From c6a4aaad62a90af9a72f9bc58650696419474239 Mon Sep 17 00:00:00 2001 From: Mohammadreza Khellat Date: Wed, 26 Aug 2020 14:53:10 +0400 Subject: Machine architecture and byte-order available as LaTeX macro Until now, no machine-related specifications were being documented in the workflow. This information can become helpful when observing differences in the outcome of both software and analysis segments of the workflow by others (some software may behave differently based on host machine). With this commit, the host machine's 'hardware class' and 'byte-order' are collected and now available as LaTeX macros for the authors to use in the paper. Currently it is placed in the acknowledgments, right after mentioning the Maneage commit. Furthermore, the project and configuration scripts are now capable of dealing with input directory names that have SPACE (and other special characters) by putting them inside double-quotes. However, having spaces and metacharacters in the address of the build directory could cause build/install failure for some software source files which are beyond the control of Maneage. So we now check the user's given build directory string, and if the string has any '@', '#', '$', '%', '^', '&', '*', '(', ')', '+', ';', and ' ' (SPACE), it will ask the user to provide a different directory. --- reproduce/analysis/make/paper.mk | 9 +- reproduce/software/make/high-level.mk | 8 +- reproduce/software/shell/configure.sh | 258 ++++++++++++++++++++--------- reproduce/software/shell/pre-make-build.sh | 86 +++++----- 4 files changed, 232 insertions(+), 129 deletions(-) (limited to 'reproduce') diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index e207337..906b4d9 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -47,8 +47,9 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex @if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" != x ]; then # Put a LaTeX input command for all the necessary macro files. + # 'hardware-parameters.tex' is created in 'configure.sh'. rm -f $(mtexdir)/project.tex - for t in $(subst paper,,$(makesrc)); do + for t in $(subst paper,,$(makesrc)) hardware-parameters; do echo "\input{tex/build/macros/$$t.tex}" >> $(mtexdir)/project.tex done else @@ -113,7 +114,7 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \ # do not use PGFPlots, then you should remove the `-shell-escape' # option for better security. See # https://savannah.nongnu.org/task/?15694 for details. - pdflatex -shell-escape -halt-on-error $$p/paper.tex + pdflatex -shell-escape -halt-on-error "$$p"/paper.tex biber paper fi @@ -142,11 +143,11 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl cd $(texbdir) # See above for a warning and brief discussion on the the # pdflatex option `-shell-escape'. - pdflatex -shell-escape -halt-on-error $$p/paper.tex + pdflatex -shell-escape -halt-on-error "$$p"/paper.tex # Come back to the top project directory and copy the built PDF # file here. - cd $$p + cd "$$p" cp $(texbdir)/$@ $(final-paper) fi diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 9f434bc..cf9c5a1 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -54,9 +54,9 @@ ibidir = $(BDIR)/software/installed/version-info/proglib # Basic directories (specific to this Makefile). il64dir = $(BDIR)/software/installed/lib64 iidir = $(BDIR)/software/installed/include -shsrcdir = $(shell pwd)/reproduce/software/shell -dtexdir = $(shell pwd)/reproduce/software/bibtex -patchdir = $(shell pwd)/reproduce/software/patches +shsrcdir = "$(shell pwd)"/reproduce/software/shell +dtexdir = "$(shell pwd)"/reproduce/software/bibtex +patchdir = "$(shell pwd)"/reproduce/software/patches itidir = $(BDIR)/software/installed/version-info/tex ictdir = $(BDIR)/software/installed/version-info/cite ipydir = $(BDIR)/software/installed/version-info/python @@ -1411,7 +1411,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf tar xf $(tdir)/install-tl-unx.tar.gz cd install-tl-* sed -e's|@installdir[@]|$(idir)|g' \ - $$topdir/reproduce/software/config/texlive.conf \ + "$$topdir"/reproduce/software/config/texlive.conf \ > texlive.conf # TeX Live's installation may fail due to any reason. But TeX Live diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index 593b1d9..2b4300b 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -48,7 +48,7 @@ need_gfortran=0 # -------------------- # # These are defined to help make this script more readable. -topdir=$(pwd) +topdir="$(pwd)" optionaldir="/optional/path" adir=reproduce/analysis/config cdir=reproduce/software/config @@ -96,7 +96,8 @@ create_file_with_notice () # an absolute address. With this function we can make sure of that. absolute_dir () { - if stat "$1" 1> /dev/null; then + address="$1" + if stat "$address" 1> /dev/null; then echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")" else exit 1; @@ -136,18 +137,18 @@ check_permission () { # Make a `junk' file, activate its executable flag and record its # permissions generally. - local junkfile=$1/check_permission_tmp_file - rm -f $junkfile - echo "Don't let my short life go to waste" > $junkfile - chmod +x $junkfile - local perm_before=$(ls -l $junkfile | awk '{print $1}') + local junkfile="$1"/check_permission_tmp_file + rm -f "$junkfile" + echo "Don't let my short life go to waste" > "$junkfile" + chmod +x "$junkfile" + local perm_before=$(ls -l "$junkfile" | awk '{print $1}') # Now, remove the executable flag and record the permissions. - chmod -x $junkfile - local perm_after=$(ls -l $junkfile | awk '{print $1}') + chmod -x "$junkfile" + local perm_after=$(ls -l "$junkfile" | awk '{print $1}') # Clean up before leaving the function - rm -f $junkfile + rm -f "$junkfile" # If the permissions are equal, the filesystem doesn't allow # permissions. @@ -187,8 +188,8 @@ check_permission () free_space_warning() { fs_threshold=$1 - fs_destpath=$2 - return $(df $fs_destpath \ + IFS='"' fs_destpath="$2" + return $(df "$fs_destpath" \ | awk 'FNR==2 {if($4>'$fs_threshold') print 1; \ else print 0; }') } @@ -224,6 +225,62 @@ fi +# Collect CPU information +# ----------------------- +# +# When the project is built, the type of a machine that built it also has +# to to be documented. This way, if different results or behaviors are +# observed in software-related or analysis-related phases of the project, +# it would be easier to track down the root cause. So far this is just +# 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=$(lscpu \ + | grep 'Byte Order' \ + | awk '{ \ + for(i=3;i /dev/null; then + if [ -d "$build_dir" ]; then + if echo "test" > "$build_dir"/$junkname ; then + rm -f "$build_dir"/$junkname instring="the already existing" - bdir=$(absolute_dir $build_dir) - rm -rf $build_dir/$junkname + bdir="$(absolute_dir "$build_dir")" else echo " ** Can't write in '$build_dir'"; fi else - if mkdir $build_dir 2> /dev/null; then + if mkdir "$build_dir" 2> /dev/null; then instring="the newly created" - bdir=$(absolute_dir $build_dir) + bdir="$(absolute_dir "$build_dir")" else echo " ** Can't create '$build_dir'"; fi fi - # If its given, make sure it isn't a subdirectory of the source + # If it is given, make sure it isn't a subdirectory of the source # directory. if ! [ x"$bdir" = x ]; then if echo "$bdir/" \ - | grep '^'$currentdir 2> /dev/null > /dev/null; then + | grep '^'"$currentdir" 2> /dev/null > /dev/null; then # If it was newly created, it will be empty, so delete it. - if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi + if ! [ "$(ls -A $bdir)" ]; then rm --dir "$bdir"; fi # Inform the user that this is not acceptable and reset `bdir'. bdir= @@ -793,10 +850,30 @@ EOF fi fi - # If everything is fine until now, see if we're able to manipulate - # file permissions. + # If things are fine so far, make sure it does not contain a space + # or other meta-characters which can cause problems during software + # building. + if ! [ x"$bdir" = x ]; then + hasmeta=0; + case $bdir in *['!'\@\#\$\%\^\&\*\(\)\+\;\ ]* ) hasmeta=1 ;; esac + if [ $hasmeta = 1 ]; then + + # If it was newly created, it will be empty, so delete it. + if ! [ "$(ls -A "$bdir")" ]; then rm --dir "$bdir"; fi + + # 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." + fi + fi + + # If everything is still fine so far, see if we're able to + # manipulate file permissions in the directory's filesystem and if + # so, see if there is atleast 5GB free space. if ! [ x"$bdir" = x ]; then - if ! $(check_permission $bdir); then + if ! $(IFS='"' check_permission "$bdir"); then # Unable to handle permissions well bdir= echo " ** File permissions can't be modified in this directory" @@ -804,7 +881,7 @@ EOF # 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 + if $(free_space_warning 5000000 "$bdir"); then echo " !! LESS THAN 5GB FREE SPACE IN: $bdir" echo " !! We recommend choosing another partition." echo " !! Build will continue in 5 seconds..." @@ -817,7 +894,7 @@ EOF # reset `build_dir' to blank, so it continues asking for another # directory and let the user know that they must select a new # directory. - if [ x$bdir = x ]; then + if [ x"$bdir" = x ]; then build_dir= echo " ** Please select another directory." echo "" @@ -834,9 +911,9 @@ fi # Input directory # --------------- if [ x"$input_dir" = x ]; then - indir=$optionaldir + indir="$optionaldir" else - indir=$input_dir + indir="$input_dir" fi noninteractive_sleep=2 if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then @@ -878,7 +955,7 @@ EOF # In case an input-directory is given, write it in 'indir'. if [ x$inindir != x ]; then - indir=$(absolute_dir $inindir) + indir="$(absolute_dir "$inindir")" echo " -- Using '$indir'" fi fi @@ -922,7 +999,7 @@ EOF # If given, write the software directory. if [ x"$tmpddir" != x ]; then - ddir=$(absolute_dir $tmpddir) + ddir="$(absolute_dir "$tmpddir")" echo " -- Using '$ddir'" fi fi @@ -946,11 +1023,18 @@ if [ $rewritepconfig = yes ]; then -e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \ $pconf.in >> $pconf else - # Read the values from existing configuration file. - inbdir=$(awk '$1=="BDIR" {print $3}' $pconf) - - # Read the software directory. - ddir=$(awk '$1=="DEPENDENCIES-DIR" {print $3}' $pconf) + # Read the values from existing configuration file. Note that the build + # directory may have space characters. Even though we currently check + # against it, we hope to be able to remove this condition in the + # future. + inbdir=$(awk '$1=="BDIR" { for(i=3; i $hwparam +.local/bin/echo "\\newcommand{\\machinebyteorder}{$byte_order}" >> $hwparam +.local/bin/echo "\\newcommand{\\machineaddresssizes}{$address_sizes}" >> $hwparam + + + + + # Clean the temporary build directory # --------------------------------- # diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh index 9188fc9..a18966f 100755 --- a/reproduce/software/shell/pre-make-build.sh +++ b/reproduce/software/shell/pre-make-build.sh @@ -30,32 +30,32 @@ set -e -# Input arguments. -bdir=$1 -ddir=$2 -downloader="$3" -user_backup_urls="$4" +# Input arguments (the 'IFS's are to allow space in the name). +IFS='"' bdir="$1" +IFS='"' ddir="$2" +IFS='"' downloader="$3" +IFS='"' user_backup_urls="$4" # Basic directories/files -topdir=$(pwd) -sdir=$bdir/software -tardir=$sdir/tarballs -instdir=$sdir/installed -tmpblddir=$sdir/build-tmp +topdir="$(pwd)" +sdir="$bdir"/software +tardir="$sdir"/tarballs +instdir="$sdir"/installed +tmpblddir="$sdir"/build-tmp confdir=reproduce/software/config -ibidir=$instdir/version-info/proglib +ibidir="$instdir"/version-info/proglib downloadwrapper=reproduce/analysis/bash/download-multi-try # Derived directories -bindir=$instdir/bin -urlfile=$confdir/urls.conf -versionsfile=$confdir/versions.conf -checksumsfile=$confdir/checksums.conf -backupfile=$confdir/servers-backup.conf +bindir="$instdir"/bin +urlfile="$confdir"/urls.conf +versionsfile="$confdir"/versions.conf +checksumsfile="$confdir"/checksums.conf +backupfile="$confdir"/servers-backup.conf @@ -87,21 +87,21 @@ done # Download the necessary tarball. download_tarball() { # Basic definitions - maneagetar=$tardir/$tarball + maneagetar="$tardir"/"$tarball" # See if the tarball already exists in Maneage. if [ -f "$maneagetar" ]; then just_a_place_holder=1 else - ucname=$tardir/$tarball.unchecked + ucname="$tardir"/"$tarball.unchecked" # If the URL is empty, use the top backup server if [ x$w = x ]; then bservers="$backupservers" - tarballurl=$topbackupserver/$tarball + tarballurl="$topbackupserver"/"$tarball" else bservers="$backupservers_all" - tarballurl=$url/$tarball + tarballurl="$url"/"$tarball" fi # See if it is in the input-software directory, if so, make a link, if @@ -111,19 +111,19 @@ download_tarball() { # link and link to an actual file. if [ -f "$ddir/$tarball" ]; then if type realpath > /dev/null 2> /dev/null; then - ln -sf "$(realpath $ddir/$tarball)" "$ucname" + ln -sf "$(realpath "$ddir/$tarball")" "$ucname" else - cp $ddir/$tarball $ucname + cp "$ddir/$tarball" "$ucname" fi else - $downloadwrapper "$downloader" nolock $tarballurl $ucname \ + $downloadwrapper "$downloader" nolock $tarballurl "$ucname" \ "$bservers" fi # Make sure this is the correct tarball. if type sha512sum > /dev/null 2> /dev/null; then checksum=$(sha512sum "$ucname" | awk '{print $1}') - expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' $checksumsfile) + expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' "$checksumsfile") if [ x$checksum = x$expectedchecksum ]; then mv "$ucname" "$maneagetar" else echo "ERROR: Non-matching checksum: $tarball" @@ -137,9 +137,9 @@ download_tarball() { # If the tarball is newer than the (possibly existing) program (the version # has changed), then delete the program. - if [ -f $ibidir/$progname ]; then - if [ $maneagetar -nt $ibidir/$progname ]; then - rm $ibidir/$progname + if [ -f "$ibidir/$progname" ]; then + if [ "$maneagetar" -nt "$ibidir/$progname" ]; then + rm "$ibidir/$progname" fi fi } @@ -151,39 +151,39 @@ download_tarball() { # Build the program from the tarball. This function takes one argument # which is the configure-time options. build_program() { - if ! [ -f $ibidir/$progname ]; then + if ! [ -f "$ibidir/$progname" ]; then # Options configoptions=$1 # Go into the temporary building directory. - cd $tmpblddir + cd "$tmpblddir" unpackdir="$progname"-"$version" # Some implementations of 'tar' don't recognize Lzip, so we need to # manually call Lzip first, then call tar afterwards. - csuffix=$(echo $tarball | sed -e's/\./ /g' | awk '{print $NF}') - rm -rf $unpackdir + csuffix=$(echo "$tarball" | sed -e's/\./ /g' | awk '{print $NF}') + rm -rf "$unpackdir" if [ x$csuffix = xlz ]; then intarrm=1 - intar=$(echo $tarball | sed -e's/.lz//') - lzip -c -d $tardir/$tarball > $intar + intar=$(echo "$tarball" | sed -e's/.lz//') + lzip -c -d "$tardir/$tarball" > $intar else intarrm=0 - intar=$tardir/$tarball + intar="$tardir"/"$tarball" fi # Unpack the tarball and go into it. - tar xf $intar - if [ x$intarrm = x1 ]; then rm $intar; fi - cd $unpackdir + tar xf "$intar" + if [ x$intarrm = x1 ]; then rm "$intar"; fi + cd "$unpackdir" # build the project, either with Make and either without it. if [ x$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 $configoptions + ./configure --prefix="$instdir" $configoptions # To build GNU Make, we don't want to assume the existance of a # Make program, so we use its 'build.sh' script and its own built @@ -198,9 +198,9 @@ build_program() { fi # Clean up the source directory - cd $topdir - rm -rf $tmpblddir/$unpackdir - echo "$progname_tex $version" > $ibidir/$progname + cd "$topdir" + rm -rf "$tmpblddir/$unpackdir" + echo "$progname_tex $version" > "$ibidir/$progname" fi } @@ -219,7 +219,7 @@ build_program() { progname="lzip" progname_tex="Lzip" url=$(awk '/^'$progname'-url/{print $3}' $urlfile) -version=$(awk '/^'$progname'-version/{print $3}' $versionsfile) +version=$(awk '/^'$progname'-version/{print $3}' "$versionsfile") tarball=$progname-$version.tar download_tarball build_program -- cgit v1.2.1 From 87948105390c035a0f0ad409db622b3850988ddb Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Thu, 27 Aug 2020 16:47:26 +0100 Subject: Plain text editors: nano in basic, emacs and vim in high-level While a project is under development, the raw analysis software are not the only necessary software in a project. We also need tools to all the edit plain-text files within the Maneaged project. Usually people use their operating system's plain-text editor. However, when working on the project on a new computer, or in a container, the plain-text editors will have different versions, or may not be present at all! This can be very annoying and frustrating! With this commit, Maneage now installs GNU Nano as part of the basic tools. GNU Nano is a very simple and small plain text editor (the installed size is only ~3.5MB, and it is friendly to new users). Therefore, any Maneaged project can assume atleast Nano will be present (in particular when no editor is available on the running system!). GNU Emacs and VIM (both without extra dependencies, in particular without GUI support) are also optionally available in 'high-level.mk' (by adding them to 'TARGETS.conf'). The basic idea for the more advanced editors (Emacs and VIM) is that project authors can add their favorite editor while they are working on the project, but upon publication they can remove them from 'TARGETS.conf'. A few other minor things came up during this work and are now also fixed: - The 'file' program and its libraries like 'libmagic' were linking to system's 'libseccomp'! This dependency then leaked into Nano (which depends on 'libmagic'). But this is just an extra feature of 'file', only for the Linux kernel. Also, we have no dependency on it so far. So 'file' is not configured to not build with 'libseccomp'. - A typo was fixed in the line where the physical core information is being read on macOS. - The top-level directories when running './project shell' are now quoted (in case they have special characters). --- reproduce/software/config/checksums.conf | 3 +++ reproduce/software/config/urls.conf | 3 +++ reproduce/software/config/versions.conf | 3 +++ reproduce/software/make/basic.mk | 25 +++++++++++++++--- reproduce/software/make/high-level.mk | 45 ++++++++++++++++++++++++++++++-- reproduce/software/shell/configure.sh | 2 +- 6 files changed, 74 insertions(+), 7 deletions(-) (limited to 'reproduce') diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index b516a61..e7a0e63 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -44,6 +44,7 @@ make-checksum = ddf0fdcb9ee1b182ef294c5da70c1275288c99bef60e63a25c0abed2ddd44aba metastore-checksum = b2a5fdde9de5ddc1e6c368d5da1b2e97e4fdbaa138a7be281ccb40a81dd4a9bb1849d36b2d5d3f01205079bace60441f82a7002097ff3a7037340a35b0f1574a mpc-checksum = 72d657958b07c7812dc9c7cbae093118ce0e454c68a585bfb0e2fa559f1bf7c5f49b93906f580ab3f1073e5b595d23c6494d4d76b765d16dde857a18dd239628 mpfr-checksum = d583555d08863bf36c89b289ae26bae353d9a31f08ee3894520992d2c26e5683c4c9c193d7ad139632f71c0a476d85ea76182702a98bf08dde7b6f65a54f8b88 +nano-checksum = d101e7f4802c079254e79340b433749dcd699fa9adec3f96e4218ec12f066a1f6b0954c27254bb6f019bc370ee2116817717870f4e2bc782c552442f2cc75195 ncurses-checksum = 4c1333dcc30e858e8a9525d4b9aefb60000cfc727bc4a1062bace06ffc4639ad9f6e54f6bdda0e3a0e5ea14de995f96b52b3327d9ec633608792c99a1e8d840d openssl-checksum = 1523985ba90f38aa91aa6c2d57652f4e243cb2a095ce6336bf34b39b5a9b5b876804299a6825c758b65990e57948da532cca761aa12b10958c97478d04dd6d34 patchelf-checksum = 39745662651cf0a9915685b2767a611ceab4286f8fa57eace342b3f44248431616e8563d4ac6709c97d8534229c73c05470239e462b7e74b36bf629a876dfbad @@ -86,6 +87,7 @@ cdsclient-checksum = 2d7abf0079189b9dd19cb8919061445fd19ea9f7dfd54e8ceee26b74321 cfitsio-checksum = 08a13931726b0ee15bd4e2ad6dd4debb8268f3b0bc33adadec5c6a29295dd536bcccb3cc949721c6cebac6f43b6118e5e38332ac0ba8a07a43553416d8debae5 cmake-checksum = e0591d5fb234f3e7b74d6d2aad44fbf3e19e69547bd428681ba6ad0461d4f3d2a154605808b4733531d2c66f0e91eb39a179ae0d89a37e92a3f20e9cae691468 eigen-checksum = 34cf600914cce719d61511577ef9cd26fbdcb7a6fad1d0ab8396f98b887fac6a5577d3967e84a8f56225cc50de38f3b91f34f447d14312028383e32b34ea1972 +emacs-checksum = dfb26531d2c19cf9fb56505f03d799654b45e5f9528e777900e8280ed2c1d21e04c52f510528e31e015977c471ae63164cedee6174b7439ebcf479a21fc18064 expat-checksum = 514ff2ef3c93af0b1715b7a08732db33c13a113c4c72422716a22ee26c09235deed71ec55510cee24c33bcd6b2347602bd71ce70a432d5583fb63765ff9e0e09 fftw-checksum = ab918b742a7c7dcb56390a0a0014f517a6dff9a2e4b4591060deeb2c652bf3c6868aa74559a422a276b853289b4b701bdcbd3d4d8c08943acf29167a7be81a38 flex-checksum = b4ef58d4a1d66b213e2f59df06959decf46d26b253cdc3f51cd26e2e2b505461ef23dafa974dd2005b1f0cafa5a83fe9258baf78004b2fdae6dfc299bc17bfd1 @@ -130,6 +132,7 @@ swarp-checksum = 80f4ade59738df3d4c9b47bda04148b53c6ba995d523fa8d1e02fb5d952b607 swig-checksum = 5eaa2e06d8e4197fd02194051db1e518325dbb074a4c55a91099ad9c55193874f577764afc9029409a41bd520a95154095f26e33ef5add5c102bb2c1d98d33eb tides-checksum = c3360ff0d023b43749ba09a33302ca059f017a157b3ce7cdcf4f1a1578e90d3e7fa420077043adbee6b1ebf94bd698c8d6b279012f36d2a05b4de5351e30e108 util-linux-checksum = c95d26b9037d6b877a247e6aeb58d17aa80f7e1bd6b523a4e0fde559fe07b3d924ece6d373300fefb65d1f206b3f990aeddb3a03605040e72ce6d6ee88591021 +vim-checksum = 06ba43386fcf308520d88d7a68e9bc1fabd824b05078b8f9112500a2ad4e50a91f1a1c2925889b7c06dbce34307f12abf508e2172b05fd283f965cc06552eb6d wcslib-checksum = 8c98c4b575056e2d966b77a4bc951256d02ecee3a11847e140fd38d93afd0f76b3e906d590c952dc9fc58ceeb1ba062b19d8e1e676ee0032f5b7ed13a9dfa892 xlsxio-checksum = 22870fda7bd4eefd5fea2a9ad7530c9049135129d9b69805091777e6b54b2fc6c3f0e69c6954f36bce54eebbfeccaf637cce9e271a593221a4296d6632470a6c yaml-checksum = dadd7d8e0d88b5ebab005e5d521d56d541580198aa497370966b98c904586e642a1cd4f3881094eb57624f218d50db77417bbfd0ffdce50340f011e35e8c4c02 diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf index 34c4d89..417f5ed 100644 --- a/reproduce/software/config/urls.conf +++ b/reproduce/software/config/urls.conf @@ -47,6 +47,7 @@ #metastore-url = http://akhlaghi.org/maneage-software #mpc-url = http://ftp.gnu.org/gnu/mpc #mpfr-url = http://www.mpfr.org/mpfr-current +#nano-url = https://www.nano-editor.org/dist/v$(word 1, $(subst ., ,$(nano-version))) #ncurses-url = http://ftp.gnu.org/gnu/ncurses #openssl-url = http://www.openssl.org/source #patchelf-url = http://nixos.org/releases/patchelf/patchelf-$(patchelf-version) @@ -88,6 +89,7 @@ #cfitsio-url = https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c #cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv) #eigen-url = http://bitbucket.org/eigen/eigen/get/$(eigen-version).tar.gz +#emacs-url = http://ftp.gnu.org/gnu/emacs #expat-url = $(shell vstr=$$(echo $(expat-version) | sed -e's/\./_/g'); echo https://github.com/libexpat/libexpat/releases/download/R_$$vstr/expat-$(expat-version).tar.lz) #fftw-url = ftp://ftp.fftw.org/pub/fftw #flex-url = https://github.com/westes/flex/files/981163 @@ -133,6 +135,7 @@ #tides-url = http://akhlaghi.org/maneage-software #util-linux-url = https://mirrors.edge.kernel.org/pub/linux/utils/util-linux/v2.35/ #valgrind-url = https://sourceware.org/pub/valgrind +#vim-url = ftp://ftp.vim.org/pub/vim/unix #wcslib-url = ftp://ftp.atnf.csiro.au/pub/software/wcslib #xlsxio-url = https://github.com/brechtsanders/xlsxio/archive #yaml-url = pyyaml.org/download/libyaml diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index 0a9e21e..0b3a4d2 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -44,6 +44,7 @@ make-version = 4.3 metastore-version = 1.1.2-23-fa9170b mpc-version = 1.1.0 mpfr-version = 4.0.2 +nano-version = 5.2 ncurses-version = 6.2 patchelf-version = 0.10 perl-version = 5.32.0 @@ -94,6 +95,7 @@ cdsclient-version = 3.84 cfitsio-version = 3.48 cmake-version = 3.18.1 eigen-version = 3.3.7 +emacs-version = 27.1 expat-version = 2.2.9 fftw-version = 3.3.8 flex-version = 2.6.4-91-ga631f5d @@ -134,6 +136,7 @@ swarp-version = 2.38.0 swig-version = 3.0.12 tides-version = 2.0 util-linux-version = 2.35 +vim-version = 8.2 xlsxio-version = 0.2.21 yaml-version = 0.2.5 diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 0b672d8..934580a 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -56,8 +56,13 @@ ibdir = $(BDIR)/software/installed/bin ildir = $(BDIR)/software/installed/lib ibidir = $(BDIR)/software/installed/version-info/proglib -# Ultimate Makefile target. -targets-proglib = low-level-links gcc-$(gcc-version) +# Ultimate Makefile target. GNU Nano (a simple and very light-weight text +# 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 is available). +targets-proglib = low-level-links \ + gcc-$(gcc-version) \ + nano-$(nano-version) all: $(foreach p, $(targets-proglib), $(ibidir)/$(p)) # Define the shell environment @@ -852,7 +857,8 @@ $(ibidir)/diffutils-$(diffutils-version): \ $(ibidir)/file-$(file-version): $(ibidir)/coreutils-$(coreutils-version) tarball=file-$(file-version).tar.gz $(call import-source, $(file-url), $(file-checksum)) - $(call gbuild, file-$(file-version), static,,V=1) + $(call gbuild, file-$(file-version), static, \ + --disable-libseccomp, V=1) echo "File $(file-version)" > $@ $(ibidir)/findutils-$(findutils-version): \ @@ -1145,11 +1151,22 @@ $(ibidir)/texinfo-$(texinfo-version): \ echo "GNU Texinfo $(texinfo-version)" > $@ $(ibidir)/which-$(which-version): $(ibidir)/coreutils-$(coreutils-version) - tarball=/which-$(which-version).tar.gz + tarball=which-$(which-version).tar.gz $(call import-source, $(which-url), $(which-checksum)) $(call gbuild, which-$(which-version), static) echo "GNU Which $(which-version)" > $@ +# GNU Nano is a very light-weight and small, command-line text editor (in +# total around 3.5 Mb after installation!). It is top-level target in the +# basic tools (nothing depends on it, it just depends on GCC). This is +# because some projects may choose to not have it by manually removing it +# from 'targets-proglib' above (it has no effect on processing after all!). +$(ibidir)/nano-$(nano-version): $(ibidir)/gcc-$(gcc-version) + tarball=nano-$(nano-version).tar.xz + $(call import-source, $(nano-url), $(nano-checksum)) + $(call gbuild, nano-$(nano-version), static) + echo "GNU Nano $(nano-version)" > $@ + diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index cf9c5a1..3c5e518 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -449,6 +449,25 @@ $(ibidir)/eigen-$(eigen-version): rm -rf $(ddir)/eigen-eigen-* echo "Eigen $(eigen-version)" > $@ +# GNU Emacs is an advanced text editor (among many other things!), so it +# isn't directly related to the analysis phase of a project. However, it +# can be useful during the development of a project on systems that don't +# have it natively. So probably after the project is finished and is ready +# for publication, you can remove it from 'TARGETS.conf'. +# +# However, the full Emacs build has a very large number of dependencies +# which aren't necessary in many scenarios so we are disabling everything +# except the core Emacs functionality (using '--without-all') and we are +# also disabling all graphic user interface features (using '--without-x'). +$(ibidir)/emacs-$(emacs-version): + tarball=emacs-$(emacs-version).tar.xz + $(call import-source, $(emacs-url), $(emacs-checksum)) + $(call gbuild, emacs-$(emacs-version), static, \ + --without-all --without-x \ + --without-gnutls --with-ns=no, \ + -j$(numthreads) V=1) + echo "GNU Emacs $(emacs-version)" > $@ + $(ibidir)/expat-$(expat-version): tarball=expat-$(expat-version).tar.lz $(call import-source, $(expat-url), $(expat-checksum)) @@ -1374,8 +1393,30 @@ $(ibidir)/xlsxio-$(xlsxio-version): \ rm $(ibdir)/example_xlsxio_* echo "XLSX I/O $(xlsxio-version)" > $@ - - +# VIM is a text editor which doesn't directly affect processing but can be +# useful in projects during its development, for more see the comment above +# GNU Emacs. +$(ibidir)/vim-$(vim-version): + tarball=vim-$(vim-version).tar.bz2 + $(call import-source, $(vim-url), $(vim-checksum)) + cd $(ddir) + tar xf $(tdir)/$$tarball + n=$$(echo $(vim-version) | sed -e's|\.||') + cd $(ddir)/vim$$n + ./configure --prefix=$(idir) \ + --disable-canberra \ + --enable-multibyte \ + --disable-netbeans \ + --disable-fontset \ + --disable-gpm \ + --disable-acl \ + --disable-gui \ + --with-x=no + make -j$(numthreads) + make install + cd .. + rm -rf vim$$n + echo "VIM $(vim-version)" > $@ diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index 2b4300b..21fe1d6 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -254,7 +254,7 @@ elif [ x$on_mac_os = xyes ]; then if [ x$hw_byteorder = x1234 ]; then byte_order="Little Endian"; elif [ x$hw_byteorder = x4321 ]; then byte_order="Big Endian"; fi - address_size_physical=$(sysctl -n machdep.cpu.address_bits.phyiscal) + address_size_physical=$(sysctl -n machdep.cpu.address_bits.physical) address_size_virtual=$(sysctl -n machdep.cpu.address_bits.virtual) address_sizes="$address_size_physical bits physical, " address_sizes+="$address_size_virtual bits virtual" -- cgit v1.2.1