Numpy and Scipy build on Mac imported into the main branch

We were developing the build of Numpy and Scipy on Mac in a parallel thread
and things seems to be working relatively nice now. There were only two
problems:

1) GCC still has some random building issues on Mac.

2) ATLAS shared libraries can't be built on Mac (so we used OpenBLAS to
   build Numpy and Scipy on both Mac and GNU/Linux).

But for now, none of these problems are critical. So, we can progress in
one branch.

There were only very minor conflicts in the merge.

8 files changed, 467 insertions, 172 deletions

diff --git a/reproduce/config/pipeline/dependency-numpy-scipy.cfg b/reproduce/config/pipeline/dependency-numpy-scipy.cfg
new file mode 100644
index 0000000..0eecf3a
--- /dev/null
+++ b/reproduce/config/pipeline/dependency-numpy-scipy.cfg
@@ -0,0 +1,39 @@
+# THIS IS A COPY OF NUMPY'S site.cfg.example, CUSTOMIZED FOR THIS PIPELINE
+# ------------------------------------------------------------------------
+
+# This file provides configuration information about non-Python dependencies for
+# numpy.distutils-using packages. Create a file like this called "site.cfg" next
+# to your package's setup.py file and fill in the appropriate sections. Not all
+# packages will use all sections so you should leave out sections that your
+# package does not use.
+
+# IMPORTANT NOTE
+# --------------
+#
+# The `ALL' grouping does't apply to ATLAS!!!!!
+
+ [ALL]
+ library_dirs = @LIBDIR@
+ include_dirs = @INCDIR@
+
+
+# FFT libraries
+# -------------
+# There are two FFT libraries that we can configure here: FFTW (2 and 3) and djbfft.
+# Note that these libraries are not used by numpy or scipy.
+#
+#   http://fftw.org/
+#   https://cr.yp.to/djbfft.html
+#
+# Given only this section, numpy.distutils will try to figure out which version
+# of FFTW you are using.
+
+# 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 .
+#[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 87b837c..2e74a45 100644
--- a/reproduce/config/pipeline/dependency-versions.mk
+++ b/reproduce/config/pipeline/dependency-versions.mk
@@ -25,6 +25,7 @@ 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
@@ -36,6 +37,7 @@ gmp-version                = 6.1.2
 gnuastro-version           = 0.8
 grep-version               = 3.3
 gzip-version               = 1.10
+hdf5-version               = 1.10.5
 isl-version                = 0.18
 libbsd-version             = 0.9.1
 libffi-version             = 3.2.1
@@ -47,6 +49,7 @@ metastore-version          = 1.1.2-23-fa9170b
 mpfr-version               = 4.0.2
 mpc-version                = 1.1.0
 ncurses-version            = 6.1
+openmpi-version            = 4.0.1
 openssl-version            = 1.1.1a
 patchelf-version           = 0.9
 pkgconfig-version          = 0.29.2
@@ -61,13 +64,26 @@ xz-version                 = 5.2.4
 zip-version                = 3.0
 
 # Libraries
+atlas-version              = 3.10.3
 cfitsio-version            = 3.45
 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
+# -----------------
+#
+# 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.
+bzip2-version              = 1.0.6
+lapack-version             = 3.8.0
+libgit2-version            = 0.26.0
+wcslib-version             = 6.2
+
 # Python packages
 # ---------------
 #
@@ -83,13 +99,15 @@ chardet-version            = 3.0.4
 cryptography-version       = 2.6.1
 cycler-version             = 0.10.0
 entrypoints-version        = 0.3
+h5py-version               = 2.9.0
 html5lib-version           = 1.0.1
 idna-version               = 2.8
 jeepney-version            = 0.4
 kiwisolver-version         = 1.0.1
 keyring-version            = 18.0.0
 matplotlib-version         = 3.0.2
-numpy-version              = 1.16.1
+mpi4py-version             = 3.0.1
+numpy-version              = 1.16.2
 pip-version                = 19.0.2
 pycparser-version          = 2.19
 pyparsing-version          = 2.3.1
@@ -104,13 +122,3 @@ soupsieve-version          = 1.8
 urllib3-version            = 1.24.1
 virtualenv-version         = 16.4.0
 webencodings-version       = 0.5.1
-
-# Special 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.
-bzip2-version              = 1.0.6
-libgit2-version            = 0.26.0
-wcslib-version             = 6.2
diff --git a/reproduce/src/make/dependencies-atlas-multiple.mk b/reproduce/src/make/dependencies-atlas-multiple.mk
new file mode 100755
index 0000000..d66890f
--- /dev/null
+++ b/reproduce/src/make/dependencies-atlas-multiple.mk
@@ -0,0 +1,47 @@
+ORIGLDFLAGS := $(LDFLAGS)
+
+include Make.inc
+
+all: libatlas.so libf77blas.so libptf77blas.so libstcblas.so libptcblas.so \
+   libblas.so libcblas.so liblapack.so.3.6.1 libptlapack.so.3.6.1 liblapack.so.3
+
+libatlas.so: libatlas.a
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname $@ -o $@ \
+	   --whole-archive libatlas.a --no-whole-archive -lc $(LIBS)
+
+libf77blas.so : libf77blas.a libatlas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname libf77blas.so.3 \
+	   -o $@ --whole-archive libf77blas.a --no-whole-archive \
+	   $(F77SYSLIB) -L. -latlas
+
+libptf77blas.so : libptf77blas.a libatlas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname libblas.so.3 \
+	   -o $@ --whole-archive libptf77blas.a --no-whole-archive \
+	   $(F77SYSLIB) -L. -latlas
+
+libstcblas.so : libcblas.a libatlas.so libblas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname libstcblas.so \
+	   -o $@ --whole-archive libcblas.a -L. -latlas -lblas
+
+libptcblas.so : libptcblas.a libatlas.so libblas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname libcblas.so \
+	   -o $@ --whole-archive libptcblas.a -L. -latlas -lblas
+
+libblas.so: libptf77blas.so
+	ln -s $< $@
+
+libcblas.so: libptcblas.so
+	ln -s $< $@
+
+liblapack.so.3.6.1 : liblapack.a libstcblas.so libf77blas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname libstlapack.so.3 \
+	   -o $@ --whole-archive liblapack.a --no-whole-archive \
+	   $(F77SYSLIB) -L. -lstcblas -lf77blas
+
+libptlapack.so.3.6.1 : libptlapack.a libcblas.so libblas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname liblapack.so.3 \
+	   -o $@ --whole-archive libptlapack.a --no-whole-archive \
+	   $(F77SYSLIB) -L. -lcblas -lblas
+
+liblapack.so.3: libptlapack.so.3.6.1
+	ln -s $< $@
diff --git a/reproduce/src/make/dependencies-atlas-single.mk b/reproduce/src/make/dependencies-atlas-single.mk
new file mode 100755
index 0000000..12dd19b
--- /dev/null
+++ b/reproduce/src/make/dependencies-atlas-single.mk
@@ -0,0 +1,29 @@
+ORIGLDFLAGS := $(LDFLAGS)
+
+include Make.inc
+
+all: libatlas.so libf77blas.so libcblas.so libblas.so liblapack.so.3.6.1
+
+libatlas.so: libatlas.a
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname $@ -o $@ \
+	   --whole-archive libatlas.a --no-whole-archive -lc $(LIBS)
+
+libf77blas.so : libf77blas.a libatlas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname libblas.so.3 \
+	   -o $@ --whole-archive libf77blas.a --no-whole-archive \
+	   $(F77SYSLIB) -L. -latlas
+
+libcblas.so : libcblas.a libatlas.so libblas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname $@ -o $@ \
+	    --whole-archive libcblas.a -L. -latlas -lblas
+
+libblas.so: libf77blas.so
+	ln -s $< $@
+
+liblapack.so.3.6.1 : liblapack.a libcblas.so libblas.so
+	ld $(ORIGLDFLAGS) $(LDFLAGS) -shared -soname liblapack.so.3 \
+	   -o $@ --whole-archive liblapack.a --no-whole-archive \
+	   $(F77SYSLIB) -L. -lcblas -lblas
+
+liblapack.so.3: liblapack.so.3.6.1
+	ln -s $< $@
diff --git a/reproduce/src/make/dependencies-basic.mk b/reproduce/src/make/dependencies-basic.mk
index cdb4a8c..52a41d9 100644
--- a/reproduce/src/make/dependencies-basic.mk
+++ b/reproduce/src/make/dependencies-basic.mk
@@ -204,12 +204,13 @@ $(tarballs): $(tdir)/%: $(lockdir)
 # is very annoying and can cause many complications. We thus remove any
 # part of PATH of that has `ccache' in it before making symbolic links to
 # the programs we are not building ourselves.
-makelink = origpath="$$PATH";                                          \
+makelink = origpath="$$PATH";                                      \
 	   export PATH=$$(echo $(syspath) | tr : '\n' | grep -v ccache \
-	                       | paste -s -d:);                        \
+	                       | tr '\n' :);                           \
 	   a=$$(which $(1) 2> /dev/null);                              \
-	   if [ -f $(ibdir)/$(1) ]; then rm $(ibdir)/$(1); fi;         \
-	   if [ x$$a != x ]; then ln -s $$a $(ibdir)/$(1); fi;         \
+	   if [ -e $(ibdir)/$(1) ]; then rm $(ibdir)/$(1); fi;         \
+	   if [ x"$(2)" = xcopy ]; then c=cp; else c="ln -s"; fi;      \
+	   if [ x$$a != x ]; then $$c $$a $(ibdir)/$(1); fi;           \
 	   export PATH="$$origpath"
 $(ibdir) $(ildir):; mkdir $@
 $(ibdir)/low-level-links: | $(ibdir) $(ildir)
@@ -576,8 +577,15 @@ $(ilidir)/openssl: $(tdir)/openssl-$(openssl-version).tar.gz         \
 	               --with-zlib-lib=$(ildir)                      \
                        --with-zlib-include=$(idir)/include, , ,      \
 	               ./config ) &&                                 \
-	cp $(tdir)/cert.pem $(idir)/etc/ssl/cert.pem &&              \
-	echo "OpenSSL is built and ready" > $@
+	cp $(tdir)/cert.pem $(idir)/etc/ssl/cert.pem;                \
+	if [ $$? = 0 ]; then                                         \
+	  if [ x$(on_mac_os) = xyes ]; then                          \
+	    echo "No need to fix rpath in libssl";                   \
+	  else                                                       \
+	    patchelf --set-rpath $(ildir) $(ildir)/libssl.so;        \
+	  fi;                                                        \
+	  echo "OpenSSL is built and ready" > $@;                    \
+	fi
 
 # GNU Wget
 #
@@ -734,13 +742,13 @@ $(ibdir)/ld: $(tdir)/binutils-$(binutils-version).tar.lz
 #
 # We are currently having problems installing GCC on macOS, so for the time
 # being, if the pipeline is being run on a macOS, we'll just set a link.
-ifeq ($(on_mac_os),yes)
-gcc-prerequisites =
-else
+#ifeq ($(on_mac_os),yes)
+#gcc-prerequisites =
+#else
 gcc-prerequisites = $(tdir)/gcc-$(gcc-version).tar.xz \
                     $(ilidir)/isl                     \
                     $(ilidir)/mpc
-endif
+#endif
 $(ibdir)/gcc: $(gcc-prerequisites)  \
               $(ibdir)/ls           \
               $(ibdir)/sed          \
@@ -752,24 +760,36 @@ $(ibdir)/gcc: $(gcc-prerequisites)  \
               $(ibdir)/which
 
         # On a macOS, we (currently!) won't build GCC because of some
-        # errors we are still trying to fix. So, we'll just make a symbolic
-        # link to the host's executables.
-	if [ "x$(on_mac_os)" = xyes ]; then                                \
+        # errors we are still trying to find. So, we'll just make a
+        # symbolic link to the host's executables.
+        #
+        # GCC builds is own libraries in '$(idir)/lib64'. But all other
+        # libraries are in '$(idir)/lib'. Since this pipeline is only for a
+        # single architecture, we can trick GCC into building its libraries
+        # in '$(idir)/lib' by defining the '$(idir)/lib64' as a symbolic
+        # link to '$(idir)/lib'.
+
+# SO FAR WE HAVEN'T BEEN ABLE TO GET A CONSISTENT BUILD OF GCC ON MAC
+# (SOMETIMES IT CRASHES IN libiberty with g++) AND SOMETIMES IT FINISHES,
+# SO, MORE TESTS ARE NEEDED ON MAC AND WE'LL USE THE HOST'S COMPILER UNTIL
+# THEN.
+	if [ "x$(on_mac_os)" = xyesno ]; then                              \
 	  $(call makelink,gfortran);                                       \
 	  $(call makelink,g++);                                            \
-	  $(call makelink,gcc);                                            \
+	  $(call makelink,gcc,copy);                                       \
 	else                                                               \
-	                                                                   \
 	  rm -f $(ibdir)/gcc* $(ibdir)/g++ $(ibdir)/gfortran $(ibdir)/gcov*;\
 	  rm -rf $(ildir)/gcc $(ildir)/libcc* $(ildir)/libgcc*;            \
 	  rm -rf $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64*;\
 	                                                                   \
+	  ln -fs $(ildir) $(idir)/lib64;                                   \
+	                                                                   \
 	  cd $(ddir);                                                      \
 	  rm -rf gcc-build gcc-$(gcc-version);                             \
-	  tar xf $< &&                                                     \
-	  mkdir $(ddir)/gcc-build &&                                       \
-	  cd $(ddir)/gcc-build &&                                          \
-	  ../gcc-$(gcc-version)/configure SHELL=$(ibdir)/bash              \
+	  tar xf $<                                                        \
+	  && mkdir $(ddir)/gcc-build                                       \
+	  && cd $(ddir)/gcc-build                                          \
+	  && ../gcc-$(gcc-version)/configure SHELL=$(ibdir)/bash           \
 	                    --prefix=$(idir)                               \
 	                    --with-mpc=$(idir)                             \
 	                    --with-mpfr=$(idir)                            \
@@ -787,9 +807,18 @@ $(ibdir)/gcc: $(gcc-prerequisites)  \
 	                    --enable-default-pie                           \
 	                    --enable-default-ssp                           \
 	                    --enable-cet=auto                              \
-	                    --enable-decimal-float &&                      \
-	  make SHELL=$(ibdir)/bash -j$$(nproc) &&                          \
-	  make SHELL=$(ibdir)/bash install &&                              \
-	  cd .. &&                                                         \
-	  rm -rf gcc-build gcc-$(gcc-version);                             \
+	                    --enable-decimal-float                         \
+	  && make SHELL=$(ibdir)/bash -j$$(nproc)                          \
+	  && make SHELL=$(ibdir)/bash install                              \
+	  && cd ..                                                         \
+	  && rm -rf gcc-build gcc-$(gcc-version)                           \
+	                                                                   \
+	  && if [ "x$(on_mac_os)" != xyes ]; then                          \
+	       for f in $$(find $(idir)/libexec/gcc); do                   \
+	         if ldd $$f &> /dev/null; then                             \
+	           patchelf --set-rpath $(ildir) $$f;                      \
+	         fi;                                                       \
+	       done;                                                       \
+	     fi;                                                           \
 	fi
+
diff --git a/reproduce/src/make/dependencies-python.mk b/reproduce/src/make/dependencies-python.mk
index 946c047..6711d17 100644
--- a/reproduce/src/make/dependencies-python.mk
+++ b/reproduce/src/make/dependencies-python.mk
@@ -29,51 +29,6 @@
 
 
 
-# Top level environment
-include reproduce/config/pipeline/LOCAL.mk
-include reproduce/src/make/dependencies-build-rules.mk
-include reproduce/config/pipeline/dependency-versions.mk
-
-ddir   = $(BDIR)/dependencies
-tdir   = $(BDIR)/dependencies/tarballs
-idir   = $(BDIR)/dependencies/installed
-ibdir  = $(BDIR)/dependencies/installed/bin
-ildir  = $(BDIR)/dependencies/installed/lib
-ilidir = $(BDIR)/dependencies/installed/lib/built
-ipydir = $(BDIR)/dependencies/installed/lib/built/python
-
-# Define the top-level programs to build (installed in `.local/bin').
-top-level-python   = astroquery matplotlib #scipy
-all: $(foreach p, $(top-level-python), $(ipydir)/$(p))
-
-# Other basic environment settings: We are only including the host
-# operating system's PATH environment variable (after our own!) for the
-# compiler and linker. For the library binaries and headers, we are only
-# using our internally built libraries.
-#
-# To investigate:
-#
-#    1) Set SHELL to `$(ibdir)/env - NAME=VALUE $(ibdir)/bash' and set all
-#       the parameters defined bellow as `NAME=VALUE' statements before
-#       calling Bash. This will enable us to completely ignore the user's
-#       native environment.
-#
-#    2) Add `--noprofile --norc' to `.SHELLFLAGS' so doesn't load the
-#       user's environment.
-.ONESHELL:
-.SHELLFLAGS              := --noprofile --norc -ec
-export CCACHE_DISABLE    := 1
-export PATH              := $(ibdir)
-export LD_RUN_PATH       := $(ildir)
-export LD_LIBRARY_PATH   := $(ildir)
-export SHELL             := $(ibdir)/bash
-export CPPFLAGS          := -I$(idir)/include
-export PKG_CONFIG_PATH   := $(ildir)/pkgconfig
-export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
-export LDFLAGS           := $(rpath_command) -L$(ildir)
-
-
-
 
 
 # Python enviroment
@@ -84,9 +39,9 @@ export LDFLAGS           := $(rpath_command) -L$(ildir)
 # systems which might interfere. To be safe, we are removing all their
 # values.
 export PYTHONPATH             := $(installdir)/lib/python/site-packages
+export PYTHONPATH2            := $(PYTHONPATH)
 export PYTHONPATH3            := $(PYTHONPATH)
 export _LMFILES_              :=
-export PYTHONPATH2            :=
 export LOADEDMODULES          :=
 export MPI_PYTHON_SITEARCH    :=
 export MPI_PYTHON2_SITEARCH   :=
@@ -106,7 +61,7 @@ export MPI_PYTHON3_SITEARCH   :=
 # convention, but include the name/version in their tarball names with
 # another format, we'll do the modification before the download so the
 # downloaded file has our desired format.
-tarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz           \
+pytarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz         \
                         astroquery-$(astroquery-version).tar.gz           \
                         astropy-$(astropy-version).tar.gz                 \
                         beautifulsoup4-$(beautifulsoup4-version).tar.gz   \
@@ -116,6 +71,7 @@ tarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz           \
                         cryptography-$(cryptography-version).tar.gz       \
                         cycler-$(cycler-version).tar.gz                   \
                         entrypoints-$(entrypoints-version).tar.gz         \
+                        h5py-$(h5py-version).tar.gz                       \
                         html5lib-$(html5lib-version).tar.gz               \
                         idna-$(idna-version).tar.gz                       \
                         jeepney-$(jeepney-version).tar.gz                 \
@@ -123,6 +79,7 @@ tarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz           \
                         keyring-$(keyring-version).tar.gz                 \
                         libffi-$(libffi-version).tar.gz                   \
                         matplotlib-$(matplotlib-version).tar.gz           \
+                        mpi4py-$(mpi4py-version).tar.gz                   \
                         numpy-$(numpy-version).zip                        \
                         pip-$(pip-version).tar.gz                         \
                         pycparser-$(pycparser-version).tar.gz             \
@@ -140,8 +97,8 @@ tarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz           \
                         webencodings-$(webencodings-version).tar.gz       \
                         virtualenv-$(virtualenv-version).tar.gz           \
                       , $(tdir)/$(t) )
-topurl=https://files.pythonhosted.org/packages
-$(tarballs): $(tdir)/%:
+pytopurl=https://files.pythonhosted.org/packages
+$(pytarballs): $(tdir)/%:
 	if [ -f $(DEPENDENCIES-DIR)/$* ]; then
 	  cp $(DEPENDENCIES-DIR)/$* $@
 	else
@@ -157,7 +114,10 @@ $(tarballs): $(tdir)/%:
           # because the tokenization above will produce `python' as the
           # first string.
 	  if [ $* = python-dateutil-$(python-dateutil-version).tar.gz ]; then
-	        n=dateutil
+	    n=dateutil
+	  elif [ $* = h5py-$(h5py-version).tar.gz ]; then
+	    n=h5py
+
           # elif [ $* = strange-tarball5name-version.tar.gz ]; then
           #  n=strange5-name
 	  else
@@ -180,7 +140,7 @@ $(tarballs): $(tdir)/%:
 	  elif [ $$n = secretstorage  ]; then
 	    mergenames=0
 	    hash=a6/89/df343dbc2957a317127e7ff2983230dc5336273be34f2e1911519d85aeb5
-	    h=$(topurl)/$$hash/SecretStorage-$(secretstorage-version).tar.gz
+	    h=$(pytopurl)/$$hash/SecretStorage-$(secretstorage-version).tar.gz
 	  elif [ $$n = asn            ]; then h=fc/f1/8db7daa71f414ddabfa056c4ef792e1461ff655c2ae2928a2b675bfed6b4
 	  elif [ $$n = astroquery     ]; then h=61/50/a7a08f9e54d7d9d97e69433cd88231e1ad2901811c9d1ae9ac7ccaef9396
 	  elif [ $$n = astropy        ]; then h=eb/f7/1251bf6881861f24239efe0c24cbcfc4191ccdbb69ac3e9bb740d0c23352
@@ -191,13 +151,15 @@ $(tarballs): $(tdir)/%:
 	  elif [ $$n = cryptography   ]; then h=07/ca/bc827c5e55918ad223d59d299fff92f3563476c3b00d0a9157d9c0217449
 	  elif [ $$n = cycler         ]; then h=c2/4b/137dea450d6e1e3d474e1d873cd1d4f7d3beed7e0dc973b06e8e10d32488
 	  elif [ $$n = entrypoints    ]; then h=b4/ef/063484f1f9ba3081e920ec9972c96664e2edb9fdc3d8669b0e3b8fc0ad7c
+	  elif [ $$n = h5py           ]; then h=43/27/a6e7dcb8ae20a4dbf3725321058923fec262b6f7835179d78ccc8d98deec
 	  elif [ $$n = html           ]; then h=85/3e/cf449cf1b5004e87510b9368e7a5f1acd8831c2d6691edd3c62a0823f98f
 	  elif [ $$n = idna           ]; then h=ad/13/eb56951b6f7950cadb579ca166e448ba77f9d24efc03edd7e55fa57d04b7
 	  elif [ $$n = jeepney        ]; then h=16/1d/74adf3b164a8d19a60d0fcf706a751ffa2a1eaa8e5bbb1b6705c92a05263
 	  elif [ $$n = keyring        ]; then h=15/88/c6ce9509438bc02d54cf214923cfba814412f90c31c95028af852b19f9b2
 	  elif [ $$n = kiwisolver     ]; then h=31/60/494fcce70d60a598c32ee00e71542e52e27c978e5f8219fae0d4ac6e2864
 	  elif [ $$n = matplotlib     ]; then h=89/0c/653aec68e9cfb775c4fbae8f71011206e5e7fe4d60fcf01ea1a9d3bc957f
-	  elif [ $$n = numpy          ]; then h=2b/26/07472b0de91851b6656cbc86e2f0d5d3a3128e7580f23295ef58b6862d6c
+	  elif [ $$n = mpi            ]; then h=55/a2/c827b196070e161357b49287fa46d69f25641930fd5f854722319d431843
+	  elif [ $$n = numpy          ]; then h=cf/8d/6345b4f32b37945fedc1e027e83970005fc9c699068d2f566b82826515f2
 	  elif [ $$n = pip            ]; then h=4c/4d/88bc9413da11702cbbace3ccc51350ae099bb351febae8acc85fec34f9af
 	  elif [ $$n = pycparser      ]; then h=68/9e/49196946aee219aead1290e00d1e7fdeab8567783e83e1b9ab5585e6206a
 	  elif [ $$n = pyparsing      ]; then h=b9/b8/6b32b3e84014148dcd60dd05795e35c2e7f4b72f918616c61fdce83d27fc
@@ -212,7 +174,7 @@ $(tarballs): $(tdir)/%:
 	  elif [ $$n = urllib         ]; then h=b1/53/37d82ab391393565f2f831b8eedbffd57db5a718216f82f1a8b4d381a1c1
 	  elif [ $$n = virtualenv     ]; then h=51/aa/c395a6e6eaaedfa5a04723b6446a1df783b16cca6fec66e671cede514688
 	  elif [ $$n = webencodings   ]; then h=0b/02/ae6ceac1baeda530866a85075641cec12989bd8d31af6d5ab4a3e8c92f47
-#         elif [ $$n = strange5-name  ]; then h=XXXXX
+#	  elif [ $$n = strange5-name  ]; then h=XXXXX
 	  else
 	    echo; echo; echo;
 	    echo "'$$n' not recognized as a dependency name to download."
@@ -227,7 +189,7 @@ $(tarballs): $(tdir)/%:
           # storing all the tarballs in one directory, we want it to have
           # the same naming convention, so we'll download it to a temporary
           # name, then rename that.
-	  if [ $$mergenames = 1 ]; then  tarballurl=$(topurl)/$$h/"$*"
+	  if [ $$mergenames = 1 ]; then  tarballurl=$(pytopurl)/$$h/"$*"
 	  else                           tarballurl=$$h
 	  fi
 
@@ -249,18 +211,24 @@ $(tarballs): $(tdir)/%:
 # --------------------
 #
 # To build Python packages with direct access to a `setup.py' (if no direct
-# access to `setup.py' is needed, pip can be used)
+# access to `setup.py' is needed, pip can be used).
 # Arguments of this function are the numbers
 #   1) Unpack command
 #   2) Package name
 #   3) Unpacked directory name after unpacking the tarball
-pybuild = cd $(ddir); rm -rf $(3);                                        \
-	 if ! $(1) $(2); then echo; echo "Tar error"; exit 1; fi;             \
-	 cd $(3);                                                             \
-	 python3 setup.py build &&                                            \
-	 python3 setup.py install &&                                          \
-	 cd .. && rm -rf $(3) &&                                              \
-	 echo "done!" > $@
+#   4) site.cfg file (optional)
+pybuild = cd $(ddir); rm -rf $(3);                                \
+	 if ! $(1) $(2); then echo; echo "Tar error"; exit 1; fi; \
+	 cd $(3);                                                 \
+	 if [ "x$(4)" != x ]; then                                \
+	   sed -e 's|@LIBDIR[@]|'"$(ildir)"'|'                    \
+	       -e 's|@INCDIR[@]|'"$(idir)/include"'|'             \
+	       $(4) > site.cfg;                                   \
+	 fi;                                                      \
+	 python3 setup.py build                                   \
+	 && python3 setup.py install                              \
+	 && cd .. && rm -rf $(3)                                  \
+	 && echo "done!" > $@
 
 
 
@@ -271,24 +239,27 @@ pybuild = cd $(ddir); rm -rf $(3);                                        \
 #
 # While this Makefile is for Python programs, in some cases, we need
 # certain programs (like Python itself), or libraries for the modules.
-$(ibdir)/python3: $(tdir)/python-$(python-version).tar.gz
+$(ilidir)/libffi: $(tdir)/libffi-$(libffi-version).tar.gz
+	$(call gbuild, $<, libffi-$(libffi-version))        \
+	echo "libffi is built" > $@
+
+$(ibdir)/python3: $(tdir)/python-$(python-version).tar.gz \
+                  $(ilidir)/libffi
         # On Mac systems, the build complains about `clang' specific
         # features, so we can't use our own GCC build here.
-#	if [ x$(on_mac_os) = xyes ]; then                   \
-#	  export CC=clang;                                  \
-#	  export CXX=clang++;                               \
-#	fi;                                                 \
-
-	$(call gbuild, $<, Python-$(python-version))        \
+	if [ x$(on_mac_os) = xyes ]; then                   \
+	  export CC=clang;                                  \
+	  export CXX=clang++;                               \
+	fi;                                                 \
+	$(call gbuild, $<, Python-$(python-version),,       \
+	       --without-ensurepip                          \
+	       --with-system-ffi                            \
+	       --enable-shared)                             \
 	&& v=$$(echo $(python-version) | awk 'BEGIN{FS="."} \
 	    {printf "%d.%d\n", $$1, $$2}')                  \
 	&& ln -s $(ildir)/python$$v $(ildir)/python         \
 	&& rm -rf $(ipydir) && mkdir $(ipydir)
 
-$(ilidir)/libffi: $(tdir)/libffi-$(libffi-version).tar.gz
-	$(call gbuild, $<, libffi-$(libffi-version))        \
-	echo "libffi is built" > $@
-
 
 
 
@@ -297,7 +268,7 @@ $(ilidir)/libffi: $(tdir)/libffi-$(libffi-version).tar.gz
 #
 # All the necessary Python modules go here.
 $(ipydir)/asn1crypto: $(tdir)/asn1crypto-$(asn1crypto-version).tar.gz \
-                      $(ibdir)/python3
+                      $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, asn1crypto-$(asn1crypto-version))
 
 $(ipydir)/astroquery: $(tdir)/astroquery-$(astroquery-version).tar.gz  \
@@ -310,7 +281,9 @@ $(ipydir)/astroquery: $(tdir)/astroquery-$(astroquery-version).tar.gz  \
 	$(call pybuild, tar xf, $<, astroquery-$(astroquery-version))
 
 $(ipydir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \
-                   $(ipydir)/numpy
+                   $(ipydir)/h5py                            \
+                   $(ipydir)/numpy                           \
+                   $(ipydir)/scipy
 	$(call pybuild, tar xf, $<, astropy-$(astropy-version))
 
 $(ipydir)/beautifulsoup4: $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.gz \
@@ -318,81 +291,107 @@ $(ipydir)/beautifulsoup4: $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.g
 	$(call pybuild, tar xf, $<, beautifulsoup4-$(beautifulsoup4-version))
 
 $(ipydir)/certifi: $(tdir)/certifi-$(certifi-version).tar.gz \
-                   $(ibdir)/python3
+                   $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, certifi-$(certifi-version))
 
 $(ipydir)/cffi: $(tdir)/cffi-$(cffi-version).tar.gz \
-                $(ipydir)/pycparser                 \
-                $(ilidir)/libffi
+                $(ilidir)/libffi                    \
+                $(ipydir)/pycparser
 	$(call pybuild, tar xf, $<, cffi-$(cffi-version))
 
 $(ipydir)/chardet: $(tdir)/chardet-$(chardet-version).tar.gz \
-                   $(ibdir)/python3
+                   $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, chardet-$(chardet-version))
 
 $(ipydir)/cryptography: $(tdir)/cryptography-$(cryptography-version).tar.gz \
-                        $(ipydir)/cffi                                      \
-                        $(ipydir)/asn1crypto
+                        $(ipydir)/asn1crypto                                \
+                        $(ipydir)/cffi
 	$(call pybuild, tar xf, $<, cryptography-$(cryptography-version))
 
 $(ipydir)/cycler: $(tdir)/cycler-$(cycler-version).tar.gz \
-                   $(ipydir)/six
+                  $(ipydir)/six
 	$(call pybuild, tar xf, $<, cycler-$(cycler-version))
 
 $(ipydir)/entrypoints: $(tdir)/entrypoints-$(entrypoints-version).tar.gz \
-                       $(ibdir)/python3
+                       $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, entrypoints-$(entrypoints-version))
 
+$(ipydir)/h5py: $(tdir)/h5py-$(h5py-version).tar.gz \
+                $(ipydir)/setuptools                \
+                $(ilidir)/hdf5
+                # $(ipydir)/mpi4py # AFTER its problem is fixed.
+	#export HDF5_MPI=ON;       # AFTER its problem is fixed.
+	export HDF5_DIR=$(ildir); \
+	$(call pybuild, tar xf, $<, h5py-$(h5py-version))
+
 $(ipydir)/html5lib: $(tdir)/html5lib-$(html5lib-version).tar.gz  \
                     $(ipydir)/six                                \
                     $(ipydir)/webencodings
 	$(call pybuild, tar xf, $<, html5lib-$(html5lib-version))
 
 $(ipydir)/idna: $(tdir)/idna-$(idna-version).tar.gz \
-                $(ibdir)/python3
+                $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, idna-$(idna-version))
 
 $(ipydir)/jeepney: $(tdir)/jeepney-$(jeepney-version).tar.gz \
-                $(ibdir)/python3
+                   $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, jeepney-$(jeepney-version))
 
 $(ipydir)/keyring: $(tdir)/keyring-$(keyring-version).tar.gz    \
-                   $(ipydir)/setuptools_scm                     \
+                   $(ipydir)/entrypoints                        \
                    $(ipydir)/secretstorage                      \
-                   $(ipydir)/entrypoints
+                   $(ipydir)/setuptools_scm
 	$(call pybuild, tar xf, $<, keyring-$(keyring-version))
 
 $(ipydir)/kiwisolver: $(tdir)/kiwisolver-$(kiwisolver-version).tar.gz    \
-                   $(ipydir)/setuptools
+                      $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, kiwisolver-$(kiwisolver-version))
 
-
 $(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz   \
                       $(ipydir)/cycler                                  \
                       $(ilidir)/freetype                                \
+                      $(ipydir)/kiwisolver                              \
                       $(ipydir)/numpy                                   \
                       $(ipydir)/pyparsing                               \
-                      $(ipydir)/python-dateutil                         \
-                      $(ipydir)/kiwisolver
+                      $(ipydir)/python-dateutil
 	$(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version))
 
+# Currently mpi4py doesn't build because of some conflict with OpenMPI:
+#
+#  In file included from src/mpi4py.MPI.c:591,
+#                  from src/MPI.c:4:
+#  src/mpi4py.MPI.c: In function '__pyx_f_6mpi4py_3MPI_del_Datatype':
+#  src/mpi4py.MPI.c:15094:36: error: expected expression before '_Static_assert'
+#  __pyx_t_1 = (((__pyx_v_ob[0]) == MPI_UB) != 0);
+#
+# But atleast on my system it fails.
+$(ipydir)/mpi4py: $(tdir)/mpi4py-$(mpi4py-version).tar.gz    \
+                  $(ipydir)/setuptools                       \
+                  $(ilidir)/openmpi
+	$(call pybuild, tar xf, $<, mpi4py-$(mpi4py-version))
+
 $(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
-                 $(ibdir)/python3
-	export BLAS=None; \
-	export ATLAS=None; \
-	export LAPACK=None; \
-	$(call pybuild, unzip, $<, numpy-$(numpy-version))
+                 $(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)
 
 $(ibdir)/pip3: $(tdir)/pip-$(pip-version).tar.gz \
-               $(ibdir)/python3
+               $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, pip-$(pip-version))
 
 $(ipydir)/pycparser: $(tdir)/pycparser-$(pycparser-version).tar.gz \
-                     $(ibdir)/python3
+                     $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, pycparser-$(pycparser-version))
 
 $(ipydir)/pyparsing: $(tdir)/pyparsing-$(pyparsing-version).tar.gz \
-                     $(ibdir)/python3
+                     $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, pyparsing-$(pyparsing-version))
 
 $(ipydir)/python-dateutil: $(tdir)/python-dateutil-$(python-dateutil-version).tar.gz  \
@@ -410,7 +409,13 @@ $(ipydir)/requests: $(tdir)/requests-$(requests-version).tar.gz   \
 
 $(ipydir)/scipy: $(tdir)/scipy-$(scipy-version).tar.gz \
                  $(ipydir)/numpy
-	$(call pybuild, tar xf, $<, scipy-$(scipy-version))
+	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)
 
 $(ipydir)/secretstorage: $(tdir)/secretstorage-$(secretstorage-version).tar.gz \
                          $(ipydir)/cryptography                                \
@@ -426,17 +431,17 @@ $(ipydir)/setuptools_scm: $(tdir)/setuptools_scm-$(setuptools_scm-version).tar.g
 	$(call pybuild, tar xf, $<, setuptools_scm-$(setuptools_scm-version))
 
 $(ipydir)/six: $(tdir)/six-$(six-version).tar.gz \
-               $(ibdir)/python3
+               $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, six-$(six-version))
 
 $(ipydir)/soupsieve: $(tdir)/soupsieve-$(soupsieve-version).tar.gz \
-                     $(ibdir)/python3
+                     $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, soupsieve-$(soupsieve-version))
 
 $(ipydir)/urllib3: $(tdir)/urllib3-$(urllib3-version).tar.gz \
-                   $(ibdir)/python3
+                   $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, urllib3-$(urllib3-version))
 
 $(ipydir)/webencodings: $(tdir)/webencodings-$(webencodings-version).tar.gz \
-                        $(ibdir)/python3
+                        $(ipydir)/setuptools
 	$(call pybuild, tar xf, $<, webencodings-$(webencodings-version))
diff --git a/reproduce/src/make/dependencies.mk b/reproduce/src/make/dependencies.mk
index 2b3b70b..fdbfd7f 100644
--- a/reproduce/src/make/dependencies.mk
+++ b/reproduce/src/make/dependencies.mk
@@ -35,19 +35,28 @@ include reproduce/src/make/dependencies-build-rules.mk
 include reproduce/config/pipeline/dependency-texlive.mk
 include reproduce/config/pipeline/dependency-versions.mk
 
+
 ddir   = $(BDIR)/dependencies
 tdir   = $(BDIR)/dependencies/tarballs
 idir   = $(BDIR)/dependencies/installed
 ibdir  = $(BDIR)/dependencies/installed/bin
 ildir  = $(BDIR)/dependencies/installed/lib
 ilidir = $(BDIR)/dependencies/installed/lib/built
+ipydir = $(BDIR)/dependencies/installed/lib/built/python
 
 # Define the top-level programs to build (installed in `.local/bin').
-top-level-programs  = astnoisechisel metastore unzip zip
-top-level-libraries = freetype
-all: $(ddir)/texlive-versions.tex                       \
-     $(foreach p, $(top-level-programs), $(ibdir)/$(p)) \
-     $(foreach p, $(top-level-libraries), $(ilidir)/$(p))
+#
+# 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-libraries = # atlas
+top-level-programs  = astnoisechisel flock metastore unzip zip
+top-level-python    = astroquery matplotlib
+all: $(ddir)/texlive-versions.tex                         \
+     $(foreach p, $(top-level-libraries), $(ilidir)/$(p)) \
+     $(foreach p, $(top-level-programs),  $(ibdir)/$(p))  \
+     $(foreach p, $(top-level-python),    $(ipydir)/$(p))
 
 # Other basic environment settings: We are only including the host
 # operating system's PATH environment variable (after our own!) for the
@@ -67,16 +76,17 @@ all: $(ddir)/texlive-versions.tex                       \
 .SHELLFLAGS              := --noprofile --norc -ec
 export CCACHE_DISABLE    := 1
 export PATH              := $(ibdir)
-export LD_RUN_PATH       := $(ildir)
-export LD_LIBRARY_PATH   := $(ildir)
 export SHELL             := $(ibdir)/bash
 export CPPFLAGS          := -I$(idir)/include
 export PKG_CONFIG_PATH   := $(ildir)/pkgconfig
 export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
+export LD_RUN_PATH       := $(ildir):$(il64dir)
+export LD_LIBRARY_PATH   := $(ildir):$(il64dir)
 export LDFLAGS           := $(rpath_command) -L$(ildir)
 
 
-
+# Python packages
+include reproduce/src/make/dependencies-python.mk
 
 
 # Tarballs
@@ -90,21 +100,27 @@ export LDFLAGS           := $(rpath_command) -L$(ildir)
 # another format, we'll do the modification before the download so the
 # downloaded file has our desired format.
 tarballs = $(foreach t, cfitsio-$(cfitsio-version).tar.gz                  \
+                        atlas-$(atlas-version).tar.bz2                     \
                         cmake-$(cmake-version).tar.gz                      \
                         curl-$(curl-version).tar.gz                        \
                         freetype-$(freetype-version).tar.gz                \
+                        fftw-$(fftw-version).tar.gz                        \
                         ghostscript-$(ghostscript-version).tar.gz          \
                         git-$(git-version).tar.xz                          \
                         gnuastro-$(gnuastro-version).tar.lz                \
                         gsl-$(gsl-version).tar.gz                          \
+                        hdf5-$(hdf5-version).tar.gz                        \
                         install-tl-unx.tar.gz                              \
                         jpegsrc.$(libjpeg-version).tar.gz                  \
+                        lapack-$(lapack-version).tar.gz                    \
                         libbsd-$(libbsd-version).tar.xz                    \
                         libpng-$(libpng-version).tar.xz                    \
                         libtool-$(libtool-version).tar.xz                  \
                         libgit2-$(libgit2-version).tar.gz                  \
                         metastore-$(metastore-version).tar.gz              \
+                        openmpi-$(openmpi-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                          \
@@ -113,12 +129,12 @@ $(tarballs): $(tdir)/%:
 	if [ -f $(DEPENDENCIES-DIR)/$* ]; then
 	  cp $(DEPENDENCIES-DIR)/$* $@
 	else
-          # Remove all numbers, `-' and `.' from the tarball name so we can
-          # search more easily only with the program name.
+	  # Remove all numbers, `-' and `.' from the tarball name so we can
+	  # search more easily only with the program name.
 	  n=$$(echo $* | sed -e's/[0-9\-]/ /g' -e's/\./ /g'           \
 	               | awk '{print $$1}' )
 
-          # Set the top download link of the requested tarball.
+	  # Set the top download link of the requested tarball.
 	  mergenames=1
 	  if [ $$n = cfitsio     ]; then
 	    mergenames=0
@@ -129,15 +145,24 @@ $(tarballs): $(tdir)/%:
 	                                 : (l==2 ? "%d00\n"           \
                                             : "%d000\n") ), $$1)}')
 	    w=https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio$$v.tar.gz
+	  elif [ $$n = atlas       ]; then
+	    mergenames=0
+	    w=https://sourceforge.net/projects/math-atlas/files/Stable/$(atlas-version)/atlas$(atlas-version).tar.bz2/download
 	  elif [ $$n = cmake       ]; then w=https://cmake.org/files/v3.12
 	  elif [ $$n = curl        ]; then w=https://curl.haxx.se/download
+	  elif [ $$n = fftw        ]; then w=ftp://ftp.fftw.org/pub/fftw
 	  elif [ $$n = freetype    ]; then w=https://download.savannah.gnu.org/releases/freetype
+	  elif [ $$n = hdf         ]; then
+	    mergenames=0
+	    majorver=$$(echo $(hdf5-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}')
+	    w=https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$$majorver/hdf5-$(hdf5-version)/src/$*
 	  elif [ $$n = ghostscript ]; then w=https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs926
 	  elif [ $$n = git         ]; then w=http://mirrors.edge.kernel.org/pub/software/scm/git
 	  elif [ $$n = gnuastro    ]; then w=http://ftp.gnu.org/gnu/gnuastro
 	  elif [ $$n = gsl         ]; then w=http://ftp.gnu.org/gnu/gsl
 	  elif [ $$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
 	  elif [ $$n = libbsd      ]; then w=http://libbsd.freedesktop.org/releases
 	  elif [ $$n = libpng      ]; then w=https://download.sourceforge.net/libpng
 	  elif [ $$n = libtool     ]; then w=http://ftp.gnu.org/gnu/libtool
@@ -145,6 +170,13 @@ $(tarballs): $(tdir)/%:
 	    mergenames=0
 	    w=https://github.com/libgit2/libgit2/archive/v$(libgit2-version).tar.gz
 	  elif [ $$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 = openmpi     ]; then
+	    mergenames=0
+	    majorver=$$(echo $(openmpi-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}')
+	    w=https://download.open-mpi.org/release/open-mpi/v$$majorver/$*
 	  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/\.//')
@@ -160,20 +192,20 @@ $(tarballs): $(tdir)/%:
 	    exit 1
 	  fi
 
-          # Download the requested tarball. Note that some packages may not
-          # follow our naming convention (where the package name is merged
-          # with its version number). In such cases, `w' will be the full
-          # address, not just the top directory address. But since we are
-          # storing all the tarballs in one directory, we want it to have
-          # the same naming convention, so we'll download it to a temporary
-          # name, then rename that.
+	  # Download the requested tarball. Note that some packages may not
+	  # follow our naming convention (where the package name is merged
+	  # with its version number). In such cases, `w' will be the full
+	  # address, not just the top directory address. But since we are
+	  # storing all the tarballs in one directory, we want it to have
+	  # the same naming convention, so we'll download it to a temporary
+	  # name, then rename that.
 	  if [ $$mergenames = 1 ]; then  tarballurl=$$w/"$*"
 	  else                           tarballurl=$$w
 	  fi
 
-          # If the download fails, Wget will write the error message in the
-          # target file, so Make will think that its done! To avoid this
-          # problem, we'll rename the output.
+	  # If the download fails, Wget will write the error message in the
+	  # target file, so Make will think that its done! To avoid this
+	  # problem, we'll rename the output.
 	  echo "Downloading $$tarballurl"
 	  if ! wget --no-use-server-timestamps -O$@ $$tarballurl; then
 	     rm -f $@
@@ -226,12 +258,26 @@ $(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
 	$(call gbuild, $<, freetype-$(freetype-version), static) \
 	&& echo "freetype is built" > $@
 
+$(ilidir)/hdf5: $(tdir)/hdf5-$(hdf5-version).tar.gz \
+                $(ilidir)/openmpi
+	export CC=mpicc;                                 \
+	export FC=mpif90;                                \
+	$(call gbuild, $<, hdf5-$(hdf5-version), static, \
+	               --enable-parallel                 \
+	               --enable-fortran, V=1)            \
+	&& echo "HDF5 library is built" > $@
+
 $(ilidir)/libbsd: $(tdir)/libbsd-$(libbsd-version).tar.xz
 	$(call gbuild, $<, libbsd-$(libbsd-version), static,,V=1) \
 	&& echo "libbsd is built" > $@
@@ -249,6 +295,100 @@ $(ilidir)/libtiff: $(tdir)/tiff-$(libtiff-version).tar.gz \
 	               --disable-webp --disable-zstd) \
 	&& echo "Libtiff is built" > $@
 
+$(ilidir)/openmpi: $(tdir)/openmpi-$(openmpi-version).tar.gz
+	$(call gbuild, $<, openmpi-$(openmpi-version), static, , V=1) \
+	&& echo "OpenMPI is built" > $@
+
+$(ilidir)/atlas: $(tdir)/atlas-$(atlas-version).tar.bz2 \
+	         $(tdir)/lapack-$(lapack-version).tar.gz
+
+        # Get the operating system specific features (how to get
+        # CPU frequency and the library suffixes). To make the steps
+        # more readable, the different library version suffixes are
+        # named with a single character: `s' for no version in the
+        # name, `m' for the major version suffix, and `f' for the
+        # full version suffix.
+        # GCC in Mac OS doesn't work. To work around this issue, on Mac
+        # systems we force ATLAS to use `clang' instead of `gcc'.
+	if [ x$(on_mac_os) = xyes ]; then
+	  s=dylib
+	  m=3.dylib
+	  f=3.6.1.dylib
+	  core=$$(sysctl hw.cpufrequency | awk '{print $$2/1000000}')
+	  clangflag="--force-clang=$(ibdir)/clang"
+	else
+	  s=so
+	  m=so.3
+	  f=so.3.6.1
+	  clangflag=
+	  core=$$(cat /proc/cpuinfo | grep "cpu MHz" \
+	              | head -n 1                    \
+	              | sed "s/.*: \([0-9.]*\).*/\1/")
+	fi
+
+        # See if the shared libraries should be build for a single CPU
+        # thread or multiple threads.
+	N=$$(nproc)
+	srcdir=$$(pwd)/reproduce/src/make
+	if [ $$N = 1 ]; then
+	  sharedmk=$$srcdir/dependencies-atlas-single.mk
+	else
+	  sharedmk=$$srcdir/dependencies-atlas-multiple.mk
+	fi
+
+        # The linking step here doesn't recognize the `-Wl' in the
+        # `rpath_command'.
+	export LDFLAGS=-L$(ildir)
+	cd $(ddir)                                                \
+	&& tar xf $<                                              \
+	&& cd ATLAS                                               \
+	&& rm -rf build                                           \
+	&& mkdir build                                            \
+	&& cd build                                               \
+	&& ../configure -b 64 -D c -DPentiumCPS=$$core            \
+	             --with-netlib-lapack-tarfile=$(word 2, $^)   \
+	             --cripple-atlas-performance                  \
+	             -Fa alg -fPIC --shared $$clangflag           \
+	             --prefix=$(idir)                             \
+	&& make                                                   \
+	&& if [ "x$(on_mac_os)" != xyes ]; then                   \
+	     cd lib && make -f $$sharedmk && cd ..                \
+	     && for l in lib/*.$$s*; do                           \
+	          patchelf --set-rpath $(ildir) $$l; done         \
+	     && cp -d lib/*.$$s* $(ildir)                         \
+	     && ln -fs $(ildir)/libblas.$$s  $(ildir)/libblas.$$m \
+	     && ln -fs $(ildir)/libf77blas.$$s $(ildir)/libf77blas.$$m \
+	     && ln -fs $(ildir)/liblapack.$$f  $(ildir)/liblapack.$$s \
+	     && ln -fs $(ildir)/liblapack.$$f  $(ildir)/liblapack.$$m; \
+	   fi                                                     \
+	&& make install
+
+        # We need to check the existance of `libptlapack.a', but we can't
+        # do this in the `&&' steps above (it will conflict). So we'll do
+        # the check after seeing if `libtatlas.so' is installed, then we'll
+        # finalize the build (delete the untarred directory).
+	if [ "x$(on_mac_os)" != xyes ]; then                       \
+	  [ -e lib/libptlapack.a ] && cp lib/libptlapack.a $(ildir); \
+	  cd $(ddir);                                              \
+	  rm -rf ATLAS;                                            \
+	fi
+
+        # We'll check the full installation with the static library (not
+        # 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" > $@
 
 
 
@@ -333,11 +473,6 @@ $(ibdir)/cmake: $(tdir)/cmake-$(cmake-version).tar.gz \
 	make install &&                                            \
 	cd ..&& rm -rf cmake-$(cmake-version)
 
-# Some programs that depend on cURL (in particular CMake) don't necessarily
-# have easiy ways to explicity tell them to also link with libcurl's
-# dependencies (libssl, libcrypto, and libz). So we won't force curl to
-# only be static.
-#
 # cURL (and its library, which is needed by several programs here) can
 # optionally link with many different network-related libraries on the host
 # system that we are not yet building in the pipeline. Many of these are
@@ -363,7 +498,7 @@ $(ibdir)/curl: $(tdir)/curl-$(curl-version).tar.gz
 	               --without-axtls                   \
 	               --disable-ldaps                   \
 	               --disable-ldap                    \
-	               --without-nss )
+	               --without-nss, V=1)
 
 # On Mac OS, libtool does different things, so to avoid confusion, we'll
 # prefix GNU's libtool executables with `glibtool'.
diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk
index 545fcc1..66e7c77 100644
--- a/reproduce/src/make/initialize.mk
+++ b/reproduce/src/make/initialize.mk
@@ -369,10 +369,6 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 	echo "\newcommand{\\grepversion}{$(grep-version)}"              >> $@
 	echo "\newcommand{\\gzipversion}{$(gzip-version)}"              >> $@
 	echo "\newcommand{\\islversion}{$(isl-version)}"                >> $@
-	echo "\newcommand{\\libbsdversion}{$(libbsd-version)}"          >> $@
-	echo "\newcommand{\\libffiversion}{$(libffi-version)}"          >> $@
-	echo "\newcommand{\\libpngversion}{$(libpng-version)}"          >> $@
-	echo "\newcommand{\\libtoolversion}{$(libtool-version)}"        >> $@
 	echo "\newcommand{\\lzipversion}{$(lzip-version)}"              >> $@
 	echo "\newcommand{\\makeversion}{$(make-version)}"              >> $@
 	echo "\newcommand{\\metastoreversion}{$(metastore-version)}"    >> $@
@@ -394,12 +390,18 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 	echo "\newcommand{\\zipversion}{$(zip-version)}"                >> $@
 
         # Libraries.
+	echo "\newcommand{\\atlasversion}{$(cfitsio-version)}"          >> $@
 	echo "\newcommand{\\cfitsioversion}{$(cfitsio-version)}"        >> $@
 	echo "\newcommand{\\curlversion}{$(curl-version)}"              >> $@
 	echo "\newcommand{\\gslversion}{$(gsl-version)}"                >> $@
+	echo "\newcommand{\\lapack}{$(lapack-version)}"                 >> $@
+	echo "\newcommand{\\libbsdversion}{$(libbsd-version)}"          >> $@
+	echo "\newcommand{\\libffiversion}{$(libffi-version)}"          >> $@
 	echo "\newcommand{\\libgittwoversion}{$(libgit2-version)}"      >> $@
 	echo "\newcommand{\\libjpegversion}{$(libjpeg-version)}"        >> $@
+	echo "\newcommand{\\libpngversion}{$(libpng-version)}"          >> $@
 	echo "\newcommand{\\libtiffversion}{$(libtiff-version)}"        >> $@
+	echo "\newcommand{\\libtoolversion}{$(libtool-version)}"        >> $@
 	echo "\newcommand{\\wcslibversion}{$(wcslib-version)}"          >> $@
 	echo "\newcommand{\\zlibversion}{$(zlib-version)}"              >> $@
 
@@ -414,8 +416,9 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 	echo "\newcommand{\\cryptographyversion}{$(cryptography-version)}" >> $@
 	echo "\newcommand{\\cyclerversion}{$(cycler-version)}"          >> $@
 	echo "\newcommand{\\entrypointsversion}{$(entrypoints-version)}" >> $@
+	echo "\newcommand{\\hpyversion}{$(h5py-version)}"               >> $@
 	echo "\newcommand{\\htmlfivelibversion}{$(html5lib-version)}"   >> $@
-	echo "\newcommand{\\indaversion}{$(idna-version)}"              >> $@
+	echo "\newcommand{\\idaversion}{$(idna-version)}"               >> $@
 	echo "\newcommand{\\jeepneyversion}{$(jeepney-version)}"        >> $@
 	echo "\newcommand{\\kiwisolverversion}{$(kiwisolver-version)}"  >> $@
 	echo "\newcommand{\\keyringversion}{$(keyring-version)}"        >> $@
@@ -433,7 +436,7 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 	echo "\newcommand{\\sixversion}{$(six-version)}"                >> $@
 	echo "\newcommand{\\soupsieveversion}{$(soupsieve-version)}"    >> $@
 	echo "\newcommand{\\urllibthreeversion}{$(urllib3-version)}"    >> $@
-	echo "\newcommand{\\virtualenvversion}{$(virtualenv-version)}"  >> $@
+#	echo "\newcommand{\\virtualenvversion}{$(virtualenv-version)}"  >> $@
 	echo "\newcommand{\\webencodingsversion}{$(webencodings-version)}" >> $@
 
         # TeX package versions