [ -f $tardir/$flocktar ]; then + if [ -f $ddir/$flocktar ]; then + cp $ddir/$flocktar $tardir/$flocktar + else + if ! $downloader $tardir/$flocktar $flockurl/$flocktar; then + rm -f $tardir/$flocktar; + echo + echo "DOWNLOAD ERROR: Couldn't download the 'flock' tarball:" + echo " $flockurl" + echo + echo "You can manually place it in '$ddir' to avoid downloading." + exit 1 + fi + fi +fi + +# If the tarball is newer than the (possibly existing) program (the version +# has changed), then delete the program. +if [ -f .local/bin/flock ]; then + if [ $tardir/$flocktar -nt $ibidir/flock ]; then + rm $ibidir/flock + fi +fi + +# Build `flock' if necessary. +if ! [ -f $ibidir/flock ]; then + cd $tmpblddir + tar xf $tardir/$flocktar + cd flock-$flockversion + ./configure --prefix=$instdir + make + make install + cd $topdir + rm -rf $tmpblddir/flock-$flockversion + echo "Discoteq flock $flockversion" > $ibidir/flock +fi + + + + + +# See if GCC can be built +# ----------------------- +# +# On some GNU/Linux distros, the C compiler is broken into `multilib' (for +# 32-bit and 64-bit support, with their own headers). On these systems, +# `/usr/include/sys/cdefs.h' and `/usr/lib/libc.a' are not available by +# default. So GCC will crash with different ugly errors! The only solution +# is that user manually installs the `multilib' part as root, before +# running the configure script. +# +# Note that `sys/cdefs.h' may be available in other directories (for +# example `/usr/include/x86_64-linux-gnu/') that are automatically included +# in an installed GCC. HOWEVER during the build of GCC, all those other +# directories are ignored. So even if they exist, they are useless. +warningsleep=0 +if [ $host_cc = 0 ]; then + if ! [ -f /usr/include/sys/cdefs.h ]; then + host_cc=1 + warningsleep=1 + cat <<EOF + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +This system doesn't have '/usr/include/sys/cdefs.h'. Because of this, the +project can't build its custom GCC to ensure better reproducibility. We +strongly recommend installing the proper package (for your operating +system) that installs this necessary file. For example on some Debian-based +GNU/Linux distros, you need these two packages: 'gcc-multilib' and +'g++-multilib'. +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + fi + + if [ -f /usr/lib/libc.a ] || [ -f /usr/lib64/libc.a ]; then + # This is just a place holder + host_cc=$host_cc + else + host_cc=1 + warningsleep=1 + cat <<EOF + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +This system doesn't have '/usr/lib/libc.a' or '/usr/lib64/libc.a'. Because +of this, the project can't build its custom GCC to ensure better +reproducibility. We strongly recommend installing the proper package (for +your operating system) that installs this necessary file. + +Some possible solutions: + 1. On some Debian-based GNU/Linux distros, these two packages may fix the + problem: 'gcc-multilib' and 'g++-multilib'. + 2. (BE CAREFUL!) If you have '/usr/lib/x86_64-linux-gnu' but don't have + '/usr/lib64', then running the following command might fix this + particular problem by making a symbolic link. + $ sudo ln -s /usr/lib/x86_64-linux-gnu /usr/lib64 + After the configure script is finished, delete the link with 'rm + /usr/lib64' (you won't need it any more as far as this project is + concerned). +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + fi + + if [ $warningsleep = 1 ]; then + cat <<EOF + +PLEASE SEE THE WARNINGS ABOVE. + +Since GCC is pretty low-level, this configuration script will continue in 5 +seconds and use your system's C compiler (it won't build a custom GCC). But +please consider installing the necessary package(s) to complete your C +compiler, then re-run './project configure'. + +EOF + sleep 5 + fi +fi + + + + + +# Fortran compiler +# ---------------- +# +# If GCC is ultimately build within the project, the user won't need to +# have a fortran compiler, we'll build it internally for high-level +# programs. However, when the host C compiler is to be used, the user needs +# to have a Fortran compiler available. +if [ $host_cc = 1 ]; then + hasfc=0; + if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi + + if [ $hasfc = 0 ]; then + cat <<EOF +______________________________________________________ +!!!!!!! Fortran Compiler NOT FOUND !!!!!!! + +Because the project won't be building its own GCC (which includes a Fortran +compiler), you need to have a Fortran compiler available. Fortran is +commonly necessary for many lower-level scientific programs. Currently we +search for 'gfortran'. If you have a Fortran compiler that is not checked, +please get in touch with us (with the form below) so we add it: + + https://savannah.nongnu.org/support/?func=additem&group=reproduce + +Note: GCC will not be built because you are either using the '--host-cc' +option, or you are using an operating system that currently has bugs when +building GCC. +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + exit 1 + fi +fi + + + + + +# Number of threads for basic builds +# ---------------------------------- +# +# Since the system might not have GNU Make at this stage, and other Make +# implementations can't deal with parallel build properly, we'll just +# default to 1 thread. This is because some versions of Make complain about +# not having enough 'pipe' (memory) on some systems. After some searching, +# I found out its because of too many threads. GNU Make will be present on +# GNU systems (that have `nproc', part of GNU Coreutils). So to simplify +# the test for GNU Make, we'll just try running `nproc'. +if which nproc &> /dev/null; then + if [ $jobs = 0 ]; then + numthreads=$(nproc --all); + else + numthreads=$jobs + fi +else + numthreads=1; +fi + + + + + +# Build basic software +# -------------------- +# +# When building these software we don't have our own un-packing software, +# Bash, Make, or AWK. In this step, we'll install such low-level basic +# tools, but we have to be very portable (and use minimal features in all). +make -f reproduce/software/make/basic.mk \ + rpath_command=$rpath_command \ + static_build=$static_build \ + needs_ldl=$needs_ldl \ + on_mac_os=$on_mac_os \ + numthreads=$numthreads \ + host_cc=$host_cc \ + -j$numthreads + + + + + +# All other software +# ------------------ +# +# We will be making all the dependencies before running the top-level +# Makefile. To make the job easier, we'll do it in a Makefile, not a +# script. Bash and Make were the tools we need to run Makefiles, so we had +# to build them in this script. But after this, we can rely on Makefiles. +if [ $jobs = 0 ]; then + numthreads=$($instdir/bin/nproc --all) +else + numthreads=$jobs +fi +.local/bin/env -i HOME=$bdir \ + .local/bin/make -f reproduce/software/make/high-level.mk \ + rpath_command=$rpath_command \ + static_build=$static_build \ + numthreads=$numthreads \ + on_mac_os=$on_mac_os \ + host_cc=$host_cc \ + -j$numthreads + + + + + +# Make sure TeX Live installed successfully +# ----------------------------------------- +# +# TeX Live is managed over the internet, so if there isn't any, or it +# suddenly gets cut, it can't be built. However, when TeX Live isn't +# installed, the project can do all its processing independent of it. It +# will just stop at the stage when all the processing is complete and it is +# only necessary to build the PDF. So we don't want to stop the project's +# configuration and building if its not present. +if [ -f $itidir/texlive-ready-tlmgr ]; then + texlive_result=$(cat $itidir/texlive-ready-tlmgr) +else + texlive_result="NOT!" +fi +if [ x"$texlive_result" = x"NOT!" ]; then + cat <<EOF + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +TeX Live couldn't be installed during the configuration (probably because +there were downloading problems). TeX Live is only necessary in making the +final PDF (which is only done after all the analysis has been complete). It +is not used at all during the analysis. + +Therefore, if you don't need the final PDF, and just want to do the +analysis, you can safely ignore this warning and continue. + +If you later have internet access and would like to add TeX live to your +project, please delete the respective files, then re-run configure as shown +below. Within configure, answer 'n' (for "no") when asked to re-write the +configuration files. + + rm .local/version-info/tex/texlive-ready-tlmgr + ./project configure + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF +fi + + + + + +# Citation of installed software +# +# After everything is installed, we'll put all the names and versions in a +# human-readable paragraph and also prepare the BibTeX citation for the +# software. +function prepare_name_version() { + + # First see if the (possible) `*' in the input arguments corresponds to + # anything. Note that some of the given directories may be empty (no + # software installed). + hasfiles=0 + for f in $@; do + if [ -f $f ]; then hasfiles=1; break; fi; + done + + # If there are any files, merge all the names in a paragraph. + if [ $hasfiles = 1 ]; then + + # Count how many names there are. This is necessary to identify the + # last element. + num=$(.local/bin/cat $@ \ + | .local/bin/sed '/^\s*$/d' \ + | .local/bin/wc -l) + + # Put them all in one paragraph. + .local/bin/cat $@ \ + | .local/bin/sort \ + | sed 's/_/\\_/' \ + | .local/bin/awk 'NF>0 { \ + c++; \ + if(c==1) \ + { \ + if('$num'==1) printf("%s", $0); \ + else printf("%s", $0); \ + } \ + else if(c=='$num') printf(" and %s\n", $0); \ + else printf(", %s", $0) \ + }' + fi +} + +# Report the different software in separate contexts (separating Python and +# TeX packages from the C/C++ programs and libraries). +proglibs=$(prepare_name_version $verdir/proglib/*) +pymodules=$(prepare_name_version $verdir/python/*) +texpkg=$(prepare_name_version $verdir/tex/texlive) + +# Write them as one paragraph for LaTeX. +pkgver=$mtexdir/dependencies.tex +.local/bin/echo "This research was done with the following free" > $pkgver +.local/bin/echo "software programs and libraries: $proglibs." >> $pkgver +if [ x"$pymodules" != x ]; then + .local/bin/echo "Within Python, the following modules" >> $pkgver + echo "were used: $pymodules." >> $pkgver +fi +.local/bin/echo "The \LaTeX{} source of the paper was compiled" >> $pkgver +.local/bin/echo "to make the PDF using the following packages:" >> $pkgver +.local/bin/echo "$texpkg. We are very grateful to all their" >> $pkgver +.local/bin/echo "creators for freely providing this necessary" >> $pkgver +.local/bin/echo "infrastructure. This research (and many " >> $pkgver +.local/bin/echo "others) would not be possible without them." >> $pkgver + +# Prepare the BibTeX entries for the used software (if there are any). +hasentry=0 +bibfiles="$ictdir/*" +for f in $bibfiles; do if [ -f $f ]; then hasentry=1; break; fi; done; + +# Make sure we start with an empty output file. +pkgbib=$mtexdir/dependencies-bib.tex +echo "" > $pkgbib + +# Fill it in with all the BibTeX entries in this directory. We'll just +# avoid writing any comments (usually copyright notices) and also put an +# empty line after each file's contents to make the output more readable. +if [ $hasentry = 1 ]; then + for f in $bibfiles; do + awk '!/^%/{print} END{print ""}' $f >> $pkgbib + done +fi + + + + + +# Clean the temporary build directory +# --------------------------------- +# +# By the time the script reaches here the temporary software build +# directory should be empty, so just delete it. Note `tmpblddir' may be a +# symbolic link to shared memory. So, to work in any scenario, first delete +# the contents of the directory (if it has any), then delete `tmpblddir'. +.local/bin/rm -rf $tmpblddir/* $tmpblddir + + + + + +# Register successful completion +# ------------------------------ +echo `.local/bin/date` > $finaltarget + + + + + + +# Final notice +# ------------ +# +# The configuration is now complete, we can inform the user on the next +# step(s) to take. +if [ x$reproducible_paper_group_name = x ]; then + buildcommand="./project make -j8" +else + buildcommand="./project make --group=$reproducible_paper_group_name -j8" +fi +cat <<EOF + +---------------- +The project and its environment are configured with no errors. + +Please run the following command to start. +(Replace '8' with the number of CPU threads) + + $buildcommand + +To change the configuration later, please re-run './project configure', DO +NOT manually edit the relevant files. + +EOF |