Dev lmod support (#36)

Co-authored-by: Ole Osterthun 

* Support Lmod #33 

RWTH switched to a different way of handling modules
Change the way modules are handled, since Lmod supports proper exit codes. 
Therefore use them and get rid of the tmpfile debacle.

* Rework guide for Lmod

Issue #34 asked for support for Lmod.
The reworked guide now explains how to use it. (Hopefully.)

* Testing module script #34

This small script allows to test whether the modules behave like the
script asserts. Mainly that is the correct exit codes when module loading fails.

* Minor Fixes, 
#37 typo in configure
#38 (rm hotfix)
#41 fix xtb link

* Fixes in configure script
Avoid using empty variables in configure
configure did not produce correct warning
moved question to where it belongs #43

* Include deprecation notices for bsub #42

* fix: Allows multithreaded crest #45 and further move quickfix for #45

* there is no need for the srun ommand on a single node; removed it

Author: polyluxus

README.md

@@ -2,7 +2,7 @@
 
 This script provides a wrapper for the
 extended tight-binding semi-empirical program package
-[xtb](https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/xtb/xtb)
+[xtb](https://www.chemie.uni-bonn.de/grimme/de/software/xtb)
 (version 6.0 or later) from Stefan Grimme's group at the University of Bonn
 (contact: xtb{at}thch.uni-bonn.de).
 It is available via [GitHub](https://github.com/grimme-lab/xtb).
@@ -24,7 +24,7 @@ Briefly:
 Obtain the latest version of xtb (and crest) from its
 [GitHub](https://github.com/grimme-lab/xtb/releases/latest) page.
 While you're at it, you might want to pick up crest, too. It is also available at
-[GithUb](https://github.com/crest-lab/crest/releases/latest).
+[GitHub](https://github.com/crest-lab/crest/releases/latest).
 Pick a directory, where you would like to install these packages, e.g.
 a separate user (here: software) and the root directory `/home/software/chemsoft/xtb`.
 Unpack the downloaded xtb archives (this may create a new directory for the downloaded version,
@@ -53,6 +53,16 @@ Alternative options (e.g. `'scriptpath'/.runxtbrc`) are also given.
 After that, the configuration script will ask about creating symbolic links in `~/bin`.
 If you choose to do that, you can basically access the script from anywhere in your file system.
 
+### Using environment modules
+
+This script can interface to environment modules.
+For the developement of this feature, [Lmod](https://lmod.readthedocs.io/) was used.
+
+More details can be found in the guides directory: [guides/module-examples.md](guides/module-examples.md).
+
+To check whether your supplied module system is supported, please find the script
+`test_modules.sh` in the [configure directory](configure) of this repository.
+
 ## Updating
 
 If you decided to clone the repository, make sure to stash your changes,
@@ -92,10 +102,10 @@ The following script options are available:
 | `-o <ARG>`  | Trap the output (without errors) of `xtb` into a file called `<ARG>`. (Default: `auto`)
 | `-s`        | Write a submit script instead of interactive execution (default: PBS). Resulting file needs to be submitted.
 | `-S`        | Write submit script and directly submit it to the queue, requires setting a queueing system with `-Q`.
-| `-Q <ARG>`  | Set a queueing system for which the submit script should be prepared, supported `pbs-gen`, `slurm-gen`, `bsub-gen`.
+| `-Q <ARG>`  | Set a queueing system for which the submit script should be prepared, supported `pbs-gen`, `slurm-gen`, (`bsub-gen`).
 | `-P <ARG>`  | Account to project or account `<ARG>`, only slurm, LSF (bsub).
 | `-M`        | Use pre-installed modules instead of path settings, also needs specified module(s). 
-| `-l <ARG>`  | Specify a module to be used, will also invoke `-M`, may be specified multiple times to create a list, `<ARG>=0` clears the list.
+| `-l <ARG>`  | Specify a module to be used, will also invoke `-M`, may be specified multiple times to create a list, `<ARG>=purge` unloads all modules and `<ARG>=0` clears the list.
 | `-i`        | Execute in interactive mode (default without configuration).
 | `-B <ARG>`  | Set the absolute path to the executable `xtb` to `<ARG>`. The name of the program needs to be included.
 | `-C <ARG>`  | Set the name of the program directly, e.g. to access a different executable like crest (if installed).
@@ -104,6 +114,8 @@ The following script options are available:
 | `-H`        | Retrieve the man page of xtb of the original xtb distribution.
 | `-X`        | Retrieve the man page of xcontrol of the original xtb distribution.
 
+Please note that support for LSF (bsub) is now deprecated and will be removed in a future update.
+
 ## Included files and directories
 
 The following files and/or directories come with this script:
@@ -163,4 +175,4 @@ See [LICENSE](LICENSE) to see the full text.
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-(Martin; 2024-01-07; wrapper version 0.5.0)
+(Martin; 2024-11-02; wrapper version 0.6.0)

VERSION

@@ -1,3 +1,3 @@
 #!/bin/bash
-version="0.5.0"
-versiondate="2024-01-07"
+version="0.6.0"
+versiondate="2024-11-02"

configure/configure.sh

@@ -470,7 +470,7 @@ ask_callname ()
 
 ask_modules ()
 {
-  ask "If a modular cluster management is available, do you want to use it?"
+  ask "If a modular path management is available, do you want to use it?"
   use_module_system=$(read_true_false)
   debug "use_module_system=$use_module_system"
   if [[ "$use_module_system" =~ ^[Tt]([Rr]([Uu]([Ee])?)?)?$ ]] ; then
@@ -482,6 +482,9 @@ ask_modules ()
       # use_module_system="false"
       # warning "Switching the use of modules off."
     fi
+    ask "Would you like to purge pre-loaded modules?"
+    use_purge_modules=$(read_true_false)
+    debug "use_purge_modules=$use_purge_modules"
     # Unsetting read in module
     unset use_module_items
     local module_index=0
@@ -506,6 +509,12 @@ ask_modules ()
   else
     debug "No modules used."
   fi
+  # Avoid empty depending variables
+  if [[ "$use_module_system" =~ ^[Ff]([Aa]([Ll]([Ss][Ee]?)?)?)?$ ]] ; then
+    use_purge_modules="false"
+    debug "use_module_system=$use_module_system"
+    debug "use_purge_modules=$use_purge_modules"
+  fi
 }
 
 ask_interactivity ()
@@ -518,13 +527,13 @@ ask_interactivity ()
     read_boolean && use_interactivity="sub"
     debug "use_interactivity=$use_interactivity"
   fi
-
-  ask "What queueing system would you like to use?"
 }
 
 ask_qsys_details ()
 {
+  ask "What queueing system would you like to use?"
   message "Currently supported: pbs-gen, bsub-gen, slurm-gen, bsub-rwth, slurm-rwth"
+  message "Please note that support for LSF (bsub) is now deprecated and will be removed in a future update."
   local test_queue
   test_queue=$(read_human_input)
   debug "test_queue=$test_queue"
@@ -550,7 +559,8 @@ ask_qsys_details ()
     '' )
       : ;;
     * )
-      [[ -z $use_queue ]] && warning "Unrecognised queueing system ($test_queue)"
+      warning "Unrecognised queueing system ($test_queue)"
+      message "Retaining recovered choice (or empty): $use_queue"
       ;;
   esac
   debug "use_queue=$use_queue"
@@ -747,9 +757,10 @@ print_settings ()
 
   echo     "## Set default queueing system for which the script should be written"
   echo     "## (pbs-gen, bsub-gen, slurm-gen, or *-rwth [special cases, see source])"
+  echo     "## Please note that support for LSF (bsub) is now deprecated and will be removed in a future update."
   echo     "#  "
   if [[ -z $use_queue ]] ; then
-    echo   "#  request_qsys=\"bsub-rwth\""
+    echo   "#  request_qsys=\"pbs-gen\""
   else
     echo   "   request_qsys=\"$use_queue\""
   fi
@@ -773,15 +784,24 @@ print_settings ()
   echo     "#"
   if [[ -z $use_module_system ]] ; then
     echo   "#  use_modules=\"true\""
+    echo   "#"
+    echo   "#  Allow to start fresh by allowing modules to be purged:"
+    echo   "#"
+    echo   "#  purge_modules=\"true\""
+    echo   "#  purge_modules=\"false\""
   else
     echo   "   use_modules=\"$use_module_system\""
+    echo   "#"
+    echo   "#  Allow to start fresh by allowing modules to be purged:"
+    echo   "#"
+    echo   "   purge_modules=\"$use_purge_modules\""
   fi
   echo     "#"
   if (( ${#use_module_items[@]} == 0 )) ; then
     echo   "#  They need to be named, too. For example:"
     echo   "#"
-    echo   "#  load_modules[0]=\"CHEMISTRY\""
-    echo   "#  load_modules[1]=\"xtb\""
+    echo   "#  load_modules[0]=\"xtb\""
+    echo   "#  load_modules[1]=\"CREST\""
   else
     echo   "#  Specified modules to be loaded:"
     echo   "#"

configure/test_modules.sh

@@ -0,0 +1,66 @@
+#!/bin/bash
+
+###
+#
+# This configuration script is part of
+# runxtb.bash --
+#   a repository to set the environment for the xtb program
+# Copyright (C) 2019 - 2024 Martin C Schwarzer
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+###
+
+# This script should be used to test the capabilities of modules
+
+#
+# Messaging functions
+#
+
+message ()
+{
+	local line
+	while read -r line || [[ -n "$line" ]] ; do
+		echo "INFO	 : $line"
+	done <<< "$*"
+}
+
+fatal ()
+{
+	echo "ERROR  : $*" >&2
+	exit 1
+}
+
+#
+# Main
+#
+
+message "This helper script will test whether modules can be used."
+cmd=$(command -v module &> /dev/null) || fatal "Command moule not available."
+message "Modules are $cmd"
+
+version=$(module --version 2>&1)
+message "Available Version: $version"
+
+message "Checking 'module purge'"
+module purge || fatal "Check failed."
+message "Ok."
+
+message "Checking whether exit codes work by loading a module 'designed2fail'."
+message "If this is actually a module on your system, then I'm sorry."
+module load designed2fail &> /dev/null && fatal "Exit status was 0; modules will not work."
+message "Ok."
+
+message "Using modules with this script should work as asserted."
+