diff options
Diffstat (limited to 'reproduce')
| -rw-r--r-- | reproduce/analysis/make/initialize.mk | 7 | ||||
| -rw-r--r-- | reproduce/analysis/make/paper.mk | 8 | ||||
| -rw-r--r-- | reproduce/analysis/make/top-make.mk | 6 | ||||
| -rw-r--r-- | reproduce/analysis/make/top-prepare.mk | 6 | ||||
| -rw-r--r-- | reproduce/software/config/LOCAL.conf.in | 28 | ||||
| -rw-r--r-- | reproduce/software/make/basic.mk | 17 | ||||
| -rw-r--r-- | reproduce/software/make/high-level.mk | 10 | ||||
| -rw-r--r-- | reproduce/software/shell/apptainer-README.md (renamed from reproduce/software/containers/README-apptainer.md) | 0 | ||||
| -rwxr-xr-x | reproduce/software/shell/apptainer.sh (renamed from reproduce/software/containers/apptainer.sh) | 121 | ||||
| -rwxr-xr-x | reproduce/software/shell/configure.sh | 1681 | ||||
| -rw-r--r-- | reproduce/software/shell/docker-README.md (renamed from reproduce/software/containers/README-docker.md) | 0 | ||||
| -rwxr-xr-x | reproduce/software/shell/docker.sh (renamed from reproduce/software/containers/docker.sh) | 129 | ||||
| -rwxr-xr-x | reproduce/software/shell/pre-make-build.sh | 57 |
13 files changed, 1124 insertions, 946 deletions
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index c51f910..5150373 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -285,7 +285,7 @@ distclean: clean # 'rm' program. So for this recipe, we'll use the host system's 'rm', # not our own. $$sys_rm -rf $(BDIR) - $$sys_rm -f .local .build $(pconfdir)/LOCAL.conf + $$sys_rm -f .local .build @@ -521,7 +521,10 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir) # Unrecognized format. *) - echo "Maneage: 'DATABASEAUTHTYPE' format not recognized! Please see the description of this variable in 'reproduce/software/config/LOCAL.conf' for the acceptable values."; exit 1;; + printf "Maneage: 'DATABASEAUTHTYPE' format not recognized! " + printf "Please see the description of this variable in " + printf "'$(bsdir)/config/LOCAL.conf' for the acceptable " + printf "values."; exit 1;; esac fi diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index 3c06ce3..b1b794c 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -105,8 +105,6 @@ else texbdir:=$(texdir)/build-$(shell whoami) endif tikzdir:=$(texbdir)/tikz -$(texbdir):; mkdir $@ -$(tikzdir): | $(texbdir); mkdir $@ @@ -120,8 +118,8 @@ $(tikzdir): | $(texbdir); mkdir $@ # on). Therefore, we should copy those macros here in the LaTeX build # directory, so the TeX directory is completely independent from each # other. -$(mtexdir)/dependencies.tex: $(bsdir)/tex/dependencies.tex - cp $(bsdir)/tex/*.tex $(mtexdir)/ +$(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex + cp $(bsdir)/config/*.tex $(mtexdir)/ @@ -140,7 +138,7 @@ $(mtexdir)/dependencies.tex: $(bsdir)/tex/dependencies.tex # been modified, we don't want to re-build the bibliography, only the final # PDF. $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \ - | $(mtexdir)/project.tex $(tikzdir) + | $(mtexdir)/project.tex # If '$(mtexdir)/project.tex' is empty, don't build PDF. @macros=$$(cat $(mtexdir)/project.tex) diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index 2689e64..e87aed8 100644 --- a/reproduce/analysis/make/top-make.mk +++ b/reproduce/analysis/make/top-make.mk @@ -19,9 +19,9 @@ -# Load the local configuration (created after running -# './project configure'). -include reproduce/software/config/LOCAL.conf +# Load the local configuration (created after running './project +# configure'). +include .build/software/config/LOCAL.conf diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk index ea40f39..d2d1c14 100644 --- a/reproduce/analysis/make/top-prepare.mk +++ b/reproduce/analysis/make/top-prepare.mk @@ -23,9 +23,9 @@ -# Load the local configuration (created after running -# './project configure'). -include reproduce/software/config/LOCAL.conf +# Load the local configuration (created after running './project +# configure'). +include .build/software/config/LOCAL.conf diff --git a/reproduce/software/config/LOCAL.conf.in b/reproduce/software/config/LOCAL.conf.in index 341a78e..e60f344 100644 --- a/reproduce/software/config/LOCAL.conf.in +++ b/reproduce/software/config/LOCAL.conf.in @@ -9,12 +9,30 @@ # permitted in any medium without royalty provided the copyright notice and # this notice are preserved. This file is offered as-is, without any # warranty. -BDIR = @bdir@ -INDIR = @indir@ + + + + +# Local system settings +# --------------------- +# +# Build directory (mandatory). All the created files of the project will be +# within this directory. +BDIR = @bdir@ + +# Input data directory. This can be empty or a non-existant location. If +# so, then the inputs will be downloaded from the 'INPUTS.conf' into the +# build directory. +INDIR = @indir@ + +# Software source code directory. This can be empty or a non-existant +# location. If so, the software tarballs will be downloaded. DEPENDENCIES-DIR = @ddir@ -SYS_CPATH = @sys_cpath@ -DOWNLOADER = @downloader@ -GROUP-NAME = @groupname@ + +# Other local settings (compiler, downloader and user). +SYS_CPATH = @sys_cpath@ +DOWNLOADER = @downloader@ +GROUP-NAME = @groupname@ diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index c9aba96..4b18c29 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -39,7 +39,7 @@ # along with this Makefile. If not, see <http://www.gnu.org/licenses/>. # Top level environment -include reproduce/software/config/LOCAL.conf +include .build/software/config/LOCAL.conf include reproduce/software/make/build-rules.mk include reproduce/software/config/versions.conf include reproduce/software/config/checksums.conf @@ -63,10 +63,13 @@ ibidir = $(BDIR)/software/installed/version-info/proglib # editor) is installed by default, it is recommended to have it in the # 'basic.mk', so Maneaged projects can be edited on any system (even when # there is no command-line text editor available). +# +# The recipe is '@echo > /dev/null' so Make does not print "make: Nothing +# to be done for 'all'." targets-proglib = low-level-links \ gcc-$(gcc-version) \ nano-$(nano-version) -all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) +all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)); @echo > /dev/null # Define the shell environment # ---------------------------- @@ -423,7 +426,7 @@ $(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version) rm -f $(ibdir)/bash* $(ibdir)/awk* $(ibdir)/gawk* # Standard build process. - export CFLAGS="-std=c17 $$CFLAGS" + export CFLAGS="-std=gnu17 $$CFLAGS" $(call gbuild, ncurses-$(ncurses-version), static, \ --with-shared --enable-rpath --without-normal \ --without-debug --with-cxx-binding \ @@ -562,7 +565,7 @@ $(ibidir)/bash-$(bash-version): \ if [ "x$(static_build)" = xyes ]; then stopt="--enable-static-link" else stopt="" fi; - export CFLAGS="$$CFLAGS -std=c17 \ + export CFLAGS="$$CFLAGS -std=gnu17 \ -DDEFAULT_PATH_VALUE='\"$(ibdir)\"' \ -DSTANDARD_UTILS_PATH='\"$(ibdir)\"' \ -DSYS_BASHRC='\"$(BASH_ENV)\"' " @@ -1015,7 +1018,7 @@ $(ibidir)/gmp-$(gmp-version): \ $(ibidir)/coreutils-$(coreutils-version) tarball=gmp-$(gmp-version).tar.lz $(call import-source, $(gmp-url), $(gmp-checksum)) - export CFLAGS="-std=c17 $$CFLAGS" + export CFLAGS="-std=gnu17 $$CFLAGS" $(call gbuild, gmp-$(gmp-version), static, \ --enable-cxx --enable-fat, \ -j$(numthreads)) @@ -1076,7 +1079,7 @@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version) $(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version) tarball=m4-$(m4-version).tar.lz $(call import-source, $(m4-url), $(m4-checksum)) - export CFLAGS="-std=c17 $$CFLAGS" + export CFLAGS="-std=gnu17 $$CFLAGS" $(call gbuild, m4-$(m4-version), static, \ --with-syscmd-shell=$(ibdir)/dash, \ -j$(numthreads) V=1) @@ -1109,7 +1112,7 @@ $(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/patchelf-$(patchelf-version if [ x$(on_mac_os) = xyes ]; then export compiler="CC=clang" else export compiler="" fi - export CFLAGS="-std=c17 $$CFLAGS" + export CFLAGS="-std=gnu17 $$CFLAGS" $(call gbuild, pkg-config-$(pkgconfig-version), static, \ $$compiler --with-internal-glib \ --with-pc-path=$(ildir)/pkgconfig, V=1) diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 4ed5d62..67ca8b6 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -29,7 +29,7 @@ # along with this Makefile. If not, see <http://www.gnu.org/licenses/>. # Top level environment (same as 'basic.mk') -include reproduce/software/config/LOCAL.conf +include .build/software/config/LOCAL.conf include reproduce/software/make/build-rules.mk include reproduce/software/config/versions.conf include reproduce/software/config/checksums.conf @@ -123,11 +123,12 @@ ifneq ($(strip $(offline)),1) target-texlive := $(itidir)/texlive endif -# Ultimate Makefile target. +# Ultimate Makefile target. The recipe is '@echo > /dev/null' so Make does +# not print "make: Nothing to be done for 'all'." all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) \ $(foreach p, $(targets-python), $(ipydir)/$(p)) \ $(foreach p, $(targets-r-cran), $(ircrandir)/$(p)) \ - $(target-texlive) + $(target-texlive); @echo > /dev/null # Define the shell environment # ---------------------------- @@ -2020,7 +2021,7 @@ $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \ # We do not build TeXLive from source and for its installation it # downloads components from the web internally; and those # components can use '/bin/sh' (which needs 'sys_library_sh_path'). - export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" + export LD_LIBRARY_PATH="$(sys_library_sh_path)" # To update itself, tlmgr needs a backup directory. backupdir=$(idir)/texlive/backups @@ -2049,7 +2050,6 @@ $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \ # files (this is because we do no yet install LaTeX from source): cdir=$$(pwd) cd $(idir)/texlive - $(shsrcdir)/prep-source.sh $(ibdir) cd $$cdir # Get all the necessary versions. diff --git a/reproduce/software/containers/README-apptainer.md b/reproduce/software/shell/apptainer-README.md index a7826ec..a7826ec 100644 --- a/reproduce/software/containers/README-apptainer.md +++ b/reproduce/software/shell/apptainer-README.md diff --git a/reproduce/software/containers/apptainer.sh b/reproduce/software/shell/apptainer.sh index 52315f6..c581ade 100755 --- a/reproduce/software/containers/apptainer.sh +++ b/reproduce/software/shell/apptainer.sh @@ -9,34 +9,35 @@ # # Usage: # -# - When you are at the top Maneage'd project directory, you can run this -# script like the example below. Just set all the '/PATH/TO/...' -# directories. See the items below for optional values. +# - When you are at the top Maneage'd project directory, run this script +# like the example below. Just set the build directory location on your +# system. See the items below for optional values to optimize the +# process (avoid downloading for exmaple). # -# ./reproduce/software/containers/apptainer.sh \ -# --build-dir=/PATH/TO/BUILD/DIRECTORY \ -# --software-dir=/PATH/TO/SOFTWARE/TARBALLS +# ./reproduce/software/shell/apptainer.sh \ +# --build-dir=/PATH/TO/BUILD/DIRECTORY # -# - Non-mandatory options: +# - Non-mandatory options: # -# - If you already have the input data that is necessary for your -# project's, use the '--input-dir' option to specify its location -# on your host file system. Otherwise the necessary analysis -# files will be downloaded directly into the build -# directory. Note that this is only necessary when '--build-only' -# is not given. +# - If you already have the input data that is necessary for your +# project, use the '--input-dir' option to specify its location +# on your host file system. Otherwise the necessary analysis +# files will be downloaded directly into the build +# directory. Note that this is only necessary when '--build-only' +# is not given. # -# - The '--software-dir' is only useful if you want to build a -# container. Even in that case, it is not mandatory: if not -# given, the software tarballs will be downloaded (thus requiring -# internet). +# - If you already have the necessary software tarballs that are +# necessary for your project, use the '--software-dir' option to +# specify its location on your host file system only when +# building the container. No problem if you don't have them, they +# will be downloaded during the configuration phase. # -# - To avoid having to set them every time you want to start the -# apptainer environment, you can put this command (with the proper -# directories) into a 'run.sh' script in the top Maneage'd project -# source directory and simply execute that. The special name 'run.sh' -# is in Maneage's '.gitignore', so it will not be included in your -# git history by mistake. +# - To avoid having to set them every time you want to start the +# apptainer environment, you can put this command (with the proper +# directories) into a 'run.sh' script in the top Maneage'd project +# source directory and simply execute that. The special name 'run.sh' +# is in Maneage's '.gitignore', so it will not be included in your +# git history by mistake. # # Known problems: # @@ -70,7 +71,7 @@ set -e # Default option values -jobs= +jobs=0 quiet=0 source_dir= build_only= @@ -105,7 +106,7 @@ Top-level script to build and run a Maneage'd project within Apptainer. --container-shell Open the container shell. Operating mode: - --quiet Do not print informative statements. + -q, --quiet Do not print informative statements. -?, --help Give this help list. -j, --jobs=INT Number of threads to use in each phase. --build-only Just build the container, don't run it. @@ -166,8 +167,8 @@ do --container_shell=*) on_off_option_error --container-shell;; # Operating mode - --quiet) quiet=1; shift;; - --quiet=*) on_off_option_error --quiet;; + -q|--quiet) quiet=1; shift;; + -q*|--quiet=*) on_off_option_error --quiet;; -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;; @@ -245,8 +246,22 @@ if ! [ x"$input_dir" = x ]; then fi # If no '--jobs' has been specified, use the maximum available jobs to the -# operating system. -if [ x$jobs = x ]; then jobs=$(nproc); fi +# operating system. Apptainer only works on GNU/Linux operating systems, so +# there is no need to account for reading the number of threads on macOS. +if [ x"$jobs" = x0 ]; then jobs=$(nproc); fi + +# Since the container is read-only and is run with the '--contain' option +# (which makes an empty '/tmp'), we need to make a dedicated directory for +# the container to be able to write to. This is necessary because some +# software (Biber in particular on the default branch) need to write there! +# See https://github.com/plk/biber/issues/494. We'll keep the directory on +# the host OS within the build directory, but as a hidden file (since it is +# not necessary in other types of build and ultimately only contains +# temporary files of programs that need it). +toptmp=$build_dir/.apptainer-tmp-$(whoami) +if ! [ -d $toptmp ]; then mkdir $toptmp; fi +chmod -R +w $toptmp/ # Some software remove writing flags on /tmp files. +if ! [ x"$( ls -A $toptmp )" = x ]; then rm -r "$toptmp"/*; fi # [APPTAINER-ONLY] Optional mounting option for the software directory. software_dir_mnt="" @@ -254,18 +269,6 @@ if ! [ x"$software_dir" = x ]; then software_dir_mnt="--mount type=bind,src=$software_dir,dst=/home/maneager/tarballs-software" fi -# [APPTAINER-ONLY] Since the container is read-only and is run with the -# '--contain' option (which makes an empty '/tmp'), we need to make a -# dedicated directory for the container to be able to write to. This is -# necessary because some software (Biber in particular on the default -# branch) need to write there! See https://github.com/plk/biber/issues/494. -# We'll keep the directory on the host OS within the build directory, but -# as a hidden file (since it is not necessary in other types of build and -# ultimately only contains temporary files of programs that need it). -toptmp=$build_dir/.apptainer-tmp-$(whoami) -if ! [ -d $toptmp ]; then mkdir $toptmp; fi -rm -rf $toptmp/* # So previous runs don't affect this run. - @@ -284,7 +287,8 @@ if [ -f $project_name ]; then fi else - # Build the basic definition, with just Debian and gcc/g++ + # Build the basic definition, with just Debian-slim with minimal + # necessary tools. if [ -f $base_name ]; then if [ $quiet = 0 ]; then printf "$scriptname: info: base OS docker image ('$base_name') " @@ -300,7 +304,7 @@ Bootstrap: docker From: $base_os %post - apt-get update && apt-get install -y gcc g++ + apt-get update && apt-get install -y gcc g++ wget EOF # Build the base operating system container and delete the # temporary definition file. @@ -321,6 +325,7 @@ EOF # software tarball directory, they will all be symbolic links that # aren't valid when the user runs the container (since we only # mount the software tarballs at build time). + intbuild=/home/maneager/build maneage_def=$build_dir/maneage.def cat <<EOF > $maneage_def Bootstrap: localimage @@ -336,24 +341,34 @@ From: $base_name cd /home/maneager/source ./project configure --jobs=$jobs \\ --input-dir=/home/maneager/input \\ - --build-dir=/home/maneager/build \\ + --build-dir=$intbuild \\ --software-dir=/home/maneager/tarballs-software rm /home/maneager/build/software/tarballs/* %runscript cd /home/maneager/source - if [ x"\$maneage_apptainer_stat" = xshell ]; then \\ - ./project shell; \\ - elif [ x"\$maneage_apptainer_stat" = xrun ]; then \\ - if [ x"\$maneage_jobs" = x ]; then \\ - ./project make; \\ + if ./project configure --build-dir=$intbuild \\ + --existing-conf --no-pause \\ + --offline --quiet; then \\ + if [ x"\$maneage_apptainer_stat" = xshell ]; then \\ + ./project shell --build-dir=$intbuild; \\ + elif [ x"\$maneage_apptainer_stat" = xrun ]; then \\ + if [ x"\$maneage_jobs" = x ]; then \\ + ./project make --build-dir=$intbuild; \\ + else \\ + ./project make --build-dir=$intbuild --jobs=\$maneage_jobs; \\ + fi; \\ else \\ - ./project make --jobs=\$maneage_jobs; \\ + printf "$scriptname: '\$maneage_apptainer_stat' (value "; \\ + printf "to 'maneage_apptainer_stat' environment variable) "; \\ + printf "is not recognized: should be either 'shell' or 'run'"; \\ + exit 1; \\ fi; \\ else \\ - printf "$scriptname: '\$maneage_apptainer_stat' (value "; \\ - printf "to 'maneage_apptainer_stat' environment variable) "; \\ - printf "is not recognized: should be either 'shell' or 'run'"; \\ + printf "$scriptname: configuration failed! This is probably "; \\ + printf "due to a mismatch between the software versions of "; \\ + printf "the container and the source that it is being "; \\ + printf "executed.\n"; \\ exit 1; \\ fi EOF diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index e291f7b..4887816 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -40,6 +40,14 @@ set -e # had the chance to implement it yet (please help if you can!). Until then, # please set them based on your project (if they differ from the core # branch). + +# If equals 1, a message will be printed, showing the nano-seconds since +# previous step: useful with '-e --offline --nopause --quiet' to find +# bottlenecks for speed optimization. Speed is important because this +# script is called automatically every time by the container scripts. +check_elapsed=0 + +# In case a fortran compiler is necessary to check. need_gfortran=0 @@ -52,14 +60,12 @@ need_gfortran=0 # These are defined to help make this script more readable. topdir="$(pwd)" optionaldir="/optional/path" -adir=reproduce/analysis/config cdir=reproduce/software/config -pconf=$cdir/LOCAL.conf -ptconf=$cdir/LOCAL_tmp.conf -poconf=$cdir/LOCAL_old.conf -depverfile=$cdir/versions.conf -depshafile=$cdir/checksums.conf + + + + @@ -73,14 +79,21 @@ depshafile=$cdir/checksums.conf # that their changes are not going to be permenant. create_file_with_notice () { - if echo "# IMPORTANT: file can be RE-WRITTEN after './project configure'" > "$1" + if printf "# IMPORTANT: " > "$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" + # These commands may look messy, but the produced comments in the + # file are the main goal and they are readable. (without having to + # break our source-code line length). + printf "file can be RE-WRITTEN after './project " >> "$1" + printf "configure'.\n" >> "$1" + printf "#\n" >> "$1" + printf "# This file was created during configuration " >> "$1" + printf "('./project configure').\n" >> "$1" + printf "# Therefore, it is not under version control " >> "$1" + printf "and any manual changes\n" >> "$1" + printf "# to it will be over-written when the " >> "$1" + printf "project is re-configured.\n" >> "$1" + printf "#\n" >> "$1" else echo; echo "Can't write to $1"; echo; exit 1 @@ -102,7 +115,7 @@ absolute_dir () if stat "$address" 1> /dev/null; then echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")" else - exit 1; + echo "$optionaldir" fi } @@ -200,30 +213,113 @@ free_space_warning() -# See if we are on a Linux-based system -# -------------------------------------- +# Function to empty the temporary software building directory. This can +# either be a symbolic link (to RAM) or an actual directory, so we can't +# simply use 'rm -r' (because a symbolic link is not a directory for 'rm'). +empty_build_tmp() { + + # 'ls -A' does not print the '.' and '..' and the '-z' option of '[' + # checks if the string is empty or not. This allows us to only attempt + # deleting the directory's contents if it actually has anything inside + # of it. Otherwise, '*' will not expand and we'll get an 'rm' error + # complaining that '$tmpblddir/*' doesn't exist. We also don't want to + # use 'rm -rf $tmpblddir/*' because in case of a typo or while + # debugging (if '$tmpblddir' becomes an empty string), this can + # accidentally delete the whole root partition (or a least the '/home' + # partition of the user). + if ! [ x"$( ls -A $tmpblddir )" = x ]; then + rm -r "$tmpblddir"/* + fi + rm -r "$tmpblddir" +} + + + + + +# Function to report the elapsed time between steps (if it was activated +# above with 'check_elapsed'). +elapsed_time_from_prev_step() { + if [ $check_elapsed = 1 ]; then + chel_now=$(date +"%N"); + chel_delta=$(echo $chel_prev $chel_now \ + | awk '{ delta=($2-$1)/1e6; \ + if(delta>0) d=delta; else d=0; \ + print d}') + chel_dsum=$(echo $chel_dsum $chel_delta | awk '{print $1+$2}') + echo $chel_counter $chel_delta "$1" \ + | awk '{ printf "Step %02d: %-6.2f [millisec]; %s\n", \ + $1, $2, $3}' + chel_counter=$((chel_counter+1)) + chel_prev=$(date +"%N") + fi +} + + + + + + + + + + +# In already-built container +# -------------------------- +# +# We need to run './project configure' at the start of every run of Maneage +# within a container (with 'shell' or 'make'). This is because we need to +# ensure the versions of all software are correct. However, the container +# filesystem (where the build/software directory is located) should be run +# as read-only when doing the analysis. So we will not be able to run some +# of the tests that require writing files or are generally not relevant +# when the container is already built (we want the configure command to be +# as fast as possible). +# +# The project source in Maneage'd containers is '/home/maneager/source'. +built_container=0 +if [ "$topdir" = /home/maneager/source ] \ + && [ -f .build/software/config/hardware-parameters.tex ]; then + built_container=1; +fi + +# Initialize the elapsed time measurement parameters. +if [ $check_elapsed = 1 ]; then + chel_dsum=0.00 + chel_counter=1 + chel_prev=$(date +"%N") + chel_start=$(date +"%N") +fi + + + + +# Identify the running OS +# ----------------------- # # Some features are tailored to GNU/Linux systems, while the BSD-based # behavior is different. Initially we only tested macOS (hence the name of # the variable), but as FreeBSD is also being inlucded in our tests. As # more systems get used, we need to tailor these kinds of things better. -kernelname=$(uname -s) -if [ x$kernelname = xLinux ]; then - on_mac_os=no - - # Don't forget to add the respective C++ compiler below (leave 'cc' in - # the end). - c_compiler_list="gcc clang cc" -elif [ x$kernelname = xDarwin ]; then - host_cc=1 - on_mac_os=yes - - # Don't forget to add the respective C++ compiler below (leave 'cc' in - # the end). - c_compiler_list="clang gcc cc" -else - on_mac_os=no - cat <<EOF +if [ $built_container = 0 ]; then + kernelname=$(uname -s) + if [ $pauseformsg = 1 ]; then pausesec=10; else pausesec=0; fi + if [ x$kernelname = xLinux ]; then + on_mac_os=no + + # Don't forget to add the respective C++ compiler below (leave 'cc' in + # the end). + c_compiler_list="gcc clang cc" + elif [ x$kernelname = xDarwin ]; then + host_cc=1 + on_mac_os=yes + + # Don't forget to add the respective C++ compiler below (leave 'cc' in + # the end). + c_compiler_list="clang gcc cc" + else + on_mac_os=no + cat <<EOF ______________________________________________________ !!!!!!! WARNING !!!!!!! @@ -234,17 +330,20 @@ web-form: https://savannah.nongnu.org/support/?func=additem&group=reproduce -The configuration will continue in 10 seconds... +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - sleep 10 + sleep $pausesec + fi + elapsed_time_from_prev_step os_identify fi - # Collect CPU information # ----------------------- # @@ -255,42 +354,43 @@ fi # later recorded as a LaTeX macro to be put in the final paper, but it # could be used in a more systematic way to optimize/revise project # workflow and build. -hw_class=$(uname -m) -if [ x$kernelname = xLinux ]; then - byte_order=$(lscpu \ - | grep 'Byte Order' \ - | awk '{ \ - for(i=3;i<NF;++i) \ - printf "%s ", $i; \ - printf "%s", $NF}') - address_sizes=$(lscpu \ - | grep 'Address sizes' \ - | awk '{ \ - for(i=3;i<NF;++i) \ - printf "%s ", $i; \ - printf "%s", $NF}') -elif [ x$on_mac_os = xyes ]; then - hw_byteorder=$(sysctl -n hw.byteorder) - if [ x$hw_byteorder = x1234 ]; then byte_order="Little Endian"; - elif [ x$hw_byteorder = x4321 ]; then byte_order="Big Endian"; - fi - # On macOS, the way of obtaining the number of cores is different - # between Intel or Apple M1 CPUs. Here we disinguish between Apple M1 - # or others. - maccputype=$(sysctl -n machdep.cpu.brand_string) - if [ x"$maccputype" = x"Apple M1" ]; then - address_size_physical=$(sysctl -n machdep.cpu.thread_count) - address_size_virtual=$(sysctl -n machdep.cpu.logical_per_package) +if [ $built_container = 0 ]; then + if [ x$kernelname = xLinux ]; then + byte_order=$(lscpu \ + | grep 'Byte Order' \ + | awk '{ \ + for(i=3;i<NF;++i) \ + printf "%s ", $i; \ + printf "%s", $NF}') + address_sizes=$(lscpu \ + | grep 'Address sizes' \ + | awk '{ \ + for(i=3;i<NF;++i) \ + printf "%s ", $i; \ + printf "%s", $NF}') + elif [ x$on_mac_os = xyes ]; then + hw_byteorder=$(sysctl -n hw.byteorder) + if [ x$hw_byteorder = x1234 ]; then byte_order="Little Endian"; + elif [ x$hw_byteorder = x4321 ]; then byte_order="Big Endian"; + fi + + # On macOS, the way of obtaining the number of cores is different + # between Intel or Apple M1 CPUs. Here we disinguish between Apple + # M1 or others. + maccputype=$(sysctl -n machdep.cpu.brand_string) + if [ x"$maccputype" = x"Apple M1" ]; then + address_size_physical=$(sysctl -n machdep.cpu.thread_count) + address_size_virtual=$(sysctl -n machdep.cpu.logical_per_package) + else + address_size_physical=$(sysctl -n machdep.cpu.address_bits.physical) + address_size_virtual=$(sysctl -n machdep.cpu.address_bits.virtual) + fi + address_sizes="$address_size_physical bits physical, " + address_sizes+="$address_size_virtual bits virtual" else - address_size_physical=$(sysctl -n machdep.cpu.address_bits.physical) - address_size_virtual=$(sysctl -n machdep.cpu.address_bits.virtual) - fi - address_sizes="$address_size_physical bits physical, " - address_sizes+="$address_size_virtual bits virtual" -else - byte_order="unrecognized" - address_sizes="unrecognized" - cat <<EOF + byte_order="unrecognized" + address_sizes="unrecognized" + cat <<EOF ______________________________________________________ !!!!!!! WARNING !!!!!!! @@ -300,10 +400,15 @@ the necessary steps in the 'reproduce/software/shell/configure.sh' script https://savannah.nongnu.org/support/?func=additem&group=reproduce +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - sleep 5 + sleep $pausesec + fi + elapsed_time_from_prev_step cpu-info fi @@ -318,7 +423,7 @@ fi # avoid these error it is highly recommended to install Xcode in the host # system. Here, it is checked that this is the case, and if not, warn the user # about not having Xcode already installed. -if [ x$on_mac_os = xyes ]; then +if [ $built_container = 0 ] && [ x$on_mac_os = xyes ]; then # 'which' isn't in POSIX, so we are using 'command -v' instead. xcode=$(command -v xcodebuild) @@ -341,12 +446,15 @@ web-form: https://savannah.nongnu.org/support/?func=additem&group=reproduce -The configuration will continue in 5 seconds ... +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - sleep 5 + sleep $pausesec fi + elapsed_time_from_prev_step compiler-of-mac-os fi @@ -359,14 +467,15 @@ fi # To build the software, we'll need some basic tools (the C/C++ compilers # in particular) to be present. has_compilers=no -for c in $c_compiler_list; do +if [ $built_container = 0 ]; then + for c in $c_compiler_list; do - # Set the respective C++ compiler. - if [ x$c = xcc ]; then cplus=c++; - elif [ x$c = xgcc ]; then cplus=g++; - elif [ x$c = xclang ]; then cplus=clang++; - else - cat <<EOF + # Set the respective C++ compiler. + if [ x$c = xcc ]; then cplus=c++; + elif [ x$c = xgcc ]; then cplus=g++; + elif [ x$c = xclang ]; then cplus=clang++; + else + cat <<EOF ______________________________________________________ !!!!!!! BUG !!!!!!! @@ -379,21 +488,21 @@ script (just above this error message), or contact us with this web-form: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - exit 1 - fi + exit 1 + fi - # Check if they exist. - if type $c > /dev/null 2>/dev/null; then - export CC=$c; - if type $cplus > /dev/null 2>/dev/null; then - export CXX=$cplus - has_compilers=yes - break + # Check if they exist. + if type $c > /dev/null 2>/dev/null; then + export CC=$c; + if type $cplus > /dev/null 2>/dev/null; then + export CXX=$cplus + has_compilers=yes + break + fi fi - fi -done -if [ x$has_compilers = xno ]; then - cat <<EOF + done + if [ x$has_compilers = xno ]; then + cat <<EOF ______________________________________________________ !!!!!!! C/C++ Compiler NOT FOUND !!!!!!! @@ -416,51 +525,52 @@ Xcode install are recommended. There are known problems with GCC on macOS. !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - exit 1 + exit 1 + fi + elapsed_time_from_prev_step compiler-present fi - -# Special directory for compiler testing -# -------------------------------------- -# -# This directory will be deleted when the compiler testing is finished. -compilertestdir=.compiler_test_dir_please_delete -if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi - - - - - # Check C compiler # ---------------- # -# Here we check if the C compiler works properly. About the "no warning" -# variable ('nowarnings'): -# -# -Wno-nullability-completeness: on macOS Big Sur 11.2.3 and Xcode 12.4, -# hundreds of 'nullability-completeness' warnings are printed which can -# be very annoying and even hide important errors or warnings. It is -# also harmless for our test here, so it is generally added. -testprog=$compilertestdir/test +# We are checking the C compiler before asking for the directories to let +# the user fix lower-level problems before giving inputs. +compilertestdir=.compiler_test_dir_please_delete testsource=$compilertestdir/test.c -if [ x$on_mac_os = xyes ]; then - noccwarnings="-Wno-nullability-completeness" -fi -echo; echo; echo "Checking host C compiler ('$CC')..."; -cat > $testsource <<EOF +testprog=$compilertestdir/test +if [ $built_container = 0 ]; then + + # Here we check if the C compiler works properly. We'll start by + # making a directory to keep the products. + if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi + + # About the "no warning" variable ('nowarnings'): + # + # -Wno-nullability-completeness: on macOS Big Sur 11.2.3 and + # Xcode 12.4, hundreds of 'nullability-completeness' warnings + # are printed which can be very annoying and even hide + # important errors or warnings. It is also harmless for our + # test here, so it is generally added. + if [ x$on_mac_os = xyes ]; then + noccwarnings="-Wno-nullability-completeness" + fi + if [ $quiet = 0 ]; then + echo; echo "Checking host C compiler ('$CC')..."; + fi + cat > $testsource <<EOF #include <stdio.h> #include <stdlib.h> -int main(void){printf("...C compiler works.\n"); - return EXIT_SUCCESS;} +int main(void){printf("Good!\n"); return EXIT_SUCCESS;} EOF -if $CC $noccwarnings $testsource -o$testprog && $testprog; then - rm $testsource $testprog -else - rm $testsource - cat <<EOF + if $CC $noccwarnings $testsource -o$testprog && $testprog > /dev/null; then + if [ $quiet = 0 ]; then echo "... yes"; fi + rm $testsource $testprog + else + rm $testsource + cat <<EOF ______________________________________________________ !!!!!!! C compiler doesn't work !!!!!!! @@ -479,13 +589,14 @@ https://savannah.nongnu.org/support/?func=additem&group=reproduce !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - exit 1 + exit 1 + fi + elapsed_time_from_prev_step compiler-c-check fi - # See if we need the dynamic-linker (-ldl) # ---------------------------------------- # @@ -493,7 +604,8 @@ fi # 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. -cat > $testsource <<EOF +if [ $built_container = 0 ]; then + cat > $testsource <<EOF #include <stdio.h> #include <dlfcn.h> int @@ -502,17 +614,17 @@ main(void) { return 0; } EOF -if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then - needs_ldl=no; -else - needs_ldl=yes; + if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then + needs_ldl=no; + else + needs_ldl=yes; + fi + elapsed_time_from_prev_step compiler-needs-dynamic-linker fi - - # See if the C compiler can build static libraries # ------------------------------------------------ # @@ -528,32 +640,30 @@ fi # the library came from the system or our build. static_build=no - - - - # Print warning if the host CC is to be used. -if [ x$host_cc = x1 ]; then +if [ $built_container = 0 ] && [ x$host_cc = x1 ]; then cat <<EOF ______________________________________________________ !!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!! The GNU Compiler Collection (GCC, including compilers for C, C++, Fortran -and etc) is currently not built on macOS systems for this project. To build -the project's necessary software on this system, we need to use your -system's C compiler. +and etc) is not going to be built for this project. Either it is a macOS, +or you have used '--host-cc'. -Project's configuration will continue in 5 seconds. -______________________________________________________ +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - sleep 5 + sleep $pausesec fi + # Necessary C library element positions # ------------------------------------- # @@ -563,7 +673,7 @@ fi # similarly different location. sys_cpath="" sys_library_path="" -if [ x"$on_mac_os" != xyes ]; then +if [ $built_container = 0 ] && [ x"$on_mac_os" != xyes ]; then # Get the GCC target name of the compiler, when its given, special # C libraries and headers are in a sub-directory of the host. @@ -581,6 +691,7 @@ if [ x"$on_mac_os" != xyes ]; then # For a check: #echo "sys_library_path: $sys_library_path" #echo "sys_cpath: $sys_cpath" + elapsed_time_from_prev_step compiler-sys-cpath fi @@ -592,25 +703,28 @@ fi # # A static C library and the 'sys/cdefs.h' header are necessary for # building GCC. -if [ x"$host_cc" = x0 ]; then - echo; echo; echo "Checking if static C library is available..."; - cat > $testsource <<EOF +if [ $built_container = 0 ]; then + if [ x"$host_cc" = x0 ]; then + if [ $quiet = 0 ]; then + echo; echo "Checking if static C library is available..."; + fi + cat > $testsource <<EOF #include <stdio.h> #include <stdlib.h> #include <sys/cdefs.h> -int main(void){printf("...yes\n"); - return EXIT_SUCCESS;} +int main(void){printf("...yes\n"); return EXIT_SUCCESS;} EOF - cc_call="$CC $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc" - if $cc_call && $testprog; then - gccwarning=0 - rm $testsource $testprog - else - echo; echo "Compilation command:"; echo "$cc_call" - rm $testsource - gccwarning=1 - host_cc=1 - cat <<EOF + cc_call="$CC $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc" + if $cc_call && $testprog > /dev/null; then + gccwarning=0 + rm $testsource $testprog + if [ $quiet = 0 ]; then echo "... yes"; fi + else + echo; echo "Compilation command:"; echo "$cc_call" + rm $testsource + gccwarning=1 + host_cc=1 + cat <<EOF _______________________________________________________ !!!!!!!!!!!! Warning !!!!!!!!!!!! @@ -637,15 +751,14 @@ re-configure the project to fix this problem. $ export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS" $ export CPPFLAGS="-I/PATH/TO/SYS/CDEFS_H \$LDFLAGS" - _______________________________________________________ EOF + fi fi -fi -# Print a warning if GCC is not meant to be built. -if [ x"$gccwarning" = x1 ]; then + # Print a warning if GCC is not meant to be built. + if [ x"$gccwarning" = x1 ]; then cat <<EOF PLEASE SEE THE WARNINGS ABOVE. @@ -655,10 +768,13 @@ 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'. -Project's configuration will continue in 5 seconds. +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. EOF - sleep 5 + sleep $pausesec + fi + elapsed_time_from_prev_step compiler-linkable-static fi @@ -672,7 +788,7 @@ fi # have a fortran compiler: we'll build it internally for high-level # programs with GCC. However, when the host C compiler is to be used, the # user needs to have a Fortran compiler available. -if [ $host_cc = 1 ]; then +if [ $built_container = 0 ] && [ $host_cc = 1 ]; then # If a Fortran compiler is necessary, see if 'gfortran' exists and can # be used. @@ -705,8 +821,9 @@ EOF # Then, see if the Fortran compiler works testsourcef=$compilertestdir/test.f echo; echo; echo "Checking host Fortran compiler..."; - echo " PRINT *, \"... Fortran Compiler works.\"" > $testsourcef - echo " END" >> $testsourcef + echo " PRINT *, \"... Fortran Compiler works.\"" \ + > $testsourcef + echo " END" >> $testsourcef if gfortran $testsourcef -o$testprog && $testprog; then rm $testsourcef $testprog else @@ -732,6 +849,68 @@ EOF exit 1 fi fi + elapsed_time_from_prev_step compiler-fortran +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. +# +# IMPORTANT NOTE: This test has to be done **AFTER** the definition of +# 'instdir', otherwise, it is going to be used as an empty string. +if [ $built_container = 0 ]; then + cat > $testsource <<EOF +#include <stdio.h> +#include <stdlib.h> +int main(void) {return EXIT_SUCCESS;} +EOF + if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null \ + > /dev/null; then + export rpath_command="-Wl,-rpath-link=$instdir/lib" + else + export rpath_command="" + fi + + # Delete the temporary directory for compiler checking. + rm -f $testprog $testsource + rm -r $compilertestdir + elapsed_time_from_prev_step compiler-rpath +fi + + + + + +# Paths needed by the host compiler (only for 'basic.mk') +# ------------------------------------------------------- +# +# At the end of the basic build, we need to build GCC. But GCC will build +# in multiple phases, making its own simple compiler in order to build +# itself completely. The intermediate/simple compiler doesn't recognize +# some system specific locations like '/usr/lib/ARCHITECTURE' that some +# operating systems use. We thus need to tell the intermediate compiler +# where its necessary libraries and headers are. +if [ $built_container = 0 ]; then + if [ x"$sys_library_path" != x ]; then + if [ x"$LIBRARY_PATH" = x ]; then + export LIBRARY_PATH="$sys_library_path" + else + export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path" + fi + if [ x"$CPATH" = x ]; then + export CPATH="$sys_cpath" + else + export CPATH="$CPATH:$sys_cpath" + fi + fi + elapsed_time_from_prev_step compiler-paths fi @@ -743,7 +922,8 @@ fi # # 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 +if [ $quiet = 0 ]; then + cat <<EOF ----------------------------- Project's local configuration @@ -758,33 +938,29 @@ components from pre-defined webpages). It is STRONGLY recommended to read the description above each question before answering it. EOF +fi - -# What to do with possibly existing configuration file -# ---------------------------------------------------- +# Previous configuration +# ---------------------- # -# 'LOCAL.conf' 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 -if [ -f $pconf ]; then +# 'LOCAL.conf' is the top-most local configuration for the project. At this +# point, if a LOCAL.conf exists within the '.build' symlink, we use it +# (instead of asking the user to interactively specify it). +rewritelconfig=yes +lconf=.build/software/config/LOCAL.conf +if [ -f $lconf ]; then if [ $existing_conf = 1 ]; then - printnotice=no - if [ -f $pconf ]; then rewritepconfig=no; fi + rewritelconfig=no; 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 [ $rewritelconfig = no ]; then + oldgroupname=$(awk '/GROUP-NAME/ {print $3; exit 0}' $lconf) if [ "x$oldgroupname" = "x$maneage_group_name" ]; then just_a_place_holder_to_avoid_not_equal_test=1; else @@ -805,65 +981,9 @@ if [ $rewritepconfig = no ]; then 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 [ $rewritepconfig = yes ]; then - if type wget > /dev/null 2>/dev/null; then - - # 'which' isn't in POSIX, so we are using 'command -v' instead. - name=$(command -v wget) - # See if the host wget has the '--no-use-server-timestamps' option - # (for example wget 1.12 doesn't have it). If not, we'll have to - # remove it. This won't affect the analysis of Maneage in anyway, - # its just to avoid re-downloading if the server timestamps are - # bad; at the worst case, it will just cause a re-download of an - # input software source code (for data inputs, we will use our own - # wget that has this option). - tsname="no-use-server-timestamps" - tscheck=$(wget --help | grep $tsname || true) - if [ x"$tscheck" = x ]; then wgetts="" - else wgetts="--$tsname"; - fi - - # By default Wget keeps the remote file's timestamp, so we'll have - # to disable it manually. - downloader="$name $wgetts -O"; - elif type curl > /dev/null 2>/dev/null; then - name=$(command -v curl) - - # - cURL doesn't keep the remote file's timestamp by default. - # - With the '-L' option, we tell cURL to follow redirects. - downloader="$name -L -o" - else - cat <<EOF - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -Couldn't find GNU Wget, or cURL on this system. These programs are used for -downloading necessary programs and data if they aren't already present (in -directories that you can specify with this configure script). Therefore if -the necessary files are not present, the project will crash. - -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - -EOF - downloader="no-downloader-found" - fi; + # Report timing of this step if necessary. + elapsed_time_from_prev_step LOCAL-and-group-check fi @@ -873,7 +993,7 @@ fi # Build directory # --------------- currentdir="$(pwd)" -if [ $rewritepconfig = yes ]; then +if [ $rewritelconfig = yes ]; then cat <<EOF =============== @@ -901,12 +1021,18 @@ Do not choose any directory under the top source directory (this directory). The build directory cannot be a subdirectory of the source. --------------- +Build directory: + - Must be writable by running user. + - Not a sub-directory of the source directory. + - No meta-characters in name: SPACE ! ' @ # $ % ^ & * ( ) + ; + EOF bdir= junkname=pure-junk-974adfkj38 while [ x"$bdir" = x ] do - # Ask the user (if not already set on the command-line). + # Ask the user (if not already set on the command-line: 'build_dir' + # comes from the 'project' script). if [ x"$build_dir" = x ]; then if read -p"Please enter the top build directory: " build_dir; then @@ -948,9 +1074,11 @@ EOF # If it was newly created, it will be empty, so delete it. if ! [ "$(ls -A $bdir)" ]; then rm --dir "$bdir"; fi - # Inform the user that this is not acceptable and reset 'bdir'. + # Inform the user that this is not acceptable and reset + # 'bdir'. bdir= - echo " ** The build-directory cannot be under the source-directory." + printf " ** The build-directory cannot be under the " + printf "source-directory." fi fi @@ -959,7 +1087,8 @@ EOF # building. if ! [ x"$bdir" = x ]; then hasmeta=0; - case $bdir in *['!'\@\#\$\%\^\&\*\(\)\+\;\ ]* ) hasmeta=1 ;; esac + case $bdir in *['!'\@\#\$\%\^\&\*\(\)\+\;\ ]* ) hasmeta=1 ;; + esac if [ $hasmeta = 1 ]; then # If it was newly created, it will be empty, so delete it. @@ -967,9 +1096,10 @@ EOF # Inform the user and set 'bdir' to empty again. bdir= - echo " ** Build directory should not contain meta-characters" - echo " ** (like SPACE, %, \$, !, ;, or parenthesis, among " - echo " ** others): they can interrup the build for some software." + printf " ** Build directory should not contain " + printf "meta-characters (like SPACE, %, \$, !, ;, or " + printf "parenthesis, among others): they can interrup " + printf "the build for some software." fi fi @@ -980,16 +1110,29 @@ EOF if ! $(check_permission "$bdir"); then # Unable to handle permissions well bdir= - echo " ** File permissions can't be modified in this directory" + printf " ** File permissions can not be modified in " + printf "this directory" else # Able to handle permissions, now check for 5GB free space # in the given partition (note that the number is in units # of 1024 bytes). If this is not the case, print a warning. if $(free_space_warning 5000000 "$bdir"); then - echo " !! LESS THAN 5GB FREE SPACE IN: $bdir" - echo " !! We recommend choosing another partition." - echo " !! Build will continue in 5 seconds..." - sleep 5 + cat <<EOF + +_______________________________________________________ +!!!!!!!!!!!! Warning !!!!!!!!!!!! + +Less than 5GB free space in '$bdir'. We recommend choosing another +partition. Note that the software environment alone will take roughly +4.5GB, so if your datasets are large, it will fill up very soon. + +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + sleep $pausesec fi fi fi @@ -1006,6 +1149,25 @@ EOF echo " -- Build directory set to ($instring): '$bdir'" fi done + + # Report timing if necessary + elapsed_time_from_prev_step build-dir + +# The directory should be extracted from the existing LOCAL.conf, not from +# the command-line or in interactive mode. +else + + # Read the build directory from existing configuration file. It is + # assumed that 'LOCAL.conf' is created by this script (above the + # 'else') and that all the sanity checks there have already been + # applied. We'll just check if it is empty or not. + bdir=$(awk '$1=="BDIR" {print $3}' $lconf) + if [ x"$bdir" = x ]; then + printf "$scriptname: no value to 'BDIR' of '$lconf'. Please run " + printf "the project configuration again, but without " + printf "'--existing-conf' (or '-e')" + exit 1 + fi fi @@ -1014,13 +1176,10 @@ fi # Input directory # --------------- -if [ x"$input_dir" = x ]; then - indir="$optionaldir" -else - indir="$input_dir" +if [ x"$input_dir" = x ]; then indir="$optionaldir" +else indir="$input_dir" fi -noninteractive_sleep=2 -if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then +if [ $rewritelconfig = yes ]; then cat <<EOF ---------------------------------- @@ -1047,35 +1206,61 @@ don't want to make duplicates, you can create symbolic links to them and put those symbolic links in the given top-level directory. EOF - # Read the input directory if interactive mode is enabled. - if read -p"(OPTIONAL) Input datasets directory ($indir): " inindir; then - just_a_place_holder_to_avoid_not_equal_test=1; - else - echo "WARNING: interactive-mode seems to be disabled!" - echo "If you have a local copy of the inputs, use '--input-dir'." - echo "... project configuration will continue in $noninteractive_sleep sec ..." - sleep $noninteractive_sleep + # In case an input directory is not given, ask the user interactively. + if [ x"$input_dir" = x ]; then + + # Read the input directory if interactive mode is enabled. + if read -p"(OPTIONAL) Input datasets directory ($indir): " \ + inindir; then + just_a_place_holder_to_avoid_not_equal_test=1; + else + cat <<EOF +______________________________________________________ +!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!! + +WARNING: interactive-mode seems to be disabled! If you have a local copy of +the inputs, use '--input-dir'. Otherwise, all the data will be downloaded. + +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + sleep $pausesec + fi + else # An input directory was given. + inindir="$input_dir" fi - # In case an input-directory is given, write it in 'indir'. + # If the given string is not empty, write it in 'indir'. if [ x$inindir != x ]; then indir="$(absolute_dir "$inindir")" echo " -- Using '$indir'" fi + + # Report timing if necessary. + elapsed_time_from_prev_step input-dir + +# The directory should be extracted from the existing LOCAL.conf, not from +# the command-line or in interactive mode; similar to 'bdir' above. +else + indir=$(awk '$1=="INDIR" {print $3}' $lconf) fi + # Dependency tarball directory # ---------------------------- -if [ x"$software_dir" = x ]; then - ddir=$optionaldir -else - ddir=$software_dir +if [ x"$software_dir" = x ]; then ddir=$optionaldir +else ddir=$software_dir fi -if [ $rewritepconfig = yes ] && [ x"$software_dir" = x ]; then +if [ $rewritelconfig = yes ]; then + + # Print information. cat <<EOF --------------------------------------- @@ -1091,14 +1276,32 @@ of a dependency, it is necessary to have an internet connection because the project will download the tarballs it needs automatically. EOF - # Read the software directory if interactive mode is enabled. - if read -p"(OPTIONAL) Directory of dependency tarballs ($ddir): " tmpddir; then - just_a_place_holder_to_avoid_not_equal_test=1; + + # Ask the user for the software directory if it is not given as an + # option. + if [ x"$software_dir" = x ]; then + if read -p"(OPTIONAL) Directory of dependency tarballs ($ddir): " \ + tmpddir; then + just_a_place_holder_to_avoid_not_equal_test=1; + else + cat <<EOF +______________________________________________________ +!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!! + +WARNING: interactive-mode seems to be disabled! If you have a local copy of +the software source tarballs, use '--software-dir'. Otherwise, all the +necessary tarballs will be downloaded. + +The configuration will continue in $pausesec seconds. To avoid the +pause on such messages use the '--no-pause' option. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +EOF + sleep $pausesec + fi else - echo "WARNING: interactive-mode seems to be disabled!" - echo "If you have a local copy of the software source, use '--software-dir'." - echo "... project configuration will continue in $noninteractive_sleep sec ..." - sleep $noninteractive_sleep + tmpddir="$software_dir" fi # If given, write the software directory. @@ -1106,105 +1309,115 @@ EOF ddir="$(absolute_dir "$tmpddir")" echo " -- Using '$ddir'" fi -fi - +# The directory should be extracted from the existing LOCAL.conf, not from +# the command-line or in interactive mode; similar to 'bdir' above. +else + indir=$(awk '$1=="DEPENDENCIES-DIR" {print $3}' $lconf) +fi +elapsed_time_from_prev_step software-dir -# 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|@sys_cpath[@]|'"$sys_cpath"'|' \ - -e's|@downloader[@]|'"$downloader"'|' \ - -e's|@groupname[@]|'"$maneage_group_name"'|' \ - $pconf.in >> $pconf -else - # Read the values from existing configuration file. Note that the build - # directory may have space characters. Even though we currently check - # against it, we hope to be able to remove this condition in the - # future. - inbdir=$(awk '$1=="BDIR" { for(i=3; i<NF; i++) \ - printf "%s ", $i; \ - printf "%s", $NF }' $pconf) - - # Read the software directory (same as 'inbdir' above about space). - ddir=$(awk '$1=="DEPENDENCIES-DIR" { for(i=3; i<NF; i++) \ - printf "%s ", $i; \ - printf "%s", $NF}' $pconf) - - # The downloader command may contain multiple elements, so we'll just - # change the (in memory) first and second tokens to empty space and - # write the full line (the original file is unchanged). - downloader=$(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 +# Downloader +# ---------- +# +# 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 [ $rewritelconfig = yes ]; then + if type wget > /dev/null 2>/dev/null; then -################################################################# -######## ERORR reading existing configuration file ############ -################################################################# -EOF - if [ $verr = 1 ]; then - cat <<EOF + # 'which' isn't in POSIX, so we are using 'command -v' instead. + name=$(command -v wget) -These variables have no value: $novalue. -EOF + # See if the host wget has the '--no-use-server-timestamps' option + # (for example wget 1.12 doesn't have it). If not, we'll have to + # remove it. This won't affect the analysis of Maneage in anyway, + # its just to avoid re-downloading if the server timestamps are + # bad; at the worst case, it will just cause a re-download of an + # input software source code (for data inputs, we will use our own + # wget that has this option). + tsname="no-use-server-timestamps" + tscheck=$(wget --help | grep $tsname || true) + if [ x"$tscheck" = x ]; then wgetts="" + else wgetts="--$tsname"; fi - if [ $berr = 1 ]; then - cat <<EOF -Couldn't create the build directory '$bdir' (value to 'BDIR') in -'$pconf'. -EOF - fi + # By default Wget keeps the remote file's timestamp, so we'll have + # to disable it manually. + downloader="$name $wgetts -O"; + elif type curl > /dev/null 2>/dev/null; then + name=$(command -v curl) + # - cURL doesn't keep the remote file's timestamp by default. + # - With the '-L' option, we tell cURL to follow redirects. + downloader="$name -L -o" + else cat <<EOF -Please run the configure script again (accepting to re-write existing -configuration file) so all the values can be filled and checked. -################################################################# +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!!!!!!!! +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + +Couldn't find GNU Wget, or cURL on this system. These programs are used for +downloading necessary programs and data if they aren't already present (in +directories that you can specify with this configure script). Therefore if +the necessary files are not present, the project will crash. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + EOF + downloader="no-downloader-found" + fi; + +# The downloader should be extracted from the existing LOCAL.conf. +else + # The value will be a command (including white spaces), so we will read + # all the "fields" from the third to the end. + downloader=$(awk '$1=="DOWNLOADER" { for(i=3; i<NF; i++) \ + printf "%s ", $i; \ + printf "%s", $NF }' $lconf) + + if [ x"$downloader" = x ]; then + printf "$scriptname: no value to 'DOWNLOADER' of '$lconf'. " + printf "Please run the project configuration again, but " + printf "without '--existing-conf' (or '-e')" + exit 1 fi fi +elapsed_time_from_prev_step downloader -# 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 "$finaltarget" +# When no local configuration existed, write the parameters into the local +# configuration file. +sdir=$bdir/software +sconfdir=$sdir/config +if ! [ -d "$sdir" ]; then mkdir "$sdir"; fi +if ! [ -d "$sconfdir" ]; then mkdir "$sconfdir"; fi +if [ $rewritelconfig = yes ]; then + + # Put the basic comments at the top of the file. + create_file_with_notice $lconf + + # Write the values. + lconfin=$cdir/LOCAL.conf.in + sed -e's|@bdir[@]|'"$bdir"'|' \ + -e's|@indir[@]|'"$indir"'|' \ + -e's|@ddir[@]|'"$ddir"'|' \ + -e's|@sys_cpath[@]|'"$sys_cpath"'|' \ + -e's|@downloader[@]|'"$downloader"'|' \ + -e's|@groupname[@]|'"$maneage_group_name"'|' \ + $lconfin >> $lconf +fi +elapsed_time_from_prev_step LOCAL-write @@ -1217,99 +1430,58 @@ rm -f "$finaltarget" # 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 +tmpblddir="$sdir"/build-tmp -# To record software versions and citation. +# Second-level directories. +instlibdir="$instdir"/lib +instbindir="$instdir"/bin verdir="$instdir"/version-info -if ! [ -d "$verdir" ]; then mkdir "$verdir"; fi - -# Program and library versions and citation. -ibidir="$verdir"/proglib -if ! [ -d "$ibidir" ]; then mkdir "$ibidir"; fi -# Python module versions and citation. +# Sub-directories of version-info +itidir="$verdir"/tex +ictdir="$verdir"/cite ipydir="$verdir"/python -if ! [ -d "$ipydir" ]; then mkdir "$ipydir"; fi - -# R module versions and citation. +ibidir="$verdir"/proglib ircrandir="$verdir"/r-cran -if ! [ -d "$ircrandir" ]; then mkdir "$ircrandir"; 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 - -# Some software install their libraries in '$(idir)/lib64'. But all other -# libraries are in '$(idir)/lib'. Since Maneage's build is only for a -# single architecture, we can set the '$(idir)/lib64' as a symbolic link to -# '$(idir)/lib' so all the libraries are always available in the same -# place. -instlibdir="$instdir"/lib -if ! [ -d "$instlibdir" ]; then mkdir "$instlibdir"; fi -ln -fs "$instlibdir" "$instdir"/lib64 - -# Wrapper over Make as a single command so it does not default to '/bin/sh' -# during installation (needed by some programs like CMake). -instbindir=$instdir/bin -if ! [ -d $instbindir ]; then mkdir $instbindir; fi -makewshell="$instbindir/make-with-shell" -echo "$instbindir/make SHELL=$instbindir/bash \$@" > $makewshell -chmod +x $makewshell - - - - - -# Project's top-level built analysis directories -# ---------------------------------------------- +if [ $built_container = 0 ]; then + + # Top-level directories. + if ! [ -d "$tardir" ]; then mkdir "$tardir"; fi + if ! [ -d "$instdir" ]; then mkdir "$instdir"; fi + + # Second-level directories. + if ! [ -d "$verdir" ]; then mkdir "$verdir"; fi + if ! [ -d "$instbindir" ]; then mkdir "$instbindir"; fi + + # Sub-directories of version-info + if ! [ -d "$itidir" ]; then mkdir "$itidir"; fi + if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi + if ! [ -d "$ipydir" ]; then mkdir "$ipydir"; fi + if ! [ -d "$ibidir" ]; then mkdir "$ibidir"; fi + if ! [ -d "$ircrandir" ]; then mkdir "$ircrandir"; fi + + # Some software install their libraries in '$(idir)/lib64'. But all + # other libraries are in '$(idir)/lib'. Since Maneage's build is only + # for a single architecture, we can set the '$(idir)/lib64' as a + # symbolic link to '$(idir)/lib' so all the libraries are always + # available in the same place. + if ! [ -d "$instlibdir" ]; then mkdir "$instlibdir"; fi + ln -fs "$instlibdir" "$instdir"/lib64 + + # Wrapper over Make as a single command so it does not default to + # '/bin/sh' during installation (needed by some programs like CMake). + makewshell="$instbindir/make-with-shell" + if ! [ -f "$makewshell" ]; then + echo "$instbindir/make SHELL=$instbindir/bash \$@" > $makewshell + chmod +x $makewshell + fi -# Top-level LaTeX. -texdir="$sdir"/tex -if ! [ -d "$texdir" ]; then mkdir "$texdir"; fi - -# If 'tex/build' and 'tex/tikz' are symbolic links then 'rm -f' will delete -# them and we can continue. However, when the project is being built from -# the tarball, these two are not symbolic links but actual directories with -# the necessary built-components to build the PDF in them. In this case, -# because 'tex/build' is a directory, 'rm -f' will fail, so we'll just -# rename the two directories (as backup) and let the project build the -# proper symbolic links afterwards. -if rm -f tex/build; then - rm -f tex/tikz -else - mv tex/tikz tex/tikz-from-tarball - mv tex/build tex/build-from-tarball + # Report the execution time of this step. + elapsed_time_from_prev_step subdirectories-of-build 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. Note that at this stage, we are using the host's 'ln', not our -# own, so its best not to assume anything (like 'ln -sf'). -rm -f .build .local - -ln -s "$bdir" .build -ln -s "$instdir" .local - -# --------- Delete for no Gnuastro --------- -rm -f .gnuastro -# ------------------------------------------ - @@ -1322,120 +1494,116 @@ rm -f .gnuastro # HDDs/SSDs and improve speed, it is therefore better to build them in the # RAM when possible. The RAM of most systems today (>8GB) is large enough # for the parallel building of the software. - +# # Set the top-level shared memory location. Currently there is only one # standard location (for GNU/Linux OSs), so doing this check here and the # main job below may seem redundant. However, it is written separately from # the main code below because later, we expect to add more possible # mounting locations (for other OSs). -if [ -d /dev/shm ]; then shmdir=/dev/shm -else shmdir="" -fi +if [ $built_container = 0 ]; then + if [ -d /dev/shm ]; then shmdir=/dev/shm + else shmdir="" + fi -# If a shared memory mounted directory exists and has the necessary -# conditions, set that directory to build software. -if [ x"$shmdir" != x ]; then - - # Make sure it has enough space. - needed_space=2000000 - available_space=$(df "$shmdir" | awk 'NR==2{print $4}') - if [ $available_space -gt $needed_space ]; then - - # Set the Maneage-specific directory within the shared - # memory. We'll use the names of the two parent directories to the - # current/running directory, separated by a '-' instead of - # '/'. We'll then appended that with the user's name (in case - # multiple users may be working on similar project names). - # - # Maybe later, we can use something like 'mktemp' to add random - # characters to this name and make it unique to every run (even for - # a single user). - dirname=$(pwd | sed -e's/\// /g' \ - | awk '{l=NF-1; printf("%s-%s", $l, $NF)}') - tbshmdir="$shmdir"/"$dirname"-$(whoami) - - # Try to make the directory if it does not yet exist. A failed - # directory creation will be tested for a few lines later, when - # testing for the existence and executability of a test file. - if ! [ -d "$tbshmdir" ]; then (mkdir "$tbshmdir" || true); fi - - # Some systems may protect '/dev/shm' against the right to execute - # programs by ordinary users. We thus need to check that the device - # allows execution within this directory by this user. - shmexecfile="$tbshmdir"/shm-execution-check.sh - rm -f $shmexecfile # We also don't want any existing flags. - - # Create the file to be executed, but do not fail fatally if it - # cannot be created. We will check a few lines later if the file - # really exists. - (cat > "$shmexecfile" <<EOF || true) + # If a shared memory mounted directory exists and has the necessary + # conditions, set that directory to build software. + if [ x"$shmdir" != x ]; then + + # Make sure it has enough space. + needed_space=2000000 + available_space=$(df "$shmdir" | awk 'NR==2{print $4}') + if [ $available_space -gt $needed_space ]; then + + # Set the Maneage-specific directory within the shared + # memory. We'll use the names of the two parent directories to + # the current/running directory, separated by a '-' instead of + # '/'. We'll then appended that with the user's name (in case + # multiple users may be working on similar project names). + # + # Maybe later, we can use something like 'mktemp' to add random + # characters to this name and make it unique to every run (even + # for a single user). + dirname=$(pwd | sed -e's/\// /g' \ + | awk '{l=NF-1; printf("%s-%s", $l, $NF)}') + tbshmdir="$shmdir"/"$dirname"-$(whoami) + + # Try to make the directory if it does not yet exist. A failed + # directory creation will be tested for a few lines later, when + # testing for the existence and executability of a test file. + if ! [ -d "$tbshmdir" ]; then (mkdir "$tbshmdir" || true); fi + + # Some systems may protect '/dev/shm' against the right to + # execute programs by ordinary users. We thus need to check + # that the device allows execution within this directory by + # this user. + shmexecfile="$tbshmdir"/shm-execution-check.sh + rm -f $shmexecfile # We also don't want any existing flags. + + # Create the file to be executed, but do not fail fatally if it + # cannot be created. We will check a few lines later if the + # file really exists. + (cat > "$shmexecfile" <<EOF || true) #!/bin/sh -echo "This file successfully executed." +a=b EOF - # If the file was successfully created, then make the file - # executable and see if it runs. If not, set 'tbshmdir' to an empty - # string so it is not used in later steps. In any case, delete the - # temporary file afterwards. - # - # We aren't adding '&> /dev/null' after the execution command - # because it can produce false failures randomly on some systems. - if [ -e "$shmexecfile" ]; then - - # Add the executable flag. - chmod +x "$shmexecfile" - - # The following line tries to execute the file. - if "$shmexecfile"; then - # Successful execution. The colon is a "no-op" (no - # operation) shell command. - : + # If the file was successfully created, then make the file + # executable and see if it runs. If not, set 'tbshmdir' to an + # empty string so it is not used in later steps. In any case, + # delete the temporary file afterwards. + # + # We aren't adding '&> /dev/null' after the execution command + # because it can produce false failures randomly on some + # systems. + if [ -e "$shmexecfile" ]; then + + # Add the executable flag. + chmod +x "$shmexecfile" + + # The following line tries to execute the file. + if "$shmexecfile"; then + # Successful execution. The colon is a "no-op" (no + # operation) shell command. + : + else + tbshmdir="" + fi + rm "$shmexecfile" else tbshmdir="" fi - rm "$shmexecfile" - else - tbshmdir="" fi + else + tbshmdir="" fi -else - tbshmdir="" -fi - - - + # If a shared memory directory was created, set the software building + # directory to be a symbolic link to it. Otherwise, just build the + # temporary build directory under the project's build directory. + # + # If it is a link, we need to empty its contents first, then itself. + if [ -d "$tmpblddir" ]; then empty_build_tmp; fi + + # Now that we are sure it doesn't exist, we'll make it (either as a + # directory or as a symbolic link). + if [ x"$tbshmdir" = x ]; then mkdir "$tmpblddir"; + else ln -s "$tbshmdir" "$tmpblddir"; + fi -# If a shared memory directory was created, set the software building -# directory to be a symbolic link to it. Otherwise, just build the -# temporary build directory under the project's build directory. -tmpblddir="$sdir"/build-tmp -rm -rf "$tmpblddir"/* "$tmpblddir" # If it is a link, we need to empty - # its contents first, then itself. -if [ x"$tbshmdir" = x ]; then mkdir "$tmpblddir"; -else ln -s "$tbshmdir" "$tmpblddir"; + # Report the time this step took. + elapsed_time_from_prev_step temporary-software-building-dir fi -# Make sure the temporary build directory is empty (un-finished -# source/build files from previous builds can remain there during debugging -# or software updates). -rm -rf $tmpblddir/* - - - - - # Inform the user that the build process is starting # ------------------------------------------------- # # Everything is ready, let the user know that the building is going to # start. -if [ $printnotice = yes ]; then - tsec=10 +if [ $quiet = 0 ]; then cat <<EOF ------------------------- @@ -1450,20 +1618,20 @@ NOTE: the built software will NOT BE INSTALLED in standard places of your OS (so no root access is required). They are only for local usage by this project. -**TIP**: you can see which software are being installed at every moment -with the following command. See "Inspecting status" section of -'README-hacking.md' for more. In short, run it while the project is being -configured (in another terminal, but in this same directory: -'$currentdir'): +TIP: you can see which software are being installed at every moment with +the following command. See "Inspecting status" section of +'README-hacking.md' for more. In short, run it in another terminal while +the project is being configured. $ ./project --check-config -Project's configuration will continue in $tsec seconds. +Project's configuration will continue in $tsec seconds. To avoid the pause +on such messages use the '--no-pause' option. ------------------------- EOF - sleep $tsec + sleep $pausesec fi @@ -1479,83 +1647,25 @@ fi # - On BSD-based systems (for example FreeBSD and macOS), we have a # 'hw.ncpu' in the output of 'sysctl'. # - When none of the above work, just set the number of threads to 1. -if [ $jobs = 0 ]; then - if type nproc > /dev/null 2> /dev/null; then - numthreads=$(nproc --all); - else - numthreads=$(sysctl -a | awk '/^hw\.ncpu/{print $2}') - if [ x"$numthreads" = x ]; then numthreads=1; fi - fi -else - numthreads=$jobs -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. -# -# IMPORTANT NOTE: This test has to be done **AFTER** the definition of -# 'instdir', otherwise, it is going to be used as an empty string. -cat > $testsource <<EOF -#include <stdio.h> -#include <stdlib.h> -int main(void) {return EXIT_SUCCESS;} -EOF -if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null > /dev/null; then - export rpath_command="-Wl,-rpath-link=$instdir/lib" -else - export rpath_command="" -fi - - - - - -# Delete the compiler testing directory -# ------------------------------------- # -# This directory was made above to make sure the necessary compilers can be -# run. -rm -f $testprog $testsource -rm -rf $compilertestdir - - - - - -# Paths needed by the host compiler (only for 'basic.mk') -# ------------------------------------------------------- -# -# At the end of the basic build, we need to build GCC. But GCC will build -# in multiple phases, making its own simple compiler in order to build -# itself completely. The intermediate/simple compiler doesn't recognize -# some system specific locations like '/usr/lib/ARCHITECTURE' that some -# operating systems use. We thus need to tell the intermediate compiler -# where its necessary libraries and headers are. -if [ x"$sys_library_path" != x ]; then - if [ x"$LIBRARY_PATH" = x ]; then - export LIBRARY_PATH="$sys_library_path" - else - export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path" - fi - if [ x"$CPATH" = x ]; then - export CPATH="$sys_cpath" +# This check is also used in 'reproduce/software/shell/docker.sh'. +if [ $built_container = 0 ]; then + if [ $jobs = 0 ]; then + if type nproc > /dev/null 2> /dev/null; then + numthreads=$(nproc --all); + else + numthreads=$(sysctl -a | awk '/^hw\.ncpu/{print $2}') + if [ x"$numthreads" = x ]; then numthreads=1; fi + fi else - export CPATH="$CPATH:$sys_cpath" + numthreads=$jobs fi + elapsed_time_from_prev_step num-threads fi - # Libraries necessary for the system's shell # ------------------------------------------ # @@ -1579,29 +1689,31 @@ fi # [1] https://savannah.nongnu.org/bugs/index.php?66847 # [2] https://stackoverflow.com/questions/34428037/how-to-interpret-the-output-of-the-ldd-program # [3] man vdso -if [ x"$on_mac_os" = xyes ]; then - sys_library_sh_path=$(otool -L /bin/sh \ - | awk '/\/lib/{print $1}' \ - | sed 's#/[^/]*$##' \ - | sort \ - | uniq \ - | awk '{if (NR==1) printf "%s", $1; \ - else printf ":%s", $1}') -else - sys_library_sh_path=$(ldd /bin/sh \ - | awk '{if($3!="") print $3}' \ - | sed 's#/[^/]*$##' \ - | grep -v "(0x[^)]*)" \ - | sort \ - | uniq \ - | awk '{if (NR==1) printf "%s", $1; \ - else printf ":%s", $1}') +if [ $built_container = 0 ]; then + if [ x"$on_mac_os" = xyes ]; then + sys_library_sh_path=$(otool -L /bin/sh \ + | awk '/\/lib/{print $1}' \ + | sed 's#/[^/]*$##' \ + | sort \ + | uniq \ + | awk '{if (NR==1) printf "%s", $1; \ + else printf ":%s", $1}') + else + sys_library_sh_path=$(ldd /bin/sh \ + | awk '{if($3!="") print $3}' \ + | sed 's#/[^/]*$##' \ + | grep -v "(0x[^)]*)" \ + | sort \ + | uniq \ + | awk '{if (NR==1) printf "%s", $1; \ + else printf ":%s", $1}') + fi + elapsed_time_from_prev_step sys-library-sh-path fi - # Find Zenodo URL for software downloading # ---------------------------------------- # @@ -1619,42 +1731,32 @@ fi # which will download the DOI-resolved webpage, and extract the Zenodo-URL # of the most recent version from there (using the 'coreutils' tarball as # an example, the directory part of the URL for all the other software are -# the same). This is not done if the options '--debug' or `--offline` are used. +# the same). This is not done if the options '--debug' or `--offline` are +# used. zenodourl="" user_backup_urls="" -zenodocheck=.build/software/zenodo-check.html -if [ x$debug = x ] && [ x$offline = x ]; then - if $downloader $zenodocheck https://doi.org/10.5281/zenodo.3883409; then - zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \ - | sed -n -e'/http/p' \ - | tr ' ' '\n' \ - | grep http \ - | sed -e 's/href="//' -e 's|/coreutils| |' \ - | awk 'NR==1{print $1}') - fi +zenodocheck="$bdir"/software/zenodo-check.html +if [ $built_container = 0 ]; then + if [ x$debug = x ] && [ x$offline = x ]; then + if $downloader $zenodocheck \ + https://doi.org/10.5281/zenodo.3883409; then + zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \ + | sed -n -e'/http/p' \ + | tr ' ' '\n' \ + | grep http \ + | sed -e 's/href="//' -e 's|/coreutils| |' \ + | awk 'NR==1{print $1}') + fi + fi + rm -f $zenodocheck + + # Add the Zenodo URL to the user's given back software URLs. Since the + # user can specify 'user_backup_urls' (not yet implemented as an option + # in './project'), we'll give preference to their specified servers, + # then add the Zenodo URL afterwards. + user_backup_urls="$user_backup_urls $zenodourl" + elapsed_time_from_prev_step zenodo-url fi -rm -f $zenodocheck - -# Add the Zenodo URL to the user's given back software URLs. Since the user -# can specify 'user_backup_urls' (not yet implemented as an option in -# './project'), we'll give preference to their specified servers, then add -# the Zenodo URL afterwards. -user_backup_urls="$user_backup_urls $zenodourl" - - - - - -# Build core tools for project -# ---------------------------- -# -# Here we build the core tools that 'basic.mk' depends on: Lzip -# (compression program), GNU Make (that 'basic.mk' is written in), Dash -# (minimal Bash-like shell) and Flock (to lock files and enable serial -# download). -export on_mac_os -./reproduce/software/shell/pre-make-build.sh \ - "$bdir" "$ddir" "$downloader" "$user_backup_urls" @@ -1682,13 +1784,29 @@ fi -# Build other basic tools our own GNU Make -# ---------------------------------------- +# Core software +# ------------- +# +# Here we build the core tools that 'basic.mk' depends on: Lzip +# (compression program), GNU Make (that 'basic.mk' is written in), Dash +# (minimal Bash-like shell) and Flock (to lock files and enable serial +# operations where necessary: mostly in download). +export on_mac_os +if [ $quiet = 0 ]; then echo "Building/validating software: pre-make"; fi +./reproduce/software/shell/pre-make-build.sh \ + "$bdir" "$ddir" "$downloader" "$user_backup_urls" +elapsed_time_from_prev_step make-software-pre-make + + + + + +# 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). -echo; echo "Building necessary software (if necessary)..." +# Having built the core tools, we are now ready to build GCC and all its +# dependencies (the "basic" software). +if [ $quiet = 0 ]; then echo "Building/validating software: basic"; fi .local/bin/make $keepgoing -f reproduce/software/make/basic.mk \ sys_library_sh_path=$sys_library_sh_path \ user_backup_urls="$user_backup_urls" \ @@ -1700,23 +1818,19 @@ echo; echo "Building necessary software (if necessary)..." on_mac_os=$on_mac_os \ host_cc=$host_cc \ -j$numthreads +elapsed_time_from_prev_step make-software-basic -# All other software -# ------------------ +# High-level 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 [ $jobs = 0 ]; then - numthreads=$(.local/bin/nproc --all) -else - numthreads=$jobs -fi +# Having our custom GCC in place, we can now build the high-level (science) +# software: we are using our custom-built 'env' to ensure that nothing from +# the host environment leaks into the high-level software environment. +if [ $quiet = 0 ]; then echo "Building/validating software: high-level"; fi .local/bin/env -i HOME=$bdir \ .local/bin/make $keepgoing \ -f reproduce/software/make/high-level.mk \ @@ -1732,16 +1846,7 @@ fi host_cc=$host_cc \ offline=$offline \ -j$numthreads - - - - - -# Delete the temporary Make wrapper -# --------------------------------- -# -# See above for its description. -rm $makewshell +elapsed_time_from_prev_step make-software-high-level @@ -1756,17 +1861,17 @@ rm $makewshell # 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 +if [ $built_container = 0 ]; then + 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 !!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +______________________________________________________ +!!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!! TeX Live couldn't be installed during the configuration (probably because there were downloading problems). TeX Live is only necessary in making the @@ -1786,18 +1891,23 @@ and re-run configure: ./project configure -e -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +The configuration will continue in $pausesec seconds. To avoid the pause on +such messages use the '--no-pause' option. + +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! EOF - sleep 10 # increase the chance that an interactive user reads this message + sleep $pausesec + fi + elapsed_time_from_prev_step check-tex-installation fi -# Citation of installed software +# Software information the paper +# ------------------------------ # # 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 @@ -1839,101 +1949,101 @@ prepare_name_version () fi } -# Import the context/sentences for placing between the list of software -# names during their acknowledgment. -. $cdir/software_acknowledge_context.sh +# Relevant files +pkgver=$sconfdir/dependencies.tex +pkgbib=$sconfdir/dependencies-bib.tex -# Report the different software in separate contexts (separating Python and -# TeX packages from the C/C++ programs and libraries). -proglibs=$(prepare_name_version $verdir/proglib/*) -pymodules=$(prepare_name_version $verdir/python/*) -texpkg=$(prepare_name_version $verdir/tex/texlive) - -# Acknowledge these software packages in a LaTeX paragraph. -pkgver=$texdir/dependencies.tex - -# Add the text to the ${pkgver} file. -.local/bin/echo "$thank_software_introduce " > $pkgver -.local/bin/echo "$thank_progs_libs $proglibs. " >> $pkgver -if [ x"$pymodules" != x ]; then - .local/bin/echo "$thank_python $pymodules. " >> $pkgver -fi -.local/bin/echo "$thank_latex $texpkg. " >> $pkgver -.local/bin/echo "$thank_software_conclude" >> $pkgver - -# Prepare the BibTeX entries for the used software (if there are any). -hasentry=0 -bibfiles="$ictdir/*" -for f in $bibfiles; do if [ -f $f ]; then hasentry=1; break; fi; done; - -# Make sure we start with an empty output file. -pkgbib=$texdir/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 +# Build the software LaTeX source but only when not in a container. +if [ $built_container = 0 ]; then + # Import the context/sentences for placing between the list of software + # names during their acknowledgment. + . $cdir/software_acknowledge_context.sh + # Report the different software in separate contexts (separating Python + # and TeX packages from the C/C++ programs and libraries). + proglibs=$(prepare_name_version $verdir/proglib/*) + pymodules=$(prepare_name_version $verdir/python/*) + texpkg=$(prepare_name_version $verdir/tex/texlive) + # Acknowledge these software packages in a LaTeX paragraph. + .local/bin/echo "$thank_software_introduce " > $pkgver + .local/bin/echo "$thank_progs_libs $proglibs. " >> $pkgver + if [ x"$pymodules" != x ]; then + .local/bin/echo "$thank_python $pymodules. " >> $pkgver + fi + .local/bin/echo "$thank_latex $texpkg. " >> $pkgver + .local/bin/echo "$thank_software_conclude" >> $pkgver + + # Prepare the BibTeX entries for the used software (if there are any). + hasentry=0 + bibfiles="$ictdir/*" + for f in $bibfiles; do if [ -f $f ]; then hasentry=1; break; fi; done; + + # 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. + echo "" > $pkgbib # We don't want to inherit any pre-existing content. + if [ $hasentry = 1 ]; then + for f in $bibfiles; do + awk '!/^%/{print} END{print ""}' $f >> $pkgbib + done + fi - -# Report machine architecture -# --------------------------- -# -# Report hardware -hwparam="$texdir/hardware-parameters.tex" - -# Add the text to the ${hwparam} file. Since harware class might include -# underscore, it must be replaced with '\_', otherwise pdftex would -# complain and break the build process when doing ./project make. -hw_class_fixed="$(echo $hw_class | sed -e 's/_/\\_/')" -.local/bin/echo "\\newcommand{\\machinearchitecture}{$hw_class_fixed}" > $hwparam -.local/bin/echo "\\newcommand{\\machinebyteorder}{$byte_order}" >> $hwparam -.local/bin/echo "\\newcommand{\\machineaddresssizes}{$address_sizes}" >> $hwparam + # Report the time that this operation took. + elapsed_time_from_prev_step tex-macros +fi -# Clean the temporary build directory -# --------------------------------- +# Report machine architecture (has to be final created file) +# ---------------------------------------------------------- # -# 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 - +# This is the final file that is created in the configuration phase: it is +# used by the high-level project script to verify that configuration has +# been completed. If any other files should be created in the final statges +# of configuration, be sure to add them before this. +# +# Since harware class might include underscore, it must be replaced with +# '\_', otherwise pdftex would complain and break the build process when +# doing ./project make. +if [ $built_container = 0 ]; then + hw_class=$(uname -m) + hwparam="$sconfdir/hardware-parameters.tex" + hw_class_fixed="$(echo $hw_class | sed -e 's/_/\\_/')" + .local/bin/echo "\\newcommand{\\machinearchitecture}{$hw_class_fixed}" \ + > $hwparam + .local/bin/echo "\\newcommand{\\machinebyteorder}{$byte_order}" \ + >> $hwparam + .local/bin/echo "\\newcommand{\\machineaddresssizes}{$address_sizes}" \ + >> $hwparam + elapsed_time_from_prev_step hardware-params +fi -# Final notice -# ------------ +# Clean up and final notice +# ------------------------- # -# The configuration is now complete, we can inform the user on the next -# step(s) to take. -if [ x$maneage_group_name = x ]; then - buildcommand="./project make -j8" -else - buildcommand="./project make --group=$maneage_group_name -j8" -fi -cat <<EOF +# The configuration is now complete. We just need to delete the temporary +# build directory and inform the user (if '--quiet' wasn't called) on the +# next step(s). +if [ -d $tmpblddir ]; then empty_build_tmp; fi +if [ $quiet = 0 ]; then + + # Suggest the command to use. + if [ x$maneage_group_name = x ]; then + buildcommand="./project make -j8" + else + buildcommand="./project make --group=$maneage_group_name -j8" + fi + + # Print the message. + cat <<EOF ---------------- The project and its environment are configured with no errors. @@ -1951,3 +2061,10 @@ Please run the following command to start the project. $buildcommand EOF +fi + + +# Total time +if [ $check_elapsed = 1 ]; then + echo $chel_dsum | awk '{printf "Total: %-6.2f [millisec]\n", $1}' +fi diff --git a/reproduce/software/containers/README-docker.md b/reproduce/software/shell/docker-README.md index d651e22..d651e22 100644 --- a/reproduce/software/containers/README-docker.md +++ b/reproduce/software/shell/docker-README.md diff --git a/reproduce/software/containers/docker.sh b/reproduce/software/shell/docker.sh index d5b5682..714c75f 100755 --- a/reproduce/software/containers/docker.sh +++ b/reproduce/software/shell/docker.sh @@ -9,35 +9,35 @@ # # Usage: # -# - When you are at the top Maneage'd project directory, you can run this -# script like the example below. Just set all the '/PATH/TO/...' -# directories (see below for '--tmp-dir'). See the items below for -# optional values. +# - When you are at the top Maneage'd project directory, run this script +# like the example below. Just set the build directory location on your +# system. See the items below for optional values to optimize the +# process (avoid downloading for exmaple). # -# ./reproduce/software/containers/docker.sh --shm-size=15gb \ -# --software-dir=/PATH/TO/SOFTWARE/TARBALLS \ -# --build-dir=/PATH/TO/BUILD/DIRECTORY +# ./reproduce/software/shell/docker.sh --shm-size=20gb \ +# --build-dir=/PATH/TO/BUILD/DIRECTORY # -# - Non-mandatory options: +# - Non-mandatory options: # -# - If you already have the input data that is necessary for your -# project's, use the '--input-dir' option to specify its location -# on your host file system. Otherwise the necessary analysis -# files will be downloaded directly into the build -# directory. Note that this is only necessary when '--build-only' -# is not given. +# - If you already have the input data that is necessary for your +# project, use the '--input-dir' option to specify its location +# on your host file system. Otherwise the necessary analysis +# files will be downloaded directly into the build +# directory. Note that this is only necessary when '--build-only' +# is not given. # -# - The '--software-dir' is only useful if you want to build a -# container. Even in that case, it is not mandatory: if not -# given, the software tarballs will be downloaded (thus requiring -# internet). +# - If you already have the necessary software tarballs that are +# necessary for your project, use the '--software-dir' option to +# specify its location on your host file system only when +# building the container. No problem if you don't have them, they +# will be downloaded during the configuration phase. # -# - To avoid having to set the directory(s) every time you want to -# start the docker environment, you can put this command (with the -# proper directories) into a 'run.sh' script in the top Maneage'd -# project source directory and simply execute that. The special name -# 'run.sh' is in Maneage's '.gitignore', so it will not be included -# in your git history by mistake. +# - To avoid having to set them every time you want to start the +# apptainer environment, you can put this command (with the proper +# directories) into a 'run.sh' script in the top Maneage'd project +# source directory and simply execute that. The special name 'run.sh' +# is in Maneage's '.gitignore', so it will not be included in your +# git history by mistake. # # Known problems: # @@ -76,7 +76,7 @@ set -e # Default option values -jobs= +jobs=0 quiet=0 source_dir= build_only= @@ -116,7 +116,7 @@ Top-level script to build and run a Maneage'd project within Docker. --container-shell Open the container shell. Operating mode: - --quiet Do not print informative statements. + -q, --quiet Do not print informative statements. -?, --help Give this help list. --shm-size=STR Passed to 'docker build' (default: $shm_size). -j, --jobs=INT Number of threads to use in each phase. @@ -168,6 +168,8 @@ do # Container options. --base-name) base_name="$2"; check_v "$1" "$base_name"; shift;shift;; --base-name=*) base_name="${1#*=}"; check_v "$1" "$base_name"; shift;; + --project-name) project_name="$2"; check_v "$1" "$project_name"; shift;shift;; + --project-name=*) project_name="${1#*=}"; check_v "$1" "$project_name"; shift;; # Interactive shell. --project-shell) project_shell=1; shift;; @@ -176,8 +178,8 @@ do --container_shell=*) on_off_option_error --container-shell;; # Operating mode - --quiet) quiet=1; shift;; - --quiet=*) on_off_option_error --quiet;; + -q|--quiet) quiet=1; shift;; + -q*|--quiet=*) on_off_option_error --quiet;; -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;; @@ -250,17 +252,43 @@ if ! [ x"$input_dir" = x ]; then input_dir_mnt="-v $input_dir:/home/maneager/input" fi -# If no '--jobs' has been specified, use the maximum available jobs to the -# operating system. -if [ x$jobs = x ]; then jobs=$(nproc); fi +# Number of threads to build software (taken from 'configure.sh'). +if [ x"$jobs" = x0 ]; then + if type nproc > /dev/null 2> /dev/null; then + numthreads=$(nproc --all); + else + numthreads=$(sysctl -a | awk '/^hw\.ncpu/{print $2}') + if [ x"$numthreads" = x ]; then numthreads=1; fi + fi +else + numthreads=$jobs +fi -# [DOCKER-ONLY] Make sure the user is a member of the 'docker' group: -glist=$(groups $(whoami) | awk '/docker/') -if [ x"$glist" = x ]; then - printf "$scriptname: you are not a member of the 'docker' group " - printf "You can run the following command as root to fix this: " - printf "'usermod -aG docker $(whoami)'\n" - exit 1 +# Since the container is read-only and is run with the '--contain' option +# (which makes an empty '/tmp'), we need to make a dedicated directory for +# the container to be able to write to. This is necessary because some +# software (Biber in particular on the default branch or Ghostscript) need +# to write there! See https://github.com/plk/biber/issues/494. We'll keep +# the directory on the host OS within the build directory, but as a hidden +# file (since it is not necessary in other types of build and ultimately +# only contains temporary files of programs that need it). +toptmp=$build_dir/.docker-tmp-$(whoami) +if ! [ -d $toptmp ]; then mkdir $toptmp; fi +chmod -R +w $toptmp/ # Some software remove writing flags on /tmp files. +if ! [ x"$( ls -A $toptmp )" = x ]; then rm -r "$toptmp"/*; fi + +# [DOCKER-ONLY] Make sure the user is a member of the 'docker' group. This +# is needed only for Linux, given that other systems uses other strategies. +# (See: https://stackoverflow.com/a/70385997) +kernelname=$(uname -s) +if [ x$kernelname = xLinux ]; then + glist=$(groups $(whoami) | awk '/docker/') + if [ x"$glist" = x ]; then + printf "$scriptname: you are not a member of the 'docker' group " + printf "You can run the following command as root to fix this: " + printf "'usermod -aG docker $(whoami)'\n" + exit 1 + fi fi # [DOCKER-ONLY] Function to check the temporary directory for building the @@ -341,6 +369,7 @@ fi # # Having the base operating system in place, we can now construct the # project's docker file. +intbuild=/home/maneager/build if docker image list | grep $project_name &> /dev/null; then if [ $quiet = 0 ]; then printf "$scriptname: info: project's image ('$project_name') " @@ -387,7 +416,7 @@ else printf " cp -r $dsr /home/maneager/source; \x5C\n" >> $df printf " cd /home/maneager/source; \x5C\n" >> $df printf " ./project configure --jobs=$jobs \x5C\n" >> $df - printf " --build-dir=/home/maneager/build \x5C\n" >> $df + printf " --build-dir=$intbuild \x5C\n" >> $df printf " --input-dir=/home/maneager/input \x5C\n" >> $df printf " --software-dir=$dts; \x5C\n" >> $df @@ -456,29 +485,33 @@ fi # The startup command of the container is managed though the 'shellopt' # variable that starts here. shellopt="" +sobase="/bin/bash -c 'cd source; " +sobase="$sobase ./project configure --build-dir=$intbuild " +sobase="$sobase --existing-conf --no-pause --offline --quiet && " +sobase="$sobase ./project MODE --build-dir=$intbuild" if [ $container_shell = 1 ] || [ $project_shell = 1 ]; then - # If the user wants to start the project shell within the container, - # add the necessary command. + # The interactive flag is necessary for both these scenarios. + interactiveopt="-it" + + # With '--project-shell' we need 'shellopt', the MODE just needs to be + # set to 'shell'. if [ $project_shell = 1 ]; then - shellopt="/bin/bash -c 'cd source; ./project shell;'" + shellopt="$(echo $sobase | sed -e's|MODE|shell|');'" fi - # Finish the 'shellop' string with a single quote (necessary in any - # case) and run Docker. - interactiveopt="-it" - # No interactive shell requested, just run the project. else interactiveopt="" - shellopt="/bin/bash -c 'cd source; ./project make --jobs=$jobs;'" + shellopt="$(echo $sobase | sed -e's|MODE|make|') --jobs=$jobs;'" fi # Execute Docker. The 'eval' is because the 'shellopt' variable contains a # single-quote that the shell should "evaluate". -eval docker run \ +eval docker run --read-only \ -v "$analysis_dir":/home/maneager/build/analysis \ -v "$source_dir":/home/maneager/source \ + -v $toptmp:/tmp \ $input_dir_mnt \ $shm_mnt \ $interactiveopt \ diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh index 28b7385..172bdb6 100755 --- a/reproduce/software/shell/pre-make-build.sh +++ b/reproduce/software/shell/pre-make-build.sh @@ -135,16 +135,6 @@ download_tarball() { else mv "$ucname" "$maneagetar" fi fi - - # If the tarball is newer than the (possibly existing) program (the - # version has changed), then delete the program. When the LaTeX name is - # not given here, the software is re-built later (close to the end of - # 'basic.mk') and the name is properly placed there. - if [ -f "$ibidir/$progname" ]; then - if [ "$maneagetar" -nt "$ibidir/$progname" ]; then - rm "$ibidir/$progname" - fi - fi } @@ -159,6 +149,9 @@ build_program() { # Options configoptions=$1 + # Inform the user. + echo; echo "Pre-make building of $progname"; echo + # Go into the temporary building directory. cd "$tmpblddir" unpackdir="$progname"-"$version" @@ -183,7 +176,8 @@ build_program() { # build the project, either with Make and either without it. if [ x$progname = xlzip ]; then - ./configure --build --check --installdir="$instdir/bin" $configoptions + ./configure --build --check --installdir="$instdir/bin" \ + $configoptions else # All others accept the configure script. ./configure --prefix="$instdir" $configoptions @@ -196,7 +190,10 @@ build_program() { case $on_mac_os in yes) sed -e's/\%1u/\%d/' src/flock.c > src/flock-new.c;; no) sed -e's/\%1u/\%ld/' src/flock.c > src/flock-new.c;; - *) echo "pre-make-build.sh: '$on_mac_os' unrecognized value for on_mac_os";; + *) + printf "pre-make-build.sh: '$on_mac_os' " + printf "unrecognized value for on_mac_os" + exit 1;; esac mv src/flock-new.c src/flock.c fi @@ -218,9 +215,9 @@ build_program() { cd "$topdir" rm -rf "$tmpblddir/$unpackdir" if [ x"$progname_tex" = x ]; then - echo "" > "$ibidir/$progname" + echo "" > "$texfile" else - echo "$progname_tex $version" > "$ibidir/$progname" + echo "$progname_tex $version" > "$texfile" fi fi } @@ -238,12 +235,12 @@ build_program() { # (without compression it is just ~400Kb). So we use its '.tar' file and # won't rely on the host's compression tools at all. progname="lzip" -progname_tex="" # Lzip re-built after GCC (empty string to avoid repetition) +progname_tex="" # Lzip is re-built after GCC (empty to avoid repetition) url=$(awk '/^'$progname'-url/{print $3}' $urlfile) version=$(awk '/^'$progname'-version/{print $3}' "$versionsfile") tarball=$progname-$version.tar -download_tarball -build_program +texfile="$ibidir/$progname-$version-pre-make" +if ! [ -f $texfile ]; then download_tarball; build_program; fi @@ -268,8 +265,11 @@ progname_tex="" # Make re-built after GCC (empty string to avoid repetition) url=$(awk '/^'$progname'-url/{print $3}' $urlfile) version=$(awk '/^'$progname'-version/{print $3}' $versionsfile) tarball=$progname-$version.tar.lz -download_tarball -build_program "--disable-dependency-tracking --without-guile" +texfile="$ibidir/$progname-$version-pre-make" +if ! [ -f $texfile ]; then + download_tarball + build_program "--disable-dependency-tracking --without-guile" +fi @@ -286,13 +286,11 @@ progname_tex="Dash" url=$(awk '/^'$progname'-url/{print $3}' $urlfile) version=$(awk '/^'$progname'-version/{print $3}' $versionsfile) tarball=$progname-$version.tar.lz -download_tarball -build_program +texfile="$ibidir/$progname-$version" +if ! [ -f $texfile ]; then download_tarball; build_program; fi # If the 'sh' symbolic link isn't set yet, set it to point to Dash. -if [ -f $bindir/sh ]; then just_a_place_holder=1 -else ln -sf $bindir/dash $bindir/sh; -fi +if ! [ -f $bindir/sh ]; then ln -sf $bindir/dash $bindir/sh; fi @@ -315,12 +313,5 @@ progname_tex="Discoteq flock" url=$(awk '/^'$progname'-url/{print $3}' $urlfile) version=$(awk '/^'$progname'-version/{print $3}' $versionsfile) tarball=$progname-$version.tar.lz -download_tarball -build_program - - - - - -# Finish this script successfully -exit 0 +texfile="$ibidir/$progname-$version" +if ! [ -f $texfile ]; then download_tarball; build_program; fi |