diff options
| -rw-r--r-- | .file-metadata | bin | 6001 -> 6119 bytes | |||
| -rw-r--r-- | reproduce/software/bibtex/imfit.tex | 24 | ||||
| -rw-r--r-- | reproduce/software/config/installation/versions.mk | 4 | ||||
| -rw-r--r-- | reproduce/software/make/basic.mk | 8 | ||||
| -rw-r--r-- | reproduce/software/make/high-level.mk | 99 |
5 files changed, 124 insertions, 11 deletions
diff --git a/.file-metadata b/.file-metadata Binary files differindex b0c648d..0be3ee1 100644 --- a/.file-metadata +++ b/.file-metadata diff --git a/reproduce/software/bibtex/imfit.tex b/reproduce/software/bibtex/imfit.tex new file mode 100644 index 0000000..bdd840b --- /dev/null +++ b/reproduce/software/bibtex/imfit.tex @@ -0,0 +1,24 @@ +%% Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com> +%% +%% 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. + +@ARTICLE{imfit2015, + author = {{Erwin}, P.}, + title = "{IMFIT: A Fast, Flexible New Program for Astronomical Image Fitting}", + journal = {ApJ}, +archivePrefix = "arXiv", + eprint = {1408.1097}, + primaryClass = "astro-ph.IM", + keywords = {galaxies: bulges, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric }, + year = 2015, + month = feb, + volume = 799, + eid = {226}, + pages = {226}, + doi = {10.1088/0004-637X/799/2/226}, + adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJ...799..226E}, + adsnote = {Provided by the SAO/NASA Astrophysics Data System} +} diff --git a/reproduce/software/config/installation/versions.mk b/reproduce/software/config/installation/versions.mk index bd3b066..d0174c8 100644 --- a/reproduce/software/config/installation/versions.mk +++ b/reproduce/software/config/installation/versions.mk @@ -25,7 +25,7 @@ bash-version = 5.0.7 binutils-version = 2.32 coreutils-version = 8.31 -curl-version = 7.63.0 +curl-version = 7.65.1 diffutils-version = 3.7 file-version = 5.36 findutils-version = 4.6.0.199-e3fc @@ -82,6 +82,7 @@ gnuastro-version = 0.9 gsl-version = 2.5 hdf5-version = 1.10.5 imagemagick-version = 7.0.8-46 +imfit-version = 1.6.1 libffi-version = 3.2.1 libjpeg-version = v9b libpng-version = 1.6.37 @@ -93,6 +94,7 @@ openmpi-version = 4.0.1 pixman-version = 0.38.0 python-version = 3.7.3 scamp-version = 2.6.7 +scons-version = 3.0.5 sextractor-version = 2.25.0 swarp-version = 2.38.0 swig-version = 3.0.12 diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk index b21e7b0..468563b 100644 --- a/reproduce/software/make/basic.mk +++ b/reproduce/software/make/basic.mk @@ -623,7 +623,7 @@ $(ibidir)/bash: $(tdir)/bash-$(bash-version).tar.lz \ # complete. # # One problem is that Coreutils installs many very basic executables which -# might be in use by other programs. So we must make sure that when +# might be in used by other programs. So we must make sure that when # Coreutils is being built, no other program is being built in # parallel. The solution to the many executables it installs is to make a # fake installation (with `DESTDIR'), and get a list of the contents of the @@ -726,7 +726,8 @@ $(ibidir)/openssl: $(tdir)/openssl-$(openssl-version).tar.gz \ # this project is avoid dependency on the host as much as possible. $(ibidir)/curl: $(tdir)/curl-$(curl-version).tar.gz \ $(ibidir)/coreutils \ - $(ibidir)/openssl #Coreutils: only so cURL is built after it. + $(ibidir)/openssl \ + $(needpatchelf) $(call gbuild, $<, curl-$(curl-version), , \ LIBS="-pthread" \ --with-zlib=$(ildir) \ @@ -744,6 +745,9 @@ $(ibidir)/curl: $(tdir)/curl-$(curl-version).tar.gz \ --disable-ldaps \ --disable-ldap \ --without-nss, V=1) \ + && if [ "x$(needpatchelf)" != x ]; then \ + $(ibdir)/patchelf --set-rpath $(ildir) $(ildir)/libcurl.so; \ + fi \ && echo "cURL $(curl-version)" > $@ diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk index 310b8e3..d609535 100644 --- a/reproduce/software/make/high-level.mk +++ b/reproduce/software/make/high-level.mk @@ -119,6 +119,7 @@ tarballs = $(foreach t, astrometry.net-$(astrometrynet-version).tar.gz \ gsl-$(gsl-version).tar.gz \ hdf5-$(hdf5-version).tar.gz \ imagemagick-$(imagemagick-version).tar.xz \ + imfit-$(imfit-version).tar.gz \ install-tl-unx.tar.gz \ jpegsrc.$(libjpeg-version).tar.gz \ lapack-$(lapack-version).tar.gz \ @@ -130,6 +131,7 @@ tarballs = $(foreach t, astrometry.net-$(astrometrynet-version).tar.gz \ openblas-$(openblas-version).tar.gz \ pixman-$(pixman-version).tar.gz \ scamp-$(scamp-version).tar.lz \ + scons-$(scons-version).tar.gz \ sextractor-$(sextractor-version).tar.lz \ swarp-$(swarp-version).tar.gz \ swig-$(swig-version).tar.gz \ @@ -173,6 +175,9 @@ $(tarballs): $(tdir)/%: | $(lockdir) elif [ $$n = imagemagick ]; then mergenames=0 w=https://www.imagemagick.org/download/releases/ImageMagick-$(imagemagick-version).tar.xz + elif [ $$n = imfit ]; then + mergenames=0 + w=http://www.mpe.mpg.de/~erwin/resources/imfit/imfit-$(imfit-version)-source.tar.gz elif [ $$n = install ]; then w=http://mirror.ctan.org/systems/texlive/tlnet elif [ $$n = jpegsrc ]; then w=http://ijg.org/files elif [ $$n = lapack ]; then w=http://www.netlib.org/lapack @@ -191,6 +196,9 @@ $(tarballs): $(tdir)/%: | $(lockdir) w=https://download.open-mpi.org/release/open-mpi/v$$majorver/$* elif [ $$n = pixman ]; then w=https://www.cairographics.org/releases elif [ $$n = scamp ]; then w=http://akhlaghi.org/src + elif [ $$n = scons ]; then + mergenames=0 + w=https://sourceforge.net/projects/scons/files/scons/$(scons-version)/scons-$(scons-version).tar.gz/download elif [ $$n = sextractor ]; then w=http://akhlaghi.org/src elif [ $$n = swarp ]; then w=https://www.astromatic.net/download/swarp elif [ $$n = swig ]; then w=https://sourceforge.net/projects/swig/files/swig/swig-$(swig-version) @@ -234,17 +242,28 @@ $(tarballs): $(tdir)/%: | $(lockdir) # libraries. Therefore, we can't use the easy `.a' suffix for static # libraries as targets and there are different conventions for shared # library names. -# -# For the actual build, the same compiler that built the library will build -# the programs, so exact knowledge of the suffix is ultimately irrelevant -# for us here. So, we'll make an `$(ildir)/built' directory and make a -# simple plain text file in it with the basic library name (an no prefix) -# and create/write into it when the library is successfully built. $(ibidir)/cfitsio: $(tdir)/cfitsio-$(cfitsio-version).tar.gz \ $(ibidir)/curl - $(call gbuild, $<, cfitsio-$(cfitsio-version), , \ + + # CFITSIO hard-codes '@rpath' inside the shared library on + # Mac systems. So we need to change it to our library + # installation path. It doesn't affect GNU/Linux, so we'll + # just do it in any case to keep things clean. + topdir=$(pwd); cd $(ddir); tar xf $< + customtar=cfitsio-$(cfitsio-version)-custom.tar.gz + cd cfitsio-$(cfitsio-version) + sed configure -e's|@rpath|$(ildir)|g' > configure_tmp + mv configure_tmp configure + chmod +x configure + cd .. + tar cf $$customtar cfitsio-$(cfitsio-version) + cd $$topdir + + # Continue the standard build on the customized tarball. + $(call gbuild, $$customtar, cfitsio-$(cfitsio-version), , \ --enable-sse2 --enable-reentrant \ --with-bzip2=$(idir), , make shared) \ + && rm $$customtar \ && echo "CFITSIO $(cfitsio-version)" > $@ $(ibidir)/cairo: $(tdir)/cairo-$(cairo-version).tar.xz \ @@ -260,8 +279,16 @@ $(ibidir)/gsl: $(tdir)/gsl-$(gsl-version).tar.gz && echo "GNU Scientific Library $(gsl-version)" > $@ $(ibidir)/fftw: $(tdir)/fftw-$(fftw-version).tar.gz + # In order to build single and double precission libraries of + # `fftw', installation of `fftw' is done twice. First time is to + # build single precission float libraries and second time is for + # building the default double precission float libraries $(call gbuild, $<, fftw-$(fftw-version), static, \ - --enable-shared --enable-single) \ + --enable-shared enable-threads \ + --enable-single --enable-type-prefix) \ + && $(call gbuild, $<, fftw-$(fftw-version), static, \ + --enable-shared --enable-threads \ + --enable-type-prefix) \ && cp $(dtexdir)/fftw.tex $(ictdir)/ \ && echo "FFTW $(fftw-version) \citep{fftw}" > $@ @@ -583,6 +610,50 @@ $(ibidir)/imagemagick: $(tdir)/imagemagick-$(imagemagick-version).tar.xz \ --without-x --disable-openmp, V=1) \ && echo "ImageMagick $(imagemagick-version)" > $@ +# `imfit' doesn't use the traditional `configure' and `make' to install +# itself. Instead of that, it uses `scons'. As a consequence, the +# installation is manually done by decompressing the tarball, and running +# `scons' with the necessary flags. Despite of that, it is necessary to +# replace the default searching paths in this script by our installation +# paths. This is done with `sed', replacing each ocurrence of `/usr/local' +# by `$(idir)'. After that, each compiled program (`imfit', `imfit-mcmc' +# and `makeimage') is copied into the installation directory and an `rpath' +# is added. +$(ibidir)/imfit: $(tdir)/imfit-$(imfit-version).tar.gz \ + $(ibidir)/cfitsio \ + $(ibidir)/scons \ + $(ibidir)/fftw \ + $(ibidir)/gsl + cd $(ddir) \ + && unpackdir=imfit-$(imfit-version) \ + && rm -rf $$unpackdir \ + && if ! tar xf $<; then echo; echo "Tar error"; exit 1; fi \ + && cd $$unpackdir \ + && sed -i 's|/usr/local|$(idir)|g' SConstruct \ + && sed -i 's|/usr/include|$(idir)/include|g' SConstruct \ + && sed -i 's|.append(|.insert(0,|g' SConstruct \ + && scons --no-openmp --no-nlopt \ + --cc=$(ibdir)/gcc --cpp=$(ibdir)/g++ \ + --header-path=$(idir)/include --lib-path=$(idir)/lib imfit \ + && cp imfit $(ibdir) \ + && scons --no-openmp --no-nlopt\ + --cc=$(ibdir)/gcc --cpp=$(ibdir)/g++ \ + --header-path=$(idir)/include --lib-path=$(idir)/lib \ + imfit-mcmc \ + && cp imfit-mcmc $(ibdir) \ + && scons --no-openmp --no-nlopt\ + --cc=$(ibdir)/gcc --cpp=$(ibdir)/g++ \ + --header-path=$(idir)/include --lib-path=$(idir)/lib \ + makeimage \ + && cp makeimage $(ibdir) \ + && cp $(dtexdir)/imfit.tex $(ictdir)/ \ + && if [ "x$(on_mac_os)" != xyes ]; then \ + for p in imfit imfit-mcmc makeimage; do \ + patchelf --set-rpath $(ildir) $(ibdir)/$$p; \ + done; \ + fi \ + && echo "Imfit $(imfit-version) \citep{imfit2015}" > $@ + # Netpbm is a prerequisite of Astrometry-net, it contains a lot of programs. # This program has a crazy dialogue installation which is override using the # printf statment. Each `\n' is a new question that the installation process @@ -633,6 +704,18 @@ $(ibidir)/scamp: $(tdir)/scamp-$(scamp-version).tar.lz \ && cp $(dtexdir)/scamp.tex $(ictdir)/ \ && echo "SCAMP $(scamp-version) \citep{scamp}" > $@ +# Since `scons' doesn't use the traditional GNU installation with +# `configure' and `make' it is installed manually using `python'. +$(ibidir)/scons: $(tdir)/scons-$(scons-version).tar.gz \ + $(ibidir)/python + cd $(ddir) \ + && unpackdir=scons-$(scons-version) \ + && rm -rf $$unpackdir \ + && if ! tar xf $<; then echo; echo "Tar error"; exit 1; fi \ + && cd $$unpackdir \ + && python setup.py install \ + && echo "SCons $(scons-version)" > $@ + # Sextractor crashes complaining about not linking with some ATLAS # libraries. But we can override this issue since we have Openblas # installed, it is just necessary to explicity tell sextractor to use it in |