#!/bin/bash

# palmrun - script for running PALM jobs

#--------------------------------------------------------------------------------#
# This file is part of the PALM model system.
#
# 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 2017-2018  Leibniz Universitaet Hannover
#--------------------------------------------------------------------------------#
#
# Current revisions:
# ------------------
# 
# 
# Former revisions:
# -----------------
# $Id: palmrun 3151 2018-07-19 08:45:38Z schwenkel $
# removed additional listing of files to be compiled, print PALM code revision
# in header
# 
# 3132 2018-07-16 11:44:58Z raasch
# create consistent error messages in case of failed restarts,
# check existence of remote job catalog
# 
# 3043 2018-05-25 10:47:54Z raasch
# check for setting of fast_io_catalog
# 
# 3033 2018-05-23 15:26:19Z raasch
# -T option not required for interactive runs (tasks per node =
# total number of cores is assumed as default, if option is not given),
# reformatting of a few messages,
# bugfix: destination output directory is created if attribute "pe" is set in
# .palm.iofiles
# 
# 2718 2018-01-02 08:49:38Z maronga
# bugfix of r2990
# 
# 2718 2018-01-02 08:49:38Z maronga
# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
#         not in the working directory from where palmrun is called
# 
# 2718 2018-01-02 08:49:38Z maronga
# svfout in the activation string will be replaced now by svfin in case of 
# automatic restarts
# 
# 2718 2018-01-02 08:49:38Z maronga
# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
# the possible output or input of sky view factors
# 
# 2718 2018-01-02 08:49:38Z maronga
# "fname" renamed to "jobname"
# 
# 2718 2018-01-02 08:49:38Z maronga
# parameters are allowed in output commands (OC:)
# 
# 2718 2018-01-02 08:49:38Z maronga
# bugfix: exit if no queue has been given neither with option -q nor in the
# configuration file 
# 
# 2718 2018-01-02 08:49:38Z maronga
# file connection file from trunk/SCRIPTS is taken by default
# 
# 2718 2018-01-02 08:49:38Z maronga
# Corrected "Former revisions" section
# 
# 2696 2017-12-14 17:12:51Z kanani
# Change in file header (GPL part)
#
# 2693 2017-12-13 12:33:49Z raasch
# replacement of variables given by {{<variable>}} in configuration file is now
# done in a more general way, variable names are written in small letters
# 
# 2670 2017-12-06 16:32:19Z raasch
# test printouts removed
# 
# 2669 2017-12-06 16:03:27Z raasch
# file attributes in .palm.iofiles restructured, "loc" attribute completely
# removed,
# wildcard (*) allowed in .palm.iofiles as file activation string for output
# files,
# informative messages in case of missing optional input files shortened
# bugfix: variable cycle explicitly interpreted with 10 as the number base
# 
# 2638 2017-11-23 12:44:23Z raasch
# use of wildcards in file connection statements enabled
# 
# 2605 2017-11-09 15:31:46Z raasch
# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
# will not be sent with the job file any more, but copied into the
# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
# 
# 2600 2017-11-01 14:11:20Z raasch
# cycle numbers are made three digits wide
# 
# 2566 2017-10-20 08:50:47Z raasch
# execute command for combine_plot_fields added
# "TEMPDIR" renamed "tempdir"
# temporary working directory for local batch jobs is created immediately within
# the user's palmrun call, due to a requirement of the "grid engine" batch
# system, where the working directory is given with batch directive -wd and must
# already exist when the job is submitted,
# informative messages in non-trace mode reduced and partly reformatted
# 
# 2551 2017-10-18 07:25:11Z raasch
# TEMPDIR added as replacement string to be used in batch directives
# 
# 2512 2017-10-04 08:26:59Z raasch
# bugfix for determining cycle numbers of NetCDF input files
# 
# 2506 2017-09-29 08:30:37Z raasch
# option -V added to check for an existing SOURCES_FOR_RUN_... folder
# host configuration added to SOURCES_FOR_RUN_... folder name
# host_identifier renamed host_configuration
# option -W added to allow for job dependencies
# 
# 2501 2017-09-26 11:41:55Z raasch
# default value for number of cores (option -X) set to 1
# bugfix for mechanism which overwrites configuration file settings with values
# provided by palmrun options
# 
# 2499 2017-09-22 16:47:58Z kanani
# option -h named configuration identifier
# 
# 2480 2017-09-19 06:24:14Z maronga
# bugfix for last revision
# 
# 2479 2017-09-19 06:12:16Z raasch
# option -A (project account number) added
# 
# 2422 2017-09-08 08:25:41Z raasch
# initial revision
# 
#--------------------------------------------------------------------------------#
# 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 nr_of_input_files=0
 typeset -i  nr_of_output_files=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=""
 combine_plot_fields=true
 compiler_name=""
 compiler_name_ser=""
 compiler_options=""
 cores=1
 cores_atmos=0
 cores_ocean=0
 coupled_dist=""
 cpp_options=""
 cpumax=0
 create_batch_job=false
 create_jobfile_only=false
 create_remote_batch_job=false
 dashes="  ----------------------------------------------------------------------------"
 defaultqueue=""
 delete_temporary_catalog=true
 do_compile=true
 do_trace=false
 executable=""
 execute_command=""
 execution_error=false
 fileconnection_file=trunk/SCRIPTS/.palm.iofiles
 jobname=test
 global_revision=""
 host_configuration="default"
 hostfile=""
 hp=""
 keep_data_from_previous_run=false
 link_local_input=false
 link_local_output=false
 linker_options=""
 local_jobcatalog=""
 locat=normal
 makefile=""
 max_par_io_str=""
 prc=$0
 while [[ $(echo $prc | grep -c "/") != 0 ]]
 do
    prc=`echo $prc | cut -f2- -d"/"`
 done
 module_calls=""
 palmrun_memory=""
 palmrun_script_name=$prc
 openmp=false
 previous_job=""
 project_account=""
 queue=none
 read_svf=""
 restart_run=false
 return_address=""
 remote_jobcatalog=""
 remote_username=""
 running_in_batch_mode=false
 run_coupled_model=false
 run_id=""
 silent=false
 source_list=""
 source_path=""
 tasks_per_node=0
 threads_per_task=1
 transfer_problems=false
 user_source_path=""
 use_existing_sources_folder=""
 use_openmp=false
 version="palmrun  1.0 Rev$Rev: 3151 $"
 working_directory=`pwd`
 write_binary=""
 write_svf=""


    # ERROR HANDLING IN CASE OF EXIT
 trap '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
          [[ $delete_temporary_catalog = true ]]  &&  (cd; rm -rf $tempdir)
          printf "\n\n+++ palmrun killed \n\n"
       elif [[ $locat != control_c ]]
       then
          printf "\n --> palmrun finished\n\n"
       fi' exit


    # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
 trap 'cd; rm -rf $tempdir
       printf "\n+++ palmrun killed by \"^C\" \n\n"
       locat=control_c
       exit
      ' 2


    # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
    # WHICH WILL BE USED TO START RESTART-JOBS
 while  getopts  :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
 do
   case  $option  in
       (a)   activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
       (A)   project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
       (b)   create_batch_job=true; prc="$prc -b";;
       (B)   delete_temporary_catalog=false; prc="$prc -B";;
       (C)   restart_run=true; prc="$prc -C";;
       (d)   jobname=$OPTARG; prc="$prc -d$OPTARG";;
       (F)   create_jobfile_only=true;;
       (G)   global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
       (h)   host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
       (j)   running_in_batch_mode=true;;
       (k)   keep_data_from_previous_run=true; prc="$prc -k";;
       (m)   palmrun_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=$OPTARG;;
       (t)   palmrun_cpumax=$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";;
       (V)   use_existing_sources_folder="-V";;
       (w)   max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
       (W)   previous_job=$OPTARG;;
       (x)   do_trace=true;set -x; prc="$prc -x";;
       (X)   palmrun_cores=$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 [[ "$1" = "?" ]]
 then
   (printf "\n  *** Description of available palmrun options:\n"
    printf "\n      Option  Description                              Default-Value"
    printf "\n        -a    activation string list                   \"\" "
    printf "\n        -A    project account number                   ---"
    printf "\n        -b    batch-job on local machine               ---"
    printf "\n        -B    do not delete temporary directory at end ---"
    printf "\n        -d    run identifier                           test"
    printf "\n        -F    create batch job file only               ---"
    printf "\n        -h    host configuration                       \"default\" "
    printf "\n        -k    keep data from previous run"
    printf "\n        -m    memory demand in MB (batch-jobs)         0 MB"
    printf "\n        -M    Makefile name                            Makefile"
    printf "\n        -O    threads per openMP task                  ---"
    printf "\n        -q    queue                                    \"$queue\" "
    printf "\n        -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                           ---"
    printf "\n        -u    username on remote machine               \"\" "
    printf "\n        -v    no prompt for confirmation               ---"
    printf "\n        -V    check if SOURCES_FOR_RUN_... exists      ---"
    printf "\n        -w    maximum parallel io streams              as given by -X"
    printf "\n        -W    name of job to wait for                  ---"
    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 ..."


    # FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
 export fname=$jobname


    # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
 config_file=.palm.config.$host_configuration
 sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname


    # 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 USER PROVIDES OWN FILE CONNECTION FILE
 if [[ -f .palm.iofiles ]]
 then
    fileconnection_file=.palm.iofiles
 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


    # CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
 if [[ "$activation_string_list" = "" ]]
 then
    printf "\n\n  +++ no activation string list given: "
    printf "\n        please set palmrun option \"-a\" "
    locat=palmrun_option; exit  
 fi


    # SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
 if [[ $(echo $activation_string_list | grep -c "restart") != 0 ]]
 then
    write_binary=true
 else
    write_binary=false
 fi

    # SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
 if [[ $(echo $activation_string_list | grep -c "svfout") != 0 ]]
 then
    write_svf=true
 else
    write_svf=false
 fi

    # SET VARIABLE TO ACTIVATE READING OF SVF DATA 
 if [[ $(echo $activation_string_list | grep -c "svfin") != 0 ]]
 then
    read_svf=true
 else
    read_svf=false
 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 [[ "$fast_io_catalog" = "" ]]
 then
    printf "\n  +++ no fast_io_catalog found in $config_file"
    printf "\n      Please add line \"fast_io_catalog ...\" to that file."
    locat=config_file; exit
 fi
 if [[ "$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 $config_file"
    printf "\n      Please add line \"compiler_options ...\" to that file."
    locat=config_file; exit
 fi
 if [[ "$linker_options" = "" ]]
 then
    printf "\n  +++ no linker options found in $config_file"
    printf "\n      Please add line \"linker_options ...\" to that file."
    locat=config_file; exit
 fi
 if [[ "$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


    # 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
 
 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

           # CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
        if [[ "$remote_jobcatalog" = "" ]]
        then
           printf "\n  +++ no remote jobcatalog found in $config_file"
           printf "\n      Please add line \"remote_jobcatalog ...\" to that file."
           locat=config_file; exit
        fi
 

     fi
     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

       # REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
    line=`echo "$line" | sed -e "s/\s\{1,\}/ /g"`

       # 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: action - field (optional)
       s1=`echo "$line" | cut -d" " -f1`
       s2=`echo "$line" | cut -d" " -s -f2`
       if [[ $(echo $s2 | grep -c ":") = 0 ]]
       then
          s2a=$s2
          s2b=""
       else
          s2a=`echo $s2 | cut -d":" -f1`
          s2b=`echo $s2 | cut -d":" -f2`
       fi
       s3=`echo "$line" | cut -d" " -f3 | sed 's/*/wildcard /g'`
       s4=`echo "$line" | cut -d" " -s -f4`
       eval s4=\"$s4\"    # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
       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 != tr), THE FILE CONNECTION
          # IS NOT CHECKED AND STORED.
       IFSALT="$IFS"; IFS="$IFS:"      # ADD ":" AS FIELD SEPARATOR
       if [[ ( "$s2a" = in  || "$s2a" = inopt )  &&  ! ( $create_remote_batch_job = true  &&  "$s2b" != tr ) ]]
       then
          found=false
          for  actual  in  $activation_string_list
          do
             for  formal  in  $s3
             do
                [[ $actual = $formal  ||  "$formal" = "-" ]]  &&  found=true
             done
          done
          if [[ $found = true ]]
          then
             (( iin = iin + 1 ))
             localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
             pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
             if [[ "$s2a" = inopt ]]
             then
                optin_pre[$iin]=yes
             else
                optin_pre[$iin]=no
             fi 

                # FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
                # FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
             if [[ $running_on_remote = true  &&  "$s2b" = tr ]]
             then
                pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
             fi

                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
                # THE WILDCARD FROM THE ENDING
             if [[ "${s5: -1}" = "*" ]]
             then
                if [[ "$s2b" = "di" ]]
                then
                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
                   printf "\n        see file \"$fileconnection_file\", line"
                   printf "\n$line"
                   locat=iofiles_file; exit
                fi
                multin[$iin]=true
                string=${endin_pre[$iin]}
                endin_pre[$iin]="${string%?}"
             else
                multin[$iin]=false
             fi
          fi
       elif [[ "$s2a" = out  &&  ! ( $create_remote_batch_job = true ) ]]
       then
          found=false
          for  actual  in  $activation_string_list
          do
             for  formal  in  $s3  
             do
                [[ $actual = $formal  ||  $formal = wildcard  ]]  &&  found=true
             done
          done
          if [[ $found = true ]]
          then
             (( iout = iout + 1 ))
             localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
             pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6

                # CHECK IF WILDCARD IS USED AS ACTIVATION STRING
                # IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
             if [[ $formal = wildcard  ]]
             then
                warnout_pre[$iout]=false
             else
                warnout_pre[$iout]=true
             fi

                # CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
                # THE WILDCARD FROM THE LOCAL FILENAME
             if [[ "${s1: -1}" = "*" ]]
             then
                if [[ "$s2b" = "di" ]]
                then
                   printf "\n    +++ wildcards (*) not allowed with \"di\" file attribute."
                   printf "\n        see file \"$fileconnection_file\", line"
                   printf "\n$line"
                   locat=iofiles_file; exit
                fi
                multout[$iout]=true
                string=${localout_pre[$iout]}
                localout_pre[$iout]="${string%?}"
             else
                multout[$iout]=false
             fi
          fi
       elif [[ "$s2a" != in  &&  "$s2a" != inopt  &&  "$s2a" != out ]]
       then
          printf "\n  +++ I/O-attribute in file $fileconnection_file has invalid"
          printf "\n      value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
          locat=connect; exit
       fi
       IFS="$IFSALT"
    fi

 done < $fileconnection_file



    # VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
 [[ "$palmrun_memory" != "" ]]  &&  memory=$palmrun_memory
 [[ "$palmrun_cpumax" != "" ]]  &&  cpumax=$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



      # 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


    # 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 ${fast_io_catalog}/${sources_for_run_catalog} ]]
    then
       printf "\n  +++ directory ${fast_io_catalog}/${sources_for_run_catalog} 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   ${base_directory}/${sources_for_run_catalog}
       mkdir -p ${base_directory}/${sources_for_run_catalog}

       if [[ "$source_list" = LM ]]
       then

             # DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
          source_list=""
          cd  $source_path


             # CHECK, IF TRUNK-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 palmrun-option \"-s LM\"\n"
          fi


             # LIST ALL MODIFIED SOURCE CODE FILES
          Filenames=""
          svn status  >  tmp_svnstatus
          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_svnstatus
          rm -rf  tmp_svnstatus


             # COPY FILES TO SOURCES_FOR_RUN_...
          for  filename  in  $Filenames
          do
             cp  $filename  ${base_directory}/${sources_for_run_catalog}
             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  ${base_directory}/${sources_for_run_catalog}
             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  ${base_directory}/${sources_for_run_catalog}/Makefile 
       fi


          # COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
       if [[ "$user_source_path" != "" ]]
       then

             # DOES THE DIRECTORY EXIST?
          if [[ ! -d $user_source_path ]]
          then

             printf "\n\n  *** INFORMATIVE: additional source code directory"
             printf "\n      \"$user_source_path\" "
             printf "\n      does not exist or is not a directory."
             printf "\n      No source code will be used from this directory!\n"
             user_source_path=""
             if [[ $silent == false ]]
             then
                sleep 2
             fi

          else

             cd $user_source_path

             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  ${base_directory}/${sources_for_run_catalog}

                # COPY MAKEFILE IF EXISTING
             if [[ -f $user_source_path/Makefile ]]
             then
                printf "\n\n  *** user Makefile from directory"
                printf "\n      \"$user_source_path\" is used \n"
                if [[ $silent == false ]]
                then
                   sleep 1
                fi
                cp  $user_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 \"$user_source_path\" "
                   printf "\n      but was also given with option \"-s\" which means that it should be taken"
                   printf "\n      from directory \"$source_path\"."
                   locat=source; exit
                fi

                cp  $user_source_path/$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
                fi
             done
             cd -  > /dev/null
          fi
       fi

          # COPY CONFIGURATION FILES
       cp  $config_file  ${base_directory}/${sources_for_run_catalog}
       cp  $fileconnection_file  ${base_directory}/${sources_for_run_catalog}

          # COPY SHELLSCRIPTS
       cp  ${source_path}/../SCRIPTS/palmrun    ${base_directory}/${sources_for_run_catalog}
       cp  ${source_path}/../SCRIPTS/batch_scp  ${base_directory}/${sources_for_run_catalog}

    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 = 0 ]]
    then
       if [[ $create_batch_job = true  ||  $create_remote_batch_job = true ]]
       then
          printf "\n"
          printf "\n  +++ option \"-T\" (tasks per node) is missing"
          printf "\n      set -T option or define tasks_per_node in the config file"
          locat=tasks_per_node; (( iec = 0 )); exit
       else
             # DEFAULT FOR INTERACTIVE RUN
          tasks_per_node=$cores
       fi
    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

 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"
       locat=queue; exit
    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 ))
 (( nr_of_input_files = 0 ))
 while (( i < iin ))
 do
    (( i = i + 1 ))

       # 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 [[ "${actionin_pre[$i]}" = di ]]
    then
       eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
    else
       eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
    fi


       # CHECK IF FILE EXISTS
    if ! ls $filename* 1>/dev/null 2>&1
    then

          # FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
       if [[ "${optin_pre[$i]}" != "yes" ]]
       then
          printf "\n\n  +++ INPUT-file: "
          if [[ "${extin_pre[$i]}" = ""  ||  "${extin_pre[$i]}" = " " ]]
          then
             printf "\n           $filename"
          else
             printf "\n           $filename.${extin_pre[$i]}"
          fi
          printf "\n      does not exist\n"
          locat=input; exit
       else
          (( nr_of_input_files = nr_of_input_files + 1 ))
          localin[$nr_of_input_files]="${localin_pre[$i]}"
          optin[$nr_of_input_files]="${optin_pre[$i]}"
          actionin[$nr_of_input_files]="unavailable"
          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
          endin[$nr_of_input_files]="${endin_pre[$i]}"
          extin[$nr_of_input_files]="${extin_pre[$i]}"
       fi

    else

          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
          # CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
       if [[ "${multin[$i]}" = true ]]
       then
             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
          ls -1 -d ${filename}    >   filelist  2>/dev/null
          ls -1 -d ${filename}.*  >>  filelist  2>/dev/null
          ls -1 -d ${filename}_*  >>  filelist  2>/dev/null

          endings=""
          while  read line
          do
                 # filename without path (i.e. after the last "/")
              basefilename=$(basename ${line})

                 # check if there is an extension and remove it
              ext=${basefilename##*.}
              if [[ "$ext" = "${extin_pre[$i]}" ]]
              then
                 basefilename=${basefilename%.*}
              fi

                 # check for an existing cycle number and remove it
              cycle=${basefilename##*.}
              if [[ $cycle =~ ^-?[0-9]+$ ]]
              then
                 basefilename=${basefilename%.*}
              fi

                 # remove the jobname from the beginning
              length_jobname=${#jobname}
              ending=${basefilename:${length_jobname}}

                 # remove the ending given in the .iofiles from the beginning
              endingstring="${endin_pre[$i]}"
              length_ending=${#endingstring}
              ending=${ending:${length_ending}}

              if [[ "$ending" = "" ]]
              then
                    # standard ending as given in the .iofiles
                 if [[ $(echo $endings | grep -c DEFAULT) = 0 ]]
                 then
                    endings="$endings DEFAULT"
                 fi
              else
                    # ending must start with "_", otherwise its a different file
                 if [[ "${ending:0:1}" = "_" ]]
                 then
                    if [[ $(echo $endings | grep -c "$ending") = 0 ]]
                    then
                       endings="$endings $ending"
                    fi
                 fi
              fi
 
          done <filelist

          rm filelist

       else

             # SINGLE NAME
          endings=DEFAULT

       fi

          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
       for  ending  in  $endings
       do

             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
          if [[ $ending = DEFAULT ]]
          then
             ending=""
          fi

             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
          (( nr_of_input_files = nr_of_input_files + 1 ))
          localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
          optin[$nr_of_input_files]="${optin_pre[$i]}"
          actionin[$nr_of_input_files]="${actionin_pre[$i]}"
          pathin[$nr_of_input_files]="${pathin_pre[$i]}"
          endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
          extin[$nr_of_input_files]="${extin_pre[$i]}"


             # 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 [[ "${actionin[$nr_of_input_files]}" = di ]]
          then
             eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
          else
             eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
          fi

             # DETERMINE THE FILE'S CYCLE NUMBER
          (( maxcycle = 0 ))
          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" = "${extin[$nr_of_input_files]}" ]]
              then
                 basefilename=${basefilename%.*}
              fi
   
                 # check for an existing cycle number
              cycle=${basefilename##*.}
              if [[ $cycle =~ ^-?[0-9]+$ ]]
              then
                    # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
                    # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
                 (( icycle = $((10#$cycle)) ))
              else
                 (( icycle = 0 ))
              fi
   
              if (( icycle > maxcycle ))
              then
                 (( maxcycle = icycle ))
   
                    # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
                    # CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
                 if [[ $(echo $cycle | cut -c1) = 0 ]]
                 then
                    leading_zero=true
                 else
                    leading_zero=false
                 fi
              fi
   
          done <filelist
          rm filelist
   
             # MAKE CYCLE NUMBER THREE DIGITS WIDE
          if [[ $leading_zero = true ]]
          then
             cyclestring=`printf "%03d" $maxcycle`
          else
             cyclestring=$maxcycle
          fi
   
             # APPEND CYCLE NUMBER TO FILENAME
          if (( maxcycle > 0 ))
          then
             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
             then
                filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
             else
                filename=${filename}.$cyclestring
             fi
          else
             if [[ "${extin[$nr_of_input_files]}" != " "  &&   "${extin[$nr_of_input_files]}" != "" ]]
             then
                filename=${filename}.${extin[$nr_of_input_files]}
             fi
          fi
          
             # STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
             # IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
          absnamein[$nr_of_input_files]=$filename
          if (( maxcycle > 0 ))
          then
             if [[ "${actionin[$nr_of_input_files]}" = di ]]
             then
                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
             else
                frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
             fi
          else
             if [[ "${actionin[$nr_of_input_files]}" = di ]]
             then
                frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
             else
                frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
             fi
          fi

       done

    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 TRANSFERRED 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_pre[$i]}" = tr || "${actionout_pre[$i]}" = tra || "${actionout_pre[$i]}" = trpe ) ) ]]
    then
       if [[ "${actionout_pre[$i]}" = tr ]]
       then
          actionout_pre[$i]=""
       elif [[ "${actionout_pre[$i]}" = trpe ]]
       then
          actionout_pre[$i]=pe
       elif [[ "${actionout_pre[$i]}" = tra ]]
       then
          actionout_pre[$i]=a
       fi
       (( maxcycle = 0 ))
       eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
       eval catalogname=${pathout_pre[$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

       fi

    fi
 done


    # DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
 if [[ $running_in_batch_mode = false ]]
 then
    run_id=$RANDOM
    job_id=${jobname}.$run_id

    tempdir=$fast_io_catalog/$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
    cputime=$cpumax
    while [[ $done = false ]]
    do
       if (( cputime == 0 ))
       then
          printf "\n  +++ cpu-time is undefined"
          printf "\n  >>> Please type CPU-time in seconds as INTEGER:"
          printf "\n  >>> "
          read  cputime   1>/dev/null  2>&1
       else
          done=true
       fi
    done
    cpumax=$cputime

       # 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 $remote_username ]]
       do
          printf "\n  +++ username on remote host with IP \"$remote_ip\" is undefined"
          printf "\n  >>> Please type username:"
          printf "\n  >>> "
          read  remote_username
       done
    fi

 else

    if [[ $running_in_batch_mode = false ]]
    then
       cputime=10000000  # NO LIMT FOR INTERACTIVE RUNS
       cpumax=$cputime
    else
       cputime=$cpumax
    fi

 fi


    # 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 "| %-35s%35s | \n" "PALM code    $global_revision" " "
 printf "|                                                                        | \n"
 column1="called on:"; column2=$(hostname)
 printf "| %-25s%-45s | \n" "$column1" "$column2"
 if [[ $create_remote_batch_job = true ]]
 then
    column1="execution on:"; column2="$host_configuration (username: $remote_username)"
 else
    if [[ $running_on_remote = true ]]
    then
       column1="host identifier:"; column2="$host_configuration (execute on IP: $remote_ip)"
    else
       column1="host identifier:"; column2="$host_configuration (execute on IP: $local_ip)"
    fi
 fi
 printf "| %-25s%-45s | \n" "$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  [[ $running_in_batch_mode = true  ||  $create_batch_job = true  ||  $create_remote_batch_job = true ]]
 then
    if [[ "$project_account" != "" ]]
    then
       column1="project account number:"
       column2="$project_account"
       printf "| %-25s%-45s | \n" "$column1" "$column2"
    fi
 fi

 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
 if [[ $create_batch_job = true  ||  $create_remote_batch_job = true  ||  $running_in_batch_mode = true ]]
 then
    column1="memory demand / PE":; column2="$memory MB"
    printf "| %-25s%-45s | \n" "$column1" "$column2"
    column1="job cpu time (h:m:s):"; column2="$timestring"
    printf "| %-25s%-45s | \n" "$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="linker options:"; column2=$(echo "$linker_options" | cut -c-45)
 printf "| %-25s%-45s | \n" "$column1" "$column2"
 line=$(echo "$linker_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="run identifier:"; column2=$jobname
 printf "| %-25s%-45s | \n" "$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 [[ "$source_list" != "" ]]
 then
    printf "|                                                                        | \n"
    printf "| Files to be compiled:                                                  | \n"
    line=$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 < nr_of_input_files ))
    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 "\n ***  batch-job will be created and submitted"
    else
       printf "\n ***  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\n"
    else
       printf "\n\n  *** creating executable and other sources for the local host\n"
    fi

       # FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
       # IT SHALL BE CREATED
    ask_for_make_depository=false
    if [[ $create_remote_batch_job = true ]]
    then

       line=`grep %base_directory $config_file`
       make_depository=`echo $line | cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
       echo  "[[ ! -d ${make_depository} ]]  &&  echo depository not found" | ssh  -q  $ssh_key  ${remote_username}@${remote_ip} 2>&1  | tee ${host_configuration}_last_make_protokoll

       if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
       then
          printf "\n\n  +++ make depository \"${make_depository}\""
          printf "\n      on remote host not found!"
          ask_for_make_depository=true
       fi
       rm ${host_configuration}_last_make_protokoll

    else

          # CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
       make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
       if [[ ! -d ${make_depository} ]]
       then
          printf "\n\n  +++ make depository \"${make_depository}\""
          printf "\n      on local host not found!"
          ask_for_make_depository=true
       fi

    fi

    if [[ $ask_for_make_depository = true ]]
    then

       antwort=dummy
       printf "\n\n"
       printf "  >>> Create a new one (y/n) ?  "
       while  read antwort
       do
          if [[ "$antwort" != y  &&  "$antwort" != Y  &&  "$antwort" != n  &&  "$antwort" != N ]]
          then
             printf "  >>> Create a new one (y/n) ?  "
          else
             break
          fi
       done
       if [[ $antwort = n  ||  $antwort = N ]]
       then
          locat=user_abort; (( iec = 0 )); exit
       fi

       if [[ $do_trace = true ]]
       then
          palmbuild  -h $host_configuration
       else
          palmbuild  -v  -h $host_configuration
       fi

       if [[ $? != 0 ]]
       then
   
              # ABORT IN CASE OF COMPILATION PROBLEMS
          printf "\n  +++ error while compiling for the MAKE_DEPOSITORY"
          locat=make_depository
          exit
       else
          echo "  *** now continue with creating executable and other sources"
       fi

    fi

       # NOW CREATE THE SOURCES_FOR_RUN FOLDER
    palmbuild  -v  $use_existing_sources_folder  -h $host_configuration  -d $jobname

    if [[ $? != 0 ]]
    then

           # ABORT IN CASE OF COMPILATION PROBLEMS
       printf "\n  +++ error while creating executable and/or other sources"
       locat=execution
       rm -rf  ${base_directory}/${sources_for_run_catalog}
       exit

    else

       printf "  *** executable and other sources created\n"
       rm -rf  ${base_directory}/${sources_for_run_catalog}

    fi

 fi


    # WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
    # WILL BE COPIED TO THE REMOTE HOST
 if [[ $create_remote_batch_job = true ]]
 then
    (( i = 0 ))
    while (( i < nr_of_input_files ))
    do
       (( i = i + 1 ))
       if [[ "${actionin[$i]}" = tr ]]
       then
          eval inputfile=${pathin[$i]}/${frelin[$i]}
          scp  -q $ssh_key  $PORTOPT  $inputfile  ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
       fi
    done
    if (( i > 0 ))
    then
       printf "\n\n  *** input files have been copied to the remote host\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
       cd  $tempdir
       cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  $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)
    optional_files_missing=false
    (( i = 0 ))
    while (( i < nr_of_input_files ))
    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 [[ "${actionin[$i]}" = unavailable ]]
       then
          optional_files_missing=true
          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 -p ${localin[$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]}" = "tr"  ||  "${actionin[$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 -p ${localin[$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 -p ${localin[$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 or 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
                   if [[ $running_on_remote = true  &&  "${actionin[$i]}" = tr ]]
                   then
                      mv  ${absnamein[$i]}  ${localin[$i]}
                   else
   		                 cp  ${absnamein[$i]}  ${localin[$i]}
                   fi
                fi
             fi
          fi
       fi

    done
    if (( i != 0 ))
    then
       if [[ $optional_files_missing = true ]]
       then
          printf "\n  *** INFORMATIVE: some optional INPUT-files are not present"
       fi
       printf "\n$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 = '$jobname', host = '$host_configuration',
          write_svf = .${write_svf}., write_binary = .${write_binary}., 
          read_svf = .${read_svf}., 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  "${execute_command}" | sed 's/{{/$/g' | sed 's/}}//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
    if [[ "$execute_command_for_combine" = "" ]]
    then
       eval line2=\"$line2\"
       execute_command_for_combine="$line2"
    fi
    


       # 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 ATMOSPHERE OCEAN COUPLING
    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
      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

          # REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
       out_command[$i]=`echo  "${out_command[$i]}" | sed 's/{{/$/g' | sed 's/}}//g'`

       printf "\n  >>> ${out_command[$i]}"
       eval  ${out_command[$i]}
       if (( i == ioc ))
       then
          printf "\n$dashes\n"
       fi
    done


       # IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
       # WILDCARDS
    (( i = 0 ))
    (( nr_of_output_files = 0 ))

    while (( i < iout ))
    do

       (( i = i + 1 ))

          # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
          # CREATE A LIST FOR THE DETECTED ENDINGS
       if [[ "${multout[$i]}" = true ]]
       then
             # DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
          ls -1 -d ${localout_pre[$i]}    >   filelist  2>/dev/null
          ls -1 -d ${localout_pre[$i]}_*  >>  filelist  2>/dev/null

          endings="DEFAULT"
          while  read line
          do
                 # remove the local name from the beginning
              localnamestring="${localout_pre[$i]}"
              length_localname=${#localnamestring}
              ending=${line:${length_localname}}

              if [[ "$ending" != "" ]]
              then
                 endings="$endings $ending"
              fi
 
          done <filelist

          rm filelist

       else

             # SINGLE NAME
          endings=DEFAULT

       fi

          # FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
       for  ending  in  $endings
       do

             # DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
          if [[ $ending = DEFAULT ]]
          then
             ending=""
          fi

             # NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
          (( nr_of_output_files = nr_of_output_files + 1 ))
          localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
          transout[$nr_of_output_files]="${transout_pre[$i]}"
          actionout[$nr_of_output_files]="${actionout_pre[$i]}"
          pathout[$nr_of_output_files]="${pathout_pre[$i]}"
          endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
          extout[$nr_of_output_files]="${extout_pre[$i]}"
          warnout[$nr_of_output_files]="${warnout_pre[$i]}"

       done

    done




       # COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
    (( i = 0 ))
    while (( i < nr_of_output_files ))
    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  *** in case of SCP transfers to local host"
             printf "\n      they will be done via remote login-node \"$remote_loginnode\" "
          fi
          printf "\n$dashes"
       fi

       if [[ ! ( $running_on_remote = true  &&  ( "${actionout[$i]}" = tr || "${actionout[$i]}" = tra || "${actionout[$i]}" = trpe ) ) ]]
       then

          eval filename=${pathout[$i]}/${jobname}${endout[$i]}

             # 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
                   # NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
                   # 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
                (( icycle = $((10#$cycle)) + 1 ))
             else
                (( icycle = 1 ))
             fi
   
             if (( icycle > maxcycle ))
             then
                (( maxcycle = icycle ))
             fi
   
          done <filelist
          rm filelist

   
             # SET THE CYCLE NUMBER
             # IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
          if [[ "${actionout[$i]}" = a ]]
          then
             (( maxcycle = maxcycle - 1 ))
          fi
          
          (( cycnum[$i] = maxcycle ))
          pathout[$i]=$filename


             # ADD CYCLE NUMBER TO FILENAME
             # 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
             cyclestring=`printf "%03d" ${cycnum[$i]}`
             pathout[$i]=${pathout[$i]}.$cyclestring
          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
          if [[ ${warnout[$i]} = true ]]
          then
             printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}  does not exist\n"
          fi
       elif [[ ! -d ${localout[$i]}  &&  $files_for_cores = true ]]
       then
          if [[ ${warnout[$i]} = true ]]
          then
             printf "\n  +++ temporary OUTPUT-file  ${localout[$i]}/....  does not exist\n"
          fi
       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]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"

                   # TRANSFER VIA SCP
                if [[ "$remote_loginnode" != "" ]]
                then
                   echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address  ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${jobname}${endout[$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]}" ${host_configuration}_${jobname}${endout[$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]}/${host_configuration}_${jobname}${endout[$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]}/${host_configuration}_${jobname}${endout[$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 -p ${pathout[$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 [[ $link_local_output = true ]]
		              then
                   printf "  --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
		              fi
		              [[ ! -d "${pathout[$i]}" ]]  &&  mkdir  ${pathout[$i]}
		              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 SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
          # SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
       if [[ $(echo $prc | grep -c "svfout") != 0 ]]
       then
          prc=`echo $prc | sed 's/svfout/svfin/g'`
       fi

          # 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/#/r/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; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address  " |  ssh -q $remote_username@$remote_loginnode  |  tee palmrun_restart.log
          else
             echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" |  ssh -q $SSH_PORTOPT  $local_username@$return_address  |  tee palmrun_restart.log
          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  |  tee palmrun_restart.log              # THE ' MUST BE EVALUATED
          cd -  > /dev/null

       fi

          # CHECK, IF RESTART JOB HAS BEEN STARTED
       if [[ $( grep -c "+++ palmrun killed"  palmrun_restart.log ) != 0 ]]
       then
          printf "\n$dashes\n  +++ creating restart run failed \n"
          locat=create_restart
          exit
          rm  palmrun_restart.log
       else
          printf "\n$dashes\n  *** restart run initiated \n"
          rm  palmrun_restart.log
       fi


          # 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 < nr_of_input_files ))
       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 -d $jobname -h $host_configuration -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"
    [[ $tasks_per_node != 0 ]]  &&  palmrun_com=${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 $max_par_io_str"
    [[ "$project_account" != "" ]]  &&  palmrun_com=${palmrun_com}" -A $project_account"
    if [[ $create_remote_batch_job = true ]]
    then
       palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
       if [[ $do_trace = true ]]
       then
          printf "\n *** PALMRUN-command on remote host:\n     $palmrun_com \n"
       fi
    elif [[ $create_batch_job = true ]]
    then
       palmrun_com=${palmrun_com}" -j"
       if [[ $do_trace = true ]]
       then
          printf "\n *** PALMRUN-command on local host:\n     $palmrun_com \n"
       fi
    fi


       # DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
       # REMOTE HOST
    job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
    job_protocol_file=$job_protocol_file_local
    if [[ $create_remote_batch_job = true ]]
    then
       job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${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/{{/$/g' | sed 's/}}//g'`
       eval line=\"$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/{{/$/g' | sed 's/}}//g'`
          eval line=\"$line\"
          echo  "$line"                            >>  $jobfile
       done
       echo " "                                    >>  $jobfile

       echo "set -x"                               >>  $jobfile
       echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp  $PORTOPT  -d  -w 10  -u $local_username $local_ip  $job_protocol_file_remote  \"$local_jobcatalog\"  ${host_configuration}_${jobname}"  >>  $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 -rf $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
    if [[ $create_remote_batch_job = true ]]
    then
       echo  "mkdir  $tempdir"           >>  $jobfile
       echo  "chmod  go+rx  $tempdir"    >>  $jobfile
    else
          # DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
          # REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
          # BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
       mkdir  $tempdir
       chmod  go+rx  $tempdir
    fi
    echo  "cd  $tempdir"                 >>  $jobfile
    echo  "export tempdir=$tempdir"      >>  $jobfile
    echo  "cp  ${fast_io_catalog}/${sources_for_run_catalog}/{*,.[!.]*}  ."  >>  $jobfile
    echo  "export PATH=.:\$PATH"         >>  $jobfile
    echo  "export execute_palmrun=true"  >>  $jobfile


       # 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=${source_path}/../SCRIPTS"   >>  $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 " "
          echo " *** transfer of job to remote host via scp"
          if [[ $do_trace = true ]]
          then
             echo "     scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
          fi
          scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}  >  /dev/null

          printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
          if [[ $do_trace = true ]]
          then
             echo "     cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}  |  ssh  -q  $ssh_key $SSH_PORTOPT  ${remote_username}@${remote_ip}  2>&1"
          fi
          echo "cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}"  |  ssh  -q  $ssh_key $SSH_PORTOPT  ${remote_username}@${remote_ip}  2>&1

       elif [[ $create_batch_job = true ]]
       then

          eval  local_jobcatalog=$local_jobcatalog
          cp  $jobfile  ${local_jobcatalog}/${host_configuration}_${job_id}
          cd $local_jobcatalog
          echo " "
          echo " *** submit the job"
          if [[ $do_trace = true ]]
          then
             echo "$submit_command ${host_configuration}_${job_id}"
          fi
          $submit_command ${host_configuration}_${job_id}
          rm ${host_configuration}_${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