diff options
Diffstat (limited to 'reproduce/software')
| -rw-r--r-- | reproduce/software/config/checksums.conf | 2 | ||||
| -rw-r--r-- | reproduce/software/config/servers-backup.conf | 2 | ||||
| -rw-r--r-- | reproduce/software/config/texlive-packages.conf | 18 | ||||
| -rw-r--r-- | reproduce/software/config/versions.conf | 5 | ||||
| -rw-r--r-- | reproduce/software/make/basic.mk | 77 | ||||
| -rw-r--r-- | reproduce/software/make/high-level.mk | 33 | ||||
| -rwxr-xr-x | reproduce/software/shell/configure.sh | 11 |
7 files changed, 78 insertions, 70 deletions
diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index 01ef8c8..130c116 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -128,7 +128,7 @@ patch-checksum = 75d4e1544484da12185418cd4a1571994398140a91ac606fa08dd067004187d pcre-checksum = abac4c4f9df9e61d7d7761a9c50843882611752e1df0842a54318f358c28f5953025eba2d78997d21ee690756b56cc9f1c04a5ed591dd60654cc78ba16d9ecfb pixman-checksum = 333732b99994f7ea636d647e0b6123075351b27601b5b6370c9bc821a1ab3921386ddb92b51e015f3fc35104ba09be1e0d7bef47f0b4f73036b01d1d70396dd9 plplot-checksum = 2c5a36d84ebd948402c924d304427b5702bc75bdd22753c9b3b910b382dfdcc26910382aae452f02d86b25c1c813bbe1f40c9305de1d2809d575975f610fdf10 -python-checksum = de940d7eceee69b8a04f12c613753f61db53ddac1c5cde5388dd342e88a09bae8da1f56b71b96f20997f6203d169e92e9e2558c43b38dbc323221d7bb362abfc +python-checksum = b3d6b4187b31167b382e195037d7ca01d5e9c112fceb0f12a30c101dbcc91079601c01aa449f9d33d2fc53c795c33305e80c891e986a0e24cbecc14beaf90199 r-cran-checksum = 54cc07956a70c09b5a533188eb063d2a9dc67a8aa5648ec7f9c107f626220c9f6e17ab7175e65dd54a8d608a1ca4106c8ad2856709eb995ab66439b5f033e725 rpcsvc-proto-checksum = c3011d7d7ef97a4a751f6921df1a23e1dd8ac50fb0690c759d37010ed7be27968a2130e3b8872cb48d5914216f9d539096a424f1ec38a75f7ed899748151c6f4 scamp-checksum = c7a192f357c6808acd16d1c5d2657c5c8c2f61e4fecb8a4b18d39b07f4c444f85d5029c21571d41ec3ba9c8d075de8bd660b0e029bf5dd63e3819e963430a938 diff --git a/reproduce/software/config/servers-backup.conf b/reproduce/software/config/servers-backup.conf index d4aa25e..f0e040e 100644 --- a/reproduce/software/config/servers-backup.conf +++ b/reproduce/software/config/servers-backup.conf @@ -9,6 +9,6 @@ # permitted in any medium without royalty provided the copyright notice and # this notice are preserved. This file is offered as-is, without any # warranty. +http://gitlab.cefca.es/maneage/tarballs-software/-/raw/master/ http://gitlab.com/maneage/tarballs-software/-/raw/master http://git.maneage.org/tarballs-software.git/plain -http://akhlaghi.org/maneage-software diff --git a/reproduce/software/config/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf index bb38d5a..e68a771 100644 --- a/reproduce/software/config/texlive-packages.conf +++ b/reproduce/software/config/texlive-packages.conf @@ -5,14 +5,20 @@ # name). # # Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2022-2025 Boud Roukema <boud@astro.uni.torun.pl> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and # this notice are preserved. This file is offered as-is, without any # warranty. -# Notes -# ----- +# Hints: +# +# - For debugging: after a partial or successful build, look through +# '.build/software/installed/texlive/maneage/tlpkg/texlive.tlpdb.main.*' +# to see what packages and files were looked at during the install. + +# Notes: # # - tex and fancyhdr: These two packages are installed along with the basic # installation scheme that we used to install tlmgr, they will be ignored @@ -22,31 +28,23 @@ # - fancyvrb: needed by R. texlive-packages = biber \ biblatex \ - bitset \ caption \ courier \ csquotes \ datetime \ - ec \ - etoolbox \ - fancyhdr \ fancyvrb \ fmtcount \ fontaxes \ footmisc \ fp \ kastrup \ - letltxmacro \ logreq \ mweights \ newtx \ - pdfescape \ - pdftexcmds \ pgf \ pgfplots \ preprint \ setspace \ - tex \ tex-gyre \ times \ titlesec \ diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index 07bdb9e..861b5c5 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -149,7 +149,6 @@ patch-version = 2.7.6 pcre-version = 8.44 pixman-version = 0.40.0 plplot-version = 5.15.0 -python-version = 3.13.2 r-cran-version = 4.1.2 rpcsvc-proto-version = 1.4 scamp-version = 2.10.0 @@ -186,6 +185,10 @@ xtrans-version = 1.5.2 lapack-version = 3.8.0 libgit2-version = 1.9.0 +# Python should only be updated by the maintainer for Python packages; see +# https://savannah.nongnu.org/task/?16622. +python-version = 3.10.6 + # Netpbm's questions in the configure steps maybe change with different or # new versions. netpbm-version = 10.73.39 diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index 628a0e2..cf155f0 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -273,46 +273,10 @@ $(ibidir)/gzip-$(gzip-version): | $(ibdir) $(ildir) $(lockdir) $(call gbuild, gzip-$(gzip-version), static, , V=1) echo "GNU Gzip $(gzip-version)" > $@ -# 2022-07-14 B Roukema -# -# xz-5.2.5 fails on (at least) CentOS 7 (Redhat) systems while trying -# to compile 'cmake' in Maneage - this is Maneage bug 62700 [1]. -# -# The fix appears to be just a few lines, although it's not clear -# how robust or long-term it is. Since we don't yet have 'patch' in -# 'basic.mk', this file has to be copied into place rather than patched. - -# xz-5.2.5_src_liblzma_liblzma.map is a patched -# version of xz-5.2.5/src/liblzma/liblzma.map based on discussion at -# [1] + [2] + the patch file [3]. -# -# [1] https://savannah.nongnu.org/bugs/index.php?62700 -# [2] https://github.com/easybuilders/easybuild-easyconfigs/issues/14991 -# [3] https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/bcebb3320ffb63f9804ca8d4d64d1822ec7c9792/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch $(ibidir)/xz-$(xz-version): $(ibidir)/gzip-$(gzip-version) - -# Prepare the tarball. tarball=xz-$(xz-version).tar.lz $(call import-source, $(xz-url), $(xz-checksum)) - -# Until the bug mentioned above is fixed, we'll can't use the generic -# rule. -# $(call gbuild, xz-$(xz-version), static) - -# Configure and build with patched file. - srcdir=$$(pwd) - unpackdir=xz-$(xz-version) - patchedfile=xz-5.2.5_src_liblzma_liblzma.map - cd $(ddir) - rm -rf $$unpackdir - tar -x -f $(tdir)/$$tarball - cd $$unpackdir - cp -pv $$srcdir/reproduce/software/patches/$$patchedfile \ - src/liblzma/liblzma.map # copy the fixed file into place - ./configure --prefix=$(idir) - make install - cd .. - rm -rf $$unpackdir + $(call gbuild, xz-$(xz-version), static) echo "XZ Utils $(xz-version)" > $@ $(ibidir)/bzip2-$(bzip2-version): $(ibidir)/gzip-$(gzip-version) @@ -1247,7 +1211,8 @@ $(ibidir)/binutils-$(binutils-version): \ # Build binutils with the standard 'gbuild' function. $(call gbuild, binutils-$(binutils-version), static, \ - --with-lib-path=$(sys_library_path), \ + --with-lib-path=$(sys_library_path) \ + --enable-gprofng=no, \ -j$(numthreads) V=1) # The 'ld' linker of Binutils needs several '*crt*.o' files from @@ -1375,21 +1340,35 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) # to avoid building so many small/temporary files and possibly # harming the hard-drive or SSD. But if the RAM doesn't have enough # space, we should use the hard-drive or SSD. During its build, -# GCC's build directory will become about 7GiB (in units of 1024^3 -# bytes, for GCC 12.1.0, which corresponds to 7.5GB, in units of -# 1000^3 bytes). So at this step, we make sure that we have more -# than 12GiB before GCC starts to build. See the figure in the link -# below for GCC's RAM consumption as a function of time: +# GCC's build directory will become several gigabytes and the build +# also needs RAM. You can track the RAM usage of the system with a +# 1-second resolution (if no other RAM consuming program is running +# while building GCC) with the command below (example outputs can +# be seen in https://savannah.nongnu.org/task/index.php?16623). # -# https://savannah.nongnu.org/task/?16244#comment12 +# c=1; while true; do POSIXLY_CORRECT=1 df -P /dev/shm/maneage-* | awk 'NR==2{print '$c', $3}'; c=$((c+1)); sleep 1; done > mem-usage.txt +# asttable mem-usage.txt -c1,'arith $2 512 x 1024 / 1024 / 1024 /' -o mem.fits # # For POSIX portability and longevity (default sizes might change), # we use the '-P' option, and we use the environment variable -# POSIXLY_CORRECT=1, so the 'block size' is 512 bytes. We'll also -# allow for about ~0.5 GB at the start. +# POSIXLY_CORRECT=1, so the 'block size' is 512 bytes. In this way, +# to get the actual GiB amount, multiply the value returned above +# by 512 (B/block), then divide by 1024^3 (B/GiB). +# +# To get the final value to use here, get the maximum used value +# after GCC is fully built and you have stopped the 'while true' +# command above. You can do this with the command below (assumes +# you have Gnuastro). +# +# aststatistics mem-usage.txt -c2 --maximum | asttable -c'arith $1 7000000 +' -Afixed -B0 +# +# The extra space is because we will assume an extra 3 GiB = 3GiB * +# 1024^3 (B/GiB) / 512 (B/block) = 6291456 blocks are necessary for +# the building (let's round it to 7000000!). # -# So we need 8 GiB * 1024^3 (B/GiB) / 512 blocks/B = 16777216 -# blocks, in blocks of 512 bytes. +# Therefore, we need to make sure that the running system more than +# the necessary amount of space in the RAM. To do this, we use 'df' +# below. # # The 4th column of 'df' is the "available" space at the time of # running, not the full space. So the 'RAM disk' that the OS @@ -1399,7 +1378,7 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version) # alone - no other Maneage software is built at the same time as # GCC - so this amount of RAM should be enough. in_ram=$$(POSIXLY_CORRECT=1 df -P $(ddir) \ - | awk 'NR==2{print ($$4>16777216) ? "yes" : "no"}'); \ + | awk 'NR==2{print ($$4>26613216) ? "yes" : "no"}'); \ if [ $$in_ram = "yes" ]; then odir=$(ddir) else odir=$(BDIR)/software/build-tmp-gcc-due-to-lack-of-space diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index fdab193..928d0a2 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -1098,18 +1098,28 @@ $(ibidir)/cmake-$(cmake-version): # SHELL=$(SHELL) and we have defined this script. export MAKE="$(makewshell)" -# Go into the unpacked directory and build CMake. +# Go into the unpacked directory and prepare CMake. cd $(ddir) rm -rf cmake-$(cmake-version) tar -xf $(tdir)/$$tarball cd cmake-$(cmake-version) $(shsrcdir)/prep-source.sh $(ibdir) - ./bootstrap --prefix=$(idir) --system-curl --system-zlib \ - --system-bzip2 --system-liblzma --no-qt-gui \ + +# Bootstrap, build and install CMake: +# - With the '--no-system-libs' option, CMake builds and statically +# links all the libraries it needs. Even though some of those (like +# liblzma, libcurl, zlib or bzip2) are within Maneage, we +# discovered that CMake can get confused and use out-of-Maneage +# libraries (https://savannah.nongnu.org/bugs/?63043). + ./bootstrap --no-qt-gui \ + --prefix=$(idir) \ + --no-system-libs \ --parallel=$(numthreads) $(makewshell) VERBOSE=1 LIBS="$$LIBS -lssl -lcrypto -lz" \ -j$(numthreads) $(makewshell) install + +# Clean up. cd .. rm -rf cmake-$(cmake-version) echo "CMake $(cmake-version)" > $@ @@ -1960,10 +1970,19 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf # Live itself (only very basic TeX and LaTeX) and the installation of its # necessary packages into two packages. # -# Note that Biber needs to link with libraries like libnsl. However, we -# don't currently build biber from source. So we can't choose the library -# version. But we have the source and build instructions for the 'nsl' -# library. When we later build biber from source, we can easily use them. +# Note that we do not build the TeXLive executables (like Biber) from +# source. So in case they need special libraries, we can't choose the +# library version here (for example see [1] and [2]). In such cases there +# is no solution but to manually add the location necessary library to +# LD_LIBRARY_PATH when calling the respective LaTeX command in +# 'reproduce/analysis/make/paper.mk'. Fortunately as of Biber 2.20, it does +# not depend on anything except the C library (all dependencies are now +# statically linked), so problems [1] and [2] will not happen. But this can +# generally happen for any other tool/OS, so it is important to build +# TeXLive from source as soon as possible [3]. +# [1] https://github.com/plk/biber/issues/445 +# [2] https://savannah.nongnu.org/bugs/index.php?63175 +# [3] https://savannah.nongnu.org/task/?15267 $(itidir)/texlive: reproduce/software/config/texlive-packages.conf \ $(itidir)/texlive-ready-tlmgr diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh index f226ced..d58a829 100755 --- a/reproduce/software/shell/configure.sh +++ b/reproduce/software/shell/configure.sh @@ -1439,6 +1439,15 @@ 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 # ------------------------------------------------- # @@ -1575,7 +1584,7 @@ fi # 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. -if [ x"$$on_mac_os" != xyes ]; then +if [ x"$on_mac_os" != xyes ]; then sys_library_sh_path=$(otool -L /bin/sh \ | awk '/\/lib/{print $1}' \ | sed 's#/[^/]*$##' \ |