From 27d3bb906b843a38c371e66372745095ccaceef6 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Thu, 28 Mar 2019 11:51:37 +0000
Subject: Configure script now has options
With the options, it is now possible to run the configure script more
easily after the initial run. The `--help' option provides a nice and
complete introduction along with a listing of the input options and the
`-j' option can be use to manually set the number of threads.
---
.file-metadata | Bin 4158 -> 4141 bytes
configure | 294 +++++++++++++++++++++++++++++++++++++++++++++++++--------
2 files changed, 254 insertions(+), 40 deletions(-)
diff --git a/.file-metadata b/.file-metadata
index ac0a6cb..18e0cd8 100644
Binary files a/.file-metadata and b/.file-metadata differ
diff --git a/configure b/configure
index c34a68a..3e0a7f0 100755
--- a/configure
+++ b/configure
@@ -34,6 +34,199 @@ set -e
+# Output of --help
+# ----------------
+me=$0 # Executable file name.
+help_print() {
+
+ if [ x"$build_dir" = x ]; then
+ bdir_status="NOT SET"
+ else
+ bdir_status="$build_dir"
+ fi
+
+ if [ x"$input_dir" = x ]; then
+ indir_status="NOT SET"
+ else
+ indir_status="$input_dir"
+ fi
+
+ if [ x"$software_dir" = x ]; then
+ software_status="NOT SET"
+ else
+ software_status="$software_dir"
+ fi
+
+ if [ $in_minmapsize = 0 ]; then
+ mm_status="NOT SET"
+ else
+ mm_status="$in_minmapsize"
+ fi
+
+ if [ $jobs = "0" ]; then
+ jobs_status="NUMBER OF THREADS ON SYSTEM"
+ else
+ jobs_status=$jobs
+ fi
+
+ if [ $existing_conf = 1 ]; then
+ ec_status="ACTIVATED"
+ else
+ ec_status="NOT SET"
+ fi
+
+ # Print the output.
+ cat <<EOF
+Usage: $me [OPTION]...
+
+Configure the reproducible paper template for this system (do local
+settings). 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 it and avoid
+re-setting the values.
+
+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.
+
+Options:
+
+ -b, --build-dir STR Top directory to build the project in.
+ Current value: $bdir_status
+
+ -i, --input-dir STR Directory containing necessary input datasets.
+ Current value: $indir_status
+
+ -s, --software-dir STR Directory containing necessary software tarballs.
+ Current value: $software_status
+
+ -m, --minmapsize INT (Specific to Gnuastro) Number of bytes to avoid
+ using RAM, use HDD/SSD instead of memory.
+ Current value: $mm_status
+
+ -j, --jobs INT Number of threads to use in building the software
+ during the pipeline. Note that on MacOS, currently
+ the first phase will be done on a single thread,
+ but higher-level software will be built in parallel.
+ Current value: $jobs_status
+
+ -e, --existing-conf Use (possibly existing) local configuration.
+ Current value: $ec_status
+
+ -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
+}
+
+
+
+
+
+# Parse the arguments
+# -------------------
+jobs=0
+build_dir=
+input_dir=
+software_dir=
+in_minmapsize=0
+existing_conf=0
+while [[ $# -gt 0 ]]
+do
+ key="$1"
+ case $key in
+ -b|--build-dir)
+ build_dir="$2"
+ if [ x"$build_dir" = x ]; then
+ echo "No argument given to '--build-dir' ('-b')."
+ exit 1;
+ fi
+ shift # past argument
+ shift # past value
+ ;;
+ -i|--input-dir)
+ input_dir="$2"
+ if [ x"$input_dir" = x ]; then
+ echo "No argument given to '--input-dir' ('-i')."
+ exit 1;
+ fi
+ shift # past argument
+ shift # past value
+ ;;
+ -s|--software-dir)
+ software_dir="$2"
+ if [ x"$software_dir" = x ]; then
+ echo "No argument given to '--software-dir' ('-s')."
+ exit 1;
+ fi
+ shift # past argument
+ shift # past value
+ ;;
+ -m|--minmapsize)
+ in_minmapsize="$2"
+ if [ x"$in_minmapsize" = x ]; then
+ echo "No argument given to '--minmapsize' ('-m')."
+ exit 1;
+ fi
+ shift # past argument
+ shift # past value
+ ;;
+ -j|--jobs)
+ jobs="$2"
+ if [ x"$jobs" = x ]; then
+ echo "No argument given to '--jobs' ('-j')."
+ exit 1;
+ fi
+ shift # past argument
+ shift # past value
+ ;;
+ -e|--existing-conf)
+ existing_conf=1
+ shift # past argument
+ ;;
+
+ -h|-P|--help|--printparams)
+ help_print
+ exit 0
+ ;;
+# -V|--version)
+# echo $version
+# exit 0
+# ;;
+ *) # unknown option
+ cat <<EOF
+Usage: $me [OPTION]...
+'$1' isn't a recognized option. Aborted.
+
+Note that for this script, option names (short or long format) and values
+must be separated by atleast one white-space character and MUST NOT have
+an '=' between them.
+EOF
+ exit 1
+ ;;
+ esac
+done
+
+
+
+
+
# Important internal locations
# ----------------------------
#
@@ -141,17 +334,7 @@ printnotice=yes
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 [ $existing_conf = 1 ]; then
printnotice=no
if [ -f $pconf ]; then rewritepconfig=no; fi
if [ -f $glconf ]; then rewritegconfig=no; fi
@@ -220,10 +403,10 @@ if [ $rewritepconfig = yes ]; then
!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-Couldn't find GNU Wget. It is used for downloading necessary programs and
-data if they aren't already present in the specified directories. Therefore
-the pipeline will crash if the necessary files are not already present on
-the system.
+Couldn't find GNU Wget, or cURL on this system. These programs are used for
+downloading necessary programs and data if they aren't already present (in
+directories that you can specify with this configure script). Therefore if
+the necessary files are not present, the pipeline will crash.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@@ -258,30 +441,36 @@ build directory in a very different address from this one (one that can be
deleted and has large volume), while having easy access to it from here.
EOF
- bdir=""
+ bdir=
junkname=pure-junk-974adfkj38
while [ x$bdir == x ]
do
- # Ask the user.
- read -p"Please enter the top build directory: " inbdir
+ # 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 $inbdir ]; then
- if mkdir $inbdir/$junkname 2> /dev/null; then
- bdir=$(absolute_dir $inbdir)
+ 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 $inbdir/$junkname
+ rm -rf $build_dir/$junkname
else
- echo " -- Can't write in '$inbdir'"
+ echo " -- Can't write in '$build_dir'"
fi
else
- if mkdir $inbdir 2> /dev/null; then
- bdir=$(absolute_dir $inbdir)
+ 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 '$inbdir'"
+ echo " -- Can't create '$build_dir'"
fi
fi
+
+ # Reset `build_dir' to blank, so it continues asking when the
+ # previous value wasn't usable.
+ build_dir=
done
fi
@@ -291,12 +480,16 @@ fi
# Input directory
# ---------------
-indir=$optionaldir
+if [ x"$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 ]; then
+if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
cat <<EOF
----------------------------------
@@ -338,12 +531,16 @@ fi
# Dependency tarball directory
# ----------------------------
-if [ $rewritepconfig = yes ]; then
+if [ x"$software_dir" = x ]; then
ddir=$optionaldir
+else
+ ddir=$software_dir
+fi
+if [ $rewritepconfig = yes ] && [ x"$software_dir" = x ]; then
cat <<EOF
---------------------------------------
-(OPTIONAL) Dependency tarball directory
+(OPTIONAL) Software tarball directory
---------------------------------------
To ensure an identical build environment, the pipeline will use its own
@@ -369,9 +566,18 @@ fi
# Memory mapping minimum size
# ---------------------------
-if [ $rewritegconfig = yes ]; then
- defaultminmapsize=10000000000
- minmapsize=$defaultminmapsize
+#
+# This option is specific to GNU Astronomy Utilities. It is primarily
+# included here as a demonstration option for software that need special
+# local settings (that are irrelevant to their processing, but necessary to
+# set based on local settings). If you do not use Gnuastro, please remove
+# this option from this script.
+if [ x"$in_minmapsize" = x ]; then
+ minmapsize=10000000000
+else
+ minmapsize=$in_minmapsize
+fi
+if [ $rewritegconfig = yes ] && [ $in_minmapsize = 0 ]; then
cat <<EOF
---------------------------
@@ -738,13 +944,21 @@ fi
# Build Basic dependencies
# ------------------------
#
-# Since the system might not have GNU Coreutils at this stage, we'll just
-# default to 4 threads if the actual number isn't found. This is because
-# some versions of Make complain about not having enough 'pipe' (memory) on
-# some systems. After some searching, I found out its because of too many
-# threads.
-if which nproc > /dev/null 2>/dev/null; then numthreads=$(nproc --all);
-else numthreads=1;
+# 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 \
--
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