Machine architecture and byte-order available as LaTeX macro

Until now, no machine-related specifications were being documented in the
workflow. This information can become helpful when observing differences in
the outcome of both software and analysis segments of the workflow by
others (some software may behave differently based on host machine).

With this commit, the host machine's 'hardware class' and 'byte-order' are
collected and now available as LaTeX macros for the authors to use in the
paper. Currently it is placed in the acknowledgments, right after
mentioning the Maneage commit.

Furthermore, the project and configuration scripts are now capable of
dealing with input directory names that have SPACE (and other special
characters) by putting them inside double-quotes. However, having spaces
and metacharacters in the address of the build directory could cause
build/install failure for some software source files which are beyond the
control of Maneage. So we now check the user's given build directory
string, and if the string has any '@', '#', '$', '%', '^', '&', '*', '(',
')', '+', ';', and ' ' (SPACE), it will ask the user to provide a different
directory.

6 files changed, 265 insertions, 161 deletions

diff --git a/paper.tex b/paper.tex
index 5367c74..3a2c2f6 100644
--- a/paper.tex
+++ b/paper.tex
@@ -250,19 +250,20 @@ to follow the ``Publication checklist'' of \texttt{README-hacking.md}.
   mentioning the reproducible paper template.}
 
 This project was developed in the reproducible framework of Maneage
-\citep[\emph{Man}aging data lin\emph{eage},][over commit
-  \maneageversion]{maneage}. Maneage has been funded partially by the
-following grants: Japanese Ministry of Education, Culture, Sports, Science,
-and Technology (MEXT) PhD scholarship to M. Akhlaghi and its Grant-in-Aid
-for Scientific Research (21244012, 24253003). The European Research Council
-(ERC) advanced grant 339659-MUSICOS. The European Union (EU) Horizon 2020
-(H2020) research and innovation programmes No 777388 under RDA EU 4.0
-project, and Marie Sk\l{}odowska-Curie grant agreement No 721463 to the
-SUNDIAL ITN. The State Research Agency (AEI) of the Spanish Ministry of
-Science, Innovation and Universities (MCIU) and the European Regional
-Development Fund (ERDF) under the grant AYA2016-76219-P. The IAC project
-P/300724, financed by the MCIU, through the Canary Islands Department of
-Economy, Knowledge and Employment.
+\citep[\emph{Man}aging data lin\emph{eage},][latest Maneage commit of
+  \maneageversion, and built on an {\machinearchitecture} machine with
+                 {\machinebyteorder} byte-order]{maneage}. Maneage has been
+funded partially by the following grants: Japanese Ministry of Education,
+Culture, Sports, Science, and Technology (MEXT) PhD scholarship to
+M. Akhlaghi and its Grant-in-Aid for Scientific Research (21244012,
+24253003). The European Research Council (ERC) advanced grant
+339659-MUSICOS. The European Union (EU) Horizon 2020 (H2020) research and
+innovation programmes No 777388 under RDA EU 4.0 project, and Marie
+Sk\l{}odowska-Curie grant agreement No 721463 to the SUNDIAL ITN. The State
+Research Agency (AEI) of the Spanish Ministry of Science, Innovation and
+Universities (MCIU) and the European Regional Development Fund (ERDF) under
+the grant AYA2016-76219-P. The IAC project P/300724, financed by the MCIU,
+through the Canary Islands Department of Economy, Knowledge and Employment.
 
 %% Tell BibLaTeX to put the bibliography list here.
 \printbibliography
diff --git a/project b/project
index 7368151..29d633d 100755
--- a/project
+++ b/project
@@ -167,27 +167,27 @@ do
 
 
   # Configure options:
-  -b|--builddir)         build_dir="$2";                             check_v "$1" "$build_dir";    shift;shift;;
-  -b=*|--build-dir=*)    build_dir="${1#*=}";                        check_v "$1" "$build_dir";    shift;;
-  -b*)                   build_dir=$(echo    "$1" | sed -e's/-b//'); check_v "$1" "$build_dir";    shift;;
-  -e|--existing-conf)    existing_conf=1;                                                          shift;;
+  -b|--build-dir)        IFS='"' build_dir="$2";                             check_v "$1" "$build_dir";    shift;shift;;
+  -b=*|--build-dir=*)    IFS='"' build_dir="${1#*=}";                        check_v "$1" "$build_dir";    shift;;
+  -b*)                   IFS='"' build_dir=$(echo    "$1" | sed -e's/-b//'); check_v "$1" "$build_dir";    shift;;
+  -e|--existing-conf)    existing_conf=1;                                                                  shift;;
   -e*|--existing-conf=*) on_off_option_error --existing-conf -e;;
-  --host-cc)             host_cc=1;                                                                shift;;
+  --host-cc)             host_cc=1;                                                                        shift;;
   --host-cc=*)           on_off_option_error --host-cc;;
-  -i|--input-dir)        input_dir="$2";                             check_v "$1" "$input_dir";    shift;shift;;
-  -i=*|--input-dir=*)    input_dir="${1#*=}";                        check_v "$1" "$input_dir";    shift;;
-  -i*)                   input_dir=$(echo    "$1" | sed -e's/-i//'); check_v "$1" "$input_dir";    shift;;
-  -m|--minmapsize)       minmapsize="$2";                            check_v "$1" "$minmapsize";   shift;shift;;
-  -m=*|--minmapsize=*)   minmapsize="${1#*=}";                       check_v "$1" "$minmapsize";   shift;;
-  -m*)                   minmapsize=$(echo   "$1" | sed -e's/-m//'); check_v "$1" "$minmapsize";   shift;;
-  -s|--software-dir)     software_dir="$2";                          check_v "$1" "$software_dir"; shift;shift;;
-  -s=*|--software-dir=*) software_dir="${1#*=}";                     check_v "$1" "$software_dir"; shift;;
-  -s*)                   software_dir=$(echo "$1" | sed -e's/-s//'); check_v "$1" "$software_dir"; shift;;
-  --check-config)        check_config=1;                                                           shift;;
+  -i|--input-dir)        IFS='"' input_dir="$2";                             check_v "$1" "$input_dir";    shift;shift;;
+  -i=*|--input-dir=*)    IFS='"' input_dir="${1#*=}";                        check_v "$1" "$input_dir";    shift;;
+  -i*)                   input_dir=$(echo    "$1" | sed -e's/-i//');         check_v "$1" "$input_dir";    shift;;
+  -m|--minmapsize)       minmapsize="$2";                                    check_v "$1" "$minmapsize";   shift;shift;;
+  -m=*|--minmapsize=*)   minmapsize="${1#*=}";                               check_v "$1" "$minmapsize";   shift;;
+  -m*)                   minmapsize=$(echo   "$1" | sed -e's/-m//');         check_v "$1" "$minmapsize";   shift;;
+  -s|--software-dir)     IFS='"' software_dir="$2";                          check_v "$1" "$software_dir"; shift;shift;;
+  -s=*|--software-dir=*) IFS='"' software_dir="${1#*=}";                     check_v "$1" "$software_dir"; shift;;
+  -s*)                   IFS='"' software_dir=$(echo "$1" | sed -e's/-s//'); check_v "$1" "$software_dir"; shift;;
+  --check-config)        check_config=1;                                                                   shift;;
   --check-config=*)      on_off_option_error --check-config;;
-  --clean-texdir)        clean_texdir=1;                                                           shift;;
+  --clean-texdir)        clean_texdir=1;                                                                   shift;;
   --clean-texdir=*)      on_off_option_error --clean-texdir;;
-  --all-highlevel)       all_highlevel=1;                                                          shift;;
+  --all-highlevel)       all_highlevel=1;                                                                  shift;;
   --all-highlevel=*)     on_off_option_error --all-highlevel;;
 
   # Configure and Make options:
@@ -279,7 +279,7 @@ EOF
             check=$(ls .local/version-info/proglib/)
             if ! [ "x$check" = x ]; then
                 printresults=1
-                ln -s $(pwd)/.local/version-info/proglib/* $checkdir/
+                ln -s "$(pwd)"/.local/version-info/proglib/* $checkdir/
             fi
 
             # If something was actually found, then print them.
@@ -304,7 +304,7 @@ EOF
         echo "========================"
 
         # Wait for the next round of checks.
-        sleep 1;
+        sleep 1
     done
     exit 0
 fi
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index e207337..906b4d9 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -47,8 +47,9 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 	@if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" != x ]; then
 
           # Put a LaTeX input command for all the necessary macro files.
+          # 'hardware-parameters.tex' is created in 'configure.sh'.
 	  rm -f $(mtexdir)/project.tex
-	  for t in $(subst paper,,$(makesrc)); do
+	  for t in $(subst paper,,$(makesrc)) hardware-parameters; do
 	    echo "\input{tex/build/macros/$$t.tex}" >> $(mtexdir)/project.tex
 	  done
 	else
@@ -113,7 +114,7 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
           # do not use PGFPlots, then you should remove the `-shell-escape'
           # option for better security. See
           # https://savannah.nongnu.org/task/?15694 for details.
-	  pdflatex -shell-escape -halt-on-error $$p/paper.tex
+	  pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
 	  biber paper
 
 	fi
@@ -142,11 +143,11 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
 	  cd $(texbdir)
           # See above for a warning and brief discussion on the the
           # pdflatex option `-shell-escape'.
-	  pdflatex -shell-escape -halt-on-error $$p/paper.tex
+	  pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
 
           # Come back to the top project directory and copy the built PDF
           # file here.
-	  cd $$p
+	  cd "$$p"
 	  cp $(texbdir)/$@ $(final-paper)
 
 	fi
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 9f434bc..cf9c5a1 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -54,9 +54,9 @@ ibidir  = $(BDIR)/software/installed/version-info/proglib
 # Basic directories (specific to this Makefile).
 il64dir  = $(BDIR)/software/installed/lib64
 iidir    = $(BDIR)/software/installed/include
-shsrcdir = $(shell pwd)/reproduce/software/shell
-dtexdir  = $(shell pwd)/reproduce/software/bibtex
-patchdir = $(shell pwd)/reproduce/software/patches
+shsrcdir = "$(shell pwd)"/reproduce/software/shell
+dtexdir  = "$(shell pwd)"/reproduce/software/bibtex
+patchdir = "$(shell pwd)"/reproduce/software/patches
 itidir   = $(BDIR)/software/installed/version-info/tex
 ictdir   = $(BDIR)/software/installed/version-info/cite
 ipydir   = $(BDIR)/software/installed/version-info/python
@@ -1411,7 +1411,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf
 	tar xf $(tdir)/install-tl-unx.tar.gz
 	cd install-tl-*
 	sed -e's|@installdir[@]|$(idir)|g' \
-	    $$topdir/reproduce/software/config/texlive.conf \
+	    "$$topdir"/reproduce/software/config/texlive.conf \
 	    > texlive.conf
 
         # TeX Live's installation may fail due to any reason. But TeX Live
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index 593b1d9..2b4300b 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -48,7 +48,7 @@ need_gfortran=0
 # --------------------
 #
 # These are defined to help make this script more readable.
-topdir=$(pwd)
+topdir="$(pwd)"
 optionaldir="/optional/path"
 adir=reproduce/analysis/config
 cdir=reproduce/software/config
@@ -96,7 +96,8 @@ create_file_with_notice ()
 # an absolute address. With this function we can make sure of that.
 absolute_dir ()
 {
-    if stat "$1" 1> /dev/null; then
+    address="$1"
+    if stat "$address" 1> /dev/null; then
         echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
     else
         exit 1;
@@ -136,18 +137,18 @@ check_permission ()
 {
     # Make a `junk' file, activate its executable flag and record its
     # permissions generally.
-    local junkfile=$1/check_permission_tmp_file
-    rm -f $junkfile
-    echo "Don't let my short life go to waste" > $junkfile
-    chmod +x $junkfile
-    local perm_before=$(ls -l $junkfile | awk '{print $1}')
+    local junkfile="$1"/check_permission_tmp_file
+    rm -f "$junkfile"
+    echo "Don't let my short life go to waste" > "$junkfile"
+    chmod +x "$junkfile"
+    local perm_before=$(ls -l "$junkfile" | awk '{print $1}')
 
     # Now, remove the executable flag and record the permissions.
-    chmod -x $junkfile
-    local perm_after=$(ls -l $junkfile | awk '{print $1}')
+    chmod -x "$junkfile"
+    local perm_after=$(ls -l "$junkfile" | awk '{print $1}')
 
     # Clean up before leaving the function
-    rm -f $junkfile
+    rm -f "$junkfile"
 
     # If the permissions are equal, the filesystem doesn't allow
     # permissions.
@@ -187,8 +188,8 @@ check_permission ()
 free_space_warning()
 {
     fs_threshold=$1
-    fs_destpath=$2
-    return $(df $fs_destpath \
+    IFS='"' fs_destpath="$2"
+    return $(df "$fs_destpath" \
                 | awk 'FNR==2 {if($4>'$fs_threshold') print 1; \
                                else                   print 0; }')
 }
@@ -224,6 +225,62 @@ fi
 
 
 
+# Collect CPU information
+# -----------------------
+#
+# When the project is built, the type of a machine that built it also has
+# to to be documented. This way, if different results or behaviors are
+# observed in software-related or analysis-related phases of the project,
+# it would be easier to track down the root cause. So far this is just
+# later recorded as a LaTeX macro to be put in the final paper, but it
+# could be used in a more systematic way to optimize/revise project
+# workflow and build.
+hw_class=$(uname -m)
+if [ x$kernelname = xLinux ]; then
+    byte_order=$(lscpu \
+                     | grep 'Byte Order' \
+                     | awk '{ \
+                             for(i=3;i<NF;++i) \
+                             printf "%s ", $i; \
+                             printf "%s", $NF}')
+    address_sizes=$(lscpu \
+                     | grep 'Address sizes' \
+                     | awk '{ \
+                             for(i=3;i<NF;++i) \
+                             printf "%s ", $i; \
+                             printf "%s", $NF}')
+elif [ x$on_mac_os = xyes ]; then
+    hw_byteorder=$(sysctl -n hw.byteorder)
+    if   [ x$hw_byteorder = x1234 ]; then byte_order="Little Endian";
+    elif [ x$hw_byteorder = x4321 ]; then byte_order="Big Endian";
+    fi
+    address_size_physical=$(sysctl -n machdep.cpu.address_bits.phyiscal)
+    address_size_virtual=$(sysctl -n machdep.cpu.address_bits.virtual)
+    address_sizes="$address_size_physical bits physical, "
+    address_sizes+="$address_size_virtual bits virtual"
+else
+    byte_order="unrecognized"
+    address_sizes="unrecognized"
+    cat <<EOF
+______________________________________________________
+!!!!!!!                 WARNING                !!!!!!!
+
+Machine byte order and address sizes could not be recognized. You can add
+the necessary steps in the 'reproduce/software/shell/configure.sh' script
+(just above this error message), or contact us with this web-form:
+
+    https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+    sleep 5
+fi
+
+
+
+
+
 # Check for C/C++ compilers
 # -------------------------
 #
@@ -717,7 +774,7 @@ fi
 
 # Build directory
 # ---------------
-currentdir=$(pwd)
+currentdir="$(pwd)"
 if [ $rewritepconfig = yes ]; then
     cat <<EOF
 
@@ -746,7 +803,7 @@ directory). The build directory cannot be a subdirectory of the source.
 EOF
     bdir=
     junkname=pure-junk-974adfkj38
-    while [ x$bdir = x ]
+    while [ x"$bdir" = x ]
     do
         # Ask the user (if not already set on the command-line).
         if [ x"$build_dir" = x ]; then
@@ -761,31 +818,31 @@ EOF
         fi
 
         # If it exists, see if we can write in it. If not, try making it.
-        if [ -d $build_dir ]; then
-            if mkdir $build_dir/$junkname 2> /dev/null; then
+        if [ -d "$build_dir" ]; then
+            if echo "test" > "$build_dir"/$junkname ; then
+                rm -f "$build_dir"/$junkname
                 instring="the already existing"
-                bdir=$(absolute_dir $build_dir)
-                rm -rf $build_dir/$junkname
+                bdir="$(absolute_dir "$build_dir")"
             else
                 echo " ** Can't write in '$build_dir'";
             fi
         else
-            if mkdir $build_dir 2> /dev/null; then
+            if mkdir "$build_dir" 2> /dev/null; then
                 instring="the newly created"
-                bdir=$(absolute_dir $build_dir)
+                bdir="$(absolute_dir "$build_dir")"
             else
                 echo " ** Can't create '$build_dir'";
             fi
         fi
 
-        # If its given, make sure it isn't a subdirectory of the source
+        # If it is given, make sure it isn't a subdirectory of the source
         # directory.
         if ! [ x"$bdir" = x ]; then
             if echo "$bdir/" \
-                    | grep '^'$currentdir 2> /dev/null > /dev/null; then
+                    | grep '^'"$currentdir" 2> /dev/null > /dev/null; then
 
                 # If it was newly created, it will be empty, so delete it.
-                if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi
+                if ! [ "$(ls -A $bdir)" ]; then rm --dir "$bdir"; fi
 
                 # Inform the user that this is not acceptable and reset `bdir'.
                 bdir=
@@ -793,10 +850,30 @@ EOF
             fi
         fi
 
-	# If everything is fine until now, see if we're able to manipulate
-	# file permissions.
+        # If things are fine so far, make sure it does not contain a space
+        # or other meta-characters which can cause problems during software
+        # building.
+        if ! [ x"$bdir" = x ]; then
+            hasmeta=0;
+            case $bdir in *['!'\@\#\$\%\^\&\*\(\)\+\;\ ]* ) hasmeta=1 ;; esac
+            if [ $hasmeta = 1 ]; then
+
+                # If it was newly created, it will be empty, so delete it.
+                if ! [ "$(ls -A "$bdir")" ]; then rm --dir "$bdir"; fi
+
+                # Inform the user and set 'bdir' to empty again.
+                bdir=
+                echo " ** Build directory should not contain meta-characters"
+                echo " ** (like SPACE, %, \$, !, ;, or parenthesis, among "
+                echo " ** others): they can interrup the build for some software."
+            fi
+        fi
+
+	# If everything is still fine so far, see if we're able to
+	# manipulate file permissions in the directory's filesystem and if
+	# so, see if there is atleast 5GB free space.
 	if ! [ x"$bdir" = x ]; then
-            if ! $(check_permission $bdir); then
+            if ! $(IFS='"' check_permission "$bdir"); then
                 # Unable to handle permissions well
                 bdir=
                 echo " ** File permissions can't be modified in this directory"
@@ -804,7 +881,7 @@ EOF
                 # Able to handle permissions, now check for 5GB free space
                 # in the given partition (note that the number is in units
                 # of 1024 bytes). If this is not the case, print a warning.
-                if $(free_space_warning 5000000 $bdir); then
+                if $(free_space_warning 5000000 "$bdir"); then
                     echo " !! LESS THAN 5GB FREE SPACE IN: $bdir"
                     echo " !! We recommend choosing another partition."
                     echo " !! Build will continue in 5 seconds..."
@@ -817,7 +894,7 @@ EOF
         # reset `build_dir' to blank, so it continues asking for another
         # directory and let the user know that they must select a new
         # directory.
-        if [ x$bdir = x ]; then
+        if [ x"$bdir" = x ]; then
             build_dir=
             echo " ** Please select another directory."
             echo ""
@@ -834,9 +911,9 @@ fi
 # Input directory
 # ---------------
 if [ x"$input_dir" = x ]; then
-    indir=$optionaldir
+    indir="$optionaldir"
 else
-    indir=$input_dir
+    indir="$input_dir"
 fi
 noninteractive_sleep=2
 if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
@@ -878,7 +955,7 @@ EOF
 
     # In case an input-directory is given, write it in 'indir'.
     if [ x$inindir != x ]; then
-        indir=$(absolute_dir $inindir)
+        indir="$(absolute_dir "$inindir")"
         echo " -- Using '$indir'"
     fi
 fi
@@ -922,7 +999,7 @@ EOF
 
     # If given, write the software directory.
     if [ x"$tmpddir" != x ]; then
-        ddir=$(absolute_dir $tmpddir)
+        ddir="$(absolute_dir "$tmpddir")"
         echo " -- Using '$ddir'"
     fi
 fi
@@ -946,11 +1023,18 @@ if [ $rewritepconfig = yes ]; then
         -e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \
         $pconf.in >> $pconf
 else
-    # Read the values from existing configuration file.
-    inbdir=$(awk '$1=="BDIR" {print $3}' $pconf)
-
-    # Read the software directory.
-    ddir=$(awk '$1=="DEPENDENCIES-DIR" {print $3}' $pconf)
+    # Read the values from existing configuration file. Note that the build
+    # directory may have space characters. Even though we currently check
+    # against it, we hope to be able to remove this condition in the
+    # future.
+    inbdir=$(awk '$1=="BDIR" { for(i=3; i<NF; i++) \
+                               printf "%s ", $i; \
+                               printf "%s", $NF }' $pconf)
+
+    # Read the software directory (same as 'inbdir' above about space).
+    ddir=$(awk '$1=="DEPENDENCIES-DIR" { for(i=3; i<NF; i++) \
+                                         printf "%s ", $i; \
+                                         printf "%s", $NF}' $pconf)
 
     # The downloader command may contain multiple elements, so we'll just
     # change the (in memory) first and second tokens to empty space and
@@ -968,9 +1052,9 @@ else
     # Make sure `bdir' is an absolute path and it exists.
     berr=0
     ierr=0
-    bdir=$(absolute_dir $inbdir)
+    bdir="$(absolute_dir "$inbdir")"
 
-    if ! [ -d $bdir  ]; then if ! mkdir $bdir; then berr=1; err=1; fi; fi
+    if ! [ -d "$bdir"  ]; then if ! mkdir "$bdir"; then berr=1; err=1; fi; fi
     if [ $err = 1 ]; then
         cat <<EOF
 
@@ -1013,10 +1097,10 @@ fi
 # (without the user noticing), in the end of this script we make a file and
 # we'll delete it here (at the start). Therefore if the script crashed in
 # the middle that file won't exist.
-sdir=$bdir/software
-finaltarget=$sdir/configuration-done.txt
-if ! [ -d $sdir ];  then mkdir $sdir; fi
-rm -f $finaltarget
+sdir="$bdir"/software
+finaltarget="$sdir"/configuration-done.txt
+if ! [ -d "$sdir" ];  then mkdir "$sdir"; fi
+rm -f "$finaltarget"
 
 
 
@@ -1030,56 +1114,56 @@ rm -f $finaltarget
 # analysis Makefiles (thus making them hard to read), we are just building
 # them here
 # Software tarballs
-tardir=$sdir/tarballs
-if ! [ -d $tardir ];  then mkdir $tardir; fi
+tardir="$sdir"/tarballs
+if ! [ -d "$tardir" ];  then mkdir "$tardir"; fi
 
 # Installed software
-instdir=$sdir/installed
-if ! [ -d $instdir ]; then mkdir $instdir; fi
+instdir="$sdir"/installed
+if ! [ -d "$instdir" ]; then mkdir "$instdir"; fi
 
 # To record software versions and citation.
-verdir=$instdir/version-info
-if ! [ -d $verdir ]; then mkdir $verdir; fi
+verdir="$instdir"/version-info
+if ! [ -d "$verdir" ]; then mkdir "$verdir"; fi
 
 # Program and library versions and citation.
-ibidir=$verdir/proglib
-if ! [ -d $ibidir ]; then mkdir $ibidir; fi
+ibidir="$verdir"/proglib
+if ! [ -d "$ibidir" ]; then mkdir "$ibidir"; fi
 
 # Python module versions and citation.
-ipydir=$verdir/python
-if ! [ -d $ipydir ]; then mkdir $ipydir; fi
+ipydir="$verdir"/python
+if ! [ -d "$ipydir" ]; then mkdir "$ipydir"; fi
 
 # Used software BibTeX entries.
-ictdir=$verdir/cite
-if ! [ -d $ictdir ]; then mkdir $ictdir; fi
+ictdir="$verdir"/cite
+if ! [ -d "$ictdir" ]; then mkdir "$ictdir"; fi
 
 # TeXLive versions.
-itidir=$verdir/tex
-if ! [ -d $itidir ]; then mkdir $itidir; fi
+itidir="$verdir"/tex
+if ! [ -d "$itidir" ]; then mkdir "$itidir"; fi
 
 # Top-level LaTeX.
-texdir=$bdir/tex
-if ! [ -d $texdir ]; then mkdir $texdir; fi
+texdir="$bdir"/tex
+if ! [ -d "$texdir" ]; then mkdir "$texdir"; fi
 
 # LaTeX macros.
-mtexdir=$texdir/macros
-if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi
+mtexdir="$texdir"/macros
+if ! [ -d "$mtexdir" ]; then mkdir "$mtexdir"; fi
 
 
 # TeX build directory. If built in a group scenario, the TeX build
 # directory must be separate for each member (so they can work on their
 # relevant parts of the paper without conflicting with each other).
 if [ "x$reproducible_paper_group_name" = x ]; then
-    texbdir=$texdir/build
+    texbdir="$texdir"/build
 else
     user=$(whoami)
-    texbdir=$texdir/build-$user
+    texbdir="$texdir"/build-$user
 fi
-if ! [ -d $texbdir ]; then mkdir $texbdir; fi
+if ! [ -d "$texbdir" ]; then mkdir "$texbdir"; fi
 
 # TiKZ (for building figures within LaTeX).
-tikzdir=$texbdir/tikz
-if ! [ -d $tikzdir ]; then mkdir $tikzdir; fi
+tikzdir="$texbdir"/tikz
+if ! [ -d "$tikzdir" ]; then mkdir "$tikzdir"; fi
 
 
 # If 'tex/build' and 'tex/tikz' are symbolic links then 'rm -f' will delete
@@ -1107,14 +1191,14 @@ fi
 # safe, we are deleting all the links on each re-configure of the project.
 rm -f .build .local
 
-ln -s $bdir .build
-ln -s $instdir .local
-ln -s $texdir tex/build
-ln -s $tikzdir tex/tikz
+ln -s "$bdir" .build
+ln -s "$instdir" .local
+ln -s "$texdir" tex/build
+ln -s "$tikzdir" tex/tikz
 
 # --------- Delete for no Gnuastro ---------
 rm -f .gnuastro
-ln -s $topdir/reproduce/analysis/config/gnuastro .gnuastro
+ln -s "$topdir"/reproduce/analysis/config/gnuastro .gnuastro
 # ------------------------------------------
 
 
@@ -1130,8 +1214,8 @@ ln -s $topdir/reproduce/analysis/config/gnuastro .gnuastro
 # project names). Maybe later, we can use something like `mktemp' to add
 # random characters to this name and make it unique to every run (even for
 # a single user).
-tmpblddir=$sdir/build-tmp
-rm -rf $tmpblddir/* $tmpblddir  # If its a link, we need to empty its
+tmpblddir="$sdir"/build-tmp
+rm -rf "$tmpblddir"/* "$tmpblddir"  # If its a link, we need to empty its
                                 # contents first, then itself.
 
 # Set the top-level shared memory location.
@@ -1143,12 +1227,12 @@ fi
 # there (in RAM), build a temporary directory for this project.
 needed_space=2000000
 if [ x"$shmdir" != x ]; then
-    available_space=$(df $shmdir | awk 'NR==2{print $4}')
+    available_space=$(df "$shmdir" | awk 'NR==2{print $4}')
     if [ $available_space -gt $needed_space ]; then
         dirname=$(pwd | sed -e's/\// /g' \
                       | awk '{l=NF-1; printf("%s-%s",$l, $NF)}')
-        tbshmdir=$shmdir/"$dirname"-$(whoami)
-        if ! [ -d $tbshmdir ]; then mkdir $tbshmdir; fi
+        tbshmdir="$shmdir"/"$dirname"-$(whoami)
+        if ! [ -d "$tbshmdir" ]; then mkdir "$tbshmdir"; fi
     fi
 else
     tbshmdir=""
@@ -1157,8 +1241,8 @@ fi
 # If a shared memory directory was created set `build-tmp' to be a
 # symbolic link to it. Otherwise, just build the temporary build
 # directory under the project build directory.
-if [ x$tbshmdir = x ]; then mkdir $tmpblddir;
-else                        ln -s $tbshmdir $tmpblddir;
+if [ x"$tbshmdir" = x ]; then mkdir "$tmpblddir";
+else                        ln -s "$tbshmdir" "$tmpblddir";
 fi
 
 
@@ -1527,6 +1611,24 @@ fi
 
 
 
+# Report machine architecture
+# ---------------------------
+#
+# Report hardware
+hwparam="$mtexdir/hardware-parameters.tex"
+
+# Add the text to the ${hwparam} file. Since harware class might include
+# underscore, it must be replaced with '\_', otherwise pdftex would
+# complain and break the build process when doing ./project make.
+hw_class_fixed="$(echo $hw_class | sed -e 's/_/\\_/')"
+.local/bin/echo "\\newcommand{\\machinearchitecture}{$hw_class_fixed}" > $hwparam
+.local/bin/echo "\\newcommand{\\machinebyteorder}{$byte_order}" >> $hwparam
+.local/bin/echo "\\newcommand{\\machineaddresssizes}{$address_sizes}" >> $hwparam
+
+
+
+
+
 # Clean the temporary build directory
 # ---------------------------------
 #
diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh
index 9188fc9..a18966f 100755
--- a/reproduce/software/shell/pre-make-build.sh
+++ b/reproduce/software/shell/pre-make-build.sh
@@ -30,32 +30,32 @@ set -e
 
 
 
-# Input arguments.
-bdir=$1
-ddir=$2
-downloader="$3"
-user_backup_urls="$4"
+# Input arguments (the 'IFS's are to allow space in the name).
+IFS='"' bdir="$1"
+IFS='"' ddir="$2"
+IFS='"' downloader="$3"
+IFS='"' user_backup_urls="$4"
 
 
 
 
 
 # Basic directories/files
-topdir=$(pwd)
-sdir=$bdir/software
-tardir=$sdir/tarballs
-instdir=$sdir/installed
-tmpblddir=$sdir/build-tmp
+topdir="$(pwd)"
+sdir="$bdir"/software
+tardir="$sdir"/tarballs
+instdir="$sdir"/installed
+tmpblddir="$sdir"/build-tmp
 confdir=reproduce/software/config
-ibidir=$instdir/version-info/proglib
+ibidir="$instdir"/version-info/proglib
 downloadwrapper=reproduce/analysis/bash/download-multi-try
 
 # Derived directories
-bindir=$instdir/bin
-urlfile=$confdir/urls.conf
-versionsfile=$confdir/versions.conf
-checksumsfile=$confdir/checksums.conf
-backupfile=$confdir/servers-backup.conf
+bindir="$instdir"/bin
+urlfile="$confdir"/urls.conf
+versionsfile="$confdir"/versions.conf
+checksumsfile="$confdir"/checksums.conf
+backupfile="$confdir"/servers-backup.conf
 
 
 
@@ -87,21 +87,21 @@ done
 # Download the necessary tarball.
 download_tarball() {
   # Basic definitions
-  maneagetar=$tardir/$tarball
+  maneagetar="$tardir"/"$tarball"
 
   # See if the tarball already exists in Maneage.
   if [ -f "$maneagetar" ]; then
     just_a_place_holder=1
   else
-    ucname=$tardir/$tarball.unchecked
+    ucname="$tardir"/"$tarball.unchecked"
 
     # If the URL is empty, use the top backup server
     if [ x$w = x ]; then
         bservers="$backupservers"
-        tarballurl=$topbackupserver/$tarball
+        tarballurl="$topbackupserver"/"$tarball"
     else
         bservers="$backupservers_all"
-        tarballurl=$url/$tarball
+        tarballurl="$url"/"$tarball"
     fi
 
     # See if it is in the input-software directory, if so, make a link, if
@@ -111,19 +111,19 @@ download_tarball() {
     # link and link to an actual file.
     if [ -f "$ddir/$tarball" ]; then
       if type realpath > /dev/null 2> /dev/null; then
-        ln -sf "$(realpath $ddir/$tarball)" "$ucname"
+        ln -sf "$(realpath "$ddir/$tarball")" "$ucname"
       else
-        cp $ddir/$tarball $ucname
+        cp "$ddir/$tarball" "$ucname"
       fi
     else
-      $downloadwrapper "$downloader" nolock $tarballurl $ucname \
+      $downloadwrapper "$downloader" nolock $tarballurl "$ucname" \
                        "$bservers"
     fi
 
     # Make sure this is the correct tarball.
     if type sha512sum > /dev/null 2> /dev/null; then
       checksum=$(sha512sum "$ucname" | awk '{print $1}')
-      expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' $checksumsfile)
+      expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' "$checksumsfile")
       if [ x$checksum = x$expectedchecksum ]; then mv "$ucname" "$maneagetar"
       else
         echo "ERROR: Non-matching checksum: $tarball"
@@ -137,9 +137,9 @@ download_tarball() {
 
   # If the tarball is newer than the (possibly existing) program (the version
   # has changed), then delete the program.
-  if [ -f $ibidir/$progname ]; then
-      if [ $maneagetar -nt $ibidir/$progname ]; then
-          rm $ibidir/$progname
+  if [ -f "$ibidir/$progname" ]; then
+      if [ "$maneagetar" -nt "$ibidir/$progname" ]; then
+          rm "$ibidir/$progname"
       fi
   fi
 }
@@ -151,39 +151,39 @@ download_tarball() {
 # Build the program from the tarball. This function takes one argument
 # which is the configure-time options.
 build_program() {
-  if ! [ -f $ibidir/$progname ]; then
+  if ! [ -f "$ibidir/$progname" ]; then
 
     # Options
     configoptions=$1
 
     # Go into the temporary building directory.
-    cd $tmpblddir
+    cd "$tmpblddir"
     unpackdir="$progname"-"$version"
 
     # Some implementations of 'tar' don't recognize Lzip, so we need to
     # manually call Lzip first, then call tar afterwards.
-    csuffix=$(echo $tarball | sed -e's/\./ /g' | awk '{print $NF}')
-    rm -rf $unpackdir
+    csuffix=$(echo "$tarball" | sed -e's/\./ /g' | awk '{print $NF}')
+    rm -rf "$unpackdir"
     if [ x$csuffix = xlz ]; then
       intarrm=1
-      intar=$(echo $tarball | sed -e's/.lz//')
-      lzip -c -d $tardir/$tarball > $intar
+      intar=$(echo "$tarball" | sed -e's/.lz//')
+      lzip -c -d "$tardir/$tarball" > $intar
     else
       intarrm=0
-      intar=$tardir/$tarball
+      intar="$tardir"/"$tarball"
     fi
 
     # Unpack the tarball and go into it.
-    tar xf $intar
-    if [ x$intarrm = x1 ]; then rm $intar; fi
-    cd $unpackdir
+    tar xf "$intar"
+    if [ x$intarrm = x1 ]; then rm "$intar"; fi
+    cd "$unpackdir"
 
     # build the project, either with Make and either without it.
     if [ x$progname = xlzip ]; then
-        ./configure --build --check --installdir=$instdir/bin $configoptions
+        ./configure --build --check --installdir="$instdir/bin" $configoptions
     else
         # All others accept the configure script.
-        ./configure --prefix=$instdir $configoptions
+        ./configure --prefix="$instdir" $configoptions
 
         # To build GNU Make, we don't want to assume the existance of a
         # Make program, so we use its 'build.sh' script and its own built
@@ -198,9 +198,9 @@ build_program() {
     fi
 
     # Clean up the source directory
-    cd $topdir
-    rm -rf $tmpblddir/$unpackdir
-    echo "$progname_tex $version" > $ibidir/$progname
+    cd "$topdir"
+    rm -rf "$tmpblddir/$unpackdir"
+    echo "$progname_tex $version" > "$ibidir/$progname"
   fi
 }
 
@@ -219,7 +219,7 @@ build_program() {
 progname="lzip"
 progname_tex="Lzip"
 url=$(awk '/^'$progname'-url/{print $3}' $urlfile)
-version=$(awk '/^'$progname'-version/{print $3}' $versionsfile)
+version=$(awk '/^'$progname'-version/{print $3}' "$versionsfile")
 tarball=$progname-$version.tar
 download_tarball
 build_program