From c151eddbcc5f4208b40dc3037a8ae8adb0ff9173 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Wed, 10 Jun 2020 23:44:13 +0100 Subject: IMPORTANT: many improvements to low-level software building phase POSSIBLE EFFECT ON YOUR PROJECT: The changes in this commit may only cause conflicts to your project if you have changed the software building Makefiles in your project's branch (e.g., 'basic.mk', 'high-level.mk' and 'python.mk'). If your project has only added analysis, it shouldn't be affected. This is a large commit, involving a long series of corrections in a differnt branch which is now finally being merged into the core Maneage branch. All changes were related and came up naturally as the low-level infrastructure was improved. So separating them in the end for the final merge would have been very time consuming and we are merging them as one commit. In general, the software building Makefiles are now much more easier to read, modify and use, along with several new features that have been added. See below for the full list. - Until now, Maneage needed the host to have a 'make' implementation because Make was necessary to build Lzip. Lzip is then used to uncompress the source of our own GNU Make. However, in the minimalist/slim versions of operating systems (for example used to build Docker images) Make isn't included by default. Since Lzip was the only program before our own GNU Make was installed, we consulting Antonio Diaz Diaz (creator of Lzip) and he kindly added the necessary functionality to a new version of Lzip, which we are using now. Hence we don't need to assume a Make implementation on the host any more. With this commit, Lzip and GNU Make are built without Make, allowing everything else to be safely built with our own custom version of GNU Make and not using the host's 'make' at all. - Until recently (Commit 3d8aa5953c4) GNU Make was built in 'basic.mk'. Therefore 'basic.mk' was written in a way that it can be used with other 'make' implementations also (i.e., important shell commands starting with '&&' and ending in '\' without any comments between them!). Furthermore, to help in style uniformity, the rules in 'high-level.mk' and 'python.mk' also followed a similar structure. But due to the point above, we can now guarantee that GNU Make is used from the very first Makefile, so this hard-to-read structure has been removed in the software build recipes and they are much more readable and edit-friendly now. - Until now, the default backup servers where at some fixed URLs, on our own pages or on Gitlab. But recently we uploaded all the necessary software to Zenodo (https://doi.org/10.5281/zenodo.3883409) which is more suitable for this task (it promises longevity, has a fixed DOI, while allowing us to add new content, or new software tarball versions). With this commit, a small script has been written to extract the most recent Zenodo upload link from the Zenodo DOI and use it for downloading the software source codes. - Until now, we primarily used the webpage of each software for downloading its tarball. But this caused many problems: 1) Some of them needed Javascript before the download, 2) Some URLs had a complex dependency on the version number, 3) some servers would be randomly down for maintenance and etc. So thanks to the point above, we now use the Zenodo server as the primary download location. However, if a user wants to use a custom software that is not (yet!) in Zenodo, the download script gives priority to a custom URL that the users can give as Make variables. If that variable is defined, then the script will use that URL before going onto Zenodo. We now have a special place for such URLs: 'reproduce/software/config/urls.conf'. The old URLs (which are a good documentation themselves) are preserved here, but are commented by default. - The software source code downloading and checksum verification step has been moved into a Make function called 'import-source' (defined in the 'build-rules.mk' and loaded in all software Makefiles). Having taken all the low-level steps there, I noticed that there is no more need for having the tarball as a separate target! So with this commit, a single rule is the only place that needs to be edited/added (greatly simplifying the software building Makefiles). - Following task #15272, A new option has been added to the './project' script called '--all-highlevel'. When this option is given, the contents of 'TARGETS.conf' are ignored and all the software in Maneage are built (selected by parsing the 'versions.conf' file). This new option was added to confirm the extensive changes made in all the software building recipes and is great for development/testing purposes. - Many of the software hadn't been tested for a long time! So after using the newly added '--all-highlevel', we noticed that some need to be updated. In general, with this commit, 'libpaper' and 'pcre' were added as new software, and the versions of the following software was updated: 'boost', 'flex', 'libtirpc', 'openblas' and 'lzip'. A 'run-parts.in' shell script was added in 'reproduce/software/shell/' which is installed with 'libpaper'. - Even though we intentionally add the necessary flags to add RPATH inside the built executable at compilation time, some software don't do it (different software on different operating systems!). Until now, for historical reasons this check was done in different ways for different software on GNU/Linux sytems. But now it is unified: if 'patchelf' is present we apply it. Because of this, 'patchelf' has been put as a top-level prerequisite, right after Tar and is installed before anything else. - In 'versions.conf', GNU Libtool is recognized as 'libtool', but in 'basic.mk', it was 'glibtool'! This caused many confusions and is corrected with this commit (in 'basic.mk', it is also 'libtool'). - A new argument is added to the './project' script to allow easy loading of the project's shell and environment for fast/temporary testing of things in the same environment as the project. Before activating the project's shell, we completely remove all host environment variables to simulate the project's environment. It can be called with this command: './project shell'. A simple prompt has also been added to highlight that the user is using the Maneage shell! --- reproduce/software/config/checksums.conf | 12 ++- reproduce/software/config/urls.conf | 159 +++++++++++++++++++++++++++++++ reproduce/software/config/versions.conf | 93 +++++++++--------- 3 files changed, 215 insertions(+), 49 deletions(-) create mode 100644 reproduce/software/config/urls.conf (limited to 'reproduce/software/config') diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf index e23df9f..2da488b 100644 --- a/reproduce/software/config/checksums.conf +++ b/reproduce/software/config/checksums.conf @@ -38,7 +38,7 @@ libiconv-checksum = 365dac0b34b4255a0066e8033a8b3db4bdb94b9b57a9dca17ebf2d779139 libtool-checksum = a6eef35f3cbccf2c9e2667f44a476ebc80ab888725eb768e91a3a6c33b8c931afc46eb23efaee76c8696d3e4eed74ab1c71157bcb924f38ee912c8a90a6521a4 libunistring-checksum = 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/dev/null +++ b/reproduce/software/config/urls.conf @@ -0,0 +1,159 @@ +# Optional URLs of software to use for downloading their source +# +# If un-commented the URLs of this file will be used. Otherwise default +# servers (primarily on 'zenodo.org') will be checked for the tarball. +# +# Copyright (C) 2020 Mohammad Akhlaghi +# Copyright (C) 2020 Raul Infante-Sainz +# +# 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. + + + + + +# Basic/low-level programs and libraires (installed in any case) +# -------------------------------------------------------------- +#bash-url = http://akhlaghi.org/maneage-software +#binutils-url = http://ftp.gnu.org/gnu/binutils +#bzip2-url = http://akhlaghi.org/maneage-software +#cert-url = http://akhlaghi.org/maneage-software +#coreutils-url = http://ftp.gnu.org/gnu/coreutils +#curl-url = https://curl.haxx.se/download +#dash-url = http://akhlaghi.org/maneage-software +#diffutils-url = http://ftp.gnu.org/gnu/diffutils +#file-url = ftp://ftp.astron.com/pub/file +#findutils-url = http://ftp.gnu.org/gnu/findutils +#flock-url = http://akhlaghi.org/src +#gawk-url = http://ftp.gnu.org/gnu/gawk +#gcc-url = http://ftp.gnu.org/gnu/gcc/gcc-$(gcc-version) +#gettext-url = https://ftp.gnu.org/gnu/gettext +#git-url = http://mirrors.edge.kernel.org/pub/software/scm/git +#gmp-url = https://gmplib.org/download/gmp +#grep-url = http://ftp.gnu.org/gnu/grep +#gzip-url = http://akhlaghi.org/src +#isl-url = ftp://gcc.gnu.org/pub/gcc/infrastructure +#libbsd-url = http://libbsd.freedesktop.org/releases +#libiconv-url = https://ftp.gnu.org/pub/gnu/libiconv +#libtool-url = http://ftp.gnu.org/gnu/libtool +#libunistring-url = http://ftp.gnu.org/gnu/libunistring +#libxml2-url = ftp://xmlsoft.org/libxml2 +#lzip-url = http://akhlaghi.org/src +#m4-url = http://akhlaghi.org/maneage-software +#make-url = http://akhlaghi.org/src +#metastore-url = http://akhlaghi.org/maneage-software +#mpc-url = http://ftp.gnu.org/gnu/mpc +#mpfr-url = http://www.mpfr.org/mpfr-current +#ncurses-url = http://ftp.gnu.org/gnu/ncurses +#openssl-url = http://www.openssl.org/source +#patchelf-url = http://nixos.org/releases/patchelf/patchelf-$(patchelf-version) +#perl-url = $(shell echo https://www.cpan.org/src/$$(echo $(perl-version) | sed -e's/\./ /g' | awk '{printf("%d.0", $$1)}')) +#pkgconfig-url = http://pkg-config.freedesktop.org/releases +#readline-url = http://ftp.gnu.org/gnu/readline +#sed-url = http://ftp.gnu.org/gnu/sed +#tar-url = http://ftp.gnu.org/gnu/tar +#texinfo-url = http://ftp.gnu.org/gnu/texinfo +#unzip-url = $(shell echo ftp://ftp.info-zip.org/pub/infozip/src/unzip$$(echo $(unzip-version) | sed -e's/\.//').tgz) +#wget-url = http://ftp.gnu.org/gnu/wget +#which-url = http://ftp.gnu.org/gnu/which +#xz-url = http://tukaani.org/xz +#zip-url = $(shell echo ftp://ftp.info-zip.org/pub/infozip/src/zip$$(echo $(zip-version) | sed -e's/\.//').tgz) +#zlib-url = http://www.zlib.net + + + + + +# Optional/high-level programs and libraries +# ------------------------------------------ +# +# These are programs and libraries that are optional, The ones in +# `reproduce/software/config/TARGETS.conf' will be built as +# part of a project. To specify a software there, just remove the +# `-url' suffix from the list below. +#apachelog4cxx-url = http://akhlaghi.org/maneage-software +#apr-url = https://www-us.apache.org/dist/apr +#apr-util-url = https://www-us.apache.org/dist/apr +#astrometrynet-url = http://astrometry.net/downloads +#atlas-url = https://sourceforge.net/projects/math-atlas/files/Stable/$(atlas-version)/atlas$(atlas-version).tar.bz2/download +#autoconf-url = http://akhlaghi.org/maneage-software +#automake-url = http://ftp.gnu.org/gnu/automake +#bison-url = http://ftp.gnu.org/gnu/bison +#boost-url = $(shell vstr=$$(echo $(boost-version) | sed -e's/\./_/g'); echo https://dl.bintray.com/boostorg/release/$(boost-version)/source) +#cairo-url = https://www.cairographics.org/releases +#cdsclient-url = http://cdsarc.u-strasbg.fr/ftp/pub/sw +#cfitsio-url = https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c +#cmake-url = $(shell majv=$$(echo $(cmake-version) | sed -e's/\./ /' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://cmake.org/files/v$$majv/cmake-$(cmake-version).tar.gz) +#eigen-url = http://bitbucket.org/eigen/eigen/get/$(eigen-version).tar.gz +#expat-url = $(shell vstr=$$(echo $(expat-version) | sed -e's/\./_/g'); echo https://github.com/libexpat/libexpat/releases/download/R_$$vstr/expat-$(expat-version).tar.lz) +#fftw-url = ftp://ftp.fftw.org/pub/fftw +#flex-url = https://github.com/westes/flex/files/981163 +#freetype-url = https://download.savannah.gnu.org/releases/freetype +#gdb-url = http://ftp.gnu.org/gnu/gdb +#ghostscript-url = $(shell v=$$(echo $(ghostscript-version) | sed -e's/\.//'); echo https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs$$v) +#gnuastro-url = http://ftp.gnu.org/gnu/gnuastro +#gsl-url = http://ftp.gnu.org/gnu/gsl +#hdf5-url = $(shell majorver=$$(echo $(hdf5-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$$majorver/hdf5-$(hdf5-version)/src) +#healpix-url = http://akhlaghi.org/maneage-software +#help2man-url = http://ftp.gnu.org/gnu/help2man +#imagemagick-url = http://akhlaghi.org/maneage-software +#imfit-url = http://www.mpe.mpg.de/~erwin/resources/imfit +#lapack-url = http://www.netlib.org/lapack +#libffi-url = ftp://sourceware.org/pub/libffi +#libgit2-url = https://github.com/libgit2/libgit2/archive +#libjpeg-url = http://ijg.org/files +#libnsl-url = http://akhlaghi.org/maneage-software +#ibpaper-url=http://ftp.debian.org/debian/pool/main/libp/libpaper/ +#libpng-url = https://download.sourceforge.net/libpng +#libtiff-url = https://download.osgeo.org/libtiff +#libtirpc-url = https://downloads.sourceforge.net/libtirpc +#minizip-url = +#missfits-url = https://www.astromatic.net/download/missfits +#netpbm-url = http://akhlaghi.org/maneage-software +#openblas-url = https://github.com/xianyi/OpenBLAS/archive +#openmpi-url = $(shell majorver=$$(echo $(openmpi-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}'); echo https://download.open-mpi.org/release/open-mpi/v$$majorver) +#openssh-url = https://artfiles.org/openbsd/OpenSSH/portable +#patch-url = http://ftp.gnu.org/gnu/patch +#pixman-url = https://www.cairographics.org/releases +#python-url = https://www.python.org/ftp/python/$(python-version) +#R-url = $(shell majver=$$(echo $(R-version) | sed -e's/\./ /g' | awk '{print $$1}'); echo https://cran.r-project.org/src/base/R-$$majver) +#rpcsvc-proto-url = https://github.com/thkukuk/rpcsvc-proto/releases/download +#scamp-url = http://akhlaghi.org/maneage-software +#scons-url = https://sourceforge.net/projects/scons/files/scons/$(scons-version)/scons-$(scons-version).tar.gz/download +#sextractor-url = http://akhlaghi.org/maneage-software +#swarp-url = https://www.astromatic.net/download/swarp +#swig-url = https://sourceforge.net/projects/swig/files/swig/swig-$(swig-version) +#tides-url = http://akhlaghi.org/maneage-software +#valgrind-url = https://sourceware.org/pub/valgrind +#wcslib-url = ftp://ftp.atnf.csiro.au/pub/software/wcslib +#xlsxio-url = https://github.com/brechtsanders/xlsxio/archive +#yaml-url = pyyaml.org/download/libyaml + + + + + +# Python packages +# --------------- +# +# Similar to optional programs and libraries above. +# +# IMPORTANT: Python packages are usually distributed on servers like +# 'https://pypi.org'. You can search for your package here and add the link +# to the tarball here for your desired software. The links in PyPi don't +# contain the names of the software, but only have hashes. So we aren't +# including them by default here. But adding them is trivial for a certain +# version. For example if you search "Numpy" and click on the "Download +# files" menu, you can download the source '.zip' file. For version 1.18.5, +# (with full filename of 'numpy-1.18.5.zip') the link will be like this. +# +# numpy-url = https://files.pythonhosted.org/packages/01/1b/d3ddcabd5817be02df0e6ee20d64f77ff6d0d97f83b77f65e98c8a651981/numpy-1.18.5.zip +# +# Hence, if the version changes, the checksum, and its two top host +# directories also change. This is why we aren't putting any URL here by +# default, if you need to add one, simply follow the numpy example above. +# But be sure to send us a link to the tarball so we upload it to Maneage's +# backup servers. diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf index 1a4172a..b395e0f 100644 --- a/reproduce/software/config/versions.conf +++ b/reproduce/software/config/versions.conf @@ -14,6 +14,8 @@ # Basic/low-level programs and libraires (installed in any case) # -------------------------------------------------------------- +# +# CLASS:BASIC (important identifier, don't modify this line) bash-version = 5.0.11 binutils-version = 2.32 coreutils-version = 8.31 @@ -22,6 +24,7 @@ dash-version = 0.5.10.2 diffutils-version = 3.7 file-version = 5.36 findutils-version = 4.7.0 +flock-version = 0.2.3 gawk-version = 5.0.1 gcc-version = 9.2.0 gettext-version = 0.20.2 @@ -35,8 +38,8 @@ libiconv-version = 1.16 libtool-version = 2.4.6 libunistring-version = 0.9.10 libxml2-version = 2.9.9 -lzip-version = 1.20 -m4-version = 1.4.18 +lzip-version = 1.22-rc2 +m4-version = 1.4.18-patched make-version = 4.3 metastore-version = 1.1.2-23-fa9170b mpc-version = 1.1.0 @@ -56,6 +59,14 @@ xz-version = 5.2.4 zip-version = 3.0 zlib-version = 1.2.11 +# Version-dependent build +# ----------------------- +# +# When updating the version of these programs/libraries, please look into +# the build rule first: In one way or another, the version string becomes +# necessary during their build and must be accounted for. +bzip2-version = 1.0.6 + @@ -67,6 +78,8 @@ zlib-version = 1.2.11 # `reproduce/software/config/TARGETS.conf' will be built as # part of a project. To specify a software there, just remove the # `-version' suffix from the list below. +# +# CLASS:HIGHLEVEL (important identifier, don't modify this line.) apachelog4cxx-version = 0.10.0-603-014954db apr-version = 1.7.0 apr-util-version = 1.6.1 @@ -75,7 +88,7 @@ atlas-version = 3.10.3 autoconf-version = 2.69.200-babc automake-version = 1.16.1 bison-version = 3.4.2 -boost-version = 1.71.0 +boost-version = 1.73.0 cairo-version = 1.16.0 cdsclient-version = 3.84 cfitsio-version = 3.47 @@ -83,8 +96,7 @@ cmake-version = 3.17.0 eigen-version = 3.3.7 expat-version = 2.2.9 fftw-version = 3.3.8 -flex-version = 2.6.4 -flock-version = 0.2.3 +flex-version = 2.6.4-91-ga631f5d freetype-version = 2.9 gdb-version = 8.3 ghostscript-version = 9.50 @@ -98,14 +110,16 @@ imfit-version = 1.6.1 libffi-version = 3.2.1 libjpeg-version = v9b libnsl-version = 1.2.0-4a062cf +libpaper-version = 1.1.28 libpng-version = 1.6.37 libtiff-version = 4.0.10 -libtirpc-version = 1.1.4 +libtirpc-version = 1.2.6 missfits-version = 2.8.0 -openblas-version = 0.3.5 +openblas-version = 0.3.10 openmpi-version = 4.0.1 openssh-version = 8.0p1 patch-version = 2.7.6 +pcre-version = 8.44 pixman-version = 0.38.0 python-version = 3.7.4 R-version = 3.6.2 @@ -119,6 +133,29 @@ tides-version = 2.0 xlsxio-version = 0.2.21 yaml-version = 0.2.2 +# Version-dependent build +# ----------------------- +lapack-version = 3.8.0 +libgit2-version = 0.28.2 +wcslib-version = 6.4 + +# Netpbm's questions in the configure steps maybe change with different or +# new versions. +netpbm-version = 10.86.99 + +# Minizip is installed with the same `zlib' tarball, and they have the same +# version. +minizip-version = $(zlib-version) + +# From version 1.2 OpenSSL may not need a manual addition, as described in +# its comments and `https://savannah.nongnu.org/bugs/?58263'. If it doesn't +# cause problems, put it back in the list of "Basic/low-level" tools. +openssl-version = 1.1.1a + +# Version 3.15.0 needs two patches, please check if they are necessary on +# any future release. +valgrind-version = 3.15.0 + @@ -131,6 +168,8 @@ yaml-version = 0.2.2 # IMPORTANT: If you intend to change the version of any of the Python # modules/libraries below, please fix the hash strings of the respective # URL in `reproduce/software/make/python.mk'. +# +# CLASS:PYTHON (important identifier, don't modify this line.) asn1crypto-version = 0.24.0 asteval-version = 0.9.16 astropy-version = 4.0 @@ -151,7 +190,6 @@ flake8-version = 3.7.8 future-version = 0.18.1 galsim-version = 2.2.1 h5py-version = 2.9.0 -healpy-version = installed-with-healpix html5lib-version = 1.0.1 idna-version = 2.8 jeepney-version = 0.4 @@ -184,42 +222,9 @@ soupsieve-version = 1.8 sympy-version = 1.4 uncertainties-version = 3.1.2 urllib3-version = 1.24.1 -virtualenv-version = 16.4.0 webencodings-version = 0.5.1 - - - - -# Special programs and libraries -# ------------------------------ -# -# When updating the version of these libraries, please look into the build -# rule first: In one way or another, the version string becomes necessary -# during their build and must be accounted for. +# Special Python modules: # -# Special notes: -# - `netpbm' questions in the configure steps maybe change with different -# or new versions. - -# Basic/low-level -bzip2-version = 1.0.6 - -# Optional/high-level -lapack-version = 3.8.0 -libgit2-version = 0.28.2 -netpbm-version = 10.86.99 -wcslib-version = 6.4 - -# Minizip is installed with the same `zlib' tarball, and they have the same -# version. -minizip-version = $(zlib-version) - -# From version 1.2 OpenSSL may not need a manual addition, as described in -# its comments and `https://savannah.nongnu.org/bugs/?58263'. If it doesn't -# cause problems, put it back in the list of "Basic/low-level" tools. -openssl-version = 1.1.1a - -# Version 3.15.0 needs two patches, please check if they are necessary on -# any future release. -valgrind-version = 3.15.0 +# Healpy: When any Python module is requested, healpix will also build its +# Python module Healpy. -- cgit v1.2.1