#! /bin/sh # # 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, 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 # Important internal locations # ---------------------------- # # These are defined to help make this script more readable. topdir=$(pwd) installedlink=.local lbdir=reproduce/build cdir=reproduce/config pdir=$cdir/pipeline pconf=$pdir/LOCAL.mk ptconf=$pdir/LOCAL_tmp.mk poconf=$pdir/LOCAL_old.mk glconf=$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 $1"; echo; exit 1 fi } # Get absolute address # -------------------- # # Since the build directory will go into a symbolic link, we want it to be # an absolute address. With this function we can make sure of that. function absolute_dir() { echo "$(cd "$(dirname "$inbdir")" && pwd )/$(basename "$inbdir")" } # 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). rewritepconfig=yes rewritegconfig=yes if [ -f $pconf ] || [ -f $glconf ]; then # If it already exits, see what the user wants to do. echo "Atleast one local configuration file already exists." echo while [ "$userread" != "y" -a "$userread" != "n" ] do read -p"Re-write existing configuration file(s) (y/n)? " userread done # Set `rewriteconfig'. if [ $userread = "n" ]; then if [ -f $pconf ]; then rewritepconfig=no; fi if [ -f $glconf ]; then rewritegconfig=no; fi fi echo fi # Identify the downloader tool # ---------------------------- # # We use Wget for the downloading. As of November 12th, cURL couldn't # download Ghostscript's source from its standard address, but Wget # could. Until November 12th, we would check for cURL or Wget, so we # defined this check system here (explained in the next paragraph of this # comment). For now its redundant, but if the fix for cURL is found later, # we can add it back (or add other downloaders). So we'll keep it. # # Since the options specifying the output filename are different between # the two, we'll also specify the output option within the `downloader' # variable. So it is important to first give the output filename after # calling `DOWNLOADER' within the Makefiles, and finish the command with # the web address. if [ $rewritepconfig = yes ]; then if type wget > /dev/null 2>/dev/null; then downloader="wget -O"; else cat <<EOF !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Couldn't find GNU Wget. It is used for downloading necessary programs and data if they aren't already present in the specified directories. Therefore the pipeline will crash if the necessary files are not already present on the system. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF downloader="no-downloader-found" fi; fi # Build directory # --------------- if [ $rewritepconfig = yes ]; then cat <<EOF =============== Build directory =============== The "source" (this directory) and "build" directories are treated separately. This greatly helps in managing the many intermediate files that are created during the build. The intermediate build files don't need to be archived or backed up: you can always re-build them with this reproduction pipeline. The build directory also needs a relatively large amount of free space (atleast serveral Giga-bytes). '$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. read -p"Please enter the top build directory: " inbdir # If it exists, see if we can write in it. If not, try making it. if [ -d $inbdir ]; then if mkdir $inbdir/$junkname 2> /dev/null; then bdir=$(absolute_dir $inbdir) echo " -- Build directory: '$bdir'" rm -rf $inbdir/$junkname else echo " -- Can't write in '$inbdir'" fi else if mkdir $inbdir 2> /dev/null; then bdir=$(absolute_dir $inbdir) echo " -- Build directory set to (the newly created): '$bdir'" else echo " -- Can't create '$inbdir'" fi fi done fi # Dependency tarball directory # ---------------------------- if [ $rewritepconfig = yes ]; then junkddir="/optional/path" ddir=$junkddir cat <<EOF --------------------------------------- (OPTIONAL) Dependency 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 echo fi # Memory mapping minimum size # --------------------------- if [ $rewritegconfig = yes ]; then defaultminmapsize=1000000000 minmapsize=$defaultminmapsize cat <<EOF --------------------------- Minimum memory mapping size --------------------------- Some programs (for example Gnuastro) can deal with cases where the local system doesn't have enough memory (RAM) to keep large files. For example, they will create memory-mapped (mmap) files on the HDD or SSD and read/write to/from them instead of RAM. This will ofcourse, slow down the processing, but atleast the program won't crash. Since the memory requirements of different systems are different and it has no effect on the software's final result, the minimum size of an allocated array to warrant a mapping to HDD/SSD instead of RAM must also be defined here. This value will be used in the programs that support this feature. EOF read -p"Minimum memory mapping size in bytes (default: $minmapsize): " \ tmpminmapsize if [ x"$tmpminmapsize" != x ]; then minmapsize=$tmpminmapsize echo " -- Using '$minmapsize'" fi fi # Write the parameters into the local configuration file. if [ $rewritepconfig = yes ]; then create_file_with_notice $pconf sed -e's|@bdir[@]|'"$bdir"'|' \ -e's|@ddir[@]|'"$ddir"'|' \ -e's|@downloader[@]|'"$downloader"'|' \ $pconf.in >> $pconf else # Read the values from existing configuration file. inbdir=$(awk '$1=="BDIR" {print $NF}' $pconf) ddir=$(awk '$1=="DEPENDENCIES-DIR" {print $NF}' $pconf) downloader=$(awk '$1=="DOWNLOADER" {print $NF}' $pconf) # Make sure `bdir' is an absolute path and it exists. bdir=$(absolute_dir $inbdir) if ! [ -d $bdir ]; then mkdir $bdir; fi fi # --------- Delete for no Gnuastro --------- # Get the version of Gnuastro that must be used. depverfile=reproduce/config/pipeline/dependency-versions.mk gversion=$(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 rm -f $installedlink ln -s $instdir $installedlink # --------- Delete for no Gnuastro --------- rm -f .gnuastro ln -s $(pwd)/reproduce/config/gnuastro .gnuastro # ------------------------------------------ # See if the C compiler can build static libraries # ------------------------------------------------ oprog=$ddir/static-test cprog=$ddir/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 [ $static_build = "no" ]; then cat <<EOF _________________________________________________________________________ !!!!!!!!!!!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!!!!!!!! Your system's C compiler ('$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 # Inform the user that the build process is starting # ------------------------------------------------- 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: $bdir/dependencies/installed EOF sleep $tsec # Build Basic dependencies # ------------------------ make -f reproduce/src/make/dependencies-basic.mk \ static_build=$static_build #-j2 # 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. ./.local/bin/make -f reproduce/src/make/dependencies.mk \ static_build=$static_build #-j8 # Print a final notice # -------------------- # # The configuration is now complete, we can inform the user on the next # step(s) to take. echo echo "----------------" echo "The reproduction pipeline and its environment are SUCCESSFULLY configured." echo echo "Please run the following command to start." echo "(Replace '8' with the number of CPU threads)" echo echo " ./.local/bin/make -j8" echo echo "To change the configuration later, please re-run './configure'," echo "DO NOT manually edit the relevant files." echo # Final target: 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-Makefile Makefile