New rule to build Coreutils, it is now built along

Recently, after the installation of Coreutils, we added a step to manually
run PatchELF over all the contents of the `$(ibdir)'. However, after a
fresh test, this method failed: because while PatchELF was updating `mv',
another program that was using `mv' couldn't do so and crashed.

To fix this problem, Coreutils is now installed in a dummy directory also
and the exact files that need `rpath' are identified and PatchELF is run on
them (to be clean). Also, higher-level `basic.mk' software (higher-level
than Bash), were re-organized so they depend on Coreutils. With this, we
are no sure that when Coreutils is being built, it is the only program that
is being built and PatchELF won't interfere with any other program.

Also, OpenSSL and CMake were set to be bulit in parallel to speed up their
build.

2 files changed, 108 insertions, 85 deletions

diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 05161e9..db779a1 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -613,38 +613,53 @@ $(ibidir)/bash: $(tdir)/bash-$(bash-version).tar.lz \
 
 
 
-# Downloaders
-# -----------
-
-# cURL
+# Coreutils
+# ---------
 #
-# cURL can optionally link with many different network-related libraries on
-# the host system that we are not yet building in the template. Many of
-# these are not relevant to most science projects, so we are explicitly
-# using `--without-XXX' or `--disable-XXX' so cURL doesn't link with
-# them. Note that if it does link with them, the configuration will crash
-# when the library is updated/changed by the host, and the whole purpose of
-# this project is avoid dependency on the host as much as possible.
-$(ibidir)/curl: $(tdir)/curl-$(curl-version).tar.gz \
-                $(ibidir)/openssl
-	$(call gbuild, $<, curl-$(curl-version), , \
-	               LIBS="-pthread" \
-	               --with-zlib=$(ildir) \
-	               --with-ssl=$(idir) \
-	               --without-mesalink \
-	               --with-ca-fallback \
-	               --without-librtmp \
-	               --without-libidn2 \
-	               --without-wolfssl \
-	               --without-brotli \
-	               --without-gnutls \
-	               --without-cyassl \
-	               --without-libpsl \
-	               --without-axtls \
-	               --disable-ldaps \
-	               --disable-ldap \
-	               --without-nss, V=1) \
-	&& echo "cURL $(curl-version)" > $@
+# For some reason, Coreutils doesn't include `rpath' in its installed
+# executables (even though it says that by default its included and that
+# even when calling `--enable-rpath=yes'). So we have to manually add
+# `rpath' to Coreutils' executables after the standard build is
+# complete.
+#
+# One problem is that Coreutils installs many very basic executables which
+# might be in use by other programs. So we must make sure that when
+# Coreutils is being built, no other program is being built in
+# parallel. The solution to the many executables it installs is to make a
+# fake installation (with `DESTDIR'), and get a list of the contents of the
+# directory to find the names.
+#
+# The echo after the PatchELF loop is to avoid a crash if the last
+# file that PatchELF encounters is not usable (and it returns with
+# an error).
+$(ibidir)/coreutils: $(tdir)/coreutils-$(coreutils-version).tar.xz \
+                     $(ibidir)/openssl \
+	             $(ibidir)/bash
+	cd $(ddir) \
+	&& rm -rf coreutils-$(coreutils-version) \
+	&& if ! tar xf $<; then echo; echo "Tar error"; exit 1; fi \
+	&& cd coreutils-$(coreutils-version) \
+	&& sed -e's|\#\! /bin/sh|\#\! $(ibdir)/bash|' \
+	       -e's|\#\!/bin/sh|\#\! $(ibdir)/bash|' \
+	       configure > configure-tmp \
+	&& mv configure-tmp configure \
+	&& chmod +x configure \
+	&& ./configure --prefix=$(idir) SHELL=$(ibdir)/bash  \
+	               LDFLAGS="$(LDFLAGS)" CPPFLAGS="$(CPPFLAGS)" \
+	               --disable-silent-rules --with-openssl=yes \
+	&& make SHELL=$(ibdir)/bash -j$(numthreads) \
+	&& make SHELL=$(ibdir)/bash install \
+	&& if [ x$(on_mac_os) != xyes ]; then \
+	     make SHELL=$(ibdir)/bash install DESTDIR=junkinst; \
+	     instprogs=$$(ls junkinst/$(ibdir)); \
+	     for f in $$instprogs; do \
+	       $(ibdir)/patchelf --set-rpath $(ildir) $(ibdir)/$$f; \
+	     done; \
+	     echo "PatchELF applied to all programs."; \
+	   fi \
+	&& cd .. \
+	&& rm -rf coreutils-$(coreutils-version) \
+	&& echo "GNU Coreutils $(coreutils-version)" > $@
 
 # OpenSSL
 #
@@ -664,7 +679,7 @@ $(ibidir)/curl: $(tdir)/curl-$(curl-version).tar.gz \
 $(idir)/etc:; mkdir $@
 $(ibidir)/openssl: $(tdir)/openssl-$(openssl-version).tar.gz \
                    $(tdir)/cert.pem \
-                   $(ibidir)/bash | $(idir)/etc
+                   $(ibidir)/make | $(idir)/etc
         # According to OpenSSL's Wiki (link bellow), it can't automatically
         # detect Mac OS's structure. It will need some help. So we'll use
         # the `on_mac_os' Make variable that we defined in the configure
@@ -682,8 +697,8 @@ $(ibidir)/openssl: $(tdir)/openssl-$(openssl-version).tar.gz \
 	               $(rpath_command) \
 	               --openssldir=$(idir)/etc/ssl \
 	               --with-zlib-lib=$(ildir) \
-	               --with-zlib-include=$(idir)/include, , , \
-	               ./config ) \
+	               --with-zlib-include=$(idir)/include, \
+	               -j$(numthreads), , ./config ) \
 	&& cp $(tdir)/cert.pem $(idir)/etc/ssl/cert.pem \
 	&& if [ $$? = 0 ]; then \
 	     if [ x$(on_mac_os) = xyes ]; then \
@@ -694,6 +709,44 @@ $(ibidir)/openssl: $(tdir)/openssl-$(openssl-version).tar.gz \
 	     echo "OpenSSL $(openssl-version)" > $@; \
 	   fi
 
+
+
+
+# Downloaders
+# -----------
+
+# cURL
+#
+# cURL can optionally link with many different network-related libraries on
+# the host system that we are not yet building in the template. Many of
+# these are not relevant to most science projects, so we are explicitly
+# using `--without-XXX' or `--disable-XXX' so cURL doesn't link with
+# them. Note that if it does link with them, the configuration will crash
+# when the library is updated/changed by the host, and the whole purpose of
+# 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.
+	$(call gbuild, $<, curl-$(curl-version), , \
+	               LIBS="-pthread" \
+	               --with-zlib=$(ildir) \
+	               --with-ssl=$(idir) \
+	               --without-mesalink \
+	               --with-ca-fallback \
+	               --without-librtmp \
+	               --without-libidn2 \
+	               --without-wolfssl \
+	               --without-brotli \
+	               --without-gnutls \
+	               --without-cyassl \
+	               --without-libpsl \
+	               --without-axtls \
+	               --disable-ldaps \
+	               --disable-ldap \
+	               --without-nss, V=1) \
+	&& echo "cURL $(curl-version)" > $@
+
+
 # GNU Wget
 #
 # Note that on some systems (for example GNU/Linux) Wget needs to explicity
@@ -709,7 +762,8 @@ $(ibidir)/openssl: $(tdir)/openssl-$(openssl-version).tar.gz \
 # host), they are disabled here.
 $(ibidir)/wget: $(tdir)/wget-$(wget-version).tar.lz \
                 $(ibidir)/pkg-config \
-                $(ibidir)/openssl
+                $(ibidir)/coreutils \
+                $(ibidir)/openssl # Coreutils only so Wget is built after it.
 	libs="-pthread"; \
 	if [ x$(needs_ldl) = xyes ]; then libs="$$libs -ldl"; fi; \
 	$(call gbuild, $<, wget-$(wget-version), , \
@@ -739,46 +793,23 @@ $(ibidir)/wget: $(tdir)/wget-$(wget-version).tar.lz \
 # process of the higher-level programs and libraries. Note that during the
 # building of those higher-level programs (after this Makefile finishes),
 # there is no access to the system's PATH.
-$(ibidir)/coreutils: $(tdir)/coreutils-$(coreutils-version).tar.xz \
-                     $(ibidir)/openssl
-        # Coreutils will use the hashing features of OpenSSL's `libcrypto'.
-        #
-        # For some reason, with this configuration (by default it says that
-        # it supports `rpath'), Coreutils doesn't include `rpath' in its
-        # installed executables. So we have to manually add them after the
-        # standard build is complete. One problem is that Coreutils
-        # installs many executables. So to simplify things, we'll just
-        # manually add `rpath' to everything in `.local/bin' using
-        # `patchelf' on non-Mac systems. It won't affect those that already
-        # have it.
-        #
-        # The echo after the PatchELF loop is to avoid a crash if the last
-        # file that PatchELF encounters is not usable (and it returns with
-        # an error).
-	$(call gbuild, $<, coreutils-$(coreutils-version), static, \
-	               LDFLAGS="$(LDFLAGS)" CPPFLAGS="$(CPPFLAGS)" \
-	               --disable-silent-rules --with-openssl=yes, \
-	               -j$(numthreads)) \
-	&& if [ x$(on_mac_os) != xyes ]; then \
-	     for f in $(ibdir)/*; do \
-	       $(ibdir)/patchelf --set-rpath $(ildir) $$f; \
-	     done; \
-	     echo "PatchELF applied to all programs."; \
-	   fi \
-	&& echo "GNU Coreutils $(coreutils-version)" > $@
-
 $(ibidir)/diffutils: $(tdir)/diffutils-$(diffutils-version).tar.xz \
-                     $(ibidir)/bash
+                     $(ibidir)/coreutils
 	$(call gbuild, $<, diffutils-$(diffutils-version), static, , V=1) \
 	&& echo "GNU Diffutils $(diffutils-version)" > $@
 
+$(ibidir)/file: $(tdir)/file-$(file-version).tar.gz \
+                $(ibidir)/coreutils
+	$(call gbuild, $<, file-$(file-version), static) \
+	&& echo "File $(file-version)" > $@
+
 $(ibidir)/findutils: $(tdir)/findutils-$(findutils-version).tar.lz \
-                     $(ibidir)/bash
+                     $(ibidir)/coreutils
 	$(call gbuild, $<, findutils-$(findutils-version), static, , V=1) \
 	&& echo "GNU Findutils $(findutils-version)" > $@
 
 $(ibidir)/gawk: $(tdir)/gawk-$(gawk-version).tar.lz \
-                $(ibidir)/bash \
+                $(ibidir)/coreutils \
                 $(ibidir)/mpfr \
                 $(ibidir)/gmp
         # AWK doesn't include RPATH by default, so we'll have to manually
@@ -800,14 +831,15 @@ $(ibidir)/gawk: $(tdir)/gawk-$(gawk-version).tar.lz \
 	&& echo "GNU AWK $(gawk-version)" > $@
 
 $(ibidir)/git: $(tdir)/git-$(git-version).tar.xz \
-               $(ibidir)/curl
+	       $(ibidir)/coreutils \
+               $(ibidir)/curl	# Coreutils, so Git is built after it.
 	$(call gbuild, $<, git-$(git-version), static, \
                        --without-tcltk --with-shell=$(ibdir)/bash, \
 	               V=1) \
 	&& echo "Git $(git-version)" > $@
 
 $(ibidir)/gmp: $(tdir)/gmp-$(gmp-version).tar.lz \
-               $(ibidir)/bash                    \
+               $(ibidir)/coreutils \
                $(ibidir)/m4
 	$(call gbuild, $<, gmp-$(gmp-version), static, , , make check)  \
 	&& echo "GNU Multiple Precision Arithmetic Library $(gmp-version)" > $@
@@ -821,17 +853,17 @@ $(ibidir)/glibtool: $(tdir)/libtool-$(libtool-version).tar.xz \
 	&& echo "GNU Libtool $(libtool-version)" > $@
 
 $(ibidir)/grep: $(tdir)/grep-$(grep-version).tar.xz \
-                $(ibidir)/bash
+                $(ibidir)/coreutils
 	$(call gbuild, $<, grep-$(grep-version), static) \
 	&& echo "GNU Grep $(grep-version)" > $@
 
 $(ibidir)/libbsd: $(tdir)/libbsd-$(libbsd-version).tar.xz \
-                  $(ibidir)/bash
+                  $(ibidir)/coreutils
 	$(call gbuild, $<, libbsd-$(libbsd-version), static,,V=1) \
 	&& echo "Libbsd $(libbsd-version)" > $@
 
 $(ibidir)/m4: $(tdir)/m4-$(m4-version).tar.gz \
-              $(ibidir)/bash
+              $(ibidir)/coreutils
 	$(call gbuild, $<, m4-$(m4-version), static) \
 	&& echo "GNU M4 $(m4-version)" > $@
 
@@ -914,7 +946,7 @@ $(ibidir)/mpfr: $(tdir)/mpfr-$(mpfr-version).tar.xz \
 	&& echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@
 
 $(ibidir)/pkg-config: $(tdir)/pkg-config-$(pkgconfig-version).tar.gz \
-                      $(ibidir)/bash
+                      $(ibidir)/coreutils
         # Some Mac OS systems may have a version of the GNU C Compiler
         # (GCC) installed that doesn't support some necessary features of
         # building Glib (as part of pkg-config). So to be safe, for Mac
@@ -928,12 +960,12 @@ $(ibidir)/pkg-config: $(tdir)/pkg-config-$(pkgconfig-version).tar.gz \
 	&& echo "pkg-config $(pkgconfig-version)" > $@
 
 $(ibidir)/sed: $(tdir)/sed-$(sed-version).tar.xz \
-               $(ibidir)/bash
+               $(ibidir)/coreutils
 	$(call gbuild, $<, sed-$(sed-version), static) \
 	&& echo "GNU Sed $(sed-version)" > $@
 
 $(ibidir)/which: $(tdir)/which-$(which-version).tar.gz \
-                 $(ibidir)/bash
+                 $(ibidir)/coreutils
 	$(call gbuild, $<, which-$(which-version), static) \
 	&& echo "GNU Which $(which-version)" > $@
 
@@ -956,7 +988,7 @@ ifeq ($(on_mac_os),yes)
 binutils-prerequisites =
 else
 binutils-prerequisites = $(tdir)/binutils-$(binutils-version).tar.lz \
-                         $(ibidir)/bash
+                         $(ibidir)/coreutils
 endif
 $(ibidir)/binutils: $(binutils-prerequisites)
 	if [ x$(on_mac_os) = xyes ]; then \
@@ -972,13 +1004,6 @@ $(ibidir)/binutils: $(binutils-prerequisites)
 	  && echo "GNU Binutils $(binutils-version)" > $@; \
 	fi
 
-# `file' is not a prerequisite of GCC. However, since it is low level, it is
-# set as a prerequisite of GCC to have it installed.
-$(ibidir)/file: $(tdir)/file-$(file-version).tar.gz \
-                $(ibidir)/bash
-	$(call gbuild, $<, file-$(file-version), static) \
-	&& echo "File $(file-version)" > $@
-
 $(ibidir)/isl: $(tdir)/isl-$(isl-version).tar.bz2 \
                $(ibidir)/gmp
 	$(call gbuild, $<, isl-$(isl-version), static)  \
@@ -1012,14 +1037,12 @@ gcc-prerequisites = $(tdir)/gcc-$(gcc-version).tar.xz \
 endif
 $(ibidir)/gcc: $(gcc-prerequisites) \
                $(ibidir)/sed \
-               $(ibidir)/bash \
                $(ibidir)/file \
                $(ibidir)/gawk \
                $(ibidir)/grep \
                $(ibidir)/which \
                $(ibidir)/glibtool \
                $(ibidir)/binutils \
-               $(ibidir)/coreutils \
                $(ibidir)/diffutils \
                $(ibidir)/findutils
 
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 85120bd..1fd22b2 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -557,7 +557,7 @@ $(ibidir)/cmake: $(tdir)/cmake-$(cmake-version).tar.gz \
 	&& cd cmake-$(cmake-version) \
 	&& ./bootstrap --prefix=$(idir) --system-curl --system-zlib \
 	               --system-bzip2 --system-liblzma --no-qt-gui \
-	&& make LIBS="$$LIBS -lssl -lcrypto -lz" VERBOSE=1 \
+	&& make -j$(numthreads) LIBS="$$LIBS -lssl -lcrypto -lz" VERBOSE=1  \
 	&& make install \
 	&& cd .. \
 	&& rm -rf cmake-$(cmake-version) \