Fixing memory calculation (#24)

- minor issues that arose because there was not enough memory assigned
- empty Environment variables were writing to stderr, now  either
  suppressed, or written as log statement
- update version and dates
- include link to xtb repo

Author: polyluxus

README.md

@@ -6,6 +6,7 @@ extended tight-binding semi-empirical program package
 (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).
 
 It makes it unnecessary to set environment variables like 
 `OMP_NUM_THREADS`, `MKL_NUM_THREADS`, `OMP_STACKSIZE`, and `XTBPATH` globally,
@@ -168,7 +169,7 @@ please include the debug output when submitting a bug report to the
 ## License (GNU General Public License v3.0)
 
 runxtb.bash - a wrapper script for xtb
-Copyright (C) 2019 Martin C Schwarzer
+Copyright (C) 2019 - 2020 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
@@ -185,4 +186,4 @@ 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; 2019-09-10; wrapper version 0.3.1)
+(Martin; 2020-02-27; wrapper version 0.3.2)

VERSION

@@ -1,3 +1,3 @@
 #!/bin/bash
-version="0.3.1"
-versiondate="2019-09-10"
+version="0.3.2"
+versiondate="2020-02-27"

configure/configure.sh

@@ -5,7 +5,7 @@
 # Tis configuration script is part of 
 # runxtb.bash -- 
 #   a repository to set the environment for the xtb program
-# Copyright (C) 2019 Martin C Schwarzer
+# Copyright (C) 2019 - 2020 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

runxtb.sh

@@ -4,7 +4,7 @@
 #
 # runxtb.sh -- 
 #   a wrapper script to apply an environment for xtb
-# Copyright (C) 2019 Martin C Schwarzer
+# Copyright (C) 2019 - 2020  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
@@ -157,7 +157,7 @@ display_howto ()
     fi
   fi
   debug "XTBPATH=$XTBPATH (XTBHOME=$XTBHOME)"
-  debug "$( declare -p MANPATH )"
+  debug "$( declare -p MANPATH 2>&1 )"
 
   message "From version 6.0 onwards there is no HOWTO included, displaying man page instead."
 
@@ -513,7 +513,7 @@ backup_if_exists ()
 write_submit_script ()
 {
     message "Remote mode selected, creating job script instead."
-    # Possible values for queue are pbs-gen bsub-gen bsub-rwth
+    # Possible values for queue are pbs-gen bsub-gen bsub-rwth slurm-gen slurm-rwth
     local queue="$1" queue_short 
     local output_file_local="$2" submitscript_filename
     [[ -z $queue ]] && fatal "No queueing systen selected. Abort."
@@ -531,9 +531,9 @@ write_submit_script ()
     echo "#!/bin/bash" >&9
     echo "# Submission script automatically created with runxtb.sh" >&9
 
-    # Add some overhead
+    # Calculate the correct use of memory, add some overhead
     local corrected_memory
-    corrected_memory=$(( requested_memory + 100 ))
+    corrected_memory=$(( requested_numCPU * requested_memory + 100 ))
 
     # Header is different for the queueing systems
     if [[ "$queue" =~ [Pp][Bb][Ss] ]] ; then
@@ -931,7 +931,9 @@ else
   # Add the manual path, even though we won't need it
   [[ -d "${XTBPATH}/man" ]] && add_to_MANPATH "${XTBPATH}/man"
   export XTBPATH PATH MANPATH
-  debug "$( declare -p XTBPATH PATH MANPATH )"
+  # If for whatever reason one of these variables is unset, then write the error in the debug log, 
+  # instead of writing it directly to the error channel
+  debug "$( declare -p XTBPATH PATH MANPATH 2>&1 )"
 fi
 
 # Check whether we have the right executable