diff options
| -rw-r--r-- | .file-metadata | bin | 4672 -> 4856 bytes | |||
| -rw-r--r-- | reproduce/config/pipeline/dependency-numpy-scipy.cfg | 20 | ||||
| -rw-r--r-- | reproduce/config/pipeline/dependency-versions.mk | 2 | ||||
| -rw-r--r-- | reproduce/src/make/dependencies-python.mk | 24 | ||||
| -rw-r--r-- | reproduce/src/make/dependencies.mk | 32 |
5 files changed, 54 insertions, 24 deletions
diff --git a/.file-metadata b/.file-metadata Binary files differindex 36f3c03..781124c 100644 --- a/.file-metadata +++ b/.file-metadata diff --git a/reproduce/config/pipeline/dependency-numpy-scipy.cfg b/reproduce/config/pipeline/dependency-numpy-scipy.cfg index 55e93bc..0eecf3a 100644 --- a/reproduce/config/pipeline/dependency-numpy-scipy.cfg +++ b/reproduce/config/pipeline/dependency-numpy-scipy.cfg @@ -16,17 +16,6 @@ library_dirs = @LIBDIR@ include_dirs = @INCDIR@ -# Atlas -# ----- -# Atlas is an open source optimized implementation of the BLAS and Lapack -# routines. NumPy will try to build against Atlas by default when available in -# the system library dirs. To build numpy against a custom installation of -# Atlas you can add an explicit section such as the following. Here we assume -# that Atlas was configured with ``prefix=/opt/atlas``. -# - [atlas] - library_dirs = @LIBDIR@ - include_dirs = @INCDIR@ # FFT libraries # ------------- @@ -38,10 +27,13 @@ # # Given only this section, numpy.distutils will try to figure out which version # of FFTW you are using. -#[fftw] -#libraries = fftw3 + +# Even with this section, Numpy apparently does not use fftw. But we will +# keep it here for the future (if a solution is found). +[fftw] +libraries = fftw3 # -# For djbfft, numpy.distutils will look for either djbfft.a or libdjbfft.a . +# For djbfft, numpy.distutils will look for either djbfft.a or libdjbfft.a . #[djbfft] #include_dirs = /usr/local/djbfft/include #library_dirs = /usr/local/djbfft/lib diff --git a/reproduce/config/pipeline/dependency-versions.mk b/reproduce/config/pipeline/dependency-versions.mk index 211ebbd..cb5920e 100644 --- a/reproduce/config/pipeline/dependency-versions.mk +++ b/reproduce/config/pipeline/dependency-versions.mk @@ -6,6 +6,7 @@ binutils-version = 2.31.1 cmake-version = 3.12.4 coreutils-version = 8.30 diffutils-version = 3.7 +fftw-version = 3.3.8 findutils-version = 4.6.0.199-e3fc flock-version = 0.2.3 freetype-version = 2.9 @@ -48,6 +49,7 @@ curl-version = 7.63.0 gsl-version = 2.5 libjpeg-version = v9b libtiff-version = 4.0.10 +openblas-version = 0.3.5 zlib-version = 1.2.11 # Special libraries diff --git a/reproduce/src/make/dependencies-python.mk b/reproduce/src/make/dependencies-python.mk index c7f861b..642316c 100644 --- a/reproduce/src/make/dependencies-python.mk +++ b/reproduce/src/make/dependencies-python.mk @@ -43,10 +43,7 @@ ilidir = $(BDIR)/dependencies/installed/lib/built ipydir = $(BDIR)/dependencies/installed/lib/built/python # Define the top-level programs to build (installed in `.local/bin'). -ifneq ($(on_mac_os),yes) -withscipy=scipy -endif -top-level-python = astroquery matplotlib $(withscipy) +top-level-python = astroquery matplotlib all: $(foreach p, $(top-level-python), $(ipydir)/$(p)) # Other basic environment settings: We are only including the host @@ -328,7 +325,8 @@ $(ipydir)/astroquery: $(tdir)/astroquery-$(astroquery-version).tar.gz \ $(ipydir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \ $(ipydir)/h5py \ - $(ipydir)/numpy + $(ipydir)/numpy \ + $(ipydir)/scipy $(call pybuild, tar xf, $<, astropy-$(astropy-version)) $(ipydir)/beautifulsoup4: $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.gz \ @@ -398,8 +396,14 @@ $(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz \ $(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version)) $(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \ - $(ipydir)/setuptools - export LDFLAGS="$$LDFLAGS -shared"; \ + $(ipydir)/setuptools \ + $(ilidir)/openblas \ + $(ilidir)/fftw + if [ x$(on_mac_os) = xyes ]; then \ + export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"; \ + else \ + export LDFLAGS="$(LDFLAGS) -shared"; \ + fi; \ conf="$$(pwd)/reproduce/config/pipeline/dependency-numpy-scipy.cfg"; \ $(call pybuild, unzip, $<, numpy-$(numpy-version),$$conf) @@ -430,7 +434,11 @@ $(ipydir)/requests: $(tdir)/requests-$(requests-version).tar.gz \ $(ipydir)/scipy: $(tdir)/scipy-$(scipy-version).tar.gz \ $(ipydir)/numpy - export LDFLAGS="$$LDFLAGS -shared"; \ + if [ x$(on_mac_os) = xyes ]; then \ + export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"; \ + else \ + export LDFLAGS="$(LDFLAGS) -shared"; \ + fi; \ conf="$$(pwd)/reproduce/config/pipeline/dependency-numpy-scipy.cfg"; \ $(call pybuild, tar xf, $<, scipy-$(scipy-version),$$conf) diff --git a/reproduce/src/make/dependencies.mk b/reproduce/src/make/dependencies.mk index 9953311..ee95be9 100644 --- a/reproduce/src/make/dependencies.mk +++ b/reproduce/src/make/dependencies.mk @@ -43,8 +43,13 @@ ildir = $(BDIR)/dependencies/installed/lib ilidir = $(BDIR)/dependencies/installed/lib/built # Define the top-level programs to build (installed in `.local/bin'). +# +# About ATLAS: currently the core pipeline does not depend on ATLAS but many +# high level software depend on it. The current rule for ATLAS is tested +# successfully on Mac (only static) and GNU/Linux (shared and static). But, +# since it takes a few hours to build, it is not currently a target. top-level-programs = astnoisechisel flock metastore unzip zip -top-level-libraries = freetype atlas +top-level-libraries = freetype openblas fftw # atlas all: $(ddir)/texlive-versions.tex \ $(foreach p, $(top-level-programs), $(ibdir)/$(p)) \ $(foreach p, $(top-level-libraries), $(ilidir)/$(p)) @@ -95,6 +100,7 @@ tarballs = $(foreach t, cfitsio-$(cfitsio-version).tar.gz \ curl-$(curl-version).tar.gz \ flock-$(flock-version).tar.xz \ freetype-$(freetype-version).tar.gz \ + fftw-$(fftw-version).tar.gz \ ghostscript-$(ghostscript-version).tar.gz \ git-$(git-version).tar.xz \ gnuastro-$(gnuastro-version).tar.lz \ @@ -108,6 +114,7 @@ tarballs = $(foreach t, cfitsio-$(cfitsio-version).tar.gz \ libgit2-$(libgit2-version).tar.gz \ metastore-$(metastore-version).tar.gz \ unzip-$(unzip-version).tar.gz \ + openblas-$(openblas-version).tar.gz \ tiff-$(libtiff-version).tar.gz \ wcslib-$(wcslib-version).tar.bz2 \ zip-$(zip-version).tar.gz \ @@ -138,6 +145,7 @@ $(tarballs): $(tdir)/%: elif [ $$n = cmake ]; then w=https://cmake.org/files/v3.12 elif [ $$n = curl ]; then w=https://curl.haxx.se/download elif [ $$n = flock ]; then w=https://github.com/discoteq/flock/releases/download/v$(flock-version) + elif [ $$n = fftw ]; then w=ftp://ftp.fftw.org/pub/fftw elif [ $$n = freetype ]; then w=https://download.savannah.gnu.org/releases/freetype elif [ $$n = ghostscript ]; then w=https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs926 elif [ $$n = git ]; then w=http://mirrors.edge.kernel.org/pub/software/scm/git @@ -153,6 +161,9 @@ $(tarballs): $(tdir)/%: mergenames=0 w=https://github.com/libgit2/libgit2/archive/v$(libgit2-version).tar.gz elif [ $$n = metastore ]; then w=http://akhlaghi.org/src + elif [ $$n = openblas ]; then + mergenames=0 + w=https://github.com/xianyi/OpenBLAS/archive/v$(openblas-version).tar.gz elif [ $$n = tiff ]; then w=https://download.osgeo.org/libtiff elif [ $$n = unzip ]; then w=ftp://ftp.info-zip.org/pub/infozip/src mergenames=0; v=$$(echo $(unzip-version) | sed -e's/\.//') @@ -234,6 +245,11 @@ $(ilidir)/gsl: $(tdir)/gsl-$(gsl-version).tar.gz $(call gbuild, $<, gsl-$(gsl-version), static) \ && echo "GNU Scientific Library is built" > $@ +$(ilidir)/fftw: $(tdir)/fftw-$(fftw-version).tar.gz + $(call gbuild, $<, fftw-$(fftw-version), static, \ + --enable-shared) \ + && echo "FFTW is built" > $@ + # Freetype is necessary to install matplotlib $(ilidir)/freetype: $(tdir)/freetype-$(freetype-version).tar.gz \ $(ilidir)/libpng @@ -303,7 +319,7 @@ $(ilidir)/atlas: $(tdir)/atlas-$(atlas-version).tar.bz2 \ && rm -rf build \ && mkdir build \ && cd build \ - && echo ../configure -b 64 -D c -DPentiumCPS=$$core \ + && ../configure -b 64 -D c -DPentiumCPS=$$core \ --with-netlib-lapack-tarfile=$(word 2, $^) \ --cripple-atlas-performance \ -Fa alg -fPIC --shared $$clangflag \ @@ -335,6 +351,18 @@ $(ilidir)/atlas: $(tdir)/atlas-$(atlas-version).tar.bz2 \ # currently building shared library on Mac. if [ -f $(ildir)/libatlas.a ]; then echo "Atlas is built" > $@; fi +$(ilidir)/openblas: $(tdir)/openblas-$(openblas-version).tar.gz + if [ x$(on_mac_os) = xyes ]; then \ + export CC=clang \ + fi; \ + cd $(ddir) \ + && tar xf $< \ + && cd OpenBLAS-$(openblas-version) \ + && make \ + && make PREFIX=$(idir) install \ + && cd .. \ + && rm -rf OpenBLAS-$(openblas-version) \ + && echo "Libtiff is built" > $@ |