#! /bin/bash # # Necessary preparations/configurations for the reproduction pipeline. # # Original author: # Mohammad Akhlaghi <mohammad@akhlaghi.org> # Contributing author(s): # Your name <your@email.address> # Copyright (C) 2018-2019, Your Name. # # 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 # Default option values jobs=0 build_dir= input_dir= host_cc=0 software_dir= existing_conf=0 minmapsize=10000000000 # Output of --help # ---------------- me=$0 # Executable file name. print_help() { # Print the output. cat <<EOF Usage: $me [OPTION]... Configure the reproducible paper template for this system (set local settings for this system). The local settings can be given on the command-line through the options below. If not, the configure script will interactively ask for a value to each one (with basic necessary background information printed before them). Alternatively, if you have already configured this script for your system, you can use the '--existing-conf' to use its values directly. RECOMMENDATION: If this is the first time you are running this pipeline, please don't use the options and let the script explain each parameter in full detail by simply running './configure'. The only mandatory value for this script is the local build directory. This is where all the pipeline's outputs will be stored. Optionally, you can also provide directories that host input data, or software source codes. If the necessary files don't exist there, the template will automatically download them. With the options below you can modify the default behavior. Just note that you should not put an '=' sign between an option name and its value. Configure options: Top-level directory settings: -b, --build-dir=STR Top directory to build the project in. -i, --input-dir=STR Directory containing input datasets (optional). -s, --software-dir=STR Directory containing necessary software tarballs. Operating mode options: --host-cc Use host system's C compiler, don't build GCC. -m, --minmapsize=INT (Gnuastro) Minimum number of bytes to use RAM. -j, --jobs=INT Number of threads to build the software. -e, --existing-conf Use (possibly existing) local configuration. -h, --help Print this help list. 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 } # Functions to check option values and complain if necessary. function on_off_option_error() { cat <<EOF $scriptname: '$1' doesn't take any values. EOF exit 1 } function check_v() { if [ x"$2" = x ]; then echo "$scriptname: option '$1' requires an argument." echo "Try '$scriptname --help' for more information." exit 1; fi } # 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. while [[ $# -gt 0 ]] do case $1 in # Input parameters. -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;; -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;; -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;; -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;; # Operating mode options --host-cc) host_cc=1; shift;; --host-cc=*) on_off_option_error --host-cc;; -j|--jobs) jobs="$2"; check_v "$1" "$jobs"; shift;shift;; -j=*|--jobs=*) jobs="${1#*=}"; check_v "$1" "$jobs"; shift;; -j*) jobs=$(echo "$1" | sed -e's/-j//'); check_v "$1" "$jobs"; shift;; -e|--existing-conf) existing_conf=1; shift;; -e*|--existing-conf=*) on_off_option_error --existing-conf;; -?|--help) print_help; exit 0;; -?*|--help=*) on_off_option_error --help;; # Unrecognized option: -*) echo "$scriptname: unknown option '$1'"; exit 1;; # Not an option, an argument. *) echo "The configure script doesn't accept arguments."; echo "For a description of options, please run with '--help'."; exit 1;; esac done # Internal directories # -------------------- # # These are defined to help make this script more readable. topdir=$(pwd) lbdir=.build installedlink=.local cdir=reproduce/config optionaldir="/optional/path" pdir=$cdir/pipeline pconf=$pdir/LOCAL.mk ptconf=$pdir/LOCAL_tmp.mk poconf=$pdir/LOCAL_old.mk # --------- Delete for no Gnuastro --------- glconf=$cdir/gnuastro/gnuastro-local.conf # ------------------------------------------ # Delete final target of configuration # ------------------------------------ # # Without the top-level `Makefile' the user can't run `make' in this # directory. But we only want to make it available when we know everything # else is set up. So we'll delete it at the start of this configuration and # reset the link in the absolute end. rm -f Makefile # 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 './configure'" > "$1" then echo "#" >> "$1" echo "# This file was created during the reproduction" >> "$1" echo "# pipeline's configuration ('./configure'). Therefore," >> "$1" echo "# it is not under version control and any manual " >> "$1" echo "# changes to it will be over-written if the pipeline " >> "$1" echo "# is 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 ----------------------------------------- Reproduction pipeline 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 pipeline. 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 `./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="./configure" else status="configured for '$oldgroupname' group" confcommand="./for-group $oldgroupname configure" fi echo "Previous pipeline was $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 `./configure' 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 pipeline will crash. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF downloader="no-downloader-found" fi; fi # Build directory # --------------- if [ $rewritepconfig = yes ]; then cat <<EOF =============== Build directory =============== The project's "source" (this directory) and "build" directories are treated separately. This greatly helps in managing the many intermediate files that are created during the build. The intermediate build files don't need to be archived or backed up: you can always re-build them with the contents of the source directory. The build directory also needs a relatively large amount of free space (atleast serveral Giga-bytes), while the source directory (all plain text) will usually be a mega-byte or less. '$lbdir' (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}' $pdir/INPUTS.mk) wfpc2md5=$(awk '!/^#/ && $1=="WFPC2MD5" {print $3}' $pdir/INPUTS.mk) wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE" {print $3}' $pdir/INPUTS.mk) wfpc2url=$(awk '!/^#/ && $1=="WFPC2URL" {print $3}' $pdir/INPUTS.mk) if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then cat <<EOF ---------------------------------- (OPTIONAL) Input dataset directory ---------------------------------- This pipeline 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 pipeline will use its own build of the programs it needs. Therefore the tarball of the relevant programs are necessary for this pipeline. If a tarball isn't present in the specified directory, *IT WILL BE DOWNLOADED* by the pipeline. Therefore, 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 pipeline 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 # Make the pipeline configuration's initial comments. 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 '$pconf'. EOF fi cat <<EOF Please run the configure script again (accepting to re-write existing configuration file) so all the values can be filled and checked. ################################################################# EOF fi fi # --------- Delete for no Gnuastro --------- # Get the version of Gnuastro that must be used. depverfile=reproduce/config/pipeline/dependency-versions.mk gversion=$(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$gversion ]; then echo "______________________________________________________" echo "!!!!!!!!!!!!!!!!!!CONFIGURATION ERROR!!!!!!!!!!!!!!!!!" echo echo "Gnuastro's version in '$glconf' ($ingversion) doesn't match the tarball version that this pipeline was designed to use in '$depverfile' ($gversion). Please re-run after removing the former file:" echo echo " $ rm $glconf" echo " $ ./configure" echo echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!" echo exit 1 fi fi # ------------------------------------------ # Setup the top-level directories # ------------------------------- rm -f $lbdir ln -s $bdir $lbdir depdir=$bdir/dependencies if ! [ -d $depdir ]; then mkdir $depdir; fi tardir=$depdir/tarballs if ! [ -d $tardir ]; then mkdir $tardir; fi instdir=$depdir/installed if ! [ -d $instdir ]; then mkdir $instdir; fi verdir=$instdir/version-info if ! [ -d $verdir ]; then mkdir $verdir; fi ibidir=$verdir/bin if ! [ -d $ibidir ]; then mkdir $ibidir; fi ilidir=$verdir/lib if ! [ -d $ilidir ]; then mkdir $ilidir; fi ipydir=$verdir/python if ! [ -d $ipydir ]; then mkdir $ipydir; fi itidir=$verdir/tex if ! [ -d $itidir ]; then mkdir $itidir; fi texdir=$bdir/tex if ! [ -d $texdir ]; then mkdir $texdir; fi mtexdir=$texdir/macros if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi rm -f $installedlink ln -s $instdir $installedlink # --------- Delete for no Gnuastro --------- rm -f .gnuastro ln -s $(pwd)/reproduce/config/gnuastro .gnuastro # ------------------------------------------ # See if the C compiler can build static libraries # ------------------------------------------------ # We are manually only working with shared libraries: because some # high-level programs like Wget and cURL need dynamic linking and if we # build the libraries statically, our own builds will be ignored and these # programs will go and find their necessary libraries on the host system. # # Another good advantage of shared libraries is that we can actually use # the shared library tool of the system (`ldd' with GNU C Library) and see # exactly where each linked library comes from. But in static building, # unless you follow the build closely, its not easy to see if the source of # the library came from the system or our build. static_build=no #oprog=$depdir/static-test #cprog=$depdir/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 #'./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=$depdir/rpath-test cprog=$depdir/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 $cprog # See if we need the dynamic-linker (-ldl) # ---------------------------------------- # # Some programs (like Wget) need dynamic loading (using `libdl'). On # GNU/Linux systems, we'll need the `-ldl' flag to link such programs. But # Mac OS doesn't need any explicit calling. So we'll check here to use in # the building of programs. oprog=$depdir/ldl-test cprog=$depdir/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 reproduction pipeline. They will be installed in: $depdir/installed EOF sleep $tsec fi # If we are on a Mac OS system # ---------------------------- # # For the time being, we'll use the existance of `otool' to see if we are # on a Mac OS system or not. Some tools (for example OpenSSL) need to know # this. # # On Mac OS, the building of GCC crashes sometimes while building libiberty # with CLang's `g++'. Until we find a solution, we'll just use the host's C # compiler. if type otool > /dev/null 2>/dev/null; then host_cc=1 on_mac_os=yes else on_mac_os=no fi # Build `flock' as first program # ------------------------------ # # Flock (or file-lock) is a unique program in the pipeline that is # necessary to serialize the (generally parallel) processing of make when # necessary. GNU/Linux machines have it as part of their `util-linux' # programs. But to be consistent, we will be using our own build. # # The reason its sepecial is that we need it to serialize the download # process of the dependency tarballs. flockversion=$(awk '/flock-version/{print $3}' $pdir/dependency-versions.mk) flocktar=flock-$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 $depdir tar xf $tardir/$flocktar cd flock-$flockversion ./configure --prefix=$instdir make; make install cd $topdir rm -rf $depdir/flock-$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, # `sys/cdefs.h' is not available by default. So if the user hasn't manually # installed it before this configure script, GCC won't build. We are thus # explicitly testing a small C program here to see if the host's C compiler # won't have any problems in building GCC. if [ $host_cc = 0 ]; then tfile=$depdir/gcc-cdefs-test.c; echo "#include <sys/cdefs.h>" > $tfile; echo "int main(void){return 0;}" >> $tfile; if gcc $tfile -o $depdir/gcc-cdefs-test &> /dev/null; then rm $depdir/gcc-cdefs-test*; else host_cc=1 fi; rm -f $tfile; if [ $host_cc = 1 ]; then cat <<EOF !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! This system's C compiler (called with 'gcc') can't include 'sys/cdefs.h. Because of this, this pipeline 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'. However, 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 to complete your C compiler, then re-run the pipeline. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF sleep 5 fi fi # Build Basic dependencies # ------------------------ # # 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 2>/dev/null; then if [ $jobs = 0 ]; then numthreads=$(nproc --all); else numthreads=$jobs fi else numthreads=1; fi make -f reproduce/src/make/dependencies-basic.mk \ rpath_command=$rpath_command \ static_build=$static_build \ needs_ldl=$needs_ldl \ on_mac_os=$on_mac_os \ numthreads=$numthreads \ host_cc=$host_cc \ -j$numthreads # Rest of dependencies # -------------------- # # 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. numthreads=$($instdir/bin/nproc) ./.local/bin/make -f reproduce/src/make/dependencies.mk \ rpath_command=$rpath_command \ static_build=$static_build \ on_mac_os=$on_mac_os \ numthreads=$numthreads \ -j$numthreads # Make sure TeX Live installed successfully # ----------------------------------------- # # TeX Live is managed over the internet, so if there isn't any, or it # suddenly gets cut, it can't be built. However, when TeX Live isn't # installed, the pipeline and can do all its processing independent of # it. It will just stop at the stage when all the processing is complete # and it is only necessary to build the PDF. So we don't want to stop the # pipeline if its not present. texlive_result=$(cat $itidir/texlive-ready-tlmgr) if [ x"$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 pipeline, 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 ./configure !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF fi # Put all the names and versions in a human-readable format in LaTeX. function prepare_name_version() { # Total number of tools to report. num=$(cat "$@" | wc -l) # Put them all in one paragraph. cat "$@" \ | sort \ | awk 'NF>0{ c++; \ if(c==1) \ { \ if('$num'==1) printf("%s", $0); \ else printf("%s", $0); \ } \ else if(c=='$num') printf(" and %s\n", $0); \ else printf(", %s", $0)}' } # Separate the parts by context. proglibs=$(prepare_name_version $verdir/bin/* $verdir/lib/*) pymodules=$(prepare_name_version $verdir/python/*) texpkg=$(prepare_name_version $verdir/tex/texlive) # Write them as one paragraph for LaTeX. pkgver=$mtexdir/dependencies.tex echo "This research was done with the following free" > $pkgver echo "software programs and libraries: $proglibs." >> $pkgver npython=$(ls $verdir/python/* | wc -l) if [ $npython != 0 ]; then echo "Within Python, the following modules were used: " >> $pkgver echo "$pymodules." >> $pkgver fi echo "The \LaTeX{} source of the paper was compiled to make" >> $pkgver echo "the PDF using the following packages $texpkg. We are" >> $pkgver echo "very grateful to all their creators for freely" >> $pkgver echo "providing this necessary infrastructure. This " >> $pkgver echo "research (and many others) would not be possible" >> $pkgver echo "without them." >> $pkgver # Final step: the Makefile # -------------------------- # # To see why this is the last step of the configuration, see above (when we # delete the top-level Makefile at the start of this script). ln -s $(pwd)/reproduce/src/make/top.mk Makefile # Final notice # ------------ # # The configuration is now complete, we can inform the user on the next # step(s) to take. if [ x$reproducible_paper_group_name = x ]; then buildcommand=".local/bin/make -j8" else buildcommand="./for-group $reproducible_paper_group_name make -j8" fi cat <<EOF ---------------- The reproduction pipeline 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 './configure', DO NOT manually edit the relevant files. EOF