Index: palm/trunk/SCRIPTS/inifor_script
===================================================================
--- palm/trunk/SCRIPTS/inifor_script (revision 3790)
+++ palm/trunk/SCRIPTS/inifor_script (revision 3790)
@@ -0,0 +1,2905 @@
+#!/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 .
+#
+# Copyright 2017-2018 Leibniz Universitaet Hannover
+#--------------------------------------------------------------------------------#
+#
+# Current revisions:
+# ------------------
+# initial revision
+#
+# Former revisions:
+# -----------------
+# $Id$
+#
+#--------------------------------------------------------------------------------#
+# inifor - script for running inifor
+#--------------------------------------------------------------------------------#
+
+
+
+ # 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=""
+ configuration_identifier="default"
+ 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
+ global_revision=""
+ 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
+ running_in_test_mode=false
+ run_coupled_model=false
+ run_id=""
+ run_id_number=""
+ run_identifier=test
+ 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: 3725 $"
+ 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 crashed \n\n"
+ exit 1
+ elif [[ $locat != normal ]]
+ then
+ [[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
+ printf "\n+++ palmrun killed by \"^C\" \n\n"
+ exit 2
+ else
+ printf "\n --> palmrun finished\n\n"
+ exit 0
+ fi' exit
+
+
+ # ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
+ trap 'locat=control_c
+ exit 1
+ ' 2
+
+
+ # READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
+ # WHICH WILL BE USED TO START RESTART-JOBS
+ while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ 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="$prc -B";;
+ (c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
+ (C) restart_run=true; prc="$prc -C";;
+ (F) create_jobfile_only=true;;
+ (G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
+ (i) run_id_number=$OPTARG;;
+ (j) running_in_batch_mode=true;;
+ (k) keep_data_from_previous_run=true; prc="$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_identifier=$OPTARG; prc="$prc -r$OPTARG";;
+ (R) return_address=$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) running_in_test_mode=true;;
+ (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 [[ "$1" = "?" ]]
+ then
+ (printf "\n *** Description of available palmrun options:\n"
+ printf "\n Option Description Default-Value"
+ printf "\n -a activation string list \"\" "
+ printf "\n -A project account number ---"
+ printf "\n -b batch-job on local machine ---"
+ printf "\n -B do not delete temporary directory at end ---"
+ printf "\n -c configuration identifier \"default\" "
+ printf "\n -F create batch job file only ---"
+ printf "\n -k keep data from previous run"
+ printf "\n -m memory demand in MB (batch-jobs) 0 MB"
+ printf "\n -M Makefile name Makefile"
+ printf "\n -O threads per openMP task ---"
+ printf "\n -q queue \"$queue\" "
+ printf "\n -r run identifier test"
+ 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 :"
+ printf "\n \"?\" - this outline \n\n") | more
+ exit
+ elif [[ "$1" != "" ]]
+ then
+ printf "\n +++ positional parameter $1 unknown \n"
+ locat=parameter; exit
+ fi
+
+
+
+ # SHORT STARTING MESSAGE
+ printf "\n*** $version "
+ printf "\n will be executed. Please wait ..."
+
+
+ # BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
+ config_file=.palm.config.$configuration_identifier
+ sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
+
+
+ # 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
+
+ # CHECK VERSION MISMATCH
+ # RESTART RUNS DON'T REQUIRE A CHECK, BECAUSE THEY USE A COPY OF THAT
+ # FILE WHICH HAS ALREADY BEEN CHECKED WITHIN THE INITAL PALMRUN CALL
+ if [[ $running_in_batch_mode != true && $restart_run != true ]]
+ then
+ if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
+ then
+ printf "\n\n +++ WARNING: A file connection file has been found in your"
+ printf "\n working directory, but its revision does not match"
+ printf "\n the revision of the default (trunk) version."
+ printf "\n You may need to update your connection file"
+ printf "\n \"${working_directory}/.palm.iofiles\" !"
+ fi
+ fi
+
+ 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 $config_file"
+ printf "\n Please add line \"compiler_options ...\" to that file."
+ locat=config_file; exit
+ fi
+ if [[ "$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
+ [[ $silent = false ]] && printf "\n Reading the I/O files... "
+
+ # READ THE FILE CONNECTION FILE LINE BY LINE
+ while read line
+ do
+
+ # REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
+ # HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
+ line=`echo "$line" | tr -s " "`
+
+ # 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]}/${run_identifier}${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[$i]}"
+ fi
+
+ else
+
+ # FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
+ # ($run_identifier) 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=${basefilename%.*}
+ fi
+
+ # remove the run_identifier from the beginning
+ length_run_identifier=${#run_identifier}
+ ending=${basefilename:${length_run_identifier}}
+
+ # 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 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 $cycle | cut -c1) = 0 ]]
+ then
+ leading_zero=true
+ else
+ leading_zero=false
+ fi
+ fi
+
+ done 0 ))
+ then
+ if [[ "${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[$nr_of_input_files]=${run_identifier}${endin[$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[$nr_of_input_files]=${run_identifier}${endin[$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]}/${run_identifier}${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 [[ $running_in_batch_mode = false ]]
+ then
+ run_id_number=$RANDOM
+ run_id=${run_identifier}.$run_id_number
+
+ tempdir=$fast_io_catalog/$run_id
+
+ # FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
+ export job_id=$run_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 [[ $create_remote_batch_job = true ]]
+ then
+ column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
+ else
+ if [[ $running_on_remote = true ]]
+ then
+ column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
+ else
+ column1="config. identifier:"; column2="$configuration_identifier (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 "$line" | cut -c46-)
+ done
+ fi
+ printf "| | \n"
+ column1="run identifier:"; column2=$run_identifier
+ 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 $line | cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
+ ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 | tee ${configuration_identifier}_last_make_protokoll
+
+ if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
+ then
+ printf "\n\n +++ make depository \"${make_depository}\""
+ printf "\n on remote host not found!"
+ ask_for_make_depository=true
+ fi
+ rm ${configuration_identifier}_last_make_protokoll
+
+ else
+
+ # CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
+ make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
+ 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 -c $configuration_identifier
+ else
+ palmbuild -v -c $configuration_identifier
+ fi
+
+ if [[ ${PIPESTATUS[0]} != 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 -c $configuration_identifier -r $run_identifier
+
+ if [[ ${PIPESTATUS[0]} != 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
+
+
+ # CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
+ if [[ $running_in_batch_mode = true || $running_in_test_mode = true ]]
+ then
+ progress_bar_disabled=true
+ else
+ progress_bar_disabled=false
+ fi
+
+
+ # CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
+ # (FILE ENVPAR WILL BE READ BY PALM)
+ cat > ENVPAR << EOF
+ &envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
+ write_svf = .${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',
+ progress_bar_disabled = .${progress_bar_disabled}. /
+
+EOF
+
+
+ # STARTING THE EXECUTABLE
+ printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$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"
+
+
+ if [[ $progress_bar_disabled = true ]]
+ then
+ $execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
+ exit_code=${PIPESTATUS[0]}
+ else
+ $execute_command < coupling_steering &> >(tee STDOUT)
+ exit_code=${PIPESTATUS[0]}
+ fi
+
+ if [[ ${exit_code} != 0 ]]
+ then
+
+ # ABORT IN CASE OF RUNTIME ERRORS
+ printf "\n +++ runtime error occured"
+ locat=execution
+ exit
+
+ else
+
+ printf "\n$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 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 = 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]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
+
+ # TRANSFER VIA SCP
+ if [[ "$remote_loginnode" != "" ]]
+ then
+ ssh -q $remote_username@$remote_loginnode "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]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}"
+ else
+ batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}
+ fi
+ [[ ${PIPESTATUS[0]} != 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]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
+
+ # FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
+ eval local_catalog=${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]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
+ transfer_problems=true
+ fi
+
+ else
+
+ # UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
+ # BE COPIED OR APPENDED ON THIS MACHINE
+ if [[ "${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
+ ssh -q $remote_username@$remote_loginnode "ssh -q $SSH_PORTOPT $local_username@$return_address \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" " | tee palmrun_restart.log
+ else
+ ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" | 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
+
+ fi
+
+ # CHECK, IF RESTART JOB HAS BEEN STARTED
+ if [[ $( grep -c "+++ palmrun crashed" palmrun_restart.log ) != 0 ]]
+ then
+ printf "\n$dashes\n +++ creating restart run failed \n"
+ locat=create_restart
+ rm palmrun_restart.log
+ exit
+ elif [[ $( grep -c "*** palmrun finished" palmrun_restart.log ) != 1 ]]
+ then
+ printf "\n$dashes\n +++ creating restart run failed, probably due to network problems\n"
+ locat=create_restart
+ rm palmrun_restart.log
+ exit
+ 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 -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -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}/${configuration_identifier}_${run_id}
+ job_protocol_file=$job_protocol_file_local
+ if [[ $create_remote_batch_job = true ]]
+ then
+ job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_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_number
+ fi
+
+
+ # BUILD THE JOB-SCRIPTS ON FILE jobfile
+ jobfile=jobfile.$run_id_number
+
+
+ # FIRST CREATE THE BATCH DIRECTIVES
+ (( i = 0 ))
+ while (( i < ibd ))
+ do
+ (( i = i + 1 ))
+ line=`echo "${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_number << %%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" >> $jobfile
+ if [[ "$remote_loginnode" != "" ]]
+ then
+ echo "ssh -q $remote_username@$remote_loginnode \"cd ${remote_jobcatalog}; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \\\"$local_jobcatalog\\\" ${configuration_identifier}_${run_identifier}\" " >> $jobfile
+ else
+ echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${configuration_identifier}_${run_identifier}" >> $jobfile
+ fi
+ 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 [[ $create_jobfile_only = false ]]
+ then
+
+ # CREATE LOCAL JOB FOLDER
+ eval local_jobcatalog=$local_jobcatalog
+ if [[ ! -d $local_jobcatalog ]]
+ then
+ echo " "
+ echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
+ mkdir $local_jobcatalog
+ fi
+
+ if [[ $create_remote_batch_job = true ]]
+ then
+
+ echo " "
+ echo " *** transfer of job to remote host via scp"
+
+ # CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
+ ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
+
+ # COPY THE JOB FILE
+ if [[ $do_trace = true ]]
+ then
+ echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
+ fi
+ scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
+
+ # SUBMIT THE JOB
+ printf " *** submit the job (output of submit command, \n"
+ printf " e.g. the job-id given by the batch-system, may follow) \n"
+ if [[ $do_trace = true ]]
+ then
+ echo " ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} \"cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}\" "
+ fi
+ ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}"
+
+ elif [[ $create_batch_job = true ]]
+ then
+
+ eval local_jobcatalog=$local_jobcatalog
+ cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
+ cd $local_jobcatalog
+ echo " "
+ echo " *** submit the job"
+ if [[ $do_trace = true ]]
+ then
+ echo "$submit_command ${configuration_identifier}_${run_id}"
+ fi
+ $submit_command ${configuration_identifier}_${run_id}
+ rm ${configuration_identifier}_${run_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