flock is now built in configure, to allow serial downloads

Until now, we were using `flock' (file-lock) for downloading the input
datasets in series. But we couldn't do this when downloading the software
tarballs because `flock' wasn't yet available. Generally, unlike
processing, downloading is much better done in series than in parallel.

To enable serial downloads of the software also, with this commit we are
installing `flock' in the configure script (not in a Makefile). As a
result, besides `flock', we can also benefit from the other good features
of the `reproduce/src/bash/download-multi-try' script *(for example
attempting download again after some time).

Some GNU mirrors may have problems at the time of download, so with this
commit, we are using the main GNU FTP server for GNU programs.

6 files changed, 104 insertions, 42 deletions

diff --git a/.file-metadata b/.file-metadata
index 0fec14c..ac0a6cb 100644
--- a/.file-metadata
+++ b/.file-metadata
diff --git a/configure b/configure
index c8e2b63..c34a68a 100755
--- a/configure
+++ b/configure
@@ -418,8 +418,12 @@ if [ $rewritepconfig = yes ]; then
         $pconf.in >> $pconf
 else
     # Read the values from existing configuration file.
-    inbdir=$(awk     '$1=="BDIR"             {print $3}' $pconf)
-    downloader=$(awk '$1=="DOWNLOADER"       {print $3}' $pconf)
+    inbdir=$(awk     '$1=="BDIR"                     {print $3}' $pconf)
+
+    # The downloader command may contain multiple elements, so we'll just
+    # change the (in memory) first and second tokens to empty space and
+    # write the full line (the original file is unchanged).
+    downloader=$(awk '$1=="DOWNLOADER" {$1=""; $2=""; print $0}' $pconf)
 
     # Make sure all necessary variables have a value
     err=0
@@ -676,6 +680,61 @@ fi
 
 
 
+# Build `flock' as first program
+# ------------------------------
+#
+# Flock (or file-lock) is a unique program in the pipeline that is
+# necessary to serialize the (generally parallel) processing of make when
+# necessary. GNU/Linux machines have it as part of their `util-linux'
+# programs. But to be consistent, we will be using our own build.
+#
+# The reason its sepecial is that we need it to serialize the download
+# process of the dependency tarballs.
+flockversion=$(awk '/flock-version/{print $3}' \
+                   reproduce/config/pipeline/dependency-versions.mk)
+flocktar=flock-$flockversion.tar.gz
+flockurl=http://github.com/discoteq/flock/releases/download/v$flockversion/
+
+# Prepare/download the tarball.
+if ! [ -f $tardir/$flocktar ]; then
+    if [ -f $ddir/$flocktar ]; then
+        cp $ddir/$flocktar $tardir/$flocktar
+    else
+        if ! $downloader $tardir/$flocktar $flockurl/$flocktar; then
+            rm -f $tardir/$flocktar;
+            echo
+            echo "DOWNLOAD ERROR: Couldn't download the 'flock' tarball:"
+            echo "  $flockurl"
+            echo
+            echo "You can manually place it in '$ddir' to avoid downloading."
+            exit 1
+        fi
+    fi
+fi
+
+# If the tarball is newer than the (possibly existing) program, then delete
+# the program.
+if [ -f .local/bin/flock ]; then
+    if [ $tardir/$flocktar -nt .local/bin/flock ]; then
+        rm .local/bin/flock
+    fi
+fi
+
+# Build `flock' if necessary.
+if ! [ -f .local/bin/flock ]; then
+    cd $depdir
+    tar xf $tardir/$flocktar
+    cd flock-$flockversion
+    ./configure --prefix=$instdir
+    make; make install
+    cd $topdir
+    rm -rf $depdir/flock-$flockversion
+fi
+
+
+
+
+
 # Build Basic dependencies
 # ------------------------
 #
diff --git a/reproduce/src/bash/download-multi-try b/reproduce/src/bash/download-multi-try
index 1be2ffa..cdeca8e 100755
--- a/reproduce/src/bash/download-multi-try
+++ b/reproduce/src/bash/download-multi-try
@@ -1,11 +1,13 @@
-#!.local/bin/bash
-#
 # Attempt downloading multiple times before crashing whole pipeline. From
 # the top project directory (for the shebang above), this script must be
 # run like this:
 #
 #   $ /path/to/download-multi-try downloader lockfile input-url downloaded-name
 #
+# NOTE: The `downloader' must contain the option to specify the output name
+# in its end. For example "wget -O". Any other option can also be placed in
+# the middle.
+#
 # Due to temporary network problems, a download may fail suddenly, but
 # succeed in a second try a few seconds later. Without this script that
 # temporary glitch in the network will permanently crash the pipeline and
@@ -70,7 +72,7 @@ fi
 
 
 
-# Try downloading multiple times before crashing
+# Try downloading multiple times before crashing.
 counter=0
 maxcounter=10
 while [ ! -f "$outname" ]; do
@@ -97,9 +99,12 @@ while [ ! -f "$outname" ]; do
         sleep $tstep
     fi
 
-    # Attempt downloading the file (one-at-a-time).
+    # Attempt downloading the file (one-at-a-time). Note that the
+    # `downloader' ends with the respective option to specify the output
+    # name. For example "wget -O" (so `outname', that comes after it) will
+    # be the name of the downloaded file.
     flock "$lockfile" bash -c \
-          "if ! $downloader -O$outname $inurl; then rm -f $outname; fi"
+          "if ! $downloader $outname $inurl; then rm -f $outname; fi"
 done
 
 
diff --git a/reproduce/src/make/dependencies-basic.mk b/reproduce/src/make/dependencies-basic.mk
index 2e6caf4..cdb4a8c 100644
--- a/reproduce/src/make/dependencies-basic.mk
+++ b/reproduce/src/make/dependencies-basic.mk
@@ -43,12 +43,13 @@ 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
+lockdir = $(BDIR)/locks
+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
 
 # We'll need the system's PATH for making links to low-level programs we
 # won't be building ourselves.
@@ -94,6 +95,8 @@ all: $(foreach p, $(top-level-programs), $(ibdir)/$(p))
 #
 # However, downloading from this link is slow (because its just a link). So
 # its easier to just keep a with the others.
+$(lockdir): | $(BDIR); mkdir $@
+downloadwrapper = ./reproduce/src/bash/download-multi-try
 tarballs = $(foreach t, bash-$(bash-version).tar.gz                         \
                         binutils-$(binutils-version).tar.lz                 \
                         bzip2-$(bzip2-version).tar.gz                       \
@@ -123,7 +126,7 @@ tarballs = $(foreach t, bash-$(bash-version).tar.gz                         \
                         xz-$(xz-version).tar.gz                             \
                         zlib-$(zlib-version).tar.gz                         \
                       , $(tdir)/$(t) )
-$(tarballs): $(tdir)/%:
+$(tarballs): $(tdir)/%: $(lockdir)
 	if [ -f $(DEPENDENCIES-DIR)/$* ]; then                              \
 	  cp $(DEPENDENCIES-DIR)/$* $@;                                     \
 	else                                                                \
@@ -132,32 +135,32 @@ $(tarballs): $(tdir)/%:
 	               | awk '{print $$1}' );                               \
 	                                                                    \
 	  mergenames=1;                                                     \
-          if   [ $$n = bash      ]; then w=http://ftpmirror.gnu.org/gnu/bash; \
-          elif [ $$n = binutils  ]; then w=http://ftpmirror.gnu.org/gnu/binutils; \
+          if   [ $$n = bash      ]; then w=http://ftp.gnu.org/gnu/bash;     \
+          elif [ $$n = binutils  ]; then w=http://ftp.gnu.org/gnu/binutils; \
           elif [ $$n = bzip      ]; then w=http://akhlaghi.org/src;         \
           elif [ $$n = cert      ]; then w=http://akhlaghi.org/src;         \
-          elif [ $$n = coreutils ]; then w=http://ftpmirror.gnu.org/gnu/coreutils;\
-          elif [ $$n = diffutils ]; then w=http://ftpmirror.gnu.org/gnu/diffutils;\
+          elif [ $$n = coreutils ]; then w=http://ftp.gnu.org/gnu/coreutils;\
+          elif [ $$n = diffutils ]; then w=http://ftp.gnu.org/gnu/diffutils;\
           elif [ $$n = findutils ]; then w=http://akhlaghi.org/src;         \
-          elif [ $$n = gawk      ]; then w=http://ftpmirror.gnu.org/gnu/gawk; \
+          elif [ $$n = gawk      ]; then w=http://ftp.gnu.org/gnu/gawk;     \
           elif [ $$n = gcc       ]; then w=http://ftp.gnu.org/gnu/gcc/gcc-$(gcc-version); \
           elif [ $$n = gmp       ]; then w=https://gmplib.org/download/gmp; \
-          elif [ $$n = grep      ]; then w=http://ftpmirror.gnu.org/gnu/grep; \
-          elif [ $$n = gzip      ]; then w=http://ftpmirror.gnu.org/gnu/gzip; \
+          elif [ $$n = grep      ]; then w=http://ftp.gnu.org/gnu/grep;     \
+          elif [ $$n = gzip      ]; then w=http://ftp.gnu.org/gnu/gzip;     \
           elif [ $$n = isl       ]; then w=ftp://gcc.gnu.org/pub/gcc/infrastructure; \
           elif [ $$n = lzip      ]; then w=http://download.savannah.gnu.org/releases/lzip; \
           elif [ $$n = make      ]; then w=http://akhlaghi.org/src;         \
           elif [ $$n = mpfr      ]; then w=http://www.mpfr.org/mpfr-current;\
-          elif [ $$n = mpc       ]; then w=http://ftpmirror.gnu.org/gnu/mpc;\
-          elif [ $$n = ncurses   ]; then w=http://ftpmirror.gnu.org/gnu/ncurses;\
+          elif [ $$n = mpc       ]; then w=http://ftp.gnu.org/gnu/mpc;      \
+          elif [ $$n = ncurses   ]; then w=http://ftp.gnu.org/gnu/ncurses;  \
           elif [ $$n = openssl   ]; then w=http://www.openssl.org/source;   \
           elif [ $$n = patchelf  ]; then w=http://nixos.org/releases/patchelf/patchelf-$(patchelf-version); \
           elif [ $$n = pkg       ]; then w=http://pkg-config.freedesktop.org/releases; \
-          elif [ $$n = readline  ]; then w=http://ftpmirror.gnu.org/gnu/readline; \
-          elif [ $$n = sed       ]; then w=http://ftpmirror.gnu.org/gnu/sed;\
-          elif [ $$n = tar       ]; then w=http://ftpmirror.gnu.org/gnu/tar;\
-          elif [ $$n = wget      ]; then w=http://ftpmirror.gnu.org/gnu/wget;\
-          elif [ $$n = which     ]; then w=http://ftpmirror.gnu.org/gnu/which;\
+          elif [ $$n = readline  ]; then w=http://ftp.gnu.org/gnu/readline; \
+          elif [ $$n = sed       ]; then w=http://ftp.gnu.org/gnu/sed;      \
+          elif [ $$n = tar       ]; then w=http://ftp.gnu.org/gnu/tar;      \
+          elif [ $$n = wget      ]; then w=http://ftp.gnu.org/gnu/wget;     \
+          elif [ $$n = which     ]; then w=http://ftp.gnu.org/gnu/which;    \
           elif [ $$n = xz        ]; then w=http://tukaani.org/xz;           \
           elif [ $$n = zlib      ]; then w=http://www.zlib.net;             \
           else                                                              \
@@ -178,10 +181,9 @@ $(tarballs): $(tdir)/%:
 	    downloader="$(DOWNLOADER)";                                     \
 	  fi;                                                               \
                                                                             \
-	  if ! $$downloader $@ $$tarballurl; then                           \
-	     rm -f $@;                                                      \
-	     echo; echo "DOWNLOAD FAILED: $$tarballurl"; echo; exit 1;      \
-	  fi;                                                               \
+	  touch $(lockdir)/download;                                        \
+	  $(downloadwrapper) "$$downloader" $(lockdir)/download             \
+	                     $$tarballurl $@;                               \
 	fi
 
 
diff --git a/reproduce/src/make/dependencies.mk b/reproduce/src/make/dependencies.mk
index deb9f39..2b3b70b 100644
--- a/reproduce/src/make/dependencies.mk
+++ b/reproduce/src/make/dependencies.mk
@@ -43,7 +43,7 @@ ildir  = $(BDIR)/dependencies/installed/lib
 ilidir = $(BDIR)/dependencies/installed/lib/built
 
 # Define the top-level programs to build (installed in `.local/bin').
-top-level-programs  = astnoisechisel flock metastore unzip zip
+top-level-programs  = astnoisechisel metastore unzip zip
 top-level-libraries = freetype
 all: $(ddir)/texlive-versions.tex                       \
      $(foreach p, $(top-level-programs), $(ibdir)/$(p)) \
@@ -92,7 +92,6 @@ export LDFLAGS           := $(rpath_command) -L$(ildir)
 tarballs = $(foreach t, cfitsio-$(cfitsio-version).tar.gz                  \
                         cmake-$(cmake-version).tar.gz                      \
                         curl-$(curl-version).tar.gz                        \
-                        flock-$(flock-version).tar.xz                      \
                         freetype-$(freetype-version).tar.gz                \
                         ghostscript-$(ghostscript-version).tar.gz          \
                         git-$(git-version).tar.xz                          \
@@ -132,17 +131,16 @@ $(tarballs): $(tdir)/%:
 	    w=https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio$$v.tar.gz
 	  elif [ $$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 [ $$n = freetype    ]; then w=https://download.savannah.gnu.org/releases/freetype
 	  elif [ $$n = ghostscript ]; then w=https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs926
 	  elif [ $$n = git         ]; then w=http://mirrors.edge.kernel.org/pub/software/scm/git
-	  elif [ $$n = gnuastro    ]; then w=http://ftpmirror.gnu.org/gnu/gnuastro
-	  elif [ $$n = gsl         ]; then w=http://ftpmirror.gnu.org/gnu/gsl
+	  elif [ $$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 = libbsd      ]; then w=http://libbsd.freedesktop.org/releases
 	  elif [ $$n = libpng      ]; then w=https://download.sourceforge.net/libpng
-	  elif [ $$n = libtool     ]; then w=http://ftpmirror.gnu.org/gnu/libtool
+	  elif [ $$n = libtool     ]; then w=http://ftp.gnu.org/gnu/libtool
 	  elif [ $$n = libgit      ]; then
 	    mergenames=0
 	    w=https://github.com/libgit2/libgit2/archive/v$(libgit2-version).tar.gz
@@ -376,9 +374,6 @@ $(ibdir)/glibtool: $(tdir)/libtool-$(libtool-version).tar.xz
 $(ibdir)/gs: $(tdir)/ghostscript-$(ghostscript-version).tar.gz
 	$(call gbuild, $<, ghostscript-$(ghostscript-version))
 
-$(ibdir)/flock: $(tdir)/flock-$(flock-version).tar.xz
-	$(call gbuild, $<, flock-$(flock-version), static)
-
 $(ibdir)/git: $(tdir)/git-$(git-version).tar.xz \
               $(ibdir)/curl
 	$(call gbuild, $<, git-$(git-version), static,             \
diff --git a/reproduce/src/make/download.mk b/reproduce/src/make/download.mk
index a1efde7..036332b 100644
--- a/reproduce/src/make/download.mk
+++ b/reproduce/src/make/download.mk
@@ -69,7 +69,8 @@ $(inputdatasets): $(indir)/%.fits: | $(indir) $(lockdir)
 	  ln -s $(INDIR)/$$origname $@
 	else
 	  touch $(lockdir)/download
-	  $(downloadwrapper) wget $(lockdir)/download $$url/$$origname $@
+	  $(downloadwrapper) "wget --no-use-server-timestamps -O" \
+	                     $(lockdir)/download $$url/$$origname $@
 	fi
 
         # Check the md5 sum to see if this is the proper dataset.