diff options
Diffstat (limited to 'reproduce/software/shell/configure.sh')
| -rwxr-xr-x | reproduce/software/shell/configure.sh | 311 |
1 files changed, 190 insertions, 121 deletions
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index 4887816..19c14ac 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -2,9 +2,9 @@ # # Necessary preparations/configurations for the reproducible project. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> -# Copyright (C) 2021-2025 Raul Infante-Sainz <infantesainz@gmail.com> -# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2021-2026 Raul Infante-Sainz <infantesainz@gmail.com> +# Copyright (C) 2022-2026 Pedram Ashofteh Ardakani <pedramardakani@pm.me> # # This script is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -228,7 +228,7 @@ empty_build_tmp() { # 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"/* + rm -rf "$tmpblddir"/* fi rm -r "$tmpblddir" } @@ -375,16 +375,23 @@ if [ $built_container = 0 ]; then fi # On macOS, the way of obtaining the number of cores is different - # between Intel or Apple M1 CPUs. Here we disinguish between Apple - # M1 or others. - maccputype=$(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=$(sysctl -n machdep.cpu.address_bits.virtual) - fi + # between Intel or Apple Silicon CPUs. Here we distinguish between + # Apple Silicon (any "Apple M*" brand string, e.g. M1, M1 Pro, M1 + # Max, M2, M2 Pro, ...) and Intel-based Macs. Note that the Apple + # Silicon group can be in the formats of "Apple M1" or "Apple M1 + # Pro", so we use a prefix match via a 'case' pattern to include + # both in one check. + maccputype=$(sysctl -n machdep.cpu.brand_string 2>/dev/null) + case "$maccputype" in + "Apple M"*) + address_size_physical=$(sysctl -n machdep.cpu.thread_count) + address_size_virtual=$(sysctl -n machdep.cpu.logical_per_package) + ;; + *) + address_size_physical=$(sysctl -n machdep.cpu.address_bits.physical) + address_size_virtual=$(sysctl -n machdep.cpu.address_bits.virtual) + ;; + esac address_sizes="$address_size_physical bits physical, " address_sizes+="$address_size_virtual bits virtual" else @@ -781,6 +788,25 @@ fi +# Older C standard versions +# ------------------------- +# +# Some basic packages require an old standard of C compilation; for their +# list, see the 'Not working with C23' list in '../config/versions.conf'. +# Here, we first try 'gnu17', but if that fails on the host compiler, we +# fall back to 'gnu99'. +if [ $built_container = 0 ]; then + printf "int main(void){; return 0;}\n" > $testsource + if gcc -std=gnu17 $testsource -o $testprog 2> /dev/null; then + std_c_old="gnu17" + else std_c_old="gnu99" + fi + rm $testsource $testprog +fi + + + + # Fortran compiler # ---------------- # @@ -856,33 +882,6 @@ 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 @@ -1146,6 +1145,20 @@ EOF echo " ** Please select another directory." echo "" else + # Set the '.build' and '.local' symbolic links (and delete + # possibly existing symbolic links). These commands are also + # present in the top-level 'project' script, but they are only + # invoked when '--build-dir' is called. When it is not called + # (the user wants to insert the directories interactively: the + # scenario here), the links need to be created from + # scratch. Furthermore, in case the given directory to + # '--build-dir' has problems (fails to pass the sanity checks + # above), the symbolic links also need to be recreated. + rm -f .build .local + ln -s $bdir .build + ln -s $bdir/software/installed .local + + # Inform the user echo " -- Build directory set to ($instring): '$bdir'" fi done @@ -1329,11 +1342,17 @@ elapsed_time_from_prev_step software-dir # 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. +# +# NOTE: it is important that the name of the programs are not recorded to +# be absolute (for example 'wget' instead of '/usr/bin/wget'). This is +# because we build both 'wget' and 'curl' within 'basic.mk'. After they are +# built, Maneage's built software have higher precedence in 'PATH'. So +# without an absolute address, our own built software will be used as soon +# as they are installed/available. if [ $rewritelconfig = yes ]; then - if type wget > /dev/null 2>/dev/null; then - # 'which' isn't in POSIX, so we are using 'command -v' instead. - name=$(command -v wget) + # First look for wget on the host. + if type wget > /dev/null 2>/dev/null; then # 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 @@ -1350,13 +1369,16 @@ if [ $rewritelconfig = yes ]; then # By default Wget keeps the remote file's timestamp, so we'll have # to disable it manually. - downloader="$name $wgetts -O"; + downloader="wget $wgetts -O"; + + # In case Wget doesn't exist, try cURL. elif type curl > /dev/null 2>/dev/null; then - name=$(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" + downloader="curl -L -o" + + # Neither Wget or cURL could be found. else cat <<EOF @@ -1396,6 +1418,55 @@ elapsed_time_from_prev_step downloader +# Libraries necessary for the system's shell +# ------------------------------------------ +# +# In some cases (mostly the programs that Maneage doesn't yet build by +# itself), the programs may call the system's shell, not Maneage's +# shell. After we close-off the system environment from Maneage, this will +# cause a crash! To avoid such cases, we need to find the locations of the +# libraries that the shell needs and temporarily add them to the library +# search path. +# +# About the 'grep -v "(0x[^)]*)"' term (from bug 66847, see [1]): On some +# systems [2], the output of 'ldd /bin/sh' includes a line for the vDSO [3] +# that is different to the formats that are assumed, prior to this commit, +# by the algorithm in 'configure.sh' when evaluating the variable +# 'sys_library_sh_path'. This leads to a fatal syntax error in (at least) +# 'ncurses', because the option using 'sys_library_sh_path' contains an +# unquoted RAM address in parentheses. Even if the address were quoted, it +# would still be incorrect. This 'grep' command excludes candidate host +# path strings that look like RAM addresses to address the problem. +# +# [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 [ $built_container = 0 ]; then + if [ x"$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", $1}') + fi + elapsed_time_from_prev_step sys-library-sh-path +fi + + + + + # When no local configuration existed, write the parameters into the local # configuration file. sdir=$bdir/software @@ -1415,6 +1486,7 @@ if [ $rewritelconfig = yes ]; then -e's|@sys_cpath[@]|'"$sys_cpath"'|' \ -e's|@downloader[@]|'"$downloader"'|' \ -e's|@groupname[@]|'"$maneage_group_name"'|' \ + -e's|@sys_library_sh_path[@]|'"$sys_library_sh_path"'|' \ $lconfin >> $lconf fi elapsed_time_from_prev_step LOCAL-write @@ -1486,6 +1558,41 @@ 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, the rpath-link value set within rpath_command in +# the case of a successful test compile (if $CC ...) will be "/lib", +# i.e. the host system root /lib directory, instead of the maneage library +# directory. +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 + + + + + # Software building directory (possibly in RAM) # --------------------------------------------- # @@ -1666,53 +1773,6 @@ fi -# Libraries necessary for the system's shell -# ------------------------------------------ -# -# In some cases (mostly the programs that Maneage doesn't yet build by -# itself), the programs may call the system's shell, not Maneage's -# shell. After we close-off the system environment from Maneage, this will -# cause a crash! To avoid such cases, we need to find the locations of the -# libraries that the shell needs and temporarily add them to the library -# search path. -# -# About the 'grep -v "(0x[^)]*)"' term (from bug 66847, see [1]): On some -# systems [2], the output of 'ldd /bin/sh' includes a line for the vDSO [3] -# that is different to the formats that are assumed, prior to this commit, -# by the algorithm in 'configure.sh' when evaluating the variable -# 'sys_library_sh_path'. This leads to a fatal syntax error in (at least) -# 'ncurses', because the option using 'sys_library_sh_path' contains an -# unquoted RAM address in parentheses. Even if the address were quoted, it -# would still be incorrect. This 'grep command excludes candidate host path -# strings that look like RAM addresses to address the problem. -# -# [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 [ $built_container = 0 ]; then - if [ x"$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", $1}') - fi - elapsed_time_from_prev_step sys-library-sh-path -fi - - - # Find Zenodo URL for software downloading # ---------------------------------------- @@ -1733,30 +1793,37 @@ fi # an example, the directory part of the URL for all the other software are # the same). This is not done if the options '--debug' or `--offline` are # used. -zenodourl="" -user_backup_urls="" -zenodocheck="$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 $zenodourl" - elapsed_time_from_prev_step zenodo-url -fi +# +# NOTE on commented region below (starting with '##'): As described [1], +# Zenodo's upload strategy does not allow a repository with more than one +# hundred files. So until the solution there has been implemented, this +# step has been commented. +# +# [1] https://savannah.nongnu.org/task/?16621 +## zenodourl="" +## user_backup_urls="" +## zenodocheck="$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 @@ -1816,6 +1883,7 @@ if [ $quiet = 0 ]; then echo "Building/validating software: basic"; fi numthreads=$numthreads \ needs_ldl=$needs_ldl \ on_mac_os=$on_mac_os \ + std_c_old=$std_c_old \ host_cc=$host_cc \ -j$numthreads elapsed_time_from_prev_step make-software-basic @@ -1874,9 +1942,10 @@ ______________________________________________________ !!!!!!!!!!!!!!! Warning !!!!!!!!!!!!!!!! TeX Live couldn't be installed during the configuration (probably because -there were downloading problems). TeX Live is only necessary in making the -final PDF (which is only done after all the analysis has been complete). It -is not used at all during the analysis. +there were downloading problems, or you used the '--offline' option). TeX +Live is only necessary in making the final PDF (which is only done after +all the analysis has been complete). It is not used at all during the +analysis. Therefore, if you don't need the final PDF, and just want to do the analysis, you can safely ignore this warning and continue. |