diff options
Diffstat (limited to 'reproduce')
| -rw-r--r-- | reproduce/analysis/make/initialize.mk | 38 | ||||
| -rw-r--r-- | reproduce/analysis/make/paper.mk | 12 | ||||
| -rw-r--r-- | reproduce/software/config/LOCAL.conf.in | 3 | ||||
| -rwxr-xr-x | reproduce/software/shell/configure.sh | 111 |
4 files changed, 88 insertions, 76 deletions
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index 5150373..b57b3a9 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -265,16 +265,8 @@ clean: # executing 'build'. rm -f *.aux *.log *.synctex *.auxlock *.dvi *.out *.run.xml *.bcf -# Delete all the built outputs except the dependency programs. We'll -# use Bash's extended options builtin ('shopt') to enable "extended -# glob" (for listing of files). It allows extended features like -# ignoring the listing of a file with '!()' that we are using -# afterwards. - shopt -s extglob - rm -rf $(texdir)/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex) - rm -rf $(badir)/!(tex) $(texdir)/!(macros|$(texbtopdir)) - rm -rf $(texdir)/build/!(tikz) $(texdir)/build/tikz/* - rm -rf $(badir)/preparation-done.mk +# Delete the full 'badir' (containing all analysis outputs). + rm -rf $(badir) distclean: clean # Without cleaning the Git hooks, we won't be able to easily commit @@ -329,12 +321,11 @@ $(project-package-contents): paper.pdf | $(texdir) paper.tex > $$dir/paper.tex # Copy ONLY the version-controlled files in 'reproduce' and -# 'tex/src'. This is important because files like 'LOCAL.conf' (in -# 'reproduce/software/config') should not be archived, they contain -# information about the host computer and are irrelevant for -# others. Also some project authors may have temporary files here -# that are not under version control and thus shouldn't be archived -# (although this is bad practice, but that is up to the user). +# 'tex/src'. This is important because the git commit hash goes in +# the tarball name (should correspond to it) and some project authors +# may have temporary files here that are not under version control +# and thus shouldn't be archived (although this is bad practice, but +# that is up to the user). # # To keep the sub-directory structure, we are packaging the files # with Tar, piping it, and unpacking it in the archive directory. So @@ -362,17 +353,20 @@ $(project-package-contents): paper.pdf | $(texdir) rm -rf $$dir/tex/build/build* # If the project has any PDFs in its 'tex/tikz' directory (TiKZ or -# PGFPlots was used to generate them), copy them too. +# PGFPlots was used to generate them), copy them too. Note that in +# the main project source, 'tex/tikz' is just a symbolic link to +# 'tex/build/tikz'. But inside the tarball we do not want to have +# symbolic links and they should be independent. if ls tex/tikz/*.pdf &> /dev/null; then cp tex/tikz/*.pdf $$dir/tex/tikz fi # When submitting to places like arXiv, they will just run LaTeX once -# and won't run 'biber'. So we need to also keep the '.bbl' file into -# the distributing tarball. However, BibLaTeX is particularly -# sensitive to versioning (a '.bbl' file has to be read by the same -# BibLaTeX version that created it). This is hard to do with -# non-up-to-date places like arXiv. Therefore, we thus just copy the +# and won't run 'biber' or 'biblatex'. So we need to also keep the +# '.bbl' file into the distributing tarball. However, BibLaTeX is +# particularly sensitive to versioning (a '.bbl' file has to be read +# by the same BibLaTeX version that created it). This is hard to do +# with non-up-to-date places like arXiv. Therefore, we just copy the # whole of BibLaTeX's source (the version we are using) into the top # tarball directory. In this way, arXiv's LaTeX engine will use the # same BibLaTeX version to interpret the '.bbl' file. TIP: you can diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index b1b794c..a399637 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -164,9 +164,9 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \ # for details. # # We need the modification to 'LD_LIBRARY_PATH' because we do not -# build LaTeX from source and it uses '/bin/sh' (among other -# possible system-wide things). - export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" +# build LaTeX from source and it (or its packages) may use +# '/bin/sh' (among other possible system-wide things). + export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH" pdflatex -shell-escape -halt-on-error "$$p"/paper.tex biber paper fi @@ -198,9 +198,9 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl # option '-shell-escape'. # # We need the modification to 'LD_LIBRARY_PATH' because we do not -# build LaTeX from source and it uses '/bin/sh' (among other -# possible system-wide things). - export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" +# build LaTeX from source and it (or its packages) may use +# '/bin/sh' (among other possible system-wide things). + export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH" pdflatex -shell-escape -halt-on-error "$$p"/paper.tex # Come back to the top project directory and copy the built PDF diff --git a/reproduce/software/config/LOCAL.conf.in b/reproduce/software/config/LOCAL.conf.in index e60f344..b95bb5f 100644 --- a/reproduce/software/config/LOCAL.conf.in +++ b/reproduce/software/config/LOCAL.conf.in @@ -31,8 +31,9 @@ DEPENDENCIES-DIR = @ddir@ # Other local settings (compiler, downloader and user). SYS_CPATH = @sys_cpath@ -DOWNLOADER = @downloader@ GROUP-NAME = @groupname@ +DOWNLOADER = @downloader@ +SYS_LIBRARY_SH_PATH = @sys_library_sh_path@ diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index 4887816..a409920 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -1146,6 +1146,20 @@ 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 @@ -1396,6 +1410,55 @@ 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 +1478,7 @@ 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 @@ -1666,53 +1730,6 @@ 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 # ---------------------------------------- |