diff options
Diffstat (limited to 'reproduce/software/shell')
| -rwxr-xr-x | reproduce/software/shell/apptainer.sh | 13 | ||||
| -rwxr-xr-x | reproduce/software/shell/configure.sh | 96 | ||||
| -rw-r--r-- | reproduce/software/shell/docker-README.md | 21 | ||||
| -rwxr-xr-x | reproduce/software/shell/docker.sh | 33 | ||||
| -rwxr-xr-x | reproduce/software/shell/prep-source.sh | 16 |
5 files changed, 106 insertions, 73 deletions
diff --git a/reproduce/software/shell/apptainer.sh b/reproduce/software/shell/apptainer.sh index 1785977..8760db6 100755 --- a/reproduce/software/shell/apptainer.sh +++ b/reproduce/software/shell/apptainer.sh @@ -195,13 +195,14 @@ done # # Make sure that the build directory is given and that it exists. if [ x$build_dir = x ]; then - printf "$scriptname: '--build-dir' not provided, this is the location " - printf "that all built analysis files will be kept on the host OS\n" + printf "$scriptname: '--build-dir' not provided, this is the " + printf "location that all built analysis files will be kept on " + printf "the host OS\n" exit 1; else if ! [ -d $build_dir ]; then - printf "$scriptname: '$build_dir' (value to '--build-dir') doesn't " - printf "exist\n" + printf "$scriptname: '$build_dir' (value to '--build-dir') " + printf "doesn't exist\n" exit 1; fi fi @@ -364,7 +365,7 @@ From: $base_sif else \\ printf "$scriptname: '\$maneage_apptainer_stat' (value "; \\ printf "to 'maneage_apptainer_stat' environment variable) "; \\ - printf "is not recognized: should be either 'shell' or 'run'"; \\ + printf "is not recognized: should be either 'shell' or 'run'\n"; \\ exit 1; \\ fi; \\ else \\ @@ -399,7 +400,7 @@ fi if ! [ x"$build_only" = x ]; then if [ $quiet = 0 ]; then printf "$scriptname: info: Maneaged project has been configured " - printf "successfully in the '$sif' image" + printf "successfully in the '$sif' image\n" fi exit 0 fi diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index ca3bf6e..3e0163e 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -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" } @@ -378,7 +378,11 @@ if [ $built_container = 0 ]; then # between Intel or Apple M1 CPUs. Here we disinguish between Apple # M1 or others. maccputype=$(sysctl -n machdep.cpu.brand_string) - if [ x"$maccputype" = x"Apple M1" ]; then + if [ x"$maccputype" = x"Apple M1" ] \ + || [ x"$maccputype" = x"Apple M2" ] \ + || [ x"$maccputype" = x"Apple M3" ] \ + || [ x"$maccputype" = x"Apple M4" ] \ + || [ x"$maccputype" = x"Apple M5" ] ; then address_size_physical=$(sysctl -n machdep.cpu.thread_count) address_size_virtual=$(sysctl -n machdep.cpu.logical_per_package) else @@ -781,6 +785,25 @@ 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 +879,6 @@ 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 @@ -1426,9 +1422,9 @@ elapsed_time_from_prev_step downloader # 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. +# 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 @@ -1550,6 +1546,41 @@ 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) # --------------------------------------------- # @@ -1833,6 +1864,7 @@ 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 diff --git a/reproduce/software/shell/docker-README.md b/reproduce/software/shell/docker-README.md index 9e09282..dd46f4f 100644 --- a/reproduce/software/shell/docker-README.md +++ b/reproduce/software/shell/docker-README.md @@ -35,28 +35,25 @@ software environment) to easily move it from one computer to another. systemctl start docker ``` - 2. Using your favorite text editor, create a `run.sh` in your top Maneage - directory (as described in the comments at the start of the `docker.sh` - script in this directory). Just activate `--build-only` on the first - run so it doesn't go onto doing the analysis and just sets up the - software environment. Set the respective directory(s) based on your - filesystem (the software directory is optional). The `run.sh` file name - is already in `.gitignore` (because it contains local directories), so - Git will ignore it and it won't be committed by mistake. + 2. At the start of the `docker.sh` script in this directory, you can see + the necessary command to run. Just activate `--build-only` on the first + run so it doesn't go onto doing the analysis (that can be done at any + later time). Set the respective directory(s) based on your filesystem + (the software directory is optional). You can put the command in a + `run.sh` at the top of the project (it is already in `.gitignore`: + because it contains local directories). 3. After the setup is complete, remove the `--build-only` and run the command below to confirm that `maneage-base` (the OS of the container) and `maneaged` (your project's full Maneage'd environment) images are available. If you want different names for these images, add the - `--project-name` and `--base-name` options to the `docker.sh` call. + `--project-name` and `--base-name` options to the `docker.sh` call. You + can see the list of available images with this command: ```shell docker image list ``` - 4. You are now ready to do your analysis by removing the `--build-only` - option. - diff --git a/reproduce/software/shell/docker.sh b/reproduce/software/shell/docker.sh index ab454aa..5cd8f11 100755 --- a/reproduce/software/shell/docker.sh +++ b/reproduce/software/shell/docker.sh @@ -1,4 +1,4 @@ -#!/bin/sh +#!/usr/bin/env bash # # Create a Docker container from an existing image of the built software # environment, but with the source, data and build (analysis) directories @@ -409,22 +409,25 @@ else # that the user gave there. mkdir $tmp_dir/$tsdir cp -r "$software_dir"/* $tmp_dir/$tsdir/ - printf " --mount=type=bind,source=$tsdir,target=$dts \x5C\n" >> $df + printf " --mount=type=bind,source=$tsdir,target=$dts \x5C\n" \ + >> $df fi # Construct the rest of the 'RUN' command. 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 " ./project configure \x5C\n" >> $df + printf " --no-pause \x5C\n" >> $df + printf " --jobs=$jobs \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" >> $df + printf " --software-dir=$dts; \x5C\n" >> $df - # We are deleting the '.build/software/tarballs' directory because this - # directory is not relevant for the analysis of the project. But in - # case any tarball was downloaded, it will consume space within the - # container. - printf " rm -rf .build/software/tarballs; \x5C\n" >> $df + # We are deleting the contents of the '.build/software/tarballs' + # directory (tarballs of the sources of the software) because they are + # not relevant to the execution of the project and will consume space + # within the container. + printf " rm -rf .build/software/tarballs/*; \x5C\n" >> $df # We are deleting the source directory becaues later (at 'docker run' # time), the 'source' will be mounted directly from the host operating @@ -432,12 +435,9 @@ else printf " cd /home/maneager; \x5C\n" >> $df printf " rm -rf source\n" >> $df - # Build the Maneage container and delete the temporary directory. The - # '--progress plain' option is for Docker to print all the outputs - # (otherwise, it will only print a very small part!). + # Build the Maneage container and delete the temporary directory. cd $tmp_dir docker build ./ -t $project_name \ - --progress=plain \ --shm-size=$shm_size \ --no-cache \ 2>&1 | tee build.log @@ -453,14 +453,15 @@ if ! [ x"$image_file" = x ] && ! [ -f "$image_file" ]; then # Save the image into a tarball tarname=$(echo $image_file | sed -e's|.gz$||') if [ $quiet = 0 ]; then - printf "$scriptname: info: saving docker image to '$tarname'" + printf "$scriptname: info: saving docker image to '$tarname'\n" fi docker save -o $tarname $project_name # Compress the saved image if [ $quiet = 0 ]; then printf "$scriptname: info: compressing to '$image_file' (can " - printf "take +10 minutes, but volume decreases by more than half!)" + printf "take +10 minutes, but volume decreases by more than " + printf "half!)\n" fi gzip --best $tarname fi @@ -470,7 +471,7 @@ fi if ! [ x"$build_only" = x ]; then if [ $quiet = 0 ]; then printf "$scriptname: info: Maneaged project has been configured " - printf "successfully in the '$project_name' image" + printf "successfully in the '$project_name' image\n" fi exit 0 fi diff --git a/reproduce/software/shell/prep-source.sh b/reproduce/software/shell/prep-source.sh index 861f3bf..2959255 100755 --- a/reproduce/software/shell/prep-source.sh +++ b/reproduce/software/shell/prep-source.sh @@ -47,17 +47,18 @@ fi -# Find all the files that contain the '/bin/sh' string and correct them to -# Maneage's own Bash. We are using 'while read' to read the file names line -# by line. This is necessary to account file names that include the 'SPACE' -# character (happens in CMake for example!). +# Find all the files that contain the '/bin/sh' or '/bin/bash' strings and +# correct them to Maneage's own shell (Dash or Bash). We are using 'while +# read' to read the file names line by line. This is necessary to account +# file names that include the 'SPACE' character (happens in CMake for +# example!). # # Note that dates are important in the source directory (files depend on # each other), so we should read the original date and after making. We are # also not using GNU SED's '-i' ('--in-place') option because the host OS # may not have GNU SED. # -# Actual situation which prompted the addition of this step: a Maneage'd +# The situation which prompted the addition of this step: a Maneage'd # project (with GNU Bash 5.1.8 and Readline 8.1.1) was being built on a # system where '/bin/sh' was GNU Bash 5.2.26 and had Readline 8.2.010. The # newer version of Bash needed the newer Readline library function(s) that @@ -74,7 +75,8 @@ fi # hard-coded in the source code of almost all programs (their build # scripts); and in special programs like GNU Make, GNU M4 or CMake it is # actually hardcoded in the source code (not just build scripts). -if [ -f "$bindir/bash" ]; then shpath="$bindir"/bash +bashpath="$bindir"/bash +if [ -f "$bindir/bash" ]; then shpath="$bashpath" else shpath="$bindir"/dash fi @@ -91,7 +93,7 @@ fi # precision up to the seconds. We then use 'sed' to remove the information # regarding the timezone, as the format is not accepted by 'touch'. # LCTYPE and LANG are also required on macos systems by sed. -grep -I -r -e'/bin/sh' $(pwd)/* \ +grep -I -r -e'/bin/sh' -e'/bin/bash' $(pwd)/* \ | sed -e's|:|\t|' \ | awk 'BEGIN{FS="\t"}{print $1}' \ | sort \ |