IMPORTANT: software configuration optimized and better modularized

Summary: after merging this commit into your project, it should be
re-configured since the location of software installation files like
'LOCAL.conf' or the LaTeX macros of the software environment have
changed. But it should not affect the analysis phase of your project.

Until this commit, it was not possible to run a pre-built Maneage'd project
(in a container) on a newly cloned Maneage'd project source. This was
because the containers should be read-only, but during the various checks
of the configuration (to verify that we are using the same software
environment in the container and the source), we were writing/testing many
things in the build directory, and 'LOCAL.conf' which was actually in the
source directory!

Furthermore, the '.local' and '.build' were built at configure time, making
it hard to run the same container from a newly cloned Maneage'd project. To
make things harder for the scenario above, the 'configure.sh' script would
pause on every message and didn't have a quiet mode (making it practically
impossible to run './project configure' before './project make' on every
container run).

With this commit, all these issues have been addressed and it is now
possible to simply get a built container, clone a Maneage'd project and run
the analysis (using the built environment of the container that is verified
on every run). The respective changes/additions are described below:

 - The high-level container scripts ('apptainer.sh' and 'docker.sh', along
   with their READMEs) have been moved to the 'reproduce/software/shell'
   directory and the old 'reproduce/software/containers' directory has been
   deleted. This is because we have classified the software files by their
   language/format and the container scripts are scripts in the end.

 - The './project' script:

    - Now has two extra options: '--quiet' and '--no-pause'. Both are
      directly passed to the 'configure.sh' script. They will respectively
      disable any informative printed message or any pause after that
      message (if it is printed).

    - The '--build-dir' option is now also relevant for './project make':
      when it is given, it will re-create the two '.build' and '.local'
      symbolic links at the top source directory in all scenarios
      ('configure', 'make' or 'shell'). This will allow both the
      configuration, analysis and shell phases to safely assume they exist
      and match the user's desire at run-time.

    - The build/analysis directory's sub-directories that need to be built
      before 'top-make.mk' are now built in a separate function to help in
      readability.

 - The 'configure.sh' script:

    - For developers: a new 'check_elapsed' variable has been defined that
      will enable the newly added 'elapsed_time_from_prev_step'
      function. This function should be used from now on at the end of
      every major step to help find bottlenecks.

 - The targets of the software in 'pre-make-build.sh' now also have the
   version of the software in their file name. Until now, they didn't have
   the version, so there was no way to detect if the software has been
   updated or not in the source. For Lzip and Make (that also get built
   after GCC), the ones in this script have a '-pre-make' suffix also.

 - 'Local.conf.in' now has descriptions for every variable.

 - The '-std=gnu17' option is now used instead of '-std=c17' for basic
   software that cannot be built without specifying the C standard in GCC
   15.1 (described in previous commit: 2881fc0a6205). See [1] for more
   details; in summary: '-std=gnu17' is also supported on macOS's Clang and
   has some features that 'pkg-config' needs

 - Generally: some longer code lines have been broken or indentation
   decreased to fit the 75 character line length. This has not reduced
   readability however. For example the long 'echo' commands are now
   replaced by multiple 'printf's, or the indentation is still clearly
   visible.

The seeds of the work on this commit started by a branch containing three
commits by Giacomo Lorenzetti (133 insertions, 100 deletions). Upon merging
with the main 'maneage' branch, they were generalized and re-organized to
become this commit.

The following issues have also been addressed with this commit:

 - The LaTeX calls (during the building of 'paper.pdf') do not contain
   Maneage'd dynamic libraries. This is because we don't build the LaTeX
   binaries from source, an TeXLive manager uses the host environment.

 - The 'docker.sh' script:

    - Adds the '--project-name' option: its internal variable existed, but
      the option for the user to define it at run-time was not.

    - Ported to macOS: it does not check being a member of the 'docker'
      group, and finds the number of threads using macOS-specific tools.

 - The 'apptainer.sh' script:

    - Now installs 'wget' in the base container also (necessary when the
      user doesn't have the tarballs).

[1] https://savannah.nongnu.org/bugs/?67068#comment2

1 files changed, 199 insertions, 128 deletions

diff --git a/project b/project
index c30bfbf..f2986fb 100755
--- a/project
+++ b/project
@@ -33,6 +33,7 @@ set -e
 jobs=0     # 0 is for the default for the 'configure.sh' script.
 group=
 debug=
+quiet=0
 timing=0
 host_cc=0
 offline=
@@ -43,6 +44,7 @@ keep_going=
 check_config=
 make_targets=
 software_dir=
+pauseformsg=1
 clean_texdir=0
 prepare_redo=0
 highlightnew=0
@@ -107,16 +109,18 @@ Project 'make' special tagets
 
 With the options below you can modify the default behavior.
 Configure options:
+      --all-highlevel      Build all high-level software (for development).
   -b, --build-dir=STR      Top directory to build the project in.
-  -e, --existing-conf      Use (possibly existing) local configuration.
-      --host-cc            Use host system's C compiler, don't build GCC.
-  -i, --input-dir=STR      Directory containing input datasets (optional).
-  -s, --software-dir=STR   Directory containing necessary software tarballs.
       --check-config       During configuration, show what is being built.
       --clean-texdir       Remove possibly existing build-time subdirectories
                            under the project's 'tex/' directory (can happen
                            when source is from arXiv for example).
-      --all-highlevel      Build all high-level software (for development).
+  -e, --existing-conf      Use (possibly existing) local configuration.
+  -i, --input-dir=STR      Directory containing input datasets (optional).
+      --host-cc            Use host system's C compiler, don't build GCC.
+      --quiet              Do not print basic info messages (with '-e').
+      --no-pause           Do not sleep/pause after basic info messages.
+  -s, --software-dir=STR   Directory containing necessary software tarballs.
 
 Configure and Make options:
   -d, --debug[=FLAGS]      In configure: use -j1, no -k, and no Zenodo check.
@@ -180,67 +184,71 @@ do
   shell)        func_operation_set $1; shift;;
 
   # Configure options:
-  -b|--build-dir)        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;;
+  -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;;
-  --offline)             offline=1;                                                                        shift;;
+  --offline)             offline=1;                                                                shift;;
   --offline=*)           on_off_option_error --offline;;
-  -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;;
-  -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)        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;;
+  -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;;
   --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;;
+  --no-pause)            pauseformsg=0;                                                            shift;;
+  --no-pause=*)          on_off_option_error --no-pause;;
+  --quiet)               quiet=1;                                                                  shift;;
+  --quiet=*)             on_off_option_error --quiet;;
 
   # Configure and Make options:
-  -g|--group)             group="$2";                            check_v group "$group";   shift;shift;;
-  -g=*|--group=*)         group="${1#*=}";                       check_v group "$group";   shift;;
-  -g*)                    group=$(echo   "$1" | sed -e's/-g//'); check_v group "$group";   shift;;
-  -j|--jobs)              jobs="$2";                             check_v jobs  "$jobs";    shift;shift;;
-  -j=*|--jobs=*)          jobs="${1#*=}";                        check_v jobs  "$jobs";    shift;;
-  -j*)                    jobs=$(echo "$1" | sed -e's/-j//');    check_v jobs  "$jobs";    shift;;
-  -k|--keep-going)        keep_going="--keep-going";                                       shift;;
-  -k=*|--keep-going=*)    on_off_option_error --keep-going -k;;
-  -k*)                    on_off_option_error --keep-going -k;;
-  -'?'|--help)            print_help; exit 0;;
-  -'?'*|--help=*)         on_off_option_error --help -?;;
+  -b|--build-dir)        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;;
+  -g|--group)            group="$2";                                 check_v group "$group";   shift;shift;;
+  -g=*|--group=*)        group="${1#*=}";                            check_v group "$group";   shift;;
+  -g*)                   group=$(echo   "$1" | sed -e's/-g//');      check_v group "$group";   shift;;
+  -j|--jobs)             jobs="$2";                                  check_v jobs  "$jobs";    shift;shift;;
+  -j=*|--jobs=*)         jobs="${1#*=}";                             check_v jobs  "$jobs";    shift;;
+  -j*)                   jobs=$(echo "$1" | sed -e's/-j//');         check_v jobs  "$jobs";    shift;;
+  -k|--keep-going)       keep_going="--keep-going";                                            shift;;
+  -k=*|--keep-going=*)   on_off_option_error --keep-going -k;;
+  -k*)                   on_off_option_error --keep-going -k;;
+  -'?'|--help)           print_help; exit 0;;
+  -'?'*|--help=*)        on_off_option_error --help -?;;
 
   # Make options (analysis):
-  -p|--prepare-redo)      prepare_redo=1;                                                  shift;;
-  -p=*|--prepare-redo=*)  on_off_option_error --prepare-redo;                              shift;;
-  -t|--timing)            timing=1;                                                        shift;;
-  -t=*|--timing=*)        on_off_option_error --timing;                                    shift;;
+  -p|--prepare-redo)     prepare_redo=1;                                                  shift;;
+  -p=*|--prepare-redo=*) on_off_option_error --prepare-redo;                              shift;;
+  -t|--timing)           timing=1;                                                        shift;;
+  -t=*|--timing=*)       on_off_option_error --timing;                                    shift;;
 
   # Make options (final PDF):
-  --refresh-bib)          [ -f tex/src/references.tex ] && touch tex/src/references.tex;   shift;;
-  --highlight-all)        highlightnew=1; highlightnotes=1;                                shift;;
-  --highlight-all=*)      on_off_option_error --highlight-new;;
-  --highlight-new)        highlightnew=1;                                                  shift;;
-  --highlight-new=*)      on_off_option_error --highlight-new;;
-  --highlight-notes)      highlightnotes=1;                                                shift;;
-  --highlight-notes=*)    on_off_option_error --highlight-notes;;
-  -d|--debug)             if [ x$operation = x ]; then
-                              echo "Please set the operation before calling '--debug'"; exit 1
-                          elif [ x$operation = xconfigure ]; then debug=a;   shift;
-                          elif [ x$operation = xmake ]; then
-                              if [ x"$2" = x ]; then
-                                  echo "In make-mode, '--debug' needs a value; see GNU Make manual"; exit 1
-                              else debug="$2"; check_v debug "$debug"; shift;shift; fi
-                          else
-                              echo "Operation '$operation' not recognized, please use 'configure' or 'make'"
-                          fi;;
-  -d=*|--debug=*)         debug="${1#*=}";                       check_v debug "$debug";   shift;;
-  -d*)                    debug=$(echo "$1" | sed -e's/-d//');   check_v debug "$debug";   shift;;
+  --refresh-bib)         [ -f tex/src/references.tex ] && touch tex/src/references.tex;   shift;;
+  --highlight-all)       highlightnew=1; highlightnotes=1;                                shift;;
+  --highlight-all=*)     on_off_option_error --highlight-new;;
+  --highlight-new)       highlightnew=1;                                                  shift;;
+  --highlight-new=*)     on_off_option_error --highlight-new;;
+  --highlight-notes)     highlightnotes=1;                                                shift;;
+  --highlight-notes=*)   on_off_option_error --highlight-notes;;
+  -d|--debug)            if [ x$operation = x ]; then
+                             echo "Please set the operation before calling '--debug'"; exit 1
+                         elif [ x$operation = xconfigure ]; then debug=a;   shift;
+                         elif [ x$operation = xmake ]; then
+                             if [ x"$2" = x ]; then
+                                 echo "In make-mode, '--debug' needs a value; see GNU Make manual"; exit 1
+                             else debug="$2"; check_v debug "$debug"; shift;shift; fi
+                         else
+                             echo "Operation '$operation' not recognized, please use 'configure' or 'make'"
+                         fi;;
+  -d=*|--debug=*)        debug="${1#*=}";                       check_v debug "$debug";   shift;;
+  -d*)                   debug=$(echo "$1" | sed -e's/-d//');   check_v debug "$debug";   shift;;
 
   # Unrecognized option:
   -*) echo "$scriptname: unknown option '$1'"; exit 1;;
@@ -294,8 +302,8 @@ EOF
                 ls $coloropt .build/software/build-tmp || junk=1;
             fi
 
-            # Make the temporary directory, delete its contents, then put new
-            # links of all built software.
+            # Make the temporary directory, delete its contents, then put
+            # new links of all built software.
             if ! [ -d $checkdir ]; then mkdir $checkdir; fi
             rm -f $checkdir/*
 
@@ -316,10 +324,11 @@ EOF
             if [ $printresults = 1 ]; then
                 echo "--- Last 5 packages that were built:"
 
-                # Then sort all the links based on the most recent dates of the
-                # files they link to (with '-L').
+                # Then sort all the links based on the most recent dates of
+                # the files they link to (with '-L').
                 ls -Llt $checkdir  \
-                    | awk '/^-/ && c++<5 {printf "[at %s] %s\n", $(NF-1), $NF}'
+                    | awk '/^-/ && c++<5 {printf "[at %s] %s\n", \
+                                                 $(NF-1), $NF}'
             fi
         else
             cat <<EOF
@@ -343,14 +352,15 @@ fi
 
 
 
-# Basic group settings
-# --------------------
+# Group check
+# -----------
 if ! [ x$group = x ]; then
 
     # Check if group is usable.
     if ! sg "$group" "echo Group \'$group\' exists"; then
-        echo "$scriptname: '$group' is not a usable group name on this system.";
-        echo "(TIP: you can use the 'groups' command to see your groups)"
+        printf "$scriptname: '$group' is not a usable group name on "
+        printf "this system. TIP: you can use the 'groups' command "
+        printf "to see your groups)\n"
         exit 1
     fi
 
@@ -362,9 +372,45 @@ fi
 
 
 
-# Error when configuration isn't run
-configuration_necessary() {
-    cat <<EOF
+# Build directory symbolic links
+# ------------------------------
+#
+# The source directory will contain two symbolic links that point to the
+# build directory:
+
+#   - .build: the top build directory.
+#
+#   - .local: the second to the top software installed directory. They are
+#     used during the configuration phase to simplify commands and are also
+#     very useful during the development of a maneage'd project (to easily
+#     get to the build directory or execut Maneage'd software).
+#
+# This needs to be done on every run because:
+#   - './project configure' can be run with a new build directory, and
+#     keeping the old '.build' conflicts with the new build directory
+#     that the user gave.
+#   - './project make' or './project shell' (within a newly cloned source
+#     directory from inside a container): the links do not exist but have
+#     to be set to the container's build directory.
+#   - This is not an expensive operation.
+if ! [ x"$build_dir" = x ]; then
+    rm -f .build .local
+    ln -s $build_dir .build
+    ln -s $build_dir/software/installed .local
+fi
+
+
+
+
+
+# Function to validate configuration
+# ----------------------------------
+#
+# Check if the configuration is missing/incomplete
+configuration_check() {
+    confdone=software/config/hardware-parameters.tex
+    if ! [ -f .build/$confdone ]; then
+        cat <<EOF
 
 The project is either (1) not configured on this system, or (2) the
 configuration wasn't successful.
@@ -384,15 +430,69 @@ If there was a problem, please let us know by filling this online form:
       http://savannah.nongnu.org/support/?func=additem&group=reproduce
 
 EOF
-    exit 1
+        exit 1
+    fi
 }
 
 
 
 
 
-# Run operations in controlled environment
-# ----------------------------------------
+# Function for TeX Preparations
+# -----------------------------
+#
+# Make sure that the necessary analysis directories directory exist in the
+# build directory. These will be necessary in various phases of hte
+# analysis and having them inside the lower-level Make steps will require
+# setting them as prerequisites for many basic jobs (thus making the
+# Makefiles harder to read and add potentials for bugs: forgetting to add
+# them for example). Also, we don't want the configure phase to make any
+# edits in the analysis directory, so they are not built there.
+tex_preparations () {
+
+    # Extract the location of the build directory.
+    bdir=$(.local/bin/realpath .build)
+
+    # We are using our custom-built 'mkdir' which is guaranteed to have the
+    # '-p' option (that will also build intermediate directories) and won't
+    # complain if the directory already exists.
+    badir=$bdir/analysis
+    texdir=$badir/tex
+    btexdir=$texdir/build
+    tikzdir=$btexdir/tikz
+    mtexdir=$texdir/macros
+    .local/bin/mkdir -p $mtexdir $btexdir $tikzdir
+
+    # If 'tex/build' and 'tex/tikz' are symbolic links then 'rm -f'
+    # will delete them and we can continue. However, when the project
+    # is being built from the tarball (from arXiv for example), these
+    # two are not symbolic links but actual directories with the
+    # necessary built-components to build the PDF in them. In this
+    # case, because 'tex/build' is a directory, 'rm -f' will fail, so
+    # we'll just rename the two directories (as backup) and let the
+    # project build the proper symbolic links afterwards.
+    if rm -f tex/build; then
+        rm -f tex/tikz
+    else
+        mv tex/tikz  tex/tikz-from-tarball
+        mv tex/build tex/build-from-tarball
+    fi
+
+    # Build the symbolic links.
+    if ! [ -L tex/tikz ]; then ln -s "$tikzdir" tex/tikz; fi
+    if ! [ -L tex/build ]; then ln -s "$texdir" tex/build; fi
+}
+
+
+
+
+
+# Function to run in controlled environment
+# -----------------------------------------
+#
+# Controlling the environment is necessary for running the analysis. Like
+# the other funcitons here, this is defined to simplify the high-level code
+# within the 'make)' switch statement.
 perms="u+r,u+w,g+r,g+w,o-r,o-w,o-x"
 controlled_env() {
 
@@ -464,11 +564,13 @@ case $operation in
         # Variables to pass to the configuration script.
         export jobs=$jobs
         export debug=$debug
+        export quiet=$quiet
         export host_cc=$host_cc
         export offline=$offline
         export build_dir=$build_dir
         export input_dir=$input_dir
         export scriptname=$scriptname
+        export pauseformsg=$pauseformsg
         export maneage_group_name=$group
         export software_dir=$software_dir
         export existing_conf=$existing_conf
@@ -488,7 +590,8 @@ case $operation in
             # creates problems when another group member wants to update
             # the software for example. We thus need to manually add the
             # group writing flag to all installed software files.
-            echo "Enabling group writing permission on all installed software..."
+            printf "Enabling group writing permission on all installed "
+            printf "software...\n"
             .local/bin/chmod -R g+w .local/;
         fi
         ;;
@@ -500,43 +603,14 @@ case $operation in
     # Batch execution of the project.
     make)
 
-        # Make sure the configure script has been completed properly
-        # ('configuration-done.txt' exists).
-        if ! [ -f .build/software/configuration-done.txt ]; then
-            configuration_necessary
-        fi
+        # Make sure the configure script is complete and necessary LaTeX
+        # directories are in place.
+        configuration_check
+        tex_preparations
 
-        # Make sure that the necessary analysis directories directory exist
-        # in the build directory. These will be necessary in various phases
-        # of hte analysis and having them inside the lower-level Make steps
-        # will require setting them as prerequisites for many basic jobs
-        # (thus making the Makefiles harder to read and add potentials for
-        # bugs: forgetting to add them for example). Also, we don't want
-        # the configure phase to make any edits in the analysis directory,
-        # so they are not built there.
-        badir=.build/analysis
-        texdir=$badir/tex
-        mtexdir=$texdir/macros
-        if ! [ -d $badir   ]; then mkdir $badir;   fi
-        if ! [ -d $texdir  ]; then mkdir $texdir;  fi
-        if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi
-
-        # TeX build directory. If built in a group scenario, the TeX build
-        # directory must be separate for each member (so they can work on their
-        # relevant parts of the paper without conflicting with each other).
-        if [ "x$maneage_group_name" = x ]; then
-            texbdir="$texdir"/build
-        else
-            user=$(whoami)
-            texbdir="$texdir"/build-$user
-        fi
-        tikzdir="$texbdir"/tikz
-        if ! [ -L tex/build ]; then ln -s "$(pwd -P)/$texdir" tex/build;  fi
-        if ! [ -L tex/tikz  ]; then ln -s "$(pwd -P)/$tikzdir" tex/tikz;  fi
-
-        # Register the start of this run (we are appending the new
-        # information so previous information is preserved until the user
-        # intentionally deletes/cleans it).
+        # Register the start of this run if requested (we are appending the
+        # new information so previous information is preserved until the
+        # user intentionally deletes/cleans it).
         if [ $timing = 1 ]; then echo "start: $(date)" >> timing.txt; fi
 
         # Run data preparation phase (optionally build Makefiles with
@@ -564,36 +638,33 @@ case $operation in
     # Interactive shell of Maneage.
     shell)
 
-        # Make sure the configure script has been completed properly
-        # ('configuration-done.txt' exists).
-        if ! [ -f .build/software/configuration-done.txt ]; then
-            configuration_necessary
-        fi
+        # Make sure the configure script has been completed properly.
+        configuration_check
 
         # Run the project's own shell without inheriting any environment
         # from the host. The 'TERM' environment variable is necessary for
         # tools like some text editors.
-        bdir=`.local/bin/realpath .build`
+        bdir=$(.local/bin/realpath .build)
         instdir="$bdir"/software/installed
         bindir="$bdir"/software/installed/bin
         rcfile=$(pwd)/reproduce/software/shell/bashrc.sh
         .local/bin/env -i \
-                       HOME="$bdir" \
-                       TERM="$TERM" \
-                       PATH="$bindir" \
-                       CCACHE_DISABLE=1 \
-                       PROJECT_STATUS=shell \
-                       SHELL="$bindir"/bash \
-                       COLORTERM="$COLORTERM" \
-                       PROJECT_RCFILE="$rcfile" \
-                       LDFLAGS=-L"$instdir"/lib \
-                       CPPFLAGS=-I"$instdir"/include \
-                       LD_LIBRARY_PATH="$instdir"/lib \
-                       OMPI_MCA_plm_rsh_agent=/bin/false \
-                       PYTHONPATH="$instdir"/lib/python/site-packages \
-                       PYTHONPATH3="$instdir"/lib/python/site-packages \
-                       PS1="[\[\033[01;35m\]maneage@\h \W\[\033[32m\]\[\033[00m\]]$ " \
-                       "$bindir"/bash --noprofile --rcfile "$rcfile"
+            HOME="$bdir" \
+            TERM="$TERM" \
+            PATH="$bindir" \
+            CCACHE_DISABLE=1 \
+            PROJECT_STATUS=shell \
+            SHELL="$bindir"/bash \
+            COLORTERM="$COLORTERM" \
+            PROJECT_RCFILE="$rcfile" \
+            LDFLAGS=-L"$instdir"/lib \
+            CPPFLAGS=-I"$instdir"/include \
+            LD_LIBRARY_PATH="$instdir"/lib \
+            OMPI_MCA_plm_rsh_agent=/bin/false \
+            PYTHONPATH="$instdir"/lib/python/site-packages \
+            PYTHONPATH3="$instdir"/lib/python/site-packages \
+            PS1="[\[\033[01;35m\]maneage@\h \W\[\033[32m\]\[\033[00m\]]$ " \
+            "$bindir"/bash --noprofile --rcfile "$rcfile"
         ;;