Index: palm/trunk/SCRIPTS/palmbuild
===================================================================
--- palm/trunk/SCRIPTS/palmbuild	(revision 2380)
+++ palm/trunk/SCRIPTS/palmbuild	(revision 2380)
@@ -0,0 +1,809 @@
+#!/bin/bash
+
+# palmbuild - script for compiling the PALM code and its utility programs
+
+#------------------------------------------------------------------------------#
+# This file is part of PALM.
+#
+# PALM 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.
+#
+# PALM 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
+# PALM. If not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright 2017  Leibniz Universitaet Hannover
+#------------------------------------------------------------------------------#
+#
+# Current revisions:
+# ------------------
+# Initial revision
+# 
+# Former revisions:
+# -----------------
+# $Id$
+# 
+#------------------------------------------------------------------------------#
+# palmbuild - script for compiling the PALM code and its utility programs
+#
+# Procedure to compile code on local and remote hosts using the
+# make-mechanism. The source code must be provided on the local host.
+#
+# @note This script does not work on MAC OS
+#------------------------------------------------------------------------------#
+
+
+    # VARIABLE DECLARATIONS + DEFAULT VALUES
+ calltime=""
+ column1=""
+ column2=""
+ config_file=.palm.config
+ host=default
+ host_found=false
+ locat=normal
+ makefile=""
+ make_options=""
+ module_commands=""
+ program_name=palm
+ remote_ip=""
+ silent=false
+ ssh_key=""
+ suf=f90
+ version="PALMBUILD  0.1  Rev$Rev: 2316 $"
+ working_directory=`pwd`
+
+
+
+    # ERROR HANDLING
+    # IN CASE OF EXIT:
+ trap 'if [[ $locat != normal ]]
+       then
+          printf "\n\n +++ palmbuild killed \n\n"
+          exit 1
+       else
+          printf "\n\n *** palmbuild finished \n\n"
+          exit 0
+       fi' exit
+
+
+    # IN CASE OF TERMINAL-BREAK:
+ trap 'printf "\n\n +++ palmbuild killed by \"^C\" \n\n"
+       exit
+      ' 2
+
+
+
+    # READ SHELLSCRIPT-OPTIONS
+ while  getopts  :d:h:m:s:S:uv  option
+ do
+   case  $option  in
+       (d)   fname=$OPTARG;;
+       (h)   host=$OPTARG;;
+       (m)   makefile=$OPTARG;;
+       (s)   suf=$OPTARG;;
+       (S)   source_list="$OPTARG";;
+       (v)   silent=true;;
+       (\?)  printf "\n  +++ unknown option $OPTARG \n";
+             locat=parameter; exit;;
+   esac
+ done
+
+
+    # BUILD THE CONFIGURATION-FILE NAME
+ config_file=${config_file}.$host
+
+
+    # CHECK, IF CONFIGURATION-FILE EXISTS
+ if [[ ! -f $config_file ]]
+ then
+    printf "\n  +++ configuration file: "
+    printf "\n           $config_file"
+    printf "\n      does not exist"
+    locat=configuration; exit  
+ fi
+
+
+    # ### is this really required?
+ config_file=$PWD/$config_file
+
+
+    # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
+ while  read line
+ do
+
+       # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
+    eval  line=\"$line\"
+
+
+       # INTERPRET THE LINE
+    if [[ "$(echo $line)" = "" ]]
+    then
+
+          # EMPTY LINE, NO ACTION
+       continue
+
+    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
+    then
+
+          # LINE IS A COMMENT LINE
+       continue
+
+    elif [[ "$(echo $line | cut -c1)"  =  "%" ]]
+    then
+
+          # LINE DEFINES AN ENVIRONMENT-VARIABLE
+       var=`echo $line | cut -d" " -s -f1 | cut -c2-`
+       value=`echo $line | cut -d" " -s -f2-`
+
+          # REPLACE ":" BY " " IN COMPILER- CPP- OR LINKER-OPTIONS,
+          # "::" IS REPLACED BY ":".
+       #value=`echo $value | sed 's/::/%DUM%/g' | sed 's/:/ /g' | sed 's/%DUM%/:/g'`
+
+
+          # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
+          # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
+          # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
+          # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
+          # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
+          # CONFIGURATION-FILE.
+       if [[ "$(eval echo \$$var)" = ""  ||  "$(eval echo \$$var)" = "0" ]]
+       then
+          eval  export  $var="\$value"
+
+             # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
+          if [[ $do_trace = true ]]
+          then
+             printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
+          fi
+       fi
+
+    else
+
+          # SKIP ALL OTHER LINES
+       continue
+
+    fi
+
+ done < $config_file
+
+ 
+    # CHECK SOURCE-CODE PATH
+ if [[ "$source_path" = "" ]]
+ then
+    printf "\n  +++ no source path found in configuration file"
+    locat=config_file; exit
+ else
+    if [[ ! -d $source_path ]]
+    then
+       printf "\n\n  +++ source path \"$source_path\" "
+       printf "\n      does not exist"
+       locat=source_path; exit
+    fi
+ fi
+
+
+    # CHECK DEPOSITORY-PATH
+ if [[ "$depository_path" = "" ]]
+ then
+    printf "\n  +++ no depository path found in configuration file"
+    locat=config_file; exit
+ fi
+
+
+    # CHECK MAKEFILE
+ [[ "$makefile" = "" ]]  &&  makefile=$source_path/Makefile
+ if [[ ! -f $makefile ]]
+ then
+    printf "\n  +++ makefile: "
+    printf "\n           $makefile"
+    printf "\n      does not exist"
+    locat=makefile; exit  
+ fi
+
+
+    # CHECK COMPILERNAME
+ if [[ "$compiler_name" = "" ]]
+ then
+    printf "\n  +++ no compiler name found in configuration file"
+    locat=config_file; exit
+ fi
+
+
+    # CHECK SERIAL COMPILERNAME
+ if [[ "$compiler_name_ser" = "" ]]
+ then
+    printf "\n  +++ no compiler name for serial compilation in configuration file"
+    locat=config_file; exit
+ fi
+
+
+    # DETERMINE SSH-KEY TO BE USED
+ if [[ "$ssh_key" != "" ]]
+ then
+    ssh_key="-i $HOME/.ssh/`echo $line | cut -d" " -s -f2`"
+ fi
+
+
+    #CHECK CPP-OPTIONS
+ if [[ "$cpp_options" = "" ]]
+ then
+    printf "\n  +++ WARNING: no cpp-options found in configuration file"
+ fi
+
+
+    # CHECK SETTINGS IN CASE OF COMPILING ON REMOTE MACHINE
+ if [[ "$remote_ip" != "" ]]
+ then
+ 
+    if [[ "$remote_username" = "" ]]
+    then
+       printf "\n  +++ no user name given in configuration file"
+       locat=config_file; exit
+    fi
+
+    [[ "$remote_hostname" = "" ]]  &&  remote_hostname=$remote_ip 
+
+       # GET SOURCE AND DEPOSITORY PATH ON THE REMOTE MACHINE WITHOUT EVALUATING
+       # THE $
+       # IF NOT GIVEN, USE THE LOCAL SOURCE AND DEPOSITORY PATH
+    line=`grep %remote_source_path $config_file`
+    if [[ "$line" != "" ]]
+    then
+       remote_source_path=`echo $line | cut -d" " -s -f2`
+    else
+       line=`grep %source_path $config_file`
+       remote_source_path=`echo $line | cut -d" " -s -f2`
+    fi
+
+    line=`grep %remote_depository_path $config_file`
+    if [[ "$line" != "" ]]
+    then
+       remote_depository_path=`echo $line | cut -d" " -s -f2`
+    else
+       line=`grep %depository_path $config_file`
+       remote_depository_path=`echo $line | cut -d" " -s -f2`
+    fi
+
+    remote_make_depository=${remote_depository_path}/MAKE_DEPOSITORY_${host}
+
+ else
+
+    local_make_depository=${depository_path}/MAKE_DEPOSITORY_${host}
+
+ fi
+
+    # HEADER-OUTPUT (PART1: MESSAGES CONCERNING THE LOCAL HOST)
+ calltime=$(date)
+ printf "\n"
+ printf "#------------------------------------------------------------------------# \n"
+ printf "| %-40s%30s | \n" "$version" "$calltime"
+ printf "|                                                                        | \n"
+ printf "| %-13s%-57s | \n" "called on:" "$local_hostname"
+ column2=$(echo $config_file | cut -c1-57 )
+ printf "| %-13s%-57s | \n" "config file:" "$column2"
+ line=$(echo "$config_file" | cut -c58-)
+ while [[ "$line" != "" ]]
+ do
+    column1=""
+    column2=$(echo $line | cut -c1-57 )
+    printf "| %-13s%-57s | \n" "$column1" "$column2"
+    line=$(echo "$line" | cut -c58-)
+ done
+ column2=$(echo $makefile | cut -c1-57 )
+ printf "| %-13s%-57s | \n" "makefile:" "$column2"
+ line=$(echo "$makefile" | cut -c58-)
+ while [[ "$line" != "" ]]
+ do
+    column1=""
+    column2=$(echo $line | cut -c1-57 )
+    printf "| %-13s%-57s | \n" "$column1" "$column2"
+    line=$(echo "$line" | cut -c58-)
+ done
+ column2=$(echo $source_path | cut -c1-57 )
+ printf "| %-13s%-57s | \n" "source path:" "$column2"
+ line=$(echo "$source_path" | cut -c58-)
+ while [[ "$line" != "" ]]
+ do
+    column1=""
+    column2=$(echo $line | cut -c1-57 )
+    printf "| %-13s%-57s | \n" "$column1" "$column2"
+    line=$(echo "$line" | cut -c58-)
+ done
+ printf "#------------------------------------------------------------------------# \n"
+
+
+
+    # TAR THE SOURCES AND MAKEFILES
+    # UTILITIES ARE TEMPORARILY COPIED TO THE SOURCE DIRECTORY IN ORDER TO TAR
+    # THEM TOO
+ cd  $source_path
+ printf "\n\n  *** tar of makefile and source files in"
+ printf "\n      $source_path"
+ cp -p  ../UTIL/combine_plot_fields.f90  .
+ cp -p  ../UTIL/compare_palm_logs.f90  .
+ cp -p  ../UTIL/Makefile_utilities  .
+ tar -cf  ${program_name}_sources.tar  Makefile*  *.$suf
+ rm  combine_plot_fields.f90  compare_palm_logs.f90  Makefile_utilities
+ printf "\n"
+
+
+
+    # GET CONFIRMATION TO CONTINUE
+ printf "\n  *** update will be made for host \"$host\" "
+
+
+ if [[ $silent = false ]]
+ then
+    answer=dummy
+    printf "\n\n"
+    while [[ "$answer" != y  &&  "$answer" != Y  &&  "$answer" != n  &&  "$answer" != N ]]
+    do
+       printf " >>> continue (y/n) ?  "
+       read  answer
+    done
+    if [[ $answer = n  ||  $answer = N ]]
+    then
+       locat=user_abort; exit
+    fi
+ fi
+
+
+
+
+    printf "\n\n#------------------------------------------------------------------------# \n"
+
+    if [[ "$remote_ip" != "" ]]
+    then
+       column2=$remote_hostname
+       printf "| %-20s%-50s | \n" "remote host:" "$column2"
+       printf "|                                                                        | \n"
+       column2=$(echo "$remote_make_depository" | cut -c1-50 )
+       printf "| %-20s%-50s | \n" "remote depository:" "$column2"
+       line=$(echo "$remote_make_depository" | cut -c51-)
+       while [[ "$line" != "" ]]
+       do
+          column1=""
+          column2=$(echo "$line" | cut -c1-50 )
+          printf "| %-20s%-50s | \n" "$column1" "$column2"
+          line=$(echo "$line" | cut -c51-)
+       done
+    else
+       column2=$local_hostname
+       printf "| %-20s%-50s | \n" "local host:" "$column2"
+       printf "|                                                                        | \n"
+       column2=$(echo "$local_make_depository" | cut -c1-50 )
+       printf "| %-20s%-50s | \n" "local depository:" "$column2"
+       line=$(echo "$local_make_depository" | cut -c51-)
+       while [[ "$line" != "" ]]
+       do
+          column1=""
+          column2=$(echo "$line" | cut -c1-50 )
+          printf "| %-20s%-50s | \n" "$column1" "$column2"
+          line=$(echo "$line" | cut -c51-)
+       done
+    fi
+
+    if [[ "$remote_ip" != "" ]]
+    then
+       printf "| %-20s%-50s | \n" "remote username:" "$remote_username"
+       printf "| %-20s%-50s | \n" "remote address:" "$remote_ip"
+    else
+       printf "| %-20s%-50s | \n" "username:" "$local_username"
+       printf "| %-20s%-50s | \n" "address:" "$local_ip"
+    fi
+
+    printf "| %-20s%-50s | \n" "compiler:" "$compiler_name"
+    printf "| %-20s%-50s | \n" "serial compiler:" "$compiler_name_ser"
+
+    if [[ "$make_options" != "" ]]
+    then
+       printf "| %-20s%-50s | \n" "make options:" "$make_options"
+    fi
+    column2=$(echo "$cpp_options" | cut -c1-50 )
+    printf "| %-20s%-50s | \n" "cpp options:" "$column2"
+    line=$(echo "$cpp_options" | cut -c51-)
+    while [[ "$line" != "" ]]
+    do
+       column1=""
+       column2=$(echo "$line" | cut -c1-50 )
+       printf "| %-20s%-50s | \n" "$column1" "$column2"
+       line=$(echo "$line" | cut -c51-)
+    done
+    column2=$(echo "$compiler_options" | cut -c1-50 )
+    printf "| %-20s%-50s | \n" "compiler options:" "$column2"
+    line=$(echo "$compiler_options" | cut -c51-)
+    while [[ "$line" != "" ]]
+    do
+       column1=""
+       column2=$(echo "$line" | cut -c1-50 )
+       printf "| %-20s%-50s | \n" "$column1" "$column2"
+       line=$(echo "$line" | cut -c51-)
+    done
+    column2=$(echo "$loader_options" | cut -c1-50 )
+    printf "| %-20s%-50s | \n" "loader options:" "$column2"
+    line=$(echo "$loader_options" | cut -c51-)
+    while [[ "$line" != "" ]]
+    do
+       column1=""
+       column2=$(echo "$line" | cut -c1-50 )
+       printf "| %-20s%-50s | \n" "$column1" "$column2"
+       line=$(echo "$line" | cut -c51-)
+    done
+    if [[ "$login_init_cmd" != "" ]]
+    then
+       column2=$(echo "$login_init_cmd" | cut -c1-50 )
+       printf "| %-20s%-50s | \n" "login init command:" "$column2"
+       line=$(echo "$login_init_cmd" | cut -c51-)
+       while [[ "$line" != "" ]]
+       do
+          column1=""
+          column2=$(echo "$line" | cut -c1-50 )
+          printf "| %-20s%-50s | \n" "$column1" "$column2"
+          line=$(echo "$line" | cut -c51-)
+       done
+    fi
+    if [[ "$module_commands" != "" ]]
+    then
+       column2=$(echo "$module_commands" | cut -c1-50 )
+       printf "| %-20s%-50s | \n" "module command(s):" "$column2"
+       line=$(echo "$module_commands" | cut -c51-)
+       while [[ "$line" != "" ]]
+       do
+          column1=""
+          column2=$(echo "$line" | cut -c1-50 )
+          printf "| %-20s%-50s | \n" "$column1" "$column2"
+          line=$(echo "$line" | cut -c51-)
+       done
+    fi
+    printf "#------------------------------------------------------------------------# \n"
+
+    if [[ $silent = false ]]
+    then
+       answer=dummy
+       printf "\n\n"
+       while [[ "$answer" != y  &&  "$answer" != Y  && "$answer" != c  &&  "$answer" != C  && "$answer" != s  &&  "$answer" != S  &&  "$answer" != a  &&  "$answer" != A ]]
+       do
+          printf " >>> continue (y(es)/c(ontinue)/a(bort)/s(skip)) ?  "
+          read  answer
+       done
+       if [[ $answer = a  ||  $answer = A ]]
+       then
+          locat=user_abort; exit
+       fi
+       if [[ $answer = c  ||  $answer = C ]]
+       then
+          silent=true
+       fi
+       if [[ $answer = s  ||  $answer = S ]]
+       then
+          continue
+       fi
+    fi
+
+
+       # MAKE ON REMOTE HOST
+    if [[ "$remote_ip" != "" ]]
+    then
+
+          # NEXT IS THE BRANCH FOR CREATING THE MAKE_DEPOSITORY_...
+       if [[ "$fname" = "" ]]
+       then
+
+             # COPY CURRENT SOURCE CODE TO SOURCE-CODE DIRECTORY ON THE REMOTE HOST
+             # CREATE THIS DIRECTORY, IF IT DOES NOT EXIST
+          echo "  *** copying \"${program_name}_sources.tar\" to \"${remote_ip}:${remote_make_depository}/\" "
+          echo "[[ ! -d ${remote_make_depository} ]]  &&  (echo \"  *** ${remote_make_depository} will be created\"; mkdir -p  ${remote_make_depository})"  |  ssh  -q  $ssh_key ${remote_username}@${remote_ip}  2>&1
+
+          scp  $ssh_key ${source_path}/${program_name}_sources.tar  ${remote_username}@${remote_ip}:${remote_make_depository}/${program_name}_sources.tar
+
+
+
+             # UNTAR PREVIOUS UPDATE ON REMOTE HOST, IF EXISTING
+          echo "  *** untar previous update on remote host, if existing"
+          echo "cd ${remote_make_depository}; [[ -f ${program_name}_current_version.tar ]]  &&  tar -xf  ${program_name}_current_version.tar"  |  ssh  -q  $ssh_key  ${remote_username}@${remote_ip}  2>&1
+
+
+             # UNTAR CURRENT SOURCES ON REMOTE HOST
+          echo "  *** untar current sources on remote host"
+          echo  "cd ${remote_make_depository}; tar -xf  ${program_name}_sources.tar"  |  ssh  -q  $ssh_key  ${remote_username}@${remote_ip}  2>&1
+
+
+             # CREATE INIT AND MODULE COAMMNDS
+          [[ "$login_init_cmd" != "" ]]   &&  login_init_cmd=${login_init_cmd}";"
+          [[ "$module_commands" != "" ]]  &&  module_commands=${module_commands}";"
+
+
+             # FIRST CREATE EXECUTABLES FOR THE UTILITY ROUTINES
+          echo " "
+          echo "  *** creating utilities on remote host"
+          make_call_string="make  -f Makefile_utilities  $make_options  F90=$compiler_name  F90_SER=$compiler_name_ser  COPT=\"$cpp_options\"  F90FLAGS=\"$compiler_options\"  LDFLAGS=\"$loader_options\" "
+          echo "$login_init_cmd $module_commands cd ${remote_make_depository}; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  -q  $ssh_key  ${remote_username}@${remote_ip} 2>&1 | tee ${remote_hostname}_last_make_protokoll
+
+          if [[ $(grep -c MAKE_ERROR ${remote_hostname}_last_make_protokoll) != 0 ]]
+          then
+             printf "\a\n  +++ error(s) occurred during compiling or linking of utilities"
+             printf "\n      on host \"$remote_hostname\" "
+             if [[ $silent = false ]]
+             then
+                answer=dummy
+                printf "\n"
+                while [[ "$answer" != c  &&  "$answer" != k ]]
+                do
+                   printf "  >>> continue / list errors / kill palmbuild (c/l/k) ? "
+                   read  answer
+                   if [[ "$answer" = l ]]
+                   then
+                      more ${remote_hostname}_last_make_protokoll
+                   fi
+                done
+                if [[ $answer = k ]]
+                then
+                   locat=user_abort; exit
+                fi
+             fi
+          fi
+
+
+             # NOW COMPILE THE PALM CODE
+             # COMMANDS WILL BE COMMUNICATED TO SSH VIA PIPE, SINCE THIS WAY THE SYSTEM- AND
+             # USER-PROFILES OF THE SHELL ARE COMPLETELY EXECUTED (OTHERWISE, MAKE
+             # MAY E.G. MISS THE COMPILER-PATHS)
+          echo " "
+          echo "  *** compile PALM sources on remote host"
+          make_call_string="make  $make_options  PROG=$program_name  F90=$compiler_name  COPT=\"$cpp_options\"  F90FLAGS=\"$compiler_options\"  LDFLAGS=\"$loader_options\" "
+          echo "$login_init_cmd $module_commands cd ${remote_make_depository}; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  -q  $ssh_key  ${remote_username}@${remote_ip} 2>&1 | tee ${remote_hostname}_last_make_protokoll
+
+          if [[ $(grep -c MAKE_ERROR ${remote_hostname}_last_make_protokoll) != 0 ]]
+          then
+             printf "\a\n  +++ error(s) occurred during compiling or linking on host \"$remote_hostname\" "
+             if [[ $silent = false ]]
+             then
+                answer=dummy
+                printf "\n"
+                while [[ "$answer" != c  &&  "$answer" != k ]]
+                do
+                   printf "  >>> continue / list errors / kill palmbuild (c/l/k) ? "
+                   read  answer
+                   if [[ "$answer" = l ]]
+                   then
+                      more ${remote_hostname}_last_make_protokoll
+                   fi
+                done
+                if [[ $answer = k ]]
+                then
+                   locat=user_abort; exit
+                fi
+             fi
+          fi
+
+             # TAR UPDATED VERSION ON THE REMOTE HOST
+          printf "\n  *** tar update on remote host ..."
+          echo  "cd ${remote_make_depository}; chmod u+w *; tar -cf  ${program_name}_current_version.tar  ${program_name}  *.f90 *.o *.mod *.x"  |  ssh  -q  $ssh_key  ${remote_username}@${remote_ip}  2>&1
+
+
+          # NOW COMES THE BRANCH FOR CREATING THE EXECUTABLE FOR THE CURRENT RUN
+          # INCLUDING E.G. USER-INTERFACE ROUTINES. ALSO ADD OTHER UTILITY EXECUTABLES. EVERYTHING IS
+          # COLLECTED IN DIRECTORY SOURCES_FOR_RUN_...
+       elif [[ "$fname" != "" ]]
+       then
+
+             # FIRST CHECK, IF A DEPOSITORY EXISTS ON THE REMOTE MACHINE
+          echo  "[[ ! -d ${remote_make_depository} ]]  &&  echo depository not found" | ssh  -q  $ssh_key  ${remote_username}@${remote_ip} 2>&1 | tee ${remote_hostname}_last_make_protokoll
+
+
+             # COPY MAKE DEPOSITORY ON REMOTE MACHINE TO SOURCES_FOR_RUN_...
+          printf "\n  *** copy MAKE_DEPOSITORY on remote host to SOURCES_FOR_RUN_$fname \n"
+          echo  "rm -rf $tmp_user_catalog/SOURCES_FOR_RUN_$fname; mkdir $tmp_user_catalog/SOURCES_FOR_RUN_$fname; cp ${remote_make_depository}/${program_name}_current_version.tar  $tmp_user_catalog/SOURCES_FOR_RUN_$fname; cd $tmp_user_catalog/SOURCES_FOR_RUN_$fname; tar xf ${program_name}_current_version.tar"  |  ssh  -q  $ssh_key  ${remote_username}@${remote_ip}  2>&1
+
+
+             # COPY CONTENTS OF SOURCES_FOR_RUN_... TO SOURCES_FOR_RUN_... ON THE REMOTE MACHINE
+          printf "\n  *** copy $base_directory/SOURCES_FOR_RUN_$fname to SOURCES_FOR_RUN_$fname on remote host \n"
+          scp  -q  $ssh_key  $base_directory/SOURCES_FOR_RUN_$fname/{*,.[!.]*}  ${remote_username}@${remote_ip}:${tmp_user_catalog}/SOURCES_FOR_RUN_$fname
+
+
+             # CREATE EXECUTABLE FROM THE NEW/MODIFIED SOURCE FILES, IF THERE ARE ANY
+          if [[ $(ls -1 $base_directory/SOURCES_FOR_RUN_$fname/ | grep -c .$suf) != 0 ]]
+          then
+
+             make_call_string="make  $make_options  PROG=$program_name  F90=$compiler_name  COPT=\"$cpp_options\"  F90FLAGS=\"$compiler_options\"  LDFLAGS=\"$loader_options\" "
+             [[ "$login_init_cmd" != "" ]]   &&  login_init_cmd=${login_init_cmd}";"
+             [[ "$module_commands" != "" ]]  &&  module_commands=${module_commands}";"
+             echo "  *** execute \"make\" on remote host"
+             echo "$login_init_cmd $module_commands cd ${tmp_user_catalog}/SOURCES_FOR_RUN_$fname; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  -q  $ssh_key  ${remote_username}@${remote_ip} 2>&1 | tee ${remote_hostname}_last_make_protokoll
+
+             if [[ $(grep -c MAKE_ERROR ${remote_hostname}_last_make_protokoll) != 0 ]]
+             then
+                printf "\a\n  +++ error(s) occurred during compiling or linking on host \"$remote_hostname\" "
+                if [[ $silent = false ]]
+                then
+                   answer=dummy
+                   printf "\n"
+                   while [[ "$answer" != c  &&  "$answer" != k ]]
+                   do
+                      printf "  >>> continue / list errors / kill palmbuild (c/l/k) ? "
+                      read  answer
+                      if [[ "$answer" = l ]]
+                      then
+                         more ${remote_hostname}_last_make_protokoll
+                      fi
+                   done
+                   if [[ $answer = k ]]
+                   then
+                      locat=user_abort; exit
+                   fi
+                fi
+             fi
+
+          else
+
+             echo "  *** nothing to compile for this run"
+
+          fi
+
+       fi
+
+       rm -rf  ${remote_hostname}_last_make_protokoll
+
+
+       # MAKE ON LOCAL HOST
+    else
+
+
+          # NEXT IS THE BRANCH FOR CREATING THE MAKE_DEPOSITORY_... ON THE
+          # LOCAL HOST
+       if [[ "$fname" = "" ]]
+       then
+
+             # SET THE ENVIRONMENT (EXECUTE INIT AND MODULE COMMANDS)
+          if [[ "$login_init_cmd" != "" ]]
+          then
+             $login_init_cmd
+          fi
+
+          if [[ "$module_commands" != "" ]]
+          then
+             $module_commands
+          fi
+
+
+             # CREATE MAKE-DEPOSITORY, IF IT DOES NOT EXIST
+          eval local_make_depository=$local_make_depository
+          if [[ ! -d $local_make_depository ]]
+          then
+             if  mkdir $local_make_depository
+             then
+                printf "\n\n  *** directory for local make depository:"
+                printf "\n           $local_make_depository"
+                printf "\n      was created\n"
+             else
+                printf "\n  +++ directory for local make depository:"
+                printf "\n           $local_make_depository"
+                printf "\n      cannot be created"
+                locat=local_depository_path; exit
+             fi
+          fi
+
+             # COPY SOURCE-CODE FROM REPOSITORY TO MAKE-DEPOSITORY
+          echo " "
+          echo "  *** untar current source sources on local host in"
+          echo "      $local_make_depository"
+          cd  $local_make_depository
+          cp  $source_path/${program_name}_sources.tar  .
+          tar xf  ${program_name}_sources.tar
+
+
+             # FIRST CREATE EXECUTABLES FOR THE UTILITY ROUTINES
+          echo " "
+          echo "  *** creating utilities on local host"
+          make  -f Makefile_utilities  $make_options  F90=$compiler_name  F90_SER=$compiler_name_ser  COPT="$cpp_options"  F90FLAGS="$compiler_options"  LDFLAGS="$loader_options"
+
+
+             # CALL MAKE ON LOCAL HOST USING THE  OPTIONS DETERMINED FURTHER ABOVE
+          echo " "
+          echo "  *** compile PALM sources on local host"
+
+          make  $make_options  PROG=$program_name  F90=$compiler_name  COPT="$cpp_options"  F90FLAGS="$compiler_options"  LDFLAGS="$loader_options"  2>&1 | tee ${local_hostname}_last_make_protokoll
+
+          if [[ $? != 0 ]]
+          then
+             printf "\a\n  +++ error(s) occurred during compiling or linking on host \"$local_hostname\" "
+             if [[ $silent = false ]]
+             then
+                answer=dummy
+                printf "\n"
+                while [[ "$answer" != c  &&  "$answer" != k ]]
+                do
+                   printf "  >>> continue / list errors / kill palmbuild (c/l/k) ? "
+                   read  answer
+                   if [[ "$answer" = l ]]
+                   then
+                      more ${local_hostname}_last_make_protokoll
+                   fi
+                done
+                if [[ $answer = k ]]
+                then
+                   locat=user_abort; exit
+                fi
+             fi
+          fi
+
+
+             # TAR NEW VERSION ON LOCAL HOST
+          printf "\n  *** tar update on local host ..."
+          tar -cf  ${program_name}_current_version.tar  ${program_name} *.$suf *.o *.mod *.x
+
+       else
+
+             # NOW COMES THE BRANCH FOR CREATING THE EXECUTABLE FOR THE CURRENT RUN
+             # INCLUDING E.G. USER-INTERFACE ROUTINES. ALSO ADD OTHER UTILITY EXECUTABLES. EVERYTHING IS
+             # COLLECTED IN DIRECTORY SOURCES_FOR_RUN_...
+
+             # FIRST CHECK, IF A DEPOSITORY EXISTS ON THE LOCAL MACHINE
+          if [[ ! -d ${local_make_depository} ]]
+          then
+             printf "\n  +++ directory for local make depository:"
+             printf "\n           $local_make_depository"
+             printf "\n      not found. Please run \"palmbuild -h $host\" "
+             locat=local_make_depository; exit
+          fi
+
+
+             # COPY MAKE DEPOSITORY ON LOCAL MACHINE TO SOURCES_FOR_RUN_...
+          printf "\n  *** copy MAKE_DEPOSITORY on local host to "
+          printf "\n      $tmp_user_catalog/SOURCES_FOR_RUN_$fname \n"
+          rm -rf $tmp_user_catalog/SOURCES_FOR_RUN_$fname
+          mkdir $tmp_user_catalog/SOURCES_FOR_RUN_$fname
+          cp ${local_make_depository}/${program_name}_current_version.tar  $tmp_user_catalog/SOURCES_FOR_RUN_$fname
+          cd $tmp_user_catalog/SOURCES_FOR_RUN_$fname
+          tar xf ${program_name}_current_version.tar
+
+
+             # COPY CONTENTS OF SOURCES_FOR_RUN_... TO SOURCES_FOR_RUN_...
+             # IN THE TMP_USER_CATALOG ON THE LOCAL MACHINE
+          printf "\n  *** copy $base_directory/SOURCES_FOR_RUN_$fname to"
+          printf "\n      $tmp_user_catalog/SOURCES_FOR_RUN_$fname on local host \n"
+          cp  $base_directory/SOURCES_FOR_RUN_$fname/{*,.[!.]*}  ${tmp_user_catalog}/SOURCES_FOR_RUN_$fname
+
+
+             # CREATE EXECUTABLE FROM THE NEW/MODIFIED SOURCE FILES, IF THERE ARE ANY
+          if [[ $(ls -1 $base_directory/SOURCES_FOR_RUN_$fname/ | grep -c .$suf) != 0 ]]
+          then
+
+             echo "  *** execute \"make\" on local host"
+             [[ "$login_init_cmd" != "" ]]   &&  $login_init_cmd
+             [[ "$module_commands" != "" ]]  &&  $module_commands
+
+             make  $make_options  PROG=$program_name  F90=$compiler_name  COPT="$cpp_options"  F90FLAGS="$compiler_options"  LDFLAGS="$loader_options"
+
+             if [[ \$? != 0 ]]
+             then
+
+                printf "\a\n  +++ error(s) occurred during compiling or linking on host \"$local_hostname\" "
+                if [[ $silent = false ]]
+                then
+                   answer=dummy
+                   printf "\n"
+                   while [[ "$answer" != c  &&  "$answer" != k ]]
+                   do
+                      printf "  >>> continue / list errors / kill palmbuild (c/k) ? "
+                      read  answer
+                   done
+                   if [[ $answer = k ]]
+                   then
+                      locat=user_abort; exit
+                   fi
+                fi
+             fi
+
+          else
+
+             echo "  *** nothing to compile for this run"
+
+          fi
+
+       fi
+    fi
Index: palm/trunk/SCRIPTS/palmrun
===================================================================
--- palm/trunk/SCRIPTS/palmrun	(revision 2380)
+++ palm/trunk/SCRIPTS/palmrun	(revision 2380)
@@ -0,0 +1,2461 @@
+#!/bin/bash
+
+# palmrun - script for running PALM jobs
+
+#--------------------------------------------------------------------------------#
+# This file is part of PALM.
+#
+# PALM 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.
+#
+# PALM 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
+# PALM. If not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright 2017  Leibniz Universitaet Hannover
+#--------------------------------------------------------------------------------#
+#
+# Current revisions:
+# ------------------
+# initial revision
+# 
+# Former revisions:
+# -----------------
+# $Id$
+# 
+#
+#--------------------------------------------------------------------------------#
+# palmrun - script for running PALM jobs on local and remote hosts
+#--------------------------------------------------------------------------------#
+
+
+ 
+    # DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
+
+ set +o allexport    # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
+                     # LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
+                     # (TOO MANY ARGUMENTS - PROBLEM)
+ set +o noclobber    # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
+
+ typeset -i  ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0
+ typeset -x -i  memory=0   # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
+                           # SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
+                           # SCRIPT-OPTION ARGUMENTS
+ typeset -i  cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
+ typeset -i  icycle inode ival maxcycle mpi_tasks
+ typeset -i  nodes remaining_cores run_number tasks_per_node threads_per_task
+
+ activation_string_list=""
+ AddFilenames=""
+ add_source_path=""
+ combine_plot_fields=true
+ compiler_name=""
+ compiler_name_ser=""
+ compiler_options=""
+ config_file=""
+ cores=""
+ cores_atmos=0
+ cores_ocean=0
+ coupled_dist=""
+ cpp_options=""
+ cpumax=0
+ create_jobfile_only=false
+ delete_temporary_catalog=true
+ create_batch_job=false
+ create_remote_batch_job=false
+ dashes="  ----------------------------------------------------------------------------"
+ defaultqueue=""
+ do_compile=true
+ do_trace=false
+ executable=""
+ execute_command=""
+ execution_error=false
+ fileconnection_file=.palm.iofiles
+ fname=test
+ global_revision=""
+ host="default"
+ hostfile=""
+ hp=""
+ job_directory=""
+ keep_data_from_previous_run=false
+ link_local_input=false
+ link_local_output=false
+ loader_options=""
+ locat=normal
+ makefile=""
+ max_par_io_str=""
+ prc=$0
+ while [[ $(echo $prc | grep -c "/") != 0 ]]
+ do
+    prc=`echo $prc | cut -f2- -d"/"`
+ done
+ module_calls=""
+ palmrun_script_name=$prc
+ openmp=false
+ queue=none
+ restart_run=false
+ return_address=""
+ remote_username=""
+ running_in_batch_mode=false
+ run_coupled_model=false
+ run_id=""
+ silent=false
+ source_list=""
+ source_path=""
+ tasks_per_node=""
+ threads_per_task=1
+ tmpcreate=false
+ tmp_data_catalog=""
+ transfer_problems=false
+ use_openmp=false
+ version="palmrun  0.9 Rev$Rev: 2303 $"
+ working_directory=`pwd`
+ write_binary=""
+ TOPT=""
+
+
+    # ERROR HANDLING IN CASE OF EXIT
+ trap 'rm -rf  $working_directory/tmp_mrun
+       if [[ $locat != normal  &&  $locat != control_c ]]
+       then
+
+              # CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
+          (( i = 0 ))
+          while (( i < iec ))
+          do
+             (( i = i + 1 ))
+             printf "\n  *** Execution of ERROR-command:\n"
+             printf "  >>> ${err_command[$i]}\n"
+             eval  ${err_command[$i]}
+          done
+          if [[ $tmpcreate = true ]]
+          then
+             [[ $delete_temporary_catalog = true ]]  &&  rm -rf $TEMPDIR
+          fi
+          printf "\n\n+++ palmrun killed \n\n"
+       elif [[ $locat != control_c ]]
+       then
+          printf "\n\n --> palmrun finished\n\n"
+          if [[ $running_on_remote = true ]]
+          then
+             printf "     Bye, bye $remote_username !!\n\n"
+          else
+             printf "     Bye, bye $local_username !!\n\n"
+          fi
+       fi' exit
+
+
+    # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
+ trap 'rm -rf  $working_directory/tmp_mrun
+       [[ $tmpcreate = true ]]  &&  (cd; rm -rf $TEMPDIR)
+       printf "\n+++ palmrun killed by \"^C\" \n\n"
+       locat=control_c
+       exit
+      ' 2
+
+
+    # CHECK IF THE PATH FOR THE PALM BINARIES (SCRIPTS+UTILITY-PROGRAMS) HAS
+    # BEEN SET
+ if [[ "$PALM_BIN" = "" ]]
+ then
+    printf "\n  +++ environment variable PALM_BIN has not been set"
+    printf "\n      please set it to the directory where the PALM scripts are located"
+    locat=palm_bin; exit
+ fi
+ export PATH=$PALM_BIN:$PATH
+
+
+
+    # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
+    # WHICH WILL BE USED TO START RESTART-JOBS
+ while  getopts  :a:bBc:Cd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vw:xX:yY:Z option
+ do
+   case  $option  in
+       (a)   activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
+       (b)   create_batch_job=true; prc="$prc -b";;
+       (B)   delete_temporary_catalog=false; prc="$prc -B";;
+       (c)   config_file=$OPTARG; prc="$prc -c$OPTARG";;
+       (C)   restart_run=true; prc="$prc -C";;
+       (d)   fname=$OPTARG; prc="$prc -d$OPTARG";;
+       (F)   create_jobfile_only=true;;
+       (G)   global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
+       (h)   host=$OPTARG; prc="$prc -h$OPTARG";;
+       (j)   running_in_batch_mode=true;;
+       (k)   keep_data_from_previous_run=true; prc="$prc -k";;
+       (m)   memory=$OPTARG; prc="$prc -m$OPTARG";;
+       (M)   makefile=$OPTARG; prc="$prc -M$OPTARG";;
+       (O)   use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
+       (q)   queue=$OPTARG; prc="$prc -q$OPTARG";;
+       (r)   run_id=$OPTARG;;
+       (R)   return_address=$OPTARG;;
+       (s)   source_list=$OPTARG;;
+       (t)   cpumax=$OPTARG; prc="$prc -t$OPTARG";;
+       (T)   palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
+       (u)   remote_username=$OPTARG; prc="$prc -u$OPTARG";;
+       (U)   return_username=$OPTARG; prc="$prc -U$OPTARG";;
+       (v)   silent=true; prc="$prc -v";;
+       (w)   max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
+       (x)   do_trace=true;set -x; prc="$prc -x";;
+       (X)   cores=$OPTARG; prc="$prc -X$OPTARG";;
+       (y)   ocean_file_appendix=true; prc="$prc -y";;
+       (Y)   run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
+       (Z)   combine_plot_fields=false; prc="$prc -Z";;
+       (\?)  printf "\n  +++ unknown option $OPTARG \n"
+             printf "\n  --> type \"$0 ?\" for available options \n"
+             locat=parameter;exit;;
+   esac
+ done
+
+
+    # SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
+    # CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
+ (( to_shift = $OPTIND - 1 ))
+ shift $to_shift
+
+    # PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
+ if [[ "$1" = "?" ]]
+ then
+   (printf "\n  *** Description of available palmrun options:\n"
+    printf "\n      Option  Description                              Default-Value"
+    printf "\n        -a    activation string list                   \"\" "
+    printf "\n        -b    batch-job on local machine               ---"
+    printf "\n        -B    do not delete temporary directory at end ---"
+    printf "\n        -c    configuration file                       .mrun.config"
+    printf "\n        -d    base name of files attached to program   test"
+    printf "\n        -F    create batch job file only               ---"
+    printf "\n        -h    execution host                           \"default\" "
+    printf "\n        -k    keep data from previous run"
+    printf "\n        -K    additional conditions for controling"
+    printf "\n              usage of conditional code and"
+    printf "\n              env-variables in configuration file      \"\" "
+    printf "\n        -m    memory demand in MB (batch-jobs)         0 MB"
+    printf "\n        -M    Makefile name                            Makefile"
+    printf "\n        -O    threads per openMP task                  ---"
+    printf "\n        -q    queue                                    \"$queue\" "
+    printf "\n        -r    run control list (combines -i -o)        \"\" "
+    printf "\n        -s    filenames of routines to be compiled     \"\" "
+    printf "\n              must end with .f, .f90, .F, or .c !"
+    printf "\n              use \"..\" for more than one file and wildcards"
+    printf "\n              -s LM compiles all locally modified files"
+    printf "\n        -t    allowed cpu-time in seconds (batch)      0"
+    printf "\n        -T    tasks per node                           depending on -h"
+    printf "\n        -u    username on remote machine               \"\" "
+    printf "\n        -v    no prompt for confirmation               ---"
+    printf "\n        -w    maximum parallel io streams              as given by -X"
+    printf "\n        -x    tracing of palmrun for debug purposes    ---"
+    printf "\n        -X    # of processors (on parallel machines)   1"
+    printf "\n        -y    add appendix \"_O\" to all local output"
+    printf "\n              files (ocean precursor runs followed by"
+    printf "\n              coupled atmosphere-ocean runs)           ---"
+    printf "\n        -Y    run coupled model, \"#1 #2\" with" 
+    printf "\n              #1 atmosphere and #2 ocean processors    \"#/2 #/2\" depending on -X"
+    printf "\n        -Z    skip combine_plot_fields at the end of      "
+    printf "\n              the simulation                           ---"
+    printf "\n "
+    printf "\n      Possible values of positional parameter <modus>:"
+    printf "\n        \"?\"       -  this outline \n\n") | more
+    exit
+ elif [[ "$1" != "" ]]
+ then
+    printf "\n  +++ positional parameter $1 unknown \n"
+    locat=parameter; exit
+ fi
+
+
+
+    # SHORT STARTING MESSAGE
+ printf "\n*** $version "
+ printf "\n    will be executed.     Please wait ..."
+
+
+    # BUILD THE CONFIGURATION-FILE NAME
+ if [[ "$config_file" = "" ]]
+ then
+    config_file=.palm.config.$host
+ fi
+
+
+    # CHECK, IF CONFIGURATION FILE EXISTS
+ if [[ ! -f $config_file ]]
+ then
+    printf "\n\n  +++ configuration file: "
+    printf "\n           $config_file"
+    printf "\n      does not exist"
+    locat=connect; exit  
+ fi
+
+
+    # CHECK, IF FILE CONNECTION FILE EXISTS
+ if [[ ! -f $fileconnection_file ]]
+ then
+    printf "\n\n  +++ file connection file: "
+    printf "\n           $fileconnection_file"
+    printf "\n      does not exist"
+    locat=connect; exit  
+ fi
+
+
+    # READ AND EVALUATE THE CONFIGURATION-FILE
+ [[ $silent = false ]]  &&  printf "\n\n    Reading the configuration file... "
+
+    # READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
+ while  read line
+ do
+
+       # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
+    eval  line=\"$line\"
+
+
+       # INTERPRET THE LINE
+    if [[ "$(echo $line)" = "" ]]
+    then
+
+          # EMPTY LINE, NO ACTION
+       continue
+
+    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
+    then
+
+          # LINE IS A COMMENT LINE
+       continue
+
+    elif [[ "$(echo $line | cut -c1)"  =  "%" ]]
+    then
+
+          # LINE DEFINES AN ENVIRONMENT-VARIABLE
+       var=`echo $line | cut -d" " -s -f1 | cut -c2-`
+       value=`echo $line | cut -d" " -s -f2-`
+
+
+          # VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
+          # ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
+          # ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
+          # NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
+          # HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
+          # CONFIGURATION-FILE.
+       if [[ "$(eval echo \$$var)" = ""  ||  "$(eval echo \$$var)" = "0" ]]
+       then
+          eval  export  $var="\$value"
+
+             # TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
+          if [[ $do_trace = true ]]
+          then
+             printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
+          fi
+       fi
+
+    elif [[ "$(echo $line | cut -c1-3)" = "BD:" ]]
+    then
+
+          # LINE DEFINES BATCH-DIRECTIVE
+       (( ibd = ibd + 1 ))
+       line=$(echo $line | cut -c4-)
+       batch_directive[$ibd]="$line"
+
+    elif [[ "$(echo $line | cut -c1-4)" = "BDT:" ]]
+    then
+
+          # LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
+          # REMOTE TO A LOCAL HOST
+       (( ibdt = ibdt + 1 ))
+       line=$(echo $line | cut -c5-)
+       batch_directive_transfer[$ibdt]="$line"
+
+    elif [[ "$(echo $line | cut -c1-3)" = "EC:" ]]
+    then
+
+          # LINE DEFINES ERROR-COMMAND
+       (( iec = iec + 1 ))
+       line=$(echo $line | cut -c4-)
+       err_command[$iec]="$line"
+
+    elif [[ "$(echo $line | cut -c1-3)" = "IC:" ]]
+    then
+
+          # LINE DEFINES INPUT-COMMAND
+       (( iic = iic + 1 ))
+       line=$(echo $line | cut -c4-)
+       in_command[$iic]="$line"
+
+    elif [[ "$(echo $line | cut -c1-3)" = "OC:" ]]
+    then
+
+          # LINE DEFINES OUTPUT-COMMAND
+       (( ioc = ioc + 1 ))
+       line=$(echo $line | cut -c4-)
+       out_command[$ioc]="$line"
+
+    else
+
+          # SKIP ALL OTHER LINES
+       continue
+
+    fi
+
+ done < $config_file
+
+
+    # CHECK SETTING OF REQUIRED PARAMETERS
+ if [[ "$compiler_name" = "" ]]
+ then
+    printf "\n  +++ no compiler name found in $config_file"
+    printf "\n      Please add line \"compiler_name ...\" to that file."
+    locat=config_file; exit
+ fi
+ if [[ "$compiler_name_ser" = "" ]]
+ then
+    printf "\n  +++ no compiler name for non-paralle compilation found in $config_file"
+    printf "\n      Please add line \"compiler_name_ser ...\" to that file."
+    locat=config_file; exit
+ fi
+ if [[ "$compiler_options" = "" ]]
+ then
+    printf "\n  +++ no compiler options found in $config_file"
+    printf "\n      Please add line \"compiler_options ...\" to that file."
+    locat=config_file; exit
+ fi
+ if [[ "$loader_options" = "" ]]
+ then
+    printf "\n  +++ no loader options found in $config_file"
+    printf "\n      Please add line \"loader_options ...\" to that file."
+    locat=config_file; exit
+ fi
+ if [[ "$execute_command" = "" ]]
+ then
+    printf "\n  +++ no execute command found in $config_file"
+    printf "\n      Please add line \"execute_command ...\" to that file."
+    locat=config_file; exit
+ fi
+
+ if [[ "$hostfile" != "" ]]
+ then
+    if [[ $hostfile != auto  &&  ! -f $hostfile ]]
+    then
+       printf "\n  +++ no hostfile \"$hostfile\" found"
+       printf "\n      Please check line \"hostfile ...\" in $config_file"
+       locat=config_file; exit    
+    fi
+ fi
+
+ if [[ "$write_binary" = "" ]]
+ then
+    write_binary=false
+ fi
+
+    # DETERMINE THE CALL STATUS
+ if [[ "$return_address" != "" ]]
+ then
+ 
+       # I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
+       # BATCH MODE AND ...
+    running_on_remote=true
+    host_name=$remote_hostname
+ 
+ else
+
+       # I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
+     if [[ "$remote_ip" != "" ]]
+     then
+
+           # I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
+        create_remote_batch_job=true
+
+     fi
+     host_name=$local_hostname
+     running_on_remote=false
+ fi
+
+
+
+    # READ AND EVALUATE THE I/O-FILE LIST
+ [[ $silent = false ]]  &&  printf "\n    Reading the I/O files... "
+
+    # READ THE FILE CONNECTION FILE LINE BY LINE
+ while  read line
+ do
+
+       # FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
+    eval  line=\"$line\"
+
+
+       # INTERPRET THE LINE
+    if [[ "$(echo $line)" = "" ]]
+    then
+          # EMPTY LINE, NO ACTION
+       continue
+
+    elif [[ "$(echo $line | cut -c1)"  =  "#" ]]
+    then
+
+          # LINE IS A COMMENT LINE
+       true
+
+    else
+
+          # LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
+          # s2a: in/out - field
+          # s2b: loc    - field (optional)
+          # s2c: tr/ar  - field (optional)
+       s1=`echo $line | cut -d" " -f1`
+       s2=`echo $line | cut -d" " -s -f2`
+       s2a=$(echo $s2 | cut -d":" -f1)
+       if [[ $(echo $s2 | grep -c ":") = 0 ]]
+       then
+          s2b=""
+          s2c=""
+       else
+          s2b=`echo $s2 | cut -d":" -f2 | sed 's/:/ /g'`
+          s2c=`echo $s2 | cut -d":" -s -f3 | sed 's/:/ /g'`
+       fi
+       s3=`echo $line | cut -d" " -f3`
+       s4=`echo $line | cut -d" " -s -f4`
+       s5=`echo $line | cut -d" " -s -f5`
+       s6=`echo $line | cut -d" " -s -f6`
+
+       
+          # STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
+          # INPUT- OR OUTPUT-LIST.
+          # VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
+          # IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
+          # LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
+          # IS NOT CHECKED AND STORED.
+       IFSALT="$IFS"; IFS="$IFS:"
+       if [[ "$s2a" = in  &&  ! ( $create_remote_batch_job = true  &&  ( "$s2b" = loc  ||  "$s2b" = locopt ) ) ]]
+       then
+          found=false
+          for  actual  in  $activation_string_list
+          do
+             for  formal  in  $s3
+             do
+                [[ $actual = $formal  ||  "$formal" = "-" ]]  &&  found=true
+             done
+          done
+          if [[ $found = true ]]
+          then
+             (( iin = iin + 1 ))
+             localin[$iin]=$s1; transin[$iin]=$s2b; actionin[$iin]=$s2c;
+             typein[$iin]=$s3; pathin[$iin]=$s4; endin[$iin]=$s5;
+             extin[$iin]=$s6
+          fi
+       elif [[ "$s2a" = out  &&  ! ( $create_remote_batch_job = true  &&  "$s2b" = loc ) ]]
+       then
+          found=false
+          for  actual  in  $activation_string_list
+          do
+             for  formal  in  $s3  
+             do
+                [[ $actual = $formal  ||  "$formal" = "-"  ]]  &&  found=true
+             done
+          done
+          if [[ $found = true ]]
+          then
+             (( iout = iout + 1 ))
+             localout[$iout]=$s1; actionout[$iout]=$s2c; typeout[$iout]=$s3;
+             pathout[$iout]=$s4; endout[$iout]=$s5; extout[$iout]=$s6
+          fi
+       elif [[ "$s2a" != in  &&  "$s2a" != out ]]
+       then
+          printf "\n  +++ I/O-attribute in configuration file $config_file has the invalid"
+          printf "\n      value \"$s2\". Only \"in\" and \"out\" are allowed!"
+          locat=connect; exit
+       fi
+       IFS="$IFSALT"
+    fi
+
+ done < $fileconnection_file
+
+
+
+      # EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
+ if [[ $run_coupled_model = true ]] 
+ then
+
+    cores_atmos=`echo $coupled_dist | cut -d" " -s -f1`
+    cores_ocean=`echo $coupled_dist | cut -d" " -s -f2`
+
+    if (( $cores_ocean + $cores_atmos != $cores ))
+    then
+
+       printf "\n  +++ number of processors does not fit to specification by \"-Y\"."
+       printf "\n      PEs (total)     : $cores"
+       printf "\n      PEs (atmosphere): $cores_atmos"
+       printf "\n      PEs (ocean)     : $cores_ocean"
+       locat=coupling; exit
+
+    fi
+
+ fi
+
+
+    # SAVE VALUES OF PALMRUN-OPTIONS IN ORDER TO OVERWRITE
+    # THOSE VALUES GIVEN IN THE CONFIGURATION-FILE
+ palmrun_memory=$memory
+ palmrun_cpumax=$cpumax
+ palmrun_cores=$cores
+
+
+    # VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
+ [[ $palmrun_memory     != 0   ]]  &&  memory=$palmrun_memory
+ [[ $palmrun_cpumax     != 0   ]]  &&  cpumax=$palmrun_cpumax
+ [[ "$palmrun_cores" != ""  ]]  &&  cores=$palmrun_cores
+ [[ "$max_par_io_str" != "" ]]  &&  maximum_parallel_io_streams=$max_par_io_str
+ [[ "$palmrun_tasks_per_node" != "" ]]  &&  tasks_per_node=$palmrun_tasks_per_node
+
+
+
+    # IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
+    # HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
+    # FOLDER
+ if [[ $running_in_batch_mode = true ]]
+ then
+ 
+    if [[ ! -d ${tmp_user_catalog}/SOURCES_FOR_RUN_$fname ]]
+    then
+       printf "\n  +++ directory ${tmp_user_catalog}/SOURCES_FOR_RUN_$fname is missing"
+       printf "\n      Please check the output of the palmrun-call"
+       printf "\n      that you did on your local host."
+       locat=SOURCES_FOR_RUN; exit
+    fi
+
+ else
+
+       # CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
+       # AUTOMATIC RESTART RUN
+       # AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
+    if [[ $restart_run = false ]]
+    then
+
+          # COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
+          # THE LOCAL HOST
+       if [[ ! -d $source_path ]]
+       then
+          printf "\n\n  +++ source path \"$source_path\" on local host"
+          printf "\n      \"$(hostname)\" does not exist"
+          locat=source_path; exit
+       fi
+
+       rm -rf  SOURCES_FOR_RUN_$fname
+       mkdir   SOURCES_FOR_RUN_$fname
+
+       if [[ "$source_list" = LM ]]
+       then
+
+             # DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
+          source_list=""
+          cd  $source_path
+
+
+             # CHECK, IF DIRECTORY IS UNDER SVN CONTROL
+          if [[ ! -d .svn ]]
+          then
+             printf "\n\n  +++ source directory"
+             printf "\n         \"$source_path\" "
+             printf "\n         is not under control of \"subversion\"."
+             printf "\n         Please do not use palmmrun-option \"-s LM\"\n"
+          fi
+
+
+             # LIST ALL MODIFIED SOURCE CODE FILES
+          Filenames=""
+          svn status  >  tmp_mrun
+          while  read line
+          do
+             firstc=`echo $line | cut -c1`
+             if [[ $firstc = M  ||  $firstc = "?" ]]
+             then
+                Name=`echo "$line" | cut -c8-`
+                extension=`echo $Name | cut -d. -f2`
+                if [[ "$extension" = f90 || "$extension" = F90 || "$extension" = f || "$extension" = F || "$extension" = c ]]
+                then
+                   Filenames="$Filenames "$Name
+                fi
+             fi
+          done < tmp_mrun
+
+
+             # COPY FILES TO SOURCES_FOR_RUN_...
+          for  filename  in  $Filenames
+          do
+             cp  $filename  $working_directory/SOURCES_FOR_RUN_$fname
+             source_list=$source_list"$filename "
+          done
+
+          cd -  > /dev/null
+
+
+          # COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
+       elif [[ "$source_list" != "" ]]
+       then
+
+          cd  $source_path
+
+          for  filename  in  $source_list
+          do
+
+                # SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
+             if [[ $(echo $filename | grep -c "/") != 0 ]]
+             then
+                printf "\n  +++ source code file:  $filename"
+                printf "\n      must not contain (\"/\") "
+                locat=source; exit
+             fi
+
+             if [[ ! -f $filename ]]
+             then
+                printf "\n  +++ source code file:  $filename"
+                printf "\n      does not exist"
+                locat=source; exit
+             else
+                cp  $filename  $working_directory/SOURCES_FOR_RUN_$fname
+             fi
+
+          done
+
+          cd -  > /dev/null
+
+       fi
+
+          # CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
+       [[ "$makefile" = "" ]]  &&  makefile=$source_path/Makefile
+       if [[ ! -f $makefile ]]
+       then
+          printf "\n  +++ file \"$makefile\" does not exist"
+          locat=make; exit
+       else
+          cp  $makefile  SOURCES_FOR_RUN_$fname/Makefile 
+       fi
+
+
+          # COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
+       if [[ "$add_source_path" != "" ]]
+       then
+
+             # DOES THE DIRECTORY EXIST?
+          if [[ ! -d $add_source_path ]]
+          then
+
+             printf "\n\n  *** INFORMATIVE: additional source code directory"
+             printf "\n      \"$add_source_path\" "
+             printf "\n      does not exist or is not a directory."
+             printf "\n      No source code will be used from this directory!\n"
+             add_source_path=""
+             if [[ $silent == false ]]
+             then
+                sleep 2
+             fi
+
+          else
+
+             cd $add_source_path
+             found=false
+
+             Names=$(ls -1 *.f90 2>&1)
+             [[ $(echo $Names | grep -c '*.f90') = 0 ]]  &&  AddFilenames="$Names"
+             Names=$(ls -1 *.F90 2>&1)
+             [[ $(echo $Names | grep -c '*.F90') = 0 ]]  &&  AddFilenames="$AddFilenames $Names"
+             Names=$(ls -1 *.F 2>&1)
+             [[ $(echo $Names | grep -c '*.F') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
+             Names=$(ls -1 *.f 2>&1)
+             [[ $(echo $Names | grep -c '*.f') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
+             Names=$(ls -1 *.c 2>&1)
+             [[ $(echo $Names | grep -c '*.c') = 0   ]]  &&  AddFilenames="$AddFilenames $Names"
+
+             cd -  > /dev/null
+             cd  SOURCES_FOR_RUN_$fname
+
+                # COPY MAKEFILE IF EXISTING
+             if [[ -f $add_source_path/Makefile ]]
+             then
+                printf "\n\n  *** user Makefile from directory"
+                printf "\n      \"$add_source_path\" is used \n"
+                if [[ $silent == false ]]
+                then
+                   sleep 1
+                fi
+                cp  $add_source_path/Makefile  .
+             fi
+
+             for  filename  in  $AddFilenames
+             do
+                if [[ -f $filename ]]
+                then
+                   printf "\n  +++ source code file \"$filename\" found in additional"
+                   printf "\n      source code directory \"$add_source_path\" "
+                   printf "\n      but was also given with option \"-s\" which means that it should be taken"
+                   printf "\n      from directory \"$source_path\"."
+                   locat=source; exit
+                fi
+
+                cp  $add_source_path/$filename  .
+                source_list="$source_list $filename"
+
+                   # CHECK IF FILE IS CONTAINED IN MAKEFILE
+                if [[ $(grep -c $filename Makefile) = 0 ]]
+                then
+                   printf "\n\n  +++ user file \"$filename\" "
+                   printf "\n      is not listed in Makefile \n"
+                   locat=source; exit
+                else
+
+                   if [[ $found = false ]]
+                   then
+                      found=true
+                      printf "\n\n  *** following user file(s) added to the"
+                      printf " files to be translated:\n      "
+                   fi
+                   printf "$filename  "
+                   if [[ $silent == false ]]
+                   then
+                      sleep 0.5
+                   fi
+
+                fi
+             done
+             [[ $found = true ]]  &&  printf "\n"
+             cd -  > /dev/null
+          fi
+       fi
+
+          # COPY CONFIGURATION FILES
+       cp  $config_file  SOURCES_FOR_RUN_$fname
+       cp  $fileconnection_file  SOURCES_FOR_RUN_$fname
+
+          # COPY SHELLSCRIPTS
+       cp  ${source_path}/../SCRIPTS/palmrun    SOURCES_FOR_RUN_$fname
+       cp  ${source_path}/../SCRIPTS/batch_scp  SOURCES_FOR_RUN_$fname
+
+    fi
+
+ fi
+
+    # GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
+    # (HANDED OVER TO RESTART-RUNS USING OPTION -G)
+ if [[ "$global_revision" = "" ]]
+ then
+    global_revision=`svnversion $source_path  2>/dev/null`
+    global_revision="Rev: $global_revision"
+ fi
+
+
+    # IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
+ if [[ -n $cores ]]
+ then
+
+       # CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
+       # INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
+    if [[ "$tasks_per_node" = ""  &&  $host != lcxt5m ]]
+    then
+       printf "\n"
+       printf "\n  +++ option \"-T\" (tasks per node) is missing"
+       printf "\n      set -T option or define tasks_per_node in the config file"
+       locat=tasks_per_node; (( iec = 0 )); exit 
+    fi
+
+    if (( cores < tasks_per_node ))
+    then
+       printf "\n"
+       printf "\n  +++ tasks per node (-T) cannot exceed total number of cores (-X)"
+       printf "\n      given values: -T $tasks_per_node  -X $cores"
+       locat=tasks_per_node; (( iec = 0 )); exit 
+    fi
+
+    (( nodes = cores / ( tasks_per_node * threads_per_task ) ))
+    (( mpi_tasks = cores / threads_per_task ))
+    [[ $mpi_tasks = 0 ]]  &&  (( mpi_tasks = 1 ))
+    (( ii = cores / tasks_per_node ))
+    (( remaining_cores =  cores - ii * tasks_per_node ))
+    if (( remaining_cores > 0 ))
+    then
+       printf "\n"
+       printf "\n  +++ WARNING: tasks per node (option \"-T\") is not an integral"
+       printf "\n      divisor of the total number of cores (option \"-X\")"
+       printf "\n      values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
+       printf "\n      One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
+       (( nodes = nodes + 1 ))
+    fi
+
+       # SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
+    if [[ "$tasks_per_node" != "" ]]
+    then
+       TOPT="-T $tasks_per_node"
+    fi
+
+ fi
+
+
+    # SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
+ if [[ "$maximum_parallel_io_streams" = "" ]]
+ then
+    maximum_parallel_io_streams=$cores
+ fi
+
+
+    # SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
+ if [[ "$scp_port" != "" ]]
+ then
+    PORTOPT="-P $scp_port"
+    SSH_PORTOPT="-p $scp_port"
+ fi
+
+
+    # DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
+    # CONFIG-FILE
+ if [[ "$ssh_key" != "" ]]
+ then
+    ssh_key="-i $HOME/.ssh/$ssh_key"
+ fi
+
+
+    # SET QUEUE, IF NOT GIVEN
+ if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
+ then
+
+    if [[ $queue = none  &&  "$defaultqueue" = "" ]]
+    then
+       printf "\n"
+       printf "\n  +++ no default queue given in configuration file and no queue"
+       printf "\n      given with option -q"
+    fi
+    if [[ $queue = none ]]
+    then
+       queue=$defaultqueue
+    fi
+
+ fi
+
+
+    # GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
+    # CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
+ (( i = 0 ))
+ while (( i < iin ))
+ do
+    (( i = i + 1 ))
+    (( maxcycle = 0 ))
+
+       # GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
+       # FILE IDENTIFIER IS NOT PART OF THE FILENAME))
+    if [[ "${actionin[$i]}" = di ]]
+    then
+       remotepathin[$i]=${pathin[$i]}/${endin[$i]}  # EVALUATE REMOTE-PATH ON THE REMOTE
+                                                    # HOST ONLY
+       eval filename=${pathin[$i]}/${endin[$i]}
+    else
+       remotepathin[$i]=${pathin[$i]}/${fname}${endin[$i]}  # EVALUATE REMOTE-PATH ON THE REMOTE
+                                                             # HOST ONLY
+       eval filename=${pathin[$i]}/${fname}${endin[$i]}
+    fi
+    eval pathname=${pathin[$i]}
+
+       # CHECK IF FILE EXISTS
+    if ! ls $filename* 1>/dev/null 2>&1
+    then
+
+          # FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
+       if [[ "${transin[$i]}" != "locopt" ]]
+       then
+          printf "\n\n  +++ INPUT-file: "
+          if [[ "${extin[$i]}" = ""  ||  "${extin[$i]}" = " " ]]
+          then
+             printf "\n           $filename"
+          else
+             printf "\n           $filename.${extin[$i]}"
+          fi
+          printf "\n      does not exist\n"
+          locat=input; exit
+       else
+          transin[$i]="unavailable"
+       fi
+    else
+
+          # DETERMINE THE FILE'S CYCLE NUMBER
+       ls -1 -d $filename    >   filelist  2>/dev/null
+       ls -1 -d $filename.*  >>  filelist  2>/dev/null
+       while  read line
+       do
+              # filename without path (i.e. after the last "/")
+           basefilename=$(basename ${line})
+
+              # check if there is an extension
+           extension=${basefilename##*.}
+           if [[ "$extension" = "$extin[$i]" ]]
+           then
+              basefilename=${basefilename&.*}
+           fi
+
+              # check for an existing cycle number
+           cycle=${basefilename##*.}
+           if [[ $cycle =~ ^-?[0-9]+$ ]]
+           then
+              (( icycle = $cycle ))
+           else
+              (( icycle = 0 ))
+           fi
+
+           if (( icycle > maxcycle ))
+           then
+              (( maxcycle = icycle ))
+           fi
+
+       done <filelist
+       rm filelist
+
+          # APPEND CYCLE NUMBER TO FILENAME
+       if (( maxcycle > 0 ))
+       then
+          if [[ "${extin[$i]}" != " "  &&   "${extin[$i]}" != "" ]]
+          then
+             filename=${filename}.$maxcycle.${extin[$i]}
+          else
+             filename=${filename}.$maxcycle
+          fi
+       else
+          if [[ "${extin[$i]}" != " "  &&   "${extin[$i]}" != "" ]]
+          then
+             filename=${filename}.${extin[$i]}
+          fi
+       fi
+       
+          # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
+          # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
+       absnamein[$i]=$filename
+       if (( maxcycle > 0 ))
+       then
+          if [[ "${actionin[$i]}" = di ]]
+          then
+             frelin[$i]=${endin[$i]}.$maxcycle
+          else
+             frelin[$i]=${fname}${endin[$i]}.$maxcycle
+          fi
+       else
+          if [[ "${actionin[$i]}" = di ]]
+          then
+             frelin[$i]=${endin[$i]}
+          else
+             frelin[$i]=${fname}${endin[$i]}
+          fi
+       fi
+
+    fi
+ done
+
+    
+    # GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
+    # CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
+    # OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED  
+    # THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRASFERRED FROM THE REMOTE TO
+    # THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
+    # REMOTE HOST)
+ (( i = 0 ))
+ while (( i < iout ))
+ do
+    (( i = i + 1 ))
+    if [[ ! ( $running_on_remote = true  &&  ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]]
+    then
+       if [[ "${actionout[$i]}" = tr ]]
+       then
+          actionout[$i]=""
+       elif [[ "${actionout[$i]}" = trpe ]]
+       then
+          actionout[$i]=pe
+       elif [[ "${actionout[$i]}" = tra ]]
+       then
+          actionout[$i]=a
+       fi
+       (( maxcycle = 0 ))
+       eval filename=${pathout[$i]}/${fname}${endout[$i]}
+       eval catalogname=${pathout[$i]}
+       if ! ls $filename* 1>/dev/null 2>&1
+       then
+      
+             # IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
+          if  cat /dev/null > $filename  
+          then
+             rm  $filename
+          else
+
+                # CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
+                # IF IT DOES NOT EXIST, TRY TO CREATE IT
+             if [[ ! -d $catalogname ]]
+             then
+                if  mkdir -p  $catalogname
+                then
+                   printf "\n\n  *** directory:"
+                   printf "\n           $catalogname"
+                   printf "\n      was created\n"
+                else
+                   printf "\n\n  +++ OUTPUT-file:"
+                   printf "\n           $filename"
+                   printf "\n      cannot be created, because directory does not exist"
+                   printf "\n      and cannot be created either"
+                   printf "\n"
+                   locat=output  ; exit
+                fi 2>/dev/null 
+             else
+                printf "\n\n  +++ OUTPUT-file:"
+                printf "\n           $filename"
+                printf "\n      cannot be created, although directory exists"
+                printf "\n"
+                locat=output  ; exit
+             fi
+          fi 2>/dev/null
+       else
+
+             # DETERMINE THE CYCLE NUMBER
+          ls -1 -d $filename    >   filelist  2>/dev/null
+          ls -1 -d $filename.*  >>  filelist  2>/dev/null
+          while  read line
+          do
+
+                # filename without path (i.e. after the last "/")
+             basefilename=$(basename ${line})
+
+                # check if there is an extension
+             extension=${basefilename##*.}
+             if [[ "$extension" = "${extout[$i]}" ]]
+             then
+                basefilename=${basefilename%.*}
+             fi
+
+                # check for an existing cycle number
+             cycle=${basefilename##*.}
+             if [[ $cycle =~ ^-?[0-9]+$ ]]
+             then
+                (( icycle = $cycle + 1 ))
+             else
+                (( icycle = 1 ))
+             fi
+
+             if (( icycle > maxcycle ))
+             then
+                (( maxcycle = icycle ))
+             fi
+
+          done <filelist
+          rm filelist
+       fi
+
+          # APPEND CYCLE NUMBER TO FILENAME AND CHECK, IF FILE CAN BE CREATED
+          # IN CASE OF FILE-APPEND, FILE MUST BE APPENDED TO THE ONE WITH HIGHEST CYCLE NUMBER
+       if [[ "${actionout[$i]}" != a ]]
+       then
+          if (( maxcycle > 0 ))
+          then
+             filename_tmp=${filename}.$maxcycle
+             if  cat /dev/null > $filename_tmp 
+             then
+                rm  $filename_tmp
+             else
+                printf "\n  +++ OUTPUT-file:"
+                printf "\n           $filename_tmp"
+                printf "\n      cannot be created"
+                locat=output  ; exit
+             fi
+          fi
+       else
+          (( maxcycle = maxcycle - 1 ))
+       fi
+       
+       (( cycnum[$i] = maxcycle ))
+       pathout[$i]=$filename
+
+    fi
+ done
+
+
+    # DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
+ if [[ $running_in_batch_mode = false ]]
+ then
+    run_id=$RANDOM
+    job_id=${fname}.$run_id
+
+    TEMPDIR=$tmp_user_catalog/$job_id
+ fi
+
+
+    # CHECK SETTINGS REQUIRED FOR BATCH JOBS
+ if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
+ then
+
+       # CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
+    if [[ $ibd = 0 ]]
+    then
+       printf "\n"
+       printf "\n  +++ no batch directives found in configuration file"
+       locat=config_file_batch_directives; (( iec = 0 )); exit 
+    fi
+
+       # CHECK IF CPUTIME IS GIVEN FOR JOB
+    done=false
+    while [[ $done = false ]]
+    do
+       cputime=$cpumax
+       if (( $cputime == 0 ))
+       then
+          printf "\n  +++ cpu-time is undefined"
+          printf "\n  >>> Please type CPU-time in seconds as INTEGER:"
+          printf "\n  >>> "
+          read  cputime  1>/dev/null  2>&1
+       else
+          done=true
+       fi
+    done
+
+       # CHECK THE MEMORY DEMAND
+    done=false
+    while [[ $done = false ]]
+    do
+       if (( memory == 0 ))
+       then
+          printf "\n  +++ memory demand is undefined"
+          printf "\n  >>> Please type memory in  MByte per process  as INTEGER:"
+          printf "\n  >>> "
+          read  memory  1>/dev/null  2>&1
+       else
+          done=true
+       fi
+    done
+
+       # IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
+    if [[ $create_remote_batch_job = true  &&  -z $remote_username ]]
+    then
+       while [[ -z $remote_username ]]
+       do
+          printf "\n  +++ username on remote host \"$remote_ip\" is undefined"
+          printf "\n  >>> Please type username:"
+          printf "\n  >>> "
+          read  remote_username
+       done
+    fi
+
+ else
+
+    cputime=10000000  # NO LIMT FOR INTERACTIVE RUNS
+
+ fi
+ cpumax=$cputime
+
+
+    # CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
+ (( cpu_hours  = cputime / 3600 ))
+ (( resttime = cputime - cpu_hours * 3600 ))
+ (( cpu_minutes  = resttime / 60 ))
+ (( cpu_seconds = resttime - cpu_minutes * 60 ))
+ timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
+
+
+    # OUTPUT OF THE PALMRUN-HEADER
+ calltime=$(date)
+ printf "\n"
+ printf "#------------------------------------------------------------------------# \n"
+ printf "| %-35s%35s | \n" "$version" "$calltime"
+ printf "|                                                                        | \n"
+ column1="called on:"; column2=$(hostname)
+ printf "| %-25s%-45s | \n" "$column1" "$column2"
+ if [[ $create_remote_batch_job = true ]]
+ then
+    column1="execution on:"; column2="$remote_hostname (username: $remote_username)"
+ else
+    if [[ $running_on_remote = true ]]
+    then
+       column1="execution on:"; column2="$remote_hostname"
+    else
+       column1="execution on:"; column2="$local_hostname"
+    fi
+ fi
+ printf "| %-25s%-45s | \n" "$column1" "$column2"
+
+ column1="running in:"
+ if [[ $running_in_batch_mode = true ]]
+ then
+    column2="batch job mode"
+ else
+    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
+    then
+       column2="job creation mode"
+    else
+       column2="interactive run mode"
+    fi
+ fi
+ printf "| %-25s%-45s | \n" "$column1" "$column2"
+
+ if [[ -n $cores ]]
+ then
+    if [[ $run_coupled_model = false ]]
+    then
+       column1="number of cores:"; column2=$cores
+    else
+       column1="number of cores:"; column2="$cores  (atmosphere: $cores_atmos, ocean: $cores_ocean)"
+    fi
+    printf "| %-25s%-45s | \n" "$column1" "$column2"
+ fi
+ if [[ -n $tasks_per_node ]]
+ then
+    column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
+    printf "| %-25s%-45s | \n" "$column1" "$column2"
+    if (( remaining_cores > 0 ))
+    then
+       column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
+       printf "| %-25s%-45s | \n" "$column1" "$column2"
+    fi
+ fi
+ if [[ $maximum_parallel_io_streams != $cores ]]
+ then
+    column1="max par io streams:"; column2="$maximum_parallel_io_streams"
+    printf "| %-25s%-45s | \n" "$column1" "$column2"
+ fi
+ if [[ $use_openmp = true ]]
+ then
+    column1="threads per task:"; column2="$threads_per_task"
+    printf "| %-25s%-45s | \n" "$column1" "$column2"
+ fi
+ printf "|                                                                        | \n"
+ if [[ "$source_list" != "" ]]
+ then
+    if [[ "$make_options" != "" ]]
+    then
+       column1="make options:"; column2=$(echo "$make_options" | cut -c-45)
+       printf "| %-25s%-45s | \n" "$column1" "$column2"
+       line=$(echo "$make_options" | cut -c46-)
+       while [[ "$line" != "" ]]
+       do
+          column1=""
+          column2=$(echo "$line" | cut -c-45)
+          printf "| %-25s%-45s | \n" "$column1" "$column2"
+          line=$(echo "$line" | cut -c46-)
+       done
+    fi
+ fi
+
+ column1="cpp directives:"; column2=$(echo "$cpp_options" | cut -c-45)
+ printf "| %-25s%-45s | \n" "$column1" "$column2"
+ line=$(echo "$cpp_options" | cut -c46-)
+ while [[ "$line" != "" ]]
+ do
+    column1=""
+    column2=$(echo "$line" | cut -c-45)
+    printf "| %-25s%-45s | \n" "$column1" "$column2"
+    line=$(echo "$line" | cut -c46-)
+ done
+
+ column1="compiler options:"; column2=$(echo "$compiler_options" | cut -c-45)
+ printf "| %-25s%-45s | \n" "$column1" "$column2"
+ line=$(echo "$compiler_options" | cut -c46-)
+ while [[ "$line" != "" ]]
+ do
+    column1=""
+    column2=$(echo "$line" | cut -c-45)
+    printf "| %-25s%-45s | \n" "$column1" "$column2"
+    line=$(echo "$line" | cut -c46-)
+ done
+
+ column1="loader options:"; column2=$(echo "$loader_options" | cut -c-45)
+ printf "| %-25s%-45s | \n" "$column1" "$column2"
+ line=$(echo "$loader_options" | cut -c46-)
+ while [[ "$line" != "" ]]
+ do
+    column1=""
+    column2=$(echo "$line" | cut -c-45)
+    printf "| %-25s%-45s | \n" "$column1" "$column2"
+    line=$(echo "$line" | cut -c46-)
+ done
+
+ if [[ "$login_init_cmd" != "" ]]
+ then
+    column1="login init commands:"; column2=$(echo "$login_init_cmd" | cut -c-45)
+    printf "| %-25s%-45s | \n" "$column1" "$column2"
+    line=$(echo "$login_init_cmd" | cut -c46-)
+    while [[ "$line" != "" ]]
+    do
+       column1=""
+       column2=$(echo "$line" | cut -c-45)
+       printf "| %-25s%-45s | \n" "$column1" "$column2"
+       line=$(echo "$line" | cut -c46-)
+    done
+ fi
+
+ if [[ "$module_commands" != "" ]]
+ then
+    column1="module commands:"; column2=$(echo "$module_commands" | cut -c-45)
+    printf "| %-25s%-45s | \n" "$column1" "$column2"
+    line=$(echo "$module_commands" | cut -c46-)
+    while [[ "$line" != "" ]]
+    do
+       column1=""
+       column2=$(echo "$line" | cut -c-45)
+       printf "| %-25s%-45s | \n" "$column1" "$column2"
+       line=$(echo "$line" | cut -c46-)
+    done
+ fi
+ printf "|                                                                        | \n"
+ column1="base name of files:"; column2=$fname
+ printf "| %-25s%-45s | \n" "$column1" "$column2"
+ column1="activation string list:"; column2=$(echo $activation_string_list)
+ printf "| %-25s%-45s | \n" "$column1" "$column2"
+
+ if [[ "$ocean_file_appendix" = true ]]
+ then
+    printf "| %-35s%-35s | \n" "suffix \"_O\" is added to local files" " "
+ fi
+
+ if [[ $create_batch_job = true  ||  "$LOADLBATCH" = yes ]]
+ then
+    column1="memory demand / PE":; column2="$memory MB"
+    printf "| %-25s%-45s | \n" "$column1" "$column2"
+    column1=CPU-time:; column2="$cpu_hours:$cpu_minutes:$cpu_seconds"
+    printf "| %-25s%-45s | \n" "$column1" "$column2"
+ fi
+
+ if [[ "$source_list" != "" ]]
+ then
+    printf "|                                                                        | \n"
+    printf "| Files to be compiled:                                                  | \n"
+    line=$source_list
+    while [[ "$line" != "" ]]
+    do
+       linestart=$(echo $line | cut -c-70)
+       printf "| %-70s | \n" "$linestart"
+       line=$(echo "$line" | cut -c71-)
+    done
+ fi
+ printf "#------------------------------------------------------------------------#"
+
+
+
+    # OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
+ if [[ $do_trace = true ]]
+ then
+    (( i = 0 ))
+    while (( i < iin ))
+    do
+       (( i = i + 1 ))
+       if (( i == 1 ))
+       then
+          printf "\n\n >>> INPUT-file assignments:\n"
+       fi
+       printf "\n     ${localin[$i]} :  ${absnamein[$i]}"
+    done
+    (( i = 0 ))
+    while (( i < iout ))
+    do
+       (( i = i + 1 ))
+       if (( i == 1 ))
+       then
+          printf "\n\n >>> OUTPUT-file assignments:\n"
+       fi
+       printf "\n     ${localout[$i]} :  ${pathout[$i]}"
+    done
+    (( i = 0 ))
+    while (( i < iic ))
+    do
+       (( i = i + 1 ))
+       if (( i == 1 ))
+       then
+          printf "\n\n >>> INPUT-commands:\n"
+       fi
+       printf "\n     ${in_command[$i]}" 
+    done
+    (( i = 0 ))
+    while (( i < ioc ))
+    do
+       (( i = i + 1 ))
+       if (( i == 1 ))
+       then
+          printf "\n\n >>> OUTPUT-commands:\n"
+       fi
+       printf "\n     ${out_command[$i]}" 
+    done
+ fi
+
+    # QUERY FOR CONTINUE
+ if [[ $silent = false  &&  $running_in_batch_mode = false ]]
+ then
+    antwort=dummy
+    printf "\n\n"
+    printf " >>> everything o.k. (y/n) ?  "
+    while  read antwort
+    do
+       if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
+       then
+          printf " >>> everything o.k. (y/n) ?  "
+       else
+          break
+       fi
+    done
+    if [[ $antwort = n  ||  $antwort = N ]]
+    then
+       locat=user_abort; (( iec = 0 )); exit
+    fi
+    if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
+    then
+       printf " ***  batch-job will be created and submitted"
+    else
+       printf " ***  PALMRUN will now continue to execute on this machine"
+    fi
+ fi
+
+ 
+
+    # PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
+ if [[ $restart_run = false  &&  $running_in_batch_mode = false ]]
+ then
+
+    if [[ $create_batch_job = true  ||  $create_remote_batch_job  = true ]]
+    then
+       printf "\n\n  *** creating executable and other sources for the remote host"
+    else
+       printf "\n\n  *** creating executable and other sources for the local host"
+    fi
+
+    palmbuild  -v  -h $host  -d $fname
+    rm -rf  SOURCES_FOR_RUN_$fname
+
+    if [[ $? != 0 ]]
+    then
+
+           # ABORT IN CASE OF COMPILATION PROBLEMS
+       printf "\n  +++ error while creating executable and/or other sources"
+       locat=execution
+       exit
+
+    else
+
+       printf "\n$dashes\n  *** executable and other sources created\n"
+
+    fi
+
+ fi
+
+
+    # NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
+    # (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
+ if [[ $create_batch_job = false  &&  $create_remote_batch_job = false ]]
+ then
+
+       # CHANGE TO THE TEMPORARY WORKING DIRECTORY
+    if [[ $running_in_batch_mode = false ]]
+    then
+          # CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
+          # FOLDER
+       mkdir -p  $TEMPDIR
+       chmod  go+rx  $TEMPDIR
+       tmpcreate=true
+       cd  $TEMPDIR
+       cp  $tmp_user_catalog/SOURCES_FOR_RUN_$fname/{*,.[!.]*}  $TEMPDIR
+       printf "\n  *** changed to temporary directory: $TEMPDIR"
+
+    else
+
+          # IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
+       printf "\n  *** running in temporary directory: $TEMPDIR"
+
+    fi
+
+
+       # PROVIDE THE INPUT FILES
+       # LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
+    (( i = 0 ))
+    while (( i < iin ))
+    do
+       (( i = i + 1 ))
+       if (( i == 1 ))
+       then
+          printf "\n\n  *** providing INPUT-files:\n$dashes"
+       fi
+
+
+          # SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
+       if [[ "${transin[$i]}" = unavailable ]]
+       then
+          if [[ "${extin[$i]}" = ""  ||  "${extin[$i]}" = " " ]]
+          then
+             printf "\n  *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
+             printf "\n                   is not available!"
+          else
+             printf "\n  *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
+             printf "\n                   is not available!"
+          fi
+          continue
+       fi
+
+          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
+       files_for_cores=false; filetype=file
+       if [[ "${actionin[$i]}" = pe  &&  -n $cores ]]
+       then
+          files_for_cores=true; filetype=files
+          actionin[$i]=""
+       elif [[ "${actionin[$i]}" = pe  &&  ! -n $cores ]]
+       then
+          actionin[$i]=""
+       elif [[ "${actionin[$i]}" = lnpe  &&  -n $cores ]]
+       then
+          files_for_cores=true; filetype=files
+          actionin[$i]="ln"
+       elif [[ "${actionin[$i]}" = lnpe  &&  ! -n $cores ]]
+       then
+          actionin[$i]="ln"
+       fi
+
+       if [[ $files_for_cores = true ]]
+       then
+          printf "\n  >>> INPUT: ${absnamein[$i]}/....  to  ${localin[$i]}"
+       else
+          printf "\n  >>> INPUT: ${absnamein[$i]}  to  ${localin[$i]}"
+       fi
+
+          # INPUT-FILES TO BE LINKED
+       if [[ "${actionin[$i]}" = ln ]]
+       then
+
+          printf "\n      $filetype will be linked"
+          if [[ $files_for_cores = false ]]
+          then
+             if [[ -f "${absnamein[$i]}" ]]
+             then
+                ln  ${absnamein[$i]}  ${localin[$i]}
+                got_tmp[$i]=true
+             fi
+          else
+             if [[ -d "${absnamein[$i]}" ]]
+             then
+                mkdir  ${localin[$i]}
+                cd ${absnamein[$i]}
+                for file in $(ls *)
+                do
+                   ln $file $TEMPDIR/${localin[$i]}
+                done >|/dev/null 2>&1
+                cd $TEMPDIR
+             fi
+
+                # IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
+             if [[ ! -f "${localin[$i]}/_000000" ]]
+             then
+                printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
+                cp -r  ${absnamein[$i]}/*  ${localin[$i]}
+             fi
+
+             got_tmp[$i]=true
+          fi
+       fi
+
+          # FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
+       if [[ "${actionin[$i]}" = ""  ||  "${actionin[$i]}" = "di"  ||  "${actionin[$i]}" = "npe" ]]
+       then
+
+          if [[ "${actionin[$i]}" = "npe"  &&  -n $cores ]]
+          then
+
+                # FILE COPIES ARE PROVIDED FOR ALL CORES
+                # EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
+             printf "\n      file will be provided for $cores processors"
+             mkdir  ${localin[$i]}
+             ival=$cores
+             (( ii = 0 ))
+             while (( ii <= ival-1 ))
+             do
+                if (( ii < 10 ))
+                then
+                   cp  ${absnamein[$i]}  ${localin[$i]}/_000$ii
+                elif (( ii < 100 ))
+                then
+                   cp  ${absnamein[$i]}  ${localin[$i]}/_00$ii
+                elif (( ii < 1000 ))
+                then
+                   cp  ${absnamein[$i]}  ${localin[$i]}/_0$ii
+                else
+                   cp  ${absnamein[$i]}  ${localin[$i]}/_$ii
+                fi
+                (( ii = ii + 1 ))
+             done
+
+          else
+
+             if [[ $files_for_cores = true ]]
+             then
+
+                   # PROVIDE FILES FOR EACH CORE
+                   # FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
+                   # FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
+                printf "\n      providing $cores files for the respective cores"
+                mkdir  ${localin[$i]}
+	              	if [[ $link_local_input = true ]]
+		              then
+		                 printf "      files will be linked\n"
+		                 cd ${absnamein[$i]}
+		                 for file in $(ls *)
+		                 do
+		                    ln -f $file  ${localin[$i]}
+		                 done
+		                 cd $TEMPDIR
+		              fi
+
+                   # IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
+		              if [[ ! -f "${localin[$i]}/_000000" ]]
+		              then
+		                 if [[ $link_local_input = true ]]
+		                	then
+	                   		printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
+		                 fi
+		                 cp -r  ${absnamein[$i]}/*  ${localin[$i]}
+		              fi
+
+             else
+
+                   # PROVIDE FILE FOR RUNS ON A SINGLE CORE
+              		if [[ $link_local_input = true ]]
+	              	then
+		                 printf "      file will be linked\n"
+		                 ln -f  ${absnamein[$i]}  ${localin[$i]}
+	              	fi
+	                 	# If "ln -f" fails of if "$link_local_input = false" do a normal "cp"
+	              	if [[ ! -f "${localin[$i]}" ]]
+                then
+		                 if [[ $link_local_input = true ]]
+	                  then
+                      printf "\n  --- WARNING: ln failed, using cp instead (might be time consuming...)"
+		                 fi
+		                 cp  ${absnamein[$i]}  ${localin[$i]}
+                fi
+             fi
+          fi
+       fi
+
+    done
+    if (( i != 0 ))
+    then
+       printf "\n$dashes\n  *** all INPUT-files provided \n"
+    fi
+
+
+       # EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
+    (( i = 0 ))
+    while (( i < iic ))
+    do
+       (( i = i + 1 ))
+       if (( i == 1 ))
+       then
+          printf "\n\n  *** execution of INPUT-commands:\n$dashes"
+       fi
+       printf "\n  >>> ${in_command[$i]}"
+       eval  ${in_command[$i]}
+       if (( i == iic ))
+       then
+          printf "\n$dashes\n"
+       fi
+    done
+
+
+       # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
+       # (FILE ENVPAR WILL BE READ BY PALM)
+    cat  >  ENVPAR  <<  EOF
+ &envpar  run_identifier = '$fname', host = '$host',
+          write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
+          maximum_parallel_io_streams = $maximum_parallel_io_streams,
+          maximum_cpu_time_allowed = ${cpumax}.,
+          revision = '$global_revision',
+          batch_job = .${running_in_batch_mode}. /
+
+EOF
+
+
+       # STARTING THE EXECUTABLE
+    printf "\n\n  *** execution starts in directory\n      \"`pwd`\"\n$dashes\n"
+    PATH=$PATH:$TEMPDIR
+
+
+       # REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
+    line=`echo  "${execute_command}" | sed 's/@MPI_TASKS@/$mpi_tasks/g' | sed 's/@TASKS_PER_NODE@/$tasks_per_node/g'`
+    line2=`echo  "${execute_command}" | sed 's/@MPI_TASKS@/1/g' | sed 's/@TASKS_PER_NODE@/1/g' | sed 's/palm/combine_plot_fields.x/g'`
+    eval line=\"$line\"
+    execute_command="$line"
+
+
+       # EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
+    eval line2=\"$line2\"
+    execute_command_for_combine="$line2"
+
+
+       # PROVIDE A HOSTFILE, IF REQUIRED
+    if [[ "$hostfile" != "" ]]
+    then
+
+       if [[ $hostfile = auto ]]
+       then
+             # CREATE A NEW HOSTFILE
+          (( ii = 1 ))
+          while (( ii <= cores / threads_per_task ))
+          do
+             echo  $(hostname)  >>  hostfile
+             (( ii = ii + 1 ))
+          done
+          if (( cores / threads_per_task == 0 ))
+          then
+             echo  $(hostname)  >>  hostfile
+          fi
+       
+       else
+          cp  $hostfile  hostfile
+       fi
+       eval line=\"`head -n $ii  hostfile`\"
+       printf "\n  *** running on: $line"
+    fi
+
+
+
+       # SET THE NUMBER OF OPENMP-THREADS
+    if [[ $use_openmp = true ]]
+    then
+       export OMP_NUM_THREADS=$threads_per_task
+       printf "\n  *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
+    else
+       export OMP_NUM_THREADS=1
+    fi
+
+
+       # PROVIDE DATA FOR 
+    if [[ $run_coupled_model = false ]]
+    then
+       if [[ "$ocean_file_appendix" = true ]]
+       then
+          echo "precursor_ocean"  >  coupling_steering
+       else
+          echo "precursor_atmos"  >  coupling_steering
+      fi
+    else
+       (( iia = $cores_atmos / $threads_per_task ))
+       (( iio = $cores_ocean / $threads_per_task ))
+       printf "\n      coupled run ($iia atmosphere, $iio ocean)"
+       printf "\n\n"
+       echo "coupled_run $iia $iio"  >  coupling_steering
+    fi
+
+    printf "\n  *** execute command:"
+    printf "\n      \"$execute_command\" \n\n"
+
+    $execute_command  <  coupling_steering
+
+    if [[ $? != 0 ]]
+    then
+
+           # ABORT IN CASE OF RUNTIME ERRORS
+       printf "\n  +++ runtime error occured"
+       locat=execution
+       exit
+
+    else
+
+       printf "\n$dashes\n  *** execution finished \n"
+
+    fi
+
+
+       # CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
+       # BY EACH CORE INTO ONE FILE
+   if [[ ! -f combine_plot_fields.x ]]
+   then
+
+      printf "\n\n\n  +++ WARNING: no combine_plot_fields found"
+      printf "\n      2d- and/or 3d-data may be incomplete!"
+      printf "\n      Your previous palmbuild may have failed. Please check.\n"
+
+   elif [[ "$combine_plot_fields" == true ]]
+   then
+
+      printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
+      $execute_command_for_combine
+
+   else
+
+         # TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
+         # DATA OUTPUT. TO DO: EXTEND THIS BRANCH BY CREATING A BATCH JOB for combine_plot_fields.
+         # ??? koennen wir das streichen ???
+      printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
+   fi
+
+
+
+       # EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
+    (( i = 0 ))
+    while (( i < ioc ))
+    do
+       (( i = i + 1 ))
+       if (( i == 1 ))
+       then
+          printf "\n\n  *** execution of OUTPUT-commands:\n$dashes"
+       fi
+       printf "\n  >>> ${out_command[$i]}"
+       eval  ${out_command[$i]}
+       if (( i == ioc ))
+       then
+          printf "\n$dashes\n"
+       fi
+    done
+
+
+       # IN TRACE-MODE PRINT CONTENTS OF THE CURRENT (TEMPORARY) WORKING DIRECTORY
+    if [[ $do_trace = true ]]
+    then
+       printf "\n\n"
+       ls -al
+    fi
+    
+
+       # COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
+    (( i = 0 ))
+    while (( i < iout ))
+    do
+       (( i = i + 1 ))
+       if (( i == 1 ))
+       then
+          printf "\n\n  *** saving OUTPUT-files:"
+
+             # GET RUN NUMBER ASSIGNED BY PALM
+          if [[ -f RUN_NUMBER ]]
+          then
+              read  run_number  <  RUN_NUMBER
+              printf "\n  *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
+              usecycle_option="-U $run_number"
+          else
+              run_number=0
+              usecycle_option=""
+          fi
+          if [[ $running_on_remote = true  &&  "$remote_loginnode" != "" ]]
+          then
+             printf "\n  *** SCP transfers to local host via remote login-node \"$remote_loginnode\" "
+          fi
+          printf "\n$dashes"
+       fi
+
+          # ADD CYCLE NUMBER TO FILENAME
+       if [[ ! ( $running_on_remote = true  &&  ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]]
+       then
+
+              # IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
+          if [[ "${actionout[$i]}" != "a" ]]
+          then
+                # SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
+                # WITH AN EXISTING CYCLE NUMBER
+             if (( run_number >= cycnum[$i] ))
+             then
+                (( cycnum[$i] = run_number ))
+             else
+                if (( run_number > 0 ))
+                then
+                   printf "\n  --- INFORMATIVE: The following file cannot get a unified cycle number"
+                fi
+             fi
+          fi
+          if (( cycnum[$i] > 0 ))
+          then
+             pathout[$i]=${pathout[$i]}.${cycnum[$i]}
+          fi
+       fi           
+
+          # CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
+       files_for_cores=false; filetype=file
+       link_local_output=false
+       if [[ "${actionout[$i]}" = pe  &&  -n $cores ]]
+       then
+          files_for_cores=true; filetype=directory
+          actionout[$i]=""
+       elif [[ "${actionout[$i]}" = pe  &&  ! -n $cores ]]
+       then
+          actionout[$i]=""
+       elif [[ "${actionout[$i]}" = lnpe  &&  -n $cores ]]
+       then
+          files_for_cores=true; filetype=directory
+          link_local_output=true
+          actionout[$i]=""
+       elif [[ "${actionout[$i]}" = lnpe  &&  ! -n $cores ]]
+       then
+          link_local_output
+          actionout[$i]=""
+       elif [[ "${actionout[$i]}" = trpe  &&  -n $cores ]]
+       then
+          files_for_cores=true; filetype=directory
+          actionout[$i]="tr"
+       elif [[ "${actionout[$i]}" = trpe  &&  ! -n $cores ]]
+       then
+          actionout[$i]="tr"
+       fi
+
+       if [[ ! -f ${localout[$i]}  &&  $files_for_cores = false ]]
+       then
+          printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}  does not exist\n"
+       elif [[ ! -d ${localout[$i]}  &&  $files_for_cores = true ]]
+       then
+          printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}/....  does not exist\n"
+       else
+
+
+             # COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
+             # IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
+          if [[ "${actionout[$i]}" = tr  ||  "${actionout[$i]}" = tra ]]
+          then
+             if [[ $running_on_remote = true ]]
+             then
+
+                   # SET OPTIONS FOR TRANSFER
+                if [[ "${actionout[$i]}" = tr ]]
+                then
+                   if [[ $files_for_cores = false ]]
+                   then
+                      catalog_option=""
+                      catalog_string=""
+                   else
+                      catalog_option="-c"
+                      catalog_string="/"
+                   fi
+                   append_option=""
+                   append_string=""
+                else
+                   append_option="-A"
+                   append_string="append"
+                fi
+
+                transfer_failed=false
+                printf "\n  >>> OUTPUT: ${localout[$i]}$catalog_string  $append_string by SCP to"
+                printf "\n              ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}$catalog_string\n"
+
+                   # TRANSFER VIA SCP
+                if [[ "$remote_loginnode" != "" ]]
+                then
+                   echo "cd $TEMPDIR; ${tmp_user_catalog}/SOURCES_FOR_RUN_${fname}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address  ${localout[$i]} \"${pathout[$i]}\" ${remote_hostname}_${fname}${endout[$i]}  ${extout[$i]}"  |  ssh -q $remote_username@$remote_loginnode
+                else
+                   batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address  ${localout[$i]} "${pathout[$i]}" ${remote_hostname}_${fname}${endout[$i]}  ${extout[$i]}
+                fi
+                [[ $? != 0 ]]  &&  transfer_failed=true
+
+
+                   # IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
+                if [[ $transfer_failed = true ]]
+                then
+                   printf "  +++ transfer failed. Trying to save a copy on this host under:\n"
+                   printf "      ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}_$run_id\n"
+
+                      # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
+                   eval  local_catalog=${pathout[$i]}
+                   if [[ ! -d $local_catalog ]]
+                   then
+                      printf "  *** local directory does not exist. Trying to create:\n"
+                      printf "      $local_catalog \n"
+                      mkdir -p  $local_catalog
+                   fi
+                   eval  cp  ${localout[$i]}  ${pathout[$i]}/${remote_hostname}_${fname}${endout[$i]}_$run_id
+                   transfer_problems=true
+                fi
+
+             else
+
+                   # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
+                   # BE COPIED OR APPENDED ON THIS MACHINE
+                if [[ "${actionout[$i]}" = tr ]]
+                then
+                   actionout[$i]=""
+                else
+                   actionout[$i]="a"
+                fi
+             fi
+          fi
+
+
+             # APPEND ON THIS MACHINE
+          if [[ "${actionout[$i]}" = "a" ]]
+          then
+             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
+             then
+                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
+                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
+                cat  ${localout[$i]}  >>  ${pathout[$i]}.${extout[$i]}
+             else
+                printf "\n  >>> OUTPUT: ${localout[$i]}  append to"
+                printf "\n              ${pathout[$i]}\n"
+                cat  ${localout[$i]}  >>  ${pathout[$i]}
+             fi
+          fi
+
+             # COPY ON THIS MACHINE
+             # COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
+             # ON DIFFERENT FILE-SYSTEMS
+          if [[ "${actionout[$i]}" = ""  &&  $files_for_cores = false ]]
+          then
+
+                # COPY IN CASE OF RUNS ON SINGLE CORES
+             if [[ "${extout[$i]}" != " "  &&  "${extout[$i]}" != "" ]]
+             then
+                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
+                printf "\n              ${pathout[$i]}.${extout[$i]}\n"
+		              if [[ $link_local_output = true ]]
+		              then
+		                 printf "      file will be linked\n"
+		                 ln -f  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
+		              fi
+		                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
+		              if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
+                then
+		                 if [[ $link_local_output = true ]]
+	                  then
+                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
+		                 fi
+		                 cp  ${localout[$i]}  ${pathout[$i]}.${extout[$i]}
+		              else
+                   printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
+                fi
+             else
+                printf "\n  >>> OUTPUT: ${localout[$i]}  to"
+                printf "\n              ${pathout[$i]}\n"
+		              if [[ $link_local_output = true ]]
+		              then
+		                 printf "      file will be linked\n"
+		                 ln -f  ${localout[$i]}  ${pathout[$i]}
+		              fi
+		                 # If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
+	              	if [[ ! -f "${pathout[$i]}" ]]
+                then
+		                 if [[ $link_local_output = true ]]
+	                  then
+                      printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
+		                 fi
+		                 cp  ${localout[$i]}  ${pathout[$i]}
+		              else
+		                 printf "+++ no copy because file ${pathout[$i]} exists\n"
+                fi
+             fi
+
+          elif [[ "${actionout[$i]}" = ""  &&  $files_for_cores = true ]]
+          then
+
+                # FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
+                # AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
+             printf "\n  >>> OUTPUT: ${localout[$i]}/_....  to"
+             printf "\n              ${pathout[$i]}\n"
+	            if [[ $link_local_output = true ]]
+	            then
+		              printf "      files will be linked\n"
+		              mkdir  ${pathout[$i]}
+		              cd ${localout[$i]}
+		              for file in $(ls *)
+		              do
+		                 ln -f $file  ${pathout[$i]}
+		              done >|/dev/null 2>&1
+		              cd $TEMPDIR
+	            fi
+
+                # IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
+	            if [[ ! -f "${pathout[$i]}/_000000" ]]
+             then
+		              if [[ $link_local_output = true ]]
+		              then
+                   printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
+		              fi
+		              cp -r  ${localout[$i]}/*  ${pathout[$i]}
+       	     fi
+
+          fi
+       fi
+    done
+
+    if (( i != 0 ))
+    then
+       if [[ $transfer_problems = true ]]
+       then
+          printf "\n$dashes\n  *** OUTPUT-files saved"
+          printf "\n  +++ WARNING: some data transfers failed! \n"
+       else
+          printf "\n$dashes\n  *** all OUTPUT-files saved \n"
+       fi
+    fi
+
+
+       # IF REQUIRED, START A RESTART-JOB
+       # FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
+    if [[ -f CONTINUE_RUN ]]
+    then
+
+          # ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
+          # -C TELLS PALMRUN THAT IT IS A RESTART-RUN
+          # -v SILENT MODE WITHOUT INTERACTIVE QUERIES
+          # -b START A BATCH JOB
+       [[ $(echo $prc | grep -c "\-C") = 0 ]]  &&  prc="$prc -C"
+       [[ $(echo $prc | grep -c "\-v") = 0 ]]  &&  prc="$prc -v"
+       [[ $(echo $prc | grep -c "\-b") = 0 ]]  &&  prc="$prc -b"
+
+
+          # REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
+          # SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
+       if [[ $(echo $prc | grep -c "#") != 0 ]]
+       then
+          prc=`echo $prc | sed 's/#/f/g'`
+       fi
+
+
+          # START THE RESTART-JOB
+       printf "\n\n  *** initiating restart-run on \"$local_ip\" using command:\n"
+       echo "      $prc"
+       printf "\n$dashes\n"
+       if [[ $running_on_remote = true ]]
+       then
+
+          echo "*** ssh will be used to initiate restart-runs!"
+          echo "    return_address=\"$return_address\" "
+          echo "    return_username=\"$local_username\" "
+
+          if [[ "$remote_loginnode" != "" ]]
+          then
+             echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; export PALM_BIN=$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address  " |  ssh -q $remote_username@$remote_loginnode
+          else
+             echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; export PALM_BIN=$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address
+          fi
+
+             # WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
+          sleep 30
+
+       else
+
+             # START THE RESTART JOB ON THE LOCAL HOST
+          eval  $prc                # THE ' MUST BE EVALUATED
+          cd -  > /dev/null
+
+       fi
+       printf "\n$dashes\n  *** restart-run initiated \n"
+
+
+          # DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
+          # DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
+          # THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
+          # MAY BE VERY HUGE)
+       (( i = 0 ))
+       while (( i < iin ))
+       do
+          (( i = i + 1 ))
+          if [[ "${got_tmp[$i]}" = true   &&  $keep_data_from_previous_run = false ]]
+          then
+             rm -r  ${absnamein[$i]}
+          fi
+       done
+
+    fi
+
+
+       # ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
+    cd  $HOME
+    [[ $delete_temporary_catalog = true ]]  &&  rm -rf $TEMPDIR
+
+
+ else
+
+
+       # PREPARING ACTIONS,
+       # IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
+
+       # BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
+    palmrun_com="$palmrun_script_name -c $config_file -d $fname -h $host -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
+    [[ "$activation_string_list" != "" ]]  &&  palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
+    [[ "$global_revision" != "" ]]  &&  palmrun_com=${palmrun_com}" -G \"$global_revision\""
+    [[ $keep_data_from_previous_run = true ]]  &&  palmrun_com=${palmrun_com}" -k"
+    [[ $do_trace = true ]]        &&  palmrun_com=${palmrun_com}" -x"
+    [[ "$cores" != "" ]]       &&  palmrun_com=${palmrun_com}" -X $cores"
+    [[ $use_openmp = true ]]  &&  palmrun_com=${palmrun_com}" -O $threads_per_task"
+    [[ "$tasks_per_node" != "" ]]  &&  palmrun_com=${palmrun_com}" -T $tasks_per_node"
+    [[ $delete_temporary_catalog = false ]]  &&  palmrun_com=${palmrun_com}" -B"
+    [[ "$ocean_file_appendix" = true ]]  &&  palmrun_com=${palmrun_com}" -y"
+    [[ $run_coupled_model = true ]]  &&  palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
+    [[ "$combine_plot_fields" = false ]]  &&  palmrun_com=${palmrun_com}" -Z"
+    [[ "$max_par_io_str" != "" ]]  &&  palmrun_com=${palmrun_com}" -w $max_par_io_str"
+    if [[ $create_remote_batch_job = true ]]
+    then
+       palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
+       printf "\n *** PALMRUN-command on remote host:\n     $palmrun_com \n"
+    elif [[ $create_batch_job = true ]]
+    then
+       palmrun_com=${palmrun_com}" -j"
+       printf "\n *** PALMRUN-command on local host:\n     $palmrun_com \n"
+    fi
+
+
+       # DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
+       # REMOTE HOST
+    job_protocol_file_local=${local_jobcatalog}/${host}_${job_id}
+    job_protocol_file=$job_protocol_file_local
+    if [[ $create_remote_batch_job = true ]]
+    then
+       job_protocol_file_remote=${remote_jobcatalog}/${host}_${job_id}
+       job_protocol_file=$job_protocol_file_remote
+       job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
+       scpjob_file=${remote_jobcatalog}/scpjob.$run_id
+    fi
+
+
+       # BUILD THE JOB-SCRIPTS ON FILE jobfile
+    jobfile=jobfile.$run_id
+
+
+       # FIRST CREATE THE BATCH DIRECTIVES
+    (( i = 0 ))
+    while (( i < ibd ))
+    do
+       (( i = i + 1 ))
+       line=`echo  "${batch_directive[$i]}" | sed 's/@JOB_ID@/$job_id/g' | sed 's/@JOBFILE@/$job_protocol_file/g' | sed 's/@CPU_HOURS@/$cpu_hours/g' | sed 's/@CPU_MINUTES@/$cpu_minutes/g' | sed 's/@CPU_SECONDS@/$cpu_seconds/g' | sed 's/@NODES@/$nodes/g' | sed 's/@CORES@/$cores/g' | sed 's/@TASKS_PER_NODE@/$tasks_per_node/g' | sed 's/@LOCAL_HOSTNAME@/${local_hostname}/g' | sed 's/@HOST@/${host}/g' | sed 's/@FNAME@/$fname/g' | sed 's/@QUEUE@/$queue/g'`
+       eval line=\"$line\"
+       echo  "$line"                               >>  $jobfile
+    done
+    echo " "                                       >>  $jobfile
+
+
+       # FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
+       # PROTOCOL
+    if [[ $create_remote_batch_job = true ]]
+    then
+       echo "set +vx"                              >>  $jobfile
+       echo "trap '"                               >>  $jobfile
+       echo "set +vx"                              >>  $jobfile
+       echo "cd ${remote_jobcatalog}"              >>  $jobfile
+       echo "cat >  scpjob.$run_id << %%END%%"     >>  $jobfile
+
+          # ADD THE BATCH DIRECTIVES
+       (( i = 0 ))
+       while (( i < ibdt ))
+       do
+          (( i = i + 1 ))
+          line=`echo  "${batch_directive_transfer[$i]}" | sed 's/@JOB_ID@/$job_id/g' | sed 's/@JOBFILE@/$job_protocol_file/g' | sed 's/@JOB_TRANSFER_PROTOCOL_FILE@/$job_transfer_protocol_file/g' | sed 's/@CPU_HOURS@/$cpu_hours/g' | sed 's/@CPU_MINUTES@/$cpu_minutes/g' | sed 's/@CPU_SECONDS@/$cpu_seconds/g' | sed 's/@NODES@/$nodes/g' | sed 's/@TASKS_PER_NODE@/$tasks_per_node/g' | sed 's/@LOCAL_HOSTNAME@/${local_hostname}/g' | sed 's/@HOST@/${host}/g' | sed 's/@FNAME@/$fname/g'`
+          eval line=\"$line\"
+          echo  "$line"                            >>  $jobfile
+       done
+       echo " "                                    >>  $jobfile
+
+       echo "set -x"                               >>  $jobfile
+       echo "${tmp_user_catalog}/SOURCES_FOR_RUN_${fname}/batch_scp  $PORTOPT  -d  -w 10  -u $local_username $local_ip  $job_protocol_file_remote  \"$local_jobcatalog\"  ${host}_${fname}"  >>  $jobfile
+       echo "%%END%%"                              >>  $jobfile
+       echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" "  >>  $jobfile
+       echo "$submit_command  $scpjob_file"        >>  $jobfile
+       echo "rm $scpjob_file"                      >>  $jobfile
+       echo "rm $job_transfer_protocol_file"       >>  $jobfile
+       echo "set -x"                               >>  $jobfile
+       echo "     ' exit"                          >>  $jobfile
+    fi
+
+
+       # ACTIVATE ERROR-TRACEBACK
+    if [[ $do_trace = true ]]
+    then
+       echo  "set -x"                                    >>  $jobfile
+    else
+       echo  "set +vx"                                   >>  $jobfile
+    fi
+
+
+       # INITIALIZE THE ENVIRONMENT AND LOAD MODULES
+    if [[ "$login_init_cmd" != "" ]]
+    then
+       echo  "$login_init_cmd"        >>  $jobfile
+    fi
+    if [[ "$module_commands" != "" ]]
+    then
+       echo  "$module_commands"     >>  $jobfile
+    fi
+
+
+       # CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
+    echo  "mkdir  $TEMPDIR"              >>  $jobfile
+    echo  "cd  $TEMPDIR"                 >>  $jobfile
+    echo  "export TEMPDIR=$TEMPDIR"      >>  $jobfile
+    echo  "cp  $tmp_user_catalog/SOURCES_FOR_RUN_$fname/{*,.[!.]*}  ."  >>  $jobfile
+    echo  "export PATH=.:\$PATH"         >>  $jobfile
+    echo  "export execute_palmrun=true"  >>  $jobfile
+
+
+       # GET REQUIRED INPUT-FILES BY SCP OR BY SENDING THEM WITH THE JOB AS HERE-DOCUMENT
+       # PUT THESE FILES INTO THE USER'S RESPECTIVE PERMANENT DIRECTORIES ON THE REMOTE-HOST
+       # IF THE DIRECTORIES DO NOT EXIST, TRY TO CREATE THEM
+    if [[ $create_remote_batch_job = true ]]
+    then
+       (( i = 0 ))
+       while (( i < iin ))
+       do
+          (( i = i + 1 ))
+          echo  "[[ ! -d ${pathin[$i]} ]]  &&  mkdir -p  ${pathin[$i]}"  >>  $jobfile
+          if [[ "${transin[$i]}" = job ]]
+          then
+             echo  "cat > ${remotepathin[$i]} <<\"%END%\""    >>  $jobfile
+             eval cat   ${pathin[$i]}/${frelin[$i]}           >>  $jobfile
+             echo  " "                                        >>  $jobfile
+             echo  "%END%"                                    >>  $jobfile
+          else
+             echo  "batch_scp $PORTOPT -b -o -g -s -u $local_username $return_address ${remotepathin[$i]} \"${pathin[$i]}\" ${frelin[$i]}" >>  $jobfile
+          fi
+
+             # CHECK, IF FILE COULD BE CREATED
+          echo  "if [[ \$? = 1 ]]"                    >>  $jobfile
+          echo  "then"                                >>  $jobfile
+          echo  "   echo \" \" "                      >>  $jobfile
+          echo  "   echo \"+++ file ${remotepathin[$i]} could not be created\" "   >>  $jobfile
+          echo  "   echo \"    please check, if directory exists on $host!\" "  >>  $jobfile
+          echo  "   echo \"+++ PALMRUN will not be continued\" "  >>  $jobfile
+          echo  "   execute_palmrun=false"            >>  $jobfile
+          echo  "fi"                                  >>  $jobfile
+       done
+    fi
+
+
+       # PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
+       # STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
+       # IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
+    echo  "LOCAL_PWD=$working_directory"                >>  $jobfile
+    echo  "export LOCAL_PWD"                            >>  $jobfile
+
+
+       # PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON 
+    echo  "LOCAL_PALMRUN_PATH=$PALM_BIN"                   >>  $jobfile
+    echo  "export LOCAL_PALMRUN_PATH"                      >>  $jobfile
+
+
+       # CALL PALMRUN WITHIN THE JOB
+       # AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
+    echo  "set -x"                                              >>  $jobfile
+    echo  "[[ \$execute_palmrun = true ]]  &&  $palmrun_com"    >>  $jobfile
+
+
+       # TRANSFER JOBFILE TO THE TARGET HOST
+    if [[ $create_jobfile_only = false ]]
+    then
+
+       if [[ $create_remote_batch_job = true ]]
+       then
+
+          echo " *** transfer of job to remote host via scp"
+          echo "     scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${job_directory}/${host}_${job_id}"
+          scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${job_directory}/${host}_${job_id}
+
+          echo " "
+          echo " *** submit the job"
+          echo "     cd $job_directory; $submit_command ${host}_${job_id}; rm ${host}_${job_id}  |  ssh  -q  $ssh_key $SSH_PORTOPT  ${remote_username}@${remote_ip}  2>&1"
+          echo "cd $job_directory; $submit_command ${host}_${job_id}; rm ${host}_${job_id}"  |  ssh  -q  $ssh_key $SSH_PORTOPT  ${remote_username}@${remote_ip}  2>&1
+
+       elif [[ $create_batch_job = true ]]
+       then
+
+          eval  job_directory=$job_directory
+          cp  $jobfile  ${job_directory}/${host}_${job_id}
+          cd $job_directory
+          echo " "
+          echo "--- submit the job"
+          echo "$submit_command ${host}_${job_id}"
+          $submit_command ${host}_${job_id}
+          rm ${host}_${job_id}
+          cd -  > /dev/null
+
+       fi
+
+       rm -rf  $jobfile
+
+    else
+
+       printf "\n *** jobfile created under name \"$jobfile\" "
+       printf "\n     no batch-job has been sent!"
+
+    fi
+
+ fi  # END OF REMOTE-PART
Index: palm/trunk/UTIL/Makefile_utilities
===================================================================
--- palm/trunk/UTIL/Makefile_utilities	(revision 2380)
+++ palm/trunk/UTIL/Makefile_utilities	(revision 2380)
@@ -0,0 +1,75 @@
+#--------------------------------------------------------------------------------#
+# This file is part of PALM.
+#
+# PALM 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.
+#
+# PALM 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
+# PALM. If not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright 1997-2014  Leibniz Universitaet Hannover
+#--------------------------------------------------------------------------------#
+#
+# Current revisions:
+# -----------------
+# file renamed to Makefile_utilities
+# executables are created in current working directory
+# interpret_config removed
+#
+# Former revisions:
+# -----------------
+# $Id$
+#
+# 1046 2012-11-09 14:38:45Z maronga
+# code put under GPL (PALM 3.9)
+#
+# utility programs are created separately for each block in the configuration
+# file,
+# compare_palm_logs added
+# added PROG3 in 'all:' statement (line 39, bugfix)
+#
+# Initial revision somewhere in 2003/04
+#
+# Description:
+# ------------
+# Makefile for generating the utility programs required by mrun and palm
+#--------------------------------------------------------------------------------#
+
+PROG1 =  combine_plot_fields.x
+PROG2 =  compare_palm_logs.x
+
+OBJS1 =  combine_plot_fields.o
+OBJS2 =  compare_palm_logs.o
+
+CC = cc
+CFLAGS = -O
+
+F90 =
+F90_SER =
+COPT =
+F90FLAGS =
+LDFLAGS =
+
+.SUFFIXES: $(SUFFIXES) .f90
+
+
+all: $(PROG1) $(PROG2) $(PROG3)
+
+$(PROG1): $(OBJS1)
+	$(F90_SER) -o $(PROG1) $(OBJS1) $(LDFLAGS)
+
+$(PROG2): $(OBJS2)
+	$(F90_SER) -o $(PROG2) $(OBJS2) $(LDFLAGS)
+
+$(PROG3): $(OBJS3)
+	$(F90_SER) -o $(PROG3) $(OBJS3) $(LDFLAGS)
+
+.f90.o:
+	$(F90_SER) $(F90FLAGS) $(COPT) -c $<
+
+
