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source: palm/trunk/SCRIPTS/palmrun @ 2731

Last change on this file since 2731 was 2718, checked in by maronga, 7 years ago
deleting of deprecated files; headers updated where needed
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 94.9 KB

Rev	Line
[2380]	1	#!/bin/bash
	2
	3	# palmrun - script for running PALM jobs
	4
	5	#--------------------------------------------------------------------------------#
[2696]	6	# This file is part of the PALM model system.
[2380]	7	#
	8	# PALM is free software: you can redistribute it and/or modify it under the terms
	9	# of the GNU General Public License as published by the Free Software Foundation,
	10	# either version 3 of the License, or (at your option) any later version.
	11	#
	12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
	13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	15	#
	16	# You should have received a copy of the GNU General Public License along with
	17	# PALM. If not, see <http://www.gnu.org/licenses/>.
	18	#
[2718]	19	# Copyright 2017-2018 Leibniz Universitaet Hannover
[2380]	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
	23	# ------------------
	24	#
[2410]	25	#
[2380]	26	# Former revisions:
	27	# -----------------
	28	# $Id: palmrun 2718 2018-01-02 08:49:38Z suehring $
[2716]	29	# Corrected "Former revisions" section
	30	#
	31	# 2696 2017-12-14 17:12:51Z kanani
	32	# Change in file header (GPL part)
	33	#
	34	# 2693 2017-12-13 12:33:49Z raasch
[2693]	35	# replacement of variables given by {{<variable>}} in configuration file is now
	36	# done in a more general way, variable names are written in small letters
	37	#
	38	# 2670 2017-12-06 16:32:19Z raasch
[2670]	39	# test printouts removed
	40	#
	41	# 2669 2017-12-06 16:03:27Z raasch
[2669]	42	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	43	# removed,
	44	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	45	# files,
	46	# informative messages in case of missing optional input files shortened
	47	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	48	#
	49	# 2638 2017-11-23 12:44:23Z raasch
[2610]	50	# use of wildcards in file connection statements enabled
	51	#
	52	# 2605 2017-11-09 15:31:46Z raasch
[2605]	53	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	54	# will not be sent with the job file any more, but copied into the
[2610]	55	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	56	#
	57	# 2600 2017-11-01 14:11:20Z raasch
[2600]	58	# cycle numbers are made three digits wide
	59	#
	60	# 2566 2017-10-20 08:50:47Z raasch
[2566]	61	# execute command for combine_plot_fields added
	62	# "TEMPDIR" renamed "tempdir"
	63	# temporary working directory for local batch jobs is created immediately within
	64	# the user's palmrun call, due to a requirement of the "grid engine" batch
	65	# system, where the working directory is given with batch directive -wd and must
	66	# already exist when the job is submitted,
	67	# informative messages in non-trace mode reduced and partly reformatted
	68	#
	69	# 2551 2017-10-18 07:25:11Z raasch
[2551]	70	# TEMPDIR added as replacement string to be used in batch directives
	71	#
	72	# 2512 2017-10-04 08:26:59Z raasch
[2507]	73	# bugfix for determining cycle numbers of NetCDF input files
	74	#
	75	# 2506 2017-09-29 08:30:37Z raasch
[2506]	76	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	77	# host configuration added to SOURCES_FOR_RUN_... folder name
	78	# host_identifier renamed host_configuration
	79	# option -W added to allow for job dependencies
	80	#
	81	# 2501 2017-09-26 11:41:55Z raasch
[2501]	82	# default value for number of cores (option -X) set to 1
	83	# bugfix for mechanism which overwrites configuration file settings with values
	84	# provided by palmrun options
	85	#
	86	# 2499 2017-09-22 16:47:58Z kanani
[2499]	87	# option -h named configuration identifier
	88	#
	89	# 2480 2017-09-19 06:24:14Z maronga
[2480]	90	# bugfix for last revision
	91	#
	92	# 2479 2017-09-19 06:12:16Z raasch
[2479]	93	# option -A (project account number) added
	94	#
	95	# 2422 2017-09-08 08:25:41Z raasch
[2410]	96	# initial revision
[2380]	97	#
	98	#--------------------------------------------------------------------------------#
	99	# palmrun - script for running PALM jobs on local and remote hosts
	100	#--------------------------------------------------------------------------------#
	101
	102
	103
	104	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	105
	106	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	107	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	108	# (TOO MANY ARGUMENTS - PROBLEM)
	109	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	110
[2610]	111	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	112	typeset -i nr_of_output_files=0
[2380]	113	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	114	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	115	# SCRIPT-OPTION ARGUMENTS
	116	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	117	typeset -i icycle inode ival maxcycle mpi_tasks
	118	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	119
	120	activation_string_list=""
	121	AddFilenames=""
	122	combine_plot_fields=true
	123	compiler_name=""
	124	compiler_name_ser=""
	125	compiler_options=""
[2501]	126	cores=1
[2380]	127	cores_atmos=0
	128	cores_ocean=0
	129	coupled_dist=""
	130	cpp_options=""
	131	cpumax=0
[2506]	132	create_batch_job=false
[2380]	133	create_jobfile_only=false
	134	create_remote_batch_job=false
	135	dashes=" ----------------------------------------------------------------------------"
	136	defaultqueue=""
[2506]	137	delete_temporary_catalog=true
[2380]	138	do_compile=true
	139	do_trace=false
	140	executable=""
	141	execute_command=""
	142	execution_error=false
	143	fileconnection_file=.palm.iofiles
	144	fname=test
	145	global_revision=""
[2506]	146	host_configuration="default"
[2380]	147	hostfile=""
	148	hp=""
	149	keep_data_from_previous_run=false
	150	link_local_input=false
	151	link_local_output=false
[2388]	152	linker_options=""
[2385]	153	local_jobcatalog=""
[2380]	154	locat=normal
	155	makefile=""
	156	max_par_io_str=""
	157	prc=$0
	158	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	159	do
	160	prc=`echo $prc \| cut -f2- -d"/"`
	161	done
	162	module_calls=""
[2506]	163	palmrun_memory=""
[2380]	164	palmrun_script_name=$prc
	165	openmp=false
[2506]	166	previous_job=""
[2479]	167	project_account=""
[2380]	168	queue=none
	169	restart_run=false
	170	return_address=""
[2385]	171	remote_jobcatalog=""
[2380]	172	remote_username=""
	173	running_in_batch_mode=false
	174	run_coupled_model=false
	175	run_id=""
	176	silent=false
	177	source_list=""
	178	source_path=""
[2501]	179	tasks_per_node=0
[2380]	180	threads_per_task=1
	181	transfer_problems=false
[2384]	182	user_source_path=""
[2506]	183	use_existing_sources_folder=""
[2380]	184	use_openmp=false
[2422]	185	version="palmrun 1.0 Rev$Rev: 2303 $"
[2380]	186	working_directory=`pwd`
	187	write_binary=""
	188	TOPT=""
	189
	190
	191	# ERROR HANDLING IN CASE OF EXIT
[2404]	192	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	193	then
	194
	195	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	196	(( i = 0 ))
	197	while (( i < iec ))
	198	do
	199	(( i = i + 1 ))
	200	printf "\n *** Execution of ERROR-command:\n"
	201	printf " >>> ${err_command[$i]}\n"
	202	eval ${err_command[$i]}
	203	done
[2566]	204	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	205	printf "\n\n+++ palmrun killed \n\n"
	206	elif [[ $locat != control_c ]]
	207	then
[2566]	208	printf "\n --> palmrun finished\n\n"
[2380]	209	fi' exit
	210
	211
	212	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	213	trap 'cd; rm -rf $tempdir
[2380]	214	printf "\n+++ palmrun killed by \"^C\" \n\n"
	215	locat=control_c
	216	exit
	217	' 2
	218
	219
	220	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	221	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	222	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
[2380]	223	do
	224	case $option in
	225	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	226	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	227	(b) create_batch_job=true; prc="$prc -b";;
	228	(B) delete_temporary_catalog=false; prc="$prc -B";;
	229	(C) restart_run=true; prc="$prc -C";;
	230	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	231	(F) create_jobfile_only=true;;
	232	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	233	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	234	(j) running_in_batch_mode=true;;
	235	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	236	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	237	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	238	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	239	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	240	(r) run_id=$OPTARG;;
	241	(R) return_address=$OPTARG;;
	242	(s) source_list=$OPTARG;;
[2501]	243	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	244	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	245	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	246	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	247	(v) silent=true; prc="$prc -v";;
[2506]	248	(V) use_existing_sources_folder="-V";;
[2380]	249	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	250	(W) previous_job=$OPTARG;;
[2380]	251	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	252	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	253	(y) ocean_file_appendix=true; prc="$prc -y";;
	254	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	255	(Z) combine_plot_fields=false; prc="$prc -Z";;
	256	(\?) printf "\n +++ unknown option $OPTARG \n"
	257	printf "\n --> type \"$0 ?\" for available options \n"
	258	locat=parameter;exit;;
	259	esac
	260	done
	261
	262
	263	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	264	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	265	(( to_shift = $OPTIND - 1 ))
	266	shift $to_shift
	267
	268	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	269	if [[ "$1" = "?" ]]
	270	then
	271	(printf "\n *** Description of available palmrun options:\n"
	272	printf "\n Option Description Default-Value"
	273	printf "\n -a activation string list \"\" "
[2479]	274	printf "\n -A project account number ---"
[2380]	275	printf "\n -b batch-job on local machine ---"
	276	printf "\n -B do not delete temporary directory at end ---"
	277	printf "\n -d base name of files attached to program test"
	278	printf "\n -F create batch job file only ---"
[2506]	279	printf "\n -h host configuration \"default\" "
[2380]	280	printf "\n -k keep data from previous run"
	281	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	282	printf "\n -M Makefile name Makefile"
	283	printf "\n -O threads per openMP task ---"
	284	printf "\n -q queue \"$queue\" "
	285	printf "\n -s filenames of routines to be compiled \"\" "
	286	printf "\n must end with .f, .f90, .F, or .c !"
	287	printf "\n use \"..\" for more than one file and wildcards"
	288	printf "\n -s LM compiles all locally modified files"
	289	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	290	printf "\n -T tasks per node ---"
[2380]	291	printf "\n -u username on remote machine \"\" "
	292	printf "\n -v no prompt for confirmation ---"
[2506]	293	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	294	printf "\n -w maximum parallel io streams as given by -X"
[2506]	295	printf "\n -W name of job to wait for ---"
[2380]	296	printf "\n -x tracing of palmrun for debug purposes ---"
	297	printf "\n -X # of processors (on parallel machines) 1"
	298	printf "\n -y add appendix \"_O\" to all local output"
	299	printf "\n files (ocean precursor runs followed by"
	300	printf "\n coupled atmosphere-ocean runs) ---"
	301	printf "\n -Y run coupled model, \"#1 #2\" with"
	302	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	303	printf "\n -Z skip combine_plot_fields at the end of "
	304	printf "\n the simulation ---"
	305	printf "\n "
	306	printf "\n Possible values of positional parameter <modus>:"
	307	printf "\n \"?\" - this outline \n\n") \| more
	308	exit
	309	elif [[ "$1" != "" ]]
	310	then
	311	printf "\n +++ positional parameter $1 unknown \n"
	312	locat=parameter; exit
	313	fi
	314
	315
	316
	317	# SHORT STARTING MESSAGE
	318	printf "\n*** $version "
	319	printf "\n will be executed. Please wait ..."
	320
	321
[2506]	322	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	323	config_file=.palm.config.$host_configuration
	324	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
[2380]	325
	326
	327	# CHECK, IF CONFIGURATION FILE EXISTS
	328	if [[ ! -f $config_file ]]
	329	then
	330	printf "\n\n +++ configuration file: "
	331	printf "\n $config_file"
	332	printf "\n does not exist"
	333	locat=connect; exit
	334	fi
	335
	336
	337	# CHECK, IF FILE CONNECTION FILE EXISTS
	338	if [[ ! -f $fileconnection_file ]]
	339	then
	340	printf "\n\n +++ file connection file: "
	341	printf "\n $fileconnection_file"
	342	printf "\n does not exist"
	343	locat=connect; exit
	344	fi
	345
	346
[2404]	347	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	348	if [[ "$activation_string_list" = "" ]]
	349	then
	350	printf "\n\n +++ no activation string list given: "
	351	printf "\n please set palmrun option \"-a\" "
	352	locat=palmrun_option; exit
	353	fi
	354
	355
	356	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	357	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	358	then
	359	write_binary=true
	360	else
	361	write_binary=false
	362	fi
	363
	364
[2380]	365	# READ AND EVALUATE THE CONFIGURATION-FILE
	366	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	367
	368	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	369	while read line
	370	do
	371
	372	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	373	eval line=\"$line\"
	374
	375
	376	# INTERPRET THE LINE
	377	if [[ "$(echo $line)" = "" ]]
	378	then
	379
	380	# EMPTY LINE, NO ACTION
	381	continue
	382
	383	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	384	then
	385
	386	# LINE IS A COMMENT LINE
	387	continue
	388
	389	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	390	then
	391
	392	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	393	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	394	value=`echo $line \| cut -d" " -s -f2-`
	395
	396
	397	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	398	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	399	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	400	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	401	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	402	# CONFIGURATION-FILE.
	403	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	404	then
	405	eval export $var="\$value"
	406
	407	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	408	if [[ $do_trace = true ]]
	409	then
	410	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	411	fi
	412	fi
	413
	414	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	415	then
	416
	417	# LINE DEFINES BATCH-DIRECTIVE
	418	(( ibd = ibd + 1 ))
	419	line=$(echo $line \| cut -c4-)
	420	batch_directive[$ibd]="$line"
	421
	422	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	423	then
	424
	425	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	426	# REMOTE TO A LOCAL HOST
	427	(( ibdt = ibdt + 1 ))
	428	line=$(echo $line \| cut -c5-)
	429	batch_directive_transfer[$ibdt]="$line"
	430
	431	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	432	then
	433
	434	# LINE DEFINES ERROR-COMMAND
	435	(( iec = iec + 1 ))
	436	line=$(echo $line \| cut -c4-)
	437	err_command[$iec]="$line"
	438
	439	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	440	then
	441
	442	# LINE DEFINES INPUT-COMMAND
	443	(( iic = iic + 1 ))
	444	line=$(echo $line \| cut -c4-)
	445	in_command[$iic]="$line"
	446
	447	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	448	then
	449
	450	# LINE DEFINES OUTPUT-COMMAND
	451	(( ioc = ioc + 1 ))
	452	line=$(echo $line \| cut -c4-)
	453	out_command[$ioc]="$line"
	454
	455	else
	456
	457	# SKIP ALL OTHER LINES
	458	continue
	459
	460	fi
	461
	462	done < $config_file
	463
	464
	465	# CHECK SETTING OF REQUIRED PARAMETERS
	466	if [[ "$compiler_name" = "" ]]
	467	then
	468	printf "\n +++ no compiler name found in $config_file"
	469	printf "\n Please add line \"compiler_name ...\" to that file."
	470	locat=config_file; exit
	471	fi
	472	if [[ "$compiler_name_ser" = "" ]]
	473	then
	474	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	475	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	476	locat=config_file; exit
	477	fi
	478	if [[ "$compiler_options" = "" ]]
	479	then
	480	printf "\n +++ no compiler options found in $config_file"
	481	printf "\n Please add line \"compiler_options ...\" to that file."
	482	locat=config_file; exit
	483	fi
[2388]	484	if [[ "$linker_options" = "" ]]
[2380]	485	then
[2388]	486	printf "\n +++ no linker options found in $config_file"
	487	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	488	locat=config_file; exit
	489	fi
	490	if [[ "$execute_command" = "" ]]
	491	then
	492	printf "\n +++ no execute command found in $config_file"
	493	printf "\n Please add line \"execute_command ...\" to that file."
	494	locat=config_file; exit
	495	fi
	496
	497	if [[ "$hostfile" != "" ]]
	498	then
	499	if [[ $hostfile != auto && ! -f $hostfile ]]
	500	then
	501	printf "\n +++ no hostfile \"$hostfile\" found"
	502	printf "\n Please check line \"hostfile ...\" in $config_file"
	503	locat=config_file; exit
	504	fi
	505	fi
	506
	507
	508	# DETERMINE THE CALL STATUS
	509	if [[ "$return_address" != "" ]]
	510	then
	511
	512	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	513	# BATCH MODE AND ...
	514	running_on_remote=true
	515
	516	else
	517
	518	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	519	if [[ "$remote_ip" != "" ]]
	520	then
	521
	522	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	523	create_remote_batch_job=true
	524
	525	fi
	526	running_on_remote=false
	527	fi
	528
	529
	530
	531	# READ AND EVALUATE THE I/O-FILE LIST
	532	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	533
	534	# READ THE FILE CONNECTION FILE LINE BY LINE
	535	while read line
	536	do
	537
[2669]	538	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	539	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	540
	541	# INTERPRET THE LINE
	542	if [[ "$(echo $line)" = "" ]]
	543	then
	544	# EMPTY LINE, NO ACTION
	545	continue
	546
	547	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	548	then
	549
	550	# LINE IS A COMMENT LINE
	551	true
	552
	553	else
	554
	555	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	556	# s2a: in/out - field
[2669]	557	# s2b: action - field (optional)
	558	s1=`echo "$line" \| cut -d" " -f1`
	559	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	560	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	561	then
[2669]	562	s2a=$s2
[2380]	563	s2b=""
	564	else
[2669]	565	s2a=`echo $s2 \| cut -d":" -f1`
	566	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	567	fi
[2669]	568	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	569	s4=`echo "$line" \| cut -d" " -s -f4`
	570	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	571	s5=`echo "$line" \| cut -d" " -s -f5`
	572	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	573
	574
	575	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	576	# INPUT- OR OUTPUT-LIST.
	577	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	578	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	579	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	580	# IS NOT CHECKED AND STORED.
[2610]	581	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	582	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	583	then
	584	found=false
	585	for actual in $activation_string_list
	586	do
	587	for formal in $s3
	588	do
	589	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	590	done
	591	done
	592	if [[ $found = true ]]
	593	then
	594	(( iin = iin + 1 ))
[2669]	595	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	596	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	597	if [[ "$s2a" = inopt ]]
	598	then
	599	optin_pre[$iin]=yes
	600	else
	601	optin_pre[$iin]=no
	602	fi
[2605]	603
	604	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	605	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	606	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	607	then
[2610]	608	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	609	fi
	610
[2610]	611	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	612	# THE WILDCARD FROM THE ENDING
	613	if [[ "${s5: -1}" = "*" ]]
	614	then
[2669]	615	if [[ "$s2b" = "di" ]]
[2610]	616	then
	617	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	618	printf "\n see file \"$fileconnection_file\", line"
	619	printf "\n$line"
	620	locat=iofiles_file; exit
	621	fi
	622	multin[$iin]=true
	623	string=${endin_pre[$iin]}
	624	endin_pre[$iin]="${string%?}"
	625	else
	626	multin[$iin]=false
	627	fi
[2380]	628	fi
[2669]	629	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	630	then
	631	found=false
	632	for actual in $activation_string_list
	633	do
	634	for formal in $s3
	635	do
[2670]	636	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	637	done
	638	done
	639	if [[ $found = true ]]
	640	then
	641	(( iout = iout + 1 ))
[2669]	642	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	643	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	644
[2669]	645	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	646	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	647	if [[ $formal = wildcard ]]
	648	then
	649	warnout_pre[$iout]=false
	650	else
	651	warnout_pre[$iout]=true
	652	fi
	653
[2610]	654	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	655	# THE WILDCARD FROM THE LOCAL FILENAME
	656	if [[ "${s1: -1}" = "*" ]]
	657	then
[2669]	658	if [[ "$s2b" = "di" ]]
[2610]	659	then
	660	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	661	printf "\n see file \"$fileconnection_file\", line"
	662	printf "\n$line"
	663	locat=iofiles_file; exit
	664	fi
	665	multout[$iout]=true
	666	string=${localout_pre[$iout]}
	667	localout_pre[$iout]="${string%?}"
	668	else
	669	multout[$iout]=false
	670	fi
[2380]	671	fi
[2669]	672	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	673	then
[2669]	674	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	675	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	676	locat=connect; exit
	677	fi
	678	IFS="$IFSALT"
	679	fi
	680
	681	done < $fileconnection_file
	682
	683
	684
[2501]	685	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	686	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	687	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	688	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	689	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	690	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	691
	692
	693
[2380]	694	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	695	if [[ $run_coupled_model = true ]]
	696	then
	697
	698	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	699	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	700
	701	if (( $cores_ocean + $cores_atmos != $cores ))
	702	then
	703
	704	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	705	printf "\n PEs (total) : $cores"
	706	printf "\n PEs (atmosphere): $cores_atmos"
	707	printf "\n PEs (ocean) : $cores_ocean"
	708	locat=coupling; exit
	709
	710	fi
	711
	712	fi
	713
	714
	715	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	716	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	717	# FOLDER
	718	if [[ $running_in_batch_mode = true ]]
	719	then
	720
[2506]	721	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	722	then
[2506]	723	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	724	printf "\n Please check the output of the palmrun-call"
	725	printf "\n that you did on your local host."
	726	locat=SOURCES_FOR_RUN; exit
	727	fi
	728
	729	else
	730
	731	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	732	# AUTOMATIC RESTART RUN
	733	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	734	if [[ $restart_run = false ]]
	735	then
	736
	737	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	738	# THE LOCAL HOST
	739	if [[ ! -d $source_path ]]
	740	then
	741	printf "\n\n +++ source path \"$source_path\" on local host"
	742	printf "\n \"$(hostname)\" does not exist"
	743	locat=source_path; exit
	744	fi
	745
[2506]	746	rm -rf $sources_for_run_catalog
	747	mkdir -p $sources_for_run_catalog
[2380]	748
	749	if [[ "$source_list" = LM ]]
	750	then
	751
	752	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	753	source_list=""
	754	cd $source_path
	755
	756
[2512]	757	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	758	if [[ ! -d ../.svn ]]
[2380]	759	then
	760	printf "\n\n +++ source directory"
	761	printf "\n \"$source_path\" "
	762	printf "\n is not under control of \"subversion\"."
[2512]	763	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	764	fi
	765
	766
	767	# LIST ALL MODIFIED SOURCE CODE FILES
	768	Filenames=""
[2404]	769	svn status > tmp_svnstatus
[2380]	770	while read line
	771	do
	772	firstc=`echo $line \| cut -c1`
	773	if [[ $firstc = M \|\| $firstc = "?" ]]
	774	then
	775	Name=`echo "$line" \| cut -c8-`
	776	extension=`echo $Name \| cut -d. -f2`
	777	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	778	then
	779	Filenames="$Filenames "$Name
	780	fi
	781	fi
[2404]	782	done < tmp_svnstatus
	783	rm -rf tmp_svnstatus
[2380]	784
	785
	786	# COPY FILES TO SOURCES_FOR_RUN_...
	787	for filename in $Filenames
	788	do
[2506]	789	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	790	source_list=$source_list"$filename "
	791	done
	792
	793	cd - > /dev/null
	794
	795
	796	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	797	elif [[ "$source_list" != "" ]]
	798	then
	799
	800	cd $source_path
	801
	802	for filename in $source_list
	803	do
	804
	805	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	806	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	807	then
	808	printf "\n +++ source code file: $filename"
	809	printf "\n must not contain (\"/\") "
	810	locat=source; exit
	811	fi
	812
	813	if [[ ! -f $filename ]]
	814	then
	815	printf "\n +++ source code file: $filename"
	816	printf "\n does not exist"
	817	locat=source; exit
	818	else
[2506]	819	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	820	fi
	821
	822	done
	823
	824	cd - > /dev/null
	825
	826	fi
	827
	828	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	829	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	830	if [[ ! -f $makefile ]]
	831	then
	832	printf "\n +++ file \"$makefile\" does not exist"
	833	locat=make; exit
	834	else
[2506]	835	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	836	fi
	837
	838
	839	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	840	if [[ "$user_source_path" != "" ]]
[2380]	841	then
	842
	843	# DOES THE DIRECTORY EXIST?
[2384]	844	if [[ ! -d $user_source_path ]]
[2380]	845	then
	846
	847	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	848	printf "\n \"$user_source_path\" "
[2380]	849	printf "\n does not exist or is not a directory."
	850	printf "\n No source code will be used from this directory!\n"
[2384]	851	user_source_path=""
[2380]	852	if [[ $silent == false ]]
	853	then
	854	sleep 2
	855	fi
	856
	857	else
	858
[2384]	859	cd $user_source_path
[2380]	860	found=false
	861
	862	Names=$(ls -1 *.f90 2>&1)
	863	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	864	Names=$(ls -1 *.F90 2>&1)
	865	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	866	Names=$(ls -1 *.F 2>&1)
	867	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	868	Names=$(ls -1 *.f 2>&1)
	869	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	870	Names=$(ls -1 *.c 2>&1)
	871	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	872
	873	cd - > /dev/null
[2506]	874	cd $sources_for_run_catalog
[2380]	875
	876	# COPY MAKEFILE IF EXISTING
[2384]	877	if [[ -f $user_source_path/Makefile ]]
[2380]	878	then
	879	printf "\n\n *** user Makefile from directory"
[2384]	880	printf "\n \"$user_source_path\" is used \n"
[2380]	881	if [[ $silent == false ]]
	882	then
	883	sleep 1
	884	fi
[2384]	885	cp $user_source_path/Makefile .
[2380]	886	fi
	887
	888	for filename in $AddFilenames
	889	do
	890	if [[ -f $filename ]]
	891	then
	892	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	893	printf "\n source code directory \"$user_source_path\" "
[2380]	894	printf "\n but was also given with option \"-s\" which means that it should be taken"
	895	printf "\n from directory \"$source_path\"."
	896	locat=source; exit
	897	fi
	898
[2384]	899	cp $user_source_path/$filename .
[2380]	900	source_list="$source_list $filename"
	901
	902	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	903	if [[ $(grep -c $filename Makefile) = 0 ]]
	904	then
	905	printf "\n\n +++ user file \"$filename\" "
	906	printf "\n is not listed in Makefile \n"
	907	locat=source; exit
	908	else
	909
	910	if [[ $found = false ]]
	911	then
	912	found=true
	913	printf "\n\n *** following user file(s) added to the"
	914	printf " files to be translated:\n "
	915	fi
	916	printf "$filename "
	917	if [[ $silent == false ]]
	918	then
	919	sleep 0.5
	920	fi
	921
	922	fi
	923	done
	924	[[ $found = true ]] && printf "\n"
	925	cd - > /dev/null
	926	fi
	927	fi
	928
	929	# COPY CONFIGURATION FILES
[2506]	930	cp $config_file $sources_for_run_catalog
	931	cp $fileconnection_file $sources_for_run_catalog
[2380]	932
	933	# COPY SHELLSCRIPTS
[2506]	934	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	935	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	936
	937	fi
	938
	939	fi
	940
[2605]	941
[2380]	942	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	943	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	944	if [[ "$global_revision" = "" ]]
	945	then
	946	global_revision=`svnversion $source_path 2>/dev/null`
	947	global_revision="Rev: $global_revision"
	948	fi
	949
	950
	951	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	952	if [[ -n $cores ]]
	953	then
	954
	955	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	956	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	957	if [[ $tasks_per_node = 0 ]]
[2380]	958	then
	959	printf "\n"
	960	printf "\n +++ option \"-T\" (tasks per node) is missing"
	961	printf "\n set -T option or define tasks_per_node in the config file"
	962	locat=tasks_per_node; (( iec = 0 )); exit
	963	fi
	964
	965	if (( cores < tasks_per_node ))
	966	then
	967	printf "\n"
	968	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	969	printf "\n given values: -T $tasks_per_node -X $cores"
	970	locat=tasks_per_node; (( iec = 0 )); exit
	971	fi
	972
	973	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	974	(( mpi_tasks = cores / threads_per_task ))
	975	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	976	(( ii = cores / tasks_per_node ))
	977	(( remaining_cores = cores - ii * tasks_per_node ))
	978	if (( remaining_cores > 0 ))
	979	then
	980	printf "\n"
	981	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	982	printf "\n divisor of the total number of cores (option \"-X\")"
	983	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	984	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	985	(( nodes = nodes + 1 ))
	986	fi
	987
	988	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	989	if [[ "$tasks_per_node" != "" ]]
	990	then
	991	TOPT="-T $tasks_per_node"
	992	fi
	993
	994	fi
	995
	996
	997	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	998	if [[ "$maximum_parallel_io_streams" = "" ]]
	999	then
	1000	maximum_parallel_io_streams=$cores
	1001	fi
	1002
	1003
	1004	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1005	if [[ "$scp_port" != "" ]]
	1006	then
	1007	PORTOPT="-P $scp_port"
	1008	SSH_PORTOPT="-p $scp_port"
	1009	fi
	1010
	1011
	1012	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1013	# CONFIG-FILE
	1014	if [[ "$ssh_key" != "" ]]
	1015	then
	1016	ssh_key="-i $HOME/.ssh/$ssh_key"
	1017	fi
	1018
	1019
	1020	# SET QUEUE, IF NOT GIVEN
	1021	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1022	then
	1023
	1024	if [[ $queue = none && "$defaultqueue" = "" ]]
	1025	then
	1026	printf "\n"
	1027	printf "\n +++ no default queue given in configuration file and no queue"
	1028	printf "\n given with option -q"
	1029	fi
	1030	if [[ $queue = none ]]
	1031	then
	1032	queue=$defaultqueue
	1033	fi
	1034
	1035	fi
	1036
	1037
	1038	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1039	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1040	(( i = 0 ))
[2610]	1041	(( nr_of_input_files = 0 ))
[2380]	1042	while (( i < iin ))
	1043	do
	1044	(( i = i + 1 ))
	1045
	1046	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1047	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1048	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1049	then
[2610]	1050	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1051	else
[2610]	1052	eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]}
[2380]	1053	fi
	1054
[2610]	1055
[2380]	1056	# CHECK IF FILE EXISTS
	1057	if ! ls $filename* 1>/dev/null 2>&1
	1058	then
	1059
[2669]	1060	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1061	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1062	then
	1063	printf "\n\n +++ INPUT-file: "
[2610]	1064	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1065	then
	1066	printf "\n $filename"
	1067	else
[2610]	1068	printf "\n $filename.${extin_pre[$i]}"
[2380]	1069	fi
	1070	printf "\n does not exist\n"
	1071	locat=input; exit
	1072	else
[2610]	1073	(( nr_of_input_files = nr_of_input_files + 1 ))
	1074	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1075	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1076	actionin[$nr_of_input_files]="unavailable"
[2610]	1077	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1078	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1079	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1080	fi
[2605]	1081
[2380]	1082	else
	1083
[2610]	1084	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND
	1085	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
	1086	if [[ "${multin[$i]}" = true ]]
	1087	then
	1088	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1089	ls -1 -d ${filename} > filelist 2>/dev/null
	1090	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1091	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1092
[2610]	1093	endings=""
	1094	while read line
	1095	do
	1096	# filename without path (i.e. after the last "/")
	1097	basefilename=$(basename ${line})
[2380]	1098
[2610]	1099	# check if there is an extension and remove it
	1100	ext=${basefilename##*.}
	1101	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1102	then
	1103	basefilename=${basefilename%.*}
	1104	fi
[2380]	1105
[2610]	1106	# check for an existing cycle number and remove it
	1107	cycle=${basefilename##*.}
	1108	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1109	then
	1110	basefilename=${basefilename%.*}
	1111	fi
[2600]	1112
[2610]	1113	# remove the fname from the beginning
	1114	length_fname=${#fname}
	1115	ending=${basefilename:${length_fname}}
	1116
	1117	# remove the ending given in the .iofiles from the beginning
	1118	endingstring="${endin_pre[$i]}"
	1119	length_ending=${#endingstring}
	1120	ending=${ending:${length_ending}}
	1121
	1122	if [[ "$ending" = "" ]]
[2600]	1123	then
[2610]	1124	# standard ending as given in the .iofiles
	1125	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1126	then
	1127	endings="$endings DEFAULT"
	1128	fi
[2600]	1129	else
[2610]	1130	# ending must start with "_", otherwise its a different file
	1131	if [[ "${ending:0:1}" = "_" ]]
	1132	then
	1133	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1134	then
	1135	endings="$endings $ending"
	1136	fi
	1137	fi
[2600]	1138	fi
[2610]	1139
	1140	done <filelist
[2380]	1141
[2610]	1142	rm filelist
[2380]	1143
[2600]	1144	else
[2610]	1145
	1146	# SINGLE NAME
	1147	endings=DEFAULT
	1148
[2600]	1149	fi
	1150
[2610]	1151	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1152	for ending in $endings
	1153	do
	1154
	1155	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1156	if [[ $ending = DEFAULT ]]
[2380]	1157	then
[2610]	1158	ending=""
	1159	fi
	1160
	1161	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1162	(( nr_of_input_files = nr_of_input_files + 1 ))
	1163	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1164	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1165	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1166	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1167	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1168	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1169
	1170
	1171	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1172	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1173	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1174	then
	1175	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1176	else
[2610]	1177	eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]}
[2380]	1178	fi
[2610]	1179
	1180	# DETERMINE THE FILE'S CYCLE NUMBER
	1181	(( maxcycle = 0 ))
	1182	ls -1 -d $filename > filelist 2>/dev/null
	1183	ls -1 -d $filename.* >> filelist 2>/dev/null
	1184	while read line
	1185	do
	1186	# filename without path (i.e. after the last "/")
	1187	basefilename=$(basename ${line})
	1188
	1189	# check if there is an extension
	1190	extension=${basefilename##*.}
	1191	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1192	then
	1193	basefilename=${basefilename%.*}
	1194	fi
	1195
	1196	# check for an existing cycle number
	1197	cycle=${basefilename##*.}
	1198	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1199	then
[2669]	1200	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1201	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1202	(( icycle = $((10#$cycle)) ))
[2610]	1203	else
	1204	(( icycle = 0 ))
	1205	fi
	1206
	1207	if (( icycle > maxcycle ))
	1208	then
	1209	(( maxcycle = icycle ))
	1210
	1211	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1212	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1213	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1214	then
	1215	leading_zero=true
	1216	else
	1217	leading_zero=false
	1218	fi
	1219	fi
	1220
	1221	done <filelist
	1222	rm filelist
	1223
	1224	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1225	if [[ $leading_zero = true ]]
[2380]	1226	then
[2610]	1227	cyclestring=`printf "%03d" $maxcycle`
	1228	else
	1229	cyclestring=$maxcycle
[2380]	1230	fi
[2610]	1231
	1232	# APPEND CYCLE NUMBER TO FILENAME
	1233	if (( maxcycle > 0 ))
[2380]	1234	then
[2610]	1235	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1236	then
	1237	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1238	else
	1239	filename=${filename}.$cyclestring
	1240	fi
[2380]	1241	else
[2610]	1242	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1243	then
	1244	filename=${filename}.${extin[$nr_of_input_files]}
	1245	fi
[2380]	1246	fi
[2610]	1247
	1248	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1249	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1250	absnamein[$nr_of_input_files]=$filename
	1251	if (( maxcycle > 0 ))
[2380]	1252	then
[2610]	1253	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1254	then
	1255	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1256	else
	1257	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring
	1258	fi
[2380]	1259	else
[2610]	1260	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1261	then
	1262	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1263	else
	1264	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}
	1265	fi
[2380]	1266	fi
	1267
[2610]	1268	done
	1269
[2380]	1270	fi
[2610]	1271
[2380]	1272	done
	1273
[2610]	1274
[2380]	1275	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1276	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1277	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1278	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1279	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1280	# REMOTE HOST)
	1281	(( i = 0 ))
	1282	while (( i < iout ))
	1283	do
	1284	(( i = i + 1 ))
[2610]	1285	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1286	then
[2610]	1287	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1288	then
[2610]	1289	actionout_pre[$i]=""
	1290	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1291	then
[2610]	1292	actionout_pre[$i]=pe
	1293	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1294	then
[2610]	1295	actionout_pre[$i]=a
[2380]	1296	fi
	1297	(( maxcycle = 0 ))
[2610]	1298	eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]}
	1299	eval catalogname=${pathout_pre[$i]}
[2380]	1300	if ! ls $filename* 1>/dev/null 2>&1
	1301	then
	1302
	1303	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1304	if cat /dev/null > $filename
	1305	then
	1306	rm $filename
	1307	else
	1308
	1309	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1310	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1311	if [[ ! -d $catalogname ]]
	1312	then
	1313	if mkdir -p $catalogname
	1314	then
	1315	printf "\n\n *** directory:"
	1316	printf "\n $catalogname"
	1317	printf "\n was created\n"
	1318	else
	1319	printf "\n\n +++ OUTPUT-file:"
	1320	printf "\n $filename"
	1321	printf "\n cannot be created, because directory does not exist"
	1322	printf "\n and cannot be created either"
	1323	printf "\n"
	1324	locat=output ; exit
	1325	fi 2>/dev/null
	1326	else
	1327	printf "\n\n +++ OUTPUT-file:"
	1328	printf "\n $filename"
	1329	printf "\n cannot be created, although directory exists"
	1330	printf "\n"
	1331	locat=output ; exit
	1332	fi
	1333	fi 2>/dev/null
	1334
	1335	fi
	1336
	1337	fi
	1338	done
	1339
	1340
	1341	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1342	if [[ $running_in_batch_mode = false ]]
	1343	then
	1344	run_id=$RANDOM
	1345	job_id=${fname}.$run_id
	1346
[2566]	1347	tempdir=$fast_io_catalog/$job_id
[2380]	1348	fi
	1349
	1350
	1351	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1352	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1353	then
	1354
	1355	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1356	if [[ $ibd = 0 ]]
	1357	then
	1358	printf "\n"
	1359	printf "\n +++ no batch directives found in configuration file"
	1360	locat=config_file_batch_directives; (( iec = 0 )); exit
	1361	fi
	1362
	1363	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1364	done=false
[2384]	1365	cputime=$cpumax
[2380]	1366	while [[ $done = false ]]
	1367	do
[2384]	1368	if (( cputime == 0 ))
[2380]	1369	then
	1370	printf "\n +++ cpu-time is undefined"
	1371	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1372	printf "\n >>> "
[2384]	1373	read cputime 1>/dev/null 2>&1
[2380]	1374	else
	1375	done=true
	1376	fi
	1377	done
[2420]	1378	cpumax=$cputime
[2380]	1379
	1380	# CHECK THE MEMORY DEMAND
	1381	done=false
	1382	while [[ $done = false ]]
	1383	do
	1384	if (( memory == 0 ))
	1385	then
	1386	printf "\n +++ memory demand is undefined"
	1387	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1388	printf "\n >>> "
	1389	read memory 1>/dev/null 2>&1
	1390	else
	1391	done=true
	1392	fi
	1393	done
	1394
	1395	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1396	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1397	then
	1398	while [[ -z $remote_username ]]
	1399	do
[2420]	1400	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1401	printf "\n >>> Please type username:"
	1402	printf "\n >>> "
	1403	read remote_username
	1404	done
	1405	fi
	1406
	1407	else
	1408
[2420]	1409	if [[ $running_in_batch_mode = false ]]
	1410	then
	1411	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1412	cpumax=$cputime
	1413	else
	1414	cputime=$cpumax
	1415	fi
[2380]	1416
	1417	fi
	1418
	1419
	1420	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1421	(( cpu_hours = cputime / 3600 ))
	1422	(( resttime = cputime - cpu_hours * 3600 ))
	1423	(( cpu_minutes = resttime / 60 ))
	1424	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1425	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1426
	1427
	1428	# OUTPUT OF THE PALMRUN-HEADER
	1429	calltime=$(date)
	1430	printf "\n"
	1431	printf "#------------------------------------------------------------------------# \n"
	1432	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1433	printf "\| \| \n"
	1434	column1="called on:"; column2=$(hostname)
	1435	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1436	if [[ $create_remote_batch_job = true ]]
	1437	then
[2506]	1438	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1439	else
	1440	if [[ $running_on_remote = true ]]
	1441	then
[2506]	1442	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1443	else
[2506]	1444	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1445	fi
	1446	fi
	1447	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1448
	1449	column1="running in:"
	1450	if [[ $running_in_batch_mode = true ]]
	1451	then
	1452	column2="batch job mode"
	1453	else
	1454	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1455	then
	1456	column2="job creation mode"
	1457	else
	1458	column2="interactive run mode"
	1459	fi
	1460	fi
	1461	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1462
[2479]	1463	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1464	then
[2480]	1465	if [[ "$project_account" != "" ]]
[2479]	1466	then
	1467	column1="project account number:"
	1468	column2="$project_account"
	1469	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1470	fi
	1471	fi
	1472
[2380]	1473	if [[ -n $cores ]]
	1474	then
	1475	if [[ $run_coupled_model = false ]]
	1476	then
	1477	column1="number of cores:"; column2=$cores
	1478	else
	1479	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1480	fi
	1481	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1482	fi
	1483	if [[ -n $tasks_per_node ]]
	1484	then
	1485	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1486	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1487	if (( remaining_cores > 0 ))
	1488	then
	1489	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1490	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1491	fi
	1492	fi
	1493	if [[ $maximum_parallel_io_streams != $cores ]]
	1494	then
	1495	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1496	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1497	fi
	1498	if [[ $use_openmp = true ]]
	1499	then
	1500	column1="threads per task:"; column2="$threads_per_task"
	1501	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1502	fi
[2384]	1503	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1504	then
[2506]	1505	column1="memory demand / PE":; column2="$memory MB"
	1506	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1507	column1="job cpu time (h:m:s):"; column2="$timestring"
	1508	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1509	fi
[2380]	1510	printf "\| \| \n"
	1511	if [[ "$source_list" != "" ]]
	1512	then
	1513	if [[ "$make_options" != "" ]]
	1514	then
	1515	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1516	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1517	line=$(echo "$make_options" \| cut -c46-)
	1518	while [[ "$line" != "" ]]
	1519	do
	1520	column1=""
	1521	column2=$(echo "$line" \| cut -c-45)
	1522	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1523	line=$(echo "$line" \| cut -c46-)
	1524	done
	1525	fi
	1526	fi
	1527
	1528	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1529	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1530	line=$(echo "$cpp_options" \| cut -c46-)
	1531	while [[ "$line" != "" ]]
	1532	do
	1533	column1=""
	1534	column2=$(echo "$line" \| cut -c-45)
	1535	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1536	line=$(echo "$line" \| cut -c46-)
	1537	done
	1538
	1539	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1540	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1541	line=$(echo "$compiler_options" \| cut -c46-)
	1542	while [[ "$line" != "" ]]
	1543	do
	1544	column1=""
	1545	column2=$(echo "$line" \| cut -c-45)
	1546	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1547	line=$(echo "$line" \| cut -c46-)
	1548	done
	1549
[2388]	1550	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1551	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1552	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1553	while [[ "$line" != "" ]]
	1554	do
	1555	column1=""
	1556	column2=$(echo "$line" \| cut -c-45)
	1557	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1558	line=$(echo "$line" \| cut -c46-)
	1559	done
	1560
	1561	if [[ "$login_init_cmd" != "" ]]
	1562	then
	1563	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1564	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1565	line=$(echo "$login_init_cmd" \| cut -c46-)
	1566	while [[ "$line" != "" ]]
	1567	do
	1568	column1=""
	1569	column2=$(echo "$line" \| cut -c-45)
	1570	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1571	line=$(echo "$line" \| cut -c46-)
	1572	done
	1573	fi
	1574
	1575	if [[ "$module_commands" != "" ]]
	1576	then
	1577	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1578	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1579	line=$(echo "$module_commands" \| cut -c46-)
	1580	while [[ "$line" != "" ]]
	1581	do
	1582	column1=""
	1583	column2=$(echo "$line" \| cut -c-45)
	1584	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1585	line=$(echo "$line" \| cut -c46-)
	1586	done
	1587	fi
	1588	printf "\| \| \n"
	1589	column1="base name of files:"; column2=$fname
	1590	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1591	column1="activation string list:"; column2=$(echo $activation_string_list)
	1592	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1593
	1594	if [[ "$ocean_file_appendix" = true ]]
	1595	then
	1596	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1597	fi
	1598
	1599	if [[ "$source_list" != "" ]]
	1600	then
	1601	printf "\| \| \n"
	1602	printf "\| Files to be compiled: \| \n"
	1603	line=$source_list
	1604	while [[ "$line" != "" ]]
	1605	do
	1606	linestart=$(echo $line \| cut -c-70)
	1607	printf "\| %-70s \| \n" "$linestart"
	1608	line=$(echo "$line" \| cut -c71-)
	1609	done
	1610	fi
	1611	printf "#------------------------------------------------------------------------#"
	1612
	1613
	1614
	1615	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1616	if [[ $do_trace = true ]]
	1617	then
	1618	(( i = 0 ))
[2610]	1619	while (( i < nr_of_input_files ))
[2380]	1620	do
	1621	(( i = i + 1 ))
	1622	if (( i == 1 ))
	1623	then
	1624	printf "\n\n >>> INPUT-file assignments:\n"
	1625	fi
	1626	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1627	done
	1628	(( i = 0 ))
	1629	while (( i < iout ))
	1630	do
	1631	(( i = i + 1 ))
	1632	if (( i == 1 ))
	1633	then
	1634	printf "\n\n >>> OUTPUT-file assignments:\n"
	1635	fi
	1636	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1637	done
	1638	(( i = 0 ))
	1639	while (( i < iic ))
	1640	do
	1641	(( i = i + 1 ))
	1642	if (( i == 1 ))
	1643	then
	1644	printf "\n\n >>> INPUT-commands:\n"
	1645	fi
	1646	printf "\n ${in_command[$i]}"
	1647	done
	1648	(( i = 0 ))
	1649	while (( i < ioc ))
	1650	do
	1651	(( i = i + 1 ))
	1652	if (( i == 1 ))
	1653	then
	1654	printf "\n\n >>> OUTPUT-commands:\n"
	1655	fi
	1656	printf "\n ${out_command[$i]}"
	1657	done
	1658	fi
	1659
	1660	# QUERY FOR CONTINUE
	1661	if [[ $silent = false && $running_in_batch_mode = false ]]
	1662	then
	1663	antwort=dummy
	1664	printf "\n\n"
	1665	printf " >>> everything o.k. (y/n) ? "
	1666	while read antwort
	1667	do
	1668	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1669	then
	1670	printf " >>> everything o.k. (y/n) ? "
	1671	else
	1672	break
	1673	fi
	1674	done
	1675	if [[ $antwort = n \|\| $antwort = N ]]
	1676	then
	1677	locat=user_abort; (( iec = 0 )); exit
	1678	fi
	1679	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1680	then
[2566]	1681	printf "\n *** batch-job will be created and submitted"
[2380]	1682	else
[2566]	1683	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1684	fi
	1685	fi
	1686
	1687
	1688
	1689	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1690	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1691	then
	1692
	1693	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1694	then
[2566]	1695	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1696	else
[2566]	1697	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1698	fi
	1699
[2422]	1700	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1701	# IT SHALL BE CREATED
	1702	ask_for_make_depository=false
	1703	if [[ $create_remote_batch_job = true ]]
	1704	then
	1705
	1706	line=`grep %base_directory $config_file`
[2506]	1707	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1708	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
[2422]	1709
[2506]	1710	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1711	then
	1712	printf "\n\n +++ make depository \"${make_depository}\""
	1713	printf "\n on remote host not found!"
	1714	ask_for_make_depository=true
	1715	fi
[2506]	1716	rm ${host_configuration}_last_make_protokoll
[2422]	1717
	1718	else
	1719
	1720	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1721	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1722	if [[ ! -d ${make_depository} ]]
	1723	then
	1724	printf "\n\n +++ make depository \"${make_depository}\""
	1725	printf "\n on local host not found!"
	1726	ask_for_make_depository=true
	1727	fi
	1728
	1729	fi
	1730
	1731	if [[ $ask_for_make_depository = true ]]
	1732	then
	1733
	1734	antwort=dummy
	1735	printf "\n\n"
	1736	printf " >>> Create a new one (y/n) ? "
	1737	while read antwort
	1738	do
	1739	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1740	then
	1741	printf " >>> Create a new one (y/n) ? "
	1742	else
	1743	break
	1744	fi
	1745	done
	1746	if [[ $antwort = n \|\| $antwort = N ]]
	1747	then
	1748	locat=user_abort; (( iec = 0 )); exit
	1749	fi
	1750
[2566]	1751	if [[ $do_trace = true ]]
	1752	then
	1753	palmbuild -h $host_configuration
	1754	else
	1755	palmbuild -v -h $host_configuration
	1756	fi
[2422]	1757
	1758	if [[ $? != 0 ]]
	1759	then
	1760
	1761	# ABORT IN CASE OF COMPILATION PROBLEMS
	1762	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1763	locat=make_depository
	1764	exit
	1765	else
	1766	echo " *** now continue with creating executable and other sources"
	1767	fi
	1768
	1769	fi
	1770
[2566]	1771	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2506]	1772	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
[2380]	1773
	1774	if [[ $? != 0 ]]
	1775	then
	1776
	1777	# ABORT IN CASE OF COMPILATION PROBLEMS
	1778	printf "\n +++ error while creating executable and/or other sources"
	1779	locat=execution
[2506]	1780	rm -rf $sources_for_run_catalog
[2380]	1781	exit
	1782
	1783	else
	1784
[2566]	1785	printf " *** executable and other sources created\n"
[2506]	1786	rm -rf $sources_for_run_catalog
[2380]	1787
	1788	fi
	1789
	1790	fi
	1791
	1792
[2669]	1793	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1794	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1795	if [[ $create_remote_batch_job = true ]]
	1796	then
	1797	(( i = 0 ))
[2610]	1798	while (( i < nr_of_input_files ))
[2605]	1799	do
	1800	(( i = i + 1 ))
[2669]	1801	if [[ "${actionin[$i]}" = tr ]]
[2605]	1802	then
	1803	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1804	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1805	fi
	1806	done
	1807	if (( i > 0 ))
	1808	then
	1809	printf " *** input files have been copied to the remote host\n"
	1810	fi
	1811	fi
	1812
	1813
[2380]	1814	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1815	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1816	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1817	then
	1818
	1819	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1820	if [[ $running_in_batch_mode = false ]]
	1821	then
	1822	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1823	# FOLDER
[2566]	1824	mkdir -p $tempdir
	1825	chmod go+rx $tempdir
	1826	cd $tempdir
	1827	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1828	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1829
	1830	else
	1831
	1832	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1833	printf "\n *** running in temporary directory: $tempdir"
[2380]	1834
	1835	fi
	1836
	1837
	1838	# PROVIDE THE INPUT FILES
	1839	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1840	optional_files_missing=false
[2380]	1841	(( i = 0 ))
[2610]	1842	while (( i < nr_of_input_files ))
[2380]	1843	do
	1844	(( i = i + 1 ))
	1845	if (( i == 1 ))
	1846	then
	1847	printf "\n\n *** providing INPUT-files:\n$dashes"
	1848	fi
	1849
	1850
	1851	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1852	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1853	then
[2669]	1854	optional_files_missing=true
[2380]	1855	continue
	1856	fi
	1857
	1858	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1859	files_for_cores=false; filetype=file
	1860	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1861	then
	1862	files_for_cores=true; filetype=files
	1863	actionin[$i]=""
	1864	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1865	then
	1866	actionin[$i]=""
	1867	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1868	then
	1869	files_for_cores=true; filetype=files
	1870	actionin[$i]="ln"
	1871	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1872	then
	1873	actionin[$i]="ln"
	1874	fi
	1875
	1876	if [[ $files_for_cores = true ]]
	1877	then
	1878	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1879	else
	1880	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1881	fi
	1882
	1883	# INPUT-FILES TO BE LINKED
	1884	if [[ "${actionin[$i]}" = ln ]]
	1885	then
	1886
	1887	printf "\n $filetype will be linked"
	1888	if [[ $files_for_cores = false ]]
	1889	then
	1890	if [[ -f "${absnamein[$i]}" ]]
	1891	then
	1892	ln ${absnamein[$i]} ${localin[$i]}
	1893	got_tmp[$i]=true
	1894	fi
	1895	else
	1896	if [[ -d "${absnamein[$i]}" ]]
	1897	then
[2396]	1898	mkdir -p ${localin[$i]}
[2380]	1899	cd ${absnamein[$i]}
	1900	for file in $(ls *)
	1901	do
[2566]	1902	ln $file $tempdir/${localin[$i]}
[2380]	1903	done >\|/dev/null 2>&1
[2566]	1904	cd $tempdir
[2380]	1905	fi
	1906
	1907	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1908	if [[ ! -f "${localin[$i]}/_000000" ]]
	1909	then
	1910	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1911	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1912	fi
	1913
	1914	got_tmp[$i]=true
	1915	fi
	1916	fi
	1917
	1918	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	1919	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	1920	then
	1921
	1922	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1923	then
	1924
	1925	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1926	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1927	printf "\n file will be provided for $cores processors"
[2396]	1928	mkdir -p ${localin[$i]}
[2380]	1929	ival=$cores
	1930	(( ii = 0 ))
	1931	while (( ii <= ival-1 ))
	1932	do
	1933	if (( ii < 10 ))
	1934	then
	1935	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1936	elif (( ii < 100 ))
	1937	then
	1938	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1939	elif (( ii < 1000 ))
	1940	then
	1941	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1942	else
	1943	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1944	fi
	1945	(( ii = ii + 1 ))
	1946	done
	1947
	1948	else
	1949
	1950	if [[ $files_for_cores = true ]]
	1951	then
	1952
	1953	# PROVIDE FILES FOR EACH CORE
	1954	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1955	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1956	printf "\n providing $cores files for the respective cores"
[2396]	1957	mkdir -p ${localin[$i]}
[2380]	1958	if [[ $link_local_input = true ]]
	1959	then
	1960	printf " files will be linked\n"
	1961	cd ${absnamein[$i]}
	1962	for file in $(ls *)
	1963	do
	1964	ln -f $file ${localin[$i]}
	1965	done
[2566]	1966	cd $tempdir
[2380]	1967	fi
	1968
	1969	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1970	if [[ ! -f "${localin[$i]}/_000000" ]]
	1971	then
	1972	if [[ $link_local_input = true ]]
	1973	then
	1974	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1975	fi
	1976	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1977	fi
	1978
	1979	else
	1980
	1981	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1982	if [[ $link_local_input = true ]]
	1983	then
	1984	printf " file will be linked\n"
	1985	ln -f ${absnamein[$i]} ${localin[$i]}
	1986	fi
[2605]	1987	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	1988	if [[ ! -f "${localin[$i]}" ]]
	1989	then
	1990	if [[ $link_local_input = true ]]
	1991	then
	1992	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1993	fi
[2669]	1994	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	1995	then
	1996	mv ${absnamein[$i]} ${localin[$i]}
	1997	else
	1998	cp ${absnamein[$i]} ${localin[$i]}
	1999	fi
[2380]	2000	fi
	2001	fi
	2002	fi
	2003	fi
	2004
	2005	done
	2006	if (( i != 0 ))
	2007	then
[2669]	2008	if [[ $optional_files_missing = true ]]
	2009	then
	2010	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2011	fi
[2380]	2012	printf "\n$dashes\n *** all INPUT-files provided \n"
	2013	fi
	2014
	2015
	2016	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2017	(( i = 0 ))
	2018	while (( i < iic ))
	2019	do
	2020	(( i = i + 1 ))
	2021	if (( i == 1 ))
	2022	then
	2023	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2024	fi
	2025	printf "\n >>> ${in_command[$i]}"
	2026	eval ${in_command[$i]}
	2027	if (( i == iic ))
	2028	then
	2029	printf "\n$dashes\n"
	2030	fi
	2031	done
	2032
	2033
	2034	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2035	# (FILE ENVPAR WILL BE READ BY PALM)
	2036	cat > ENVPAR << EOF
[2506]	2037	&envpar run_identifier = '$fname', host = '$host_configuration',
[2380]	2038	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	2039	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2040	maximum_cpu_time_allowed = ${cpumax}.,
	2041	revision = '$global_revision',
	2042	batch_job = .${running_in_batch_mode}. /
	2043
	2044	EOF
	2045
	2046
	2047	# STARTING THE EXECUTABLE
	2048	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2049	PATH=$PATH:$tempdir
[2380]	2050
	2051
	2052	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2053	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2054	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2055	eval line=\"$line\"
	2056	execute_command="$line"
	2057
	2058
	2059	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2060	if [[ "$execute_command_for_combine" = "" ]]
	2061	then
	2062	eval line2=\"$line2\"
	2063	execute_command_for_combine="$line2"
	2064	fi
	2065
[2380]	2066
	2067
	2068	# PROVIDE A HOSTFILE, IF REQUIRED
	2069	if [[ "$hostfile" != "" ]]
	2070	then
	2071
	2072	if [[ $hostfile = auto ]]
	2073	then
	2074	# CREATE A NEW HOSTFILE
	2075	(( ii = 1 ))
	2076	while (( ii <= cores / threads_per_task ))
	2077	do
	2078	echo $(hostname) >> hostfile
	2079	(( ii = ii + 1 ))
	2080	done
	2081	if (( cores / threads_per_task == 0 ))
	2082	then
	2083	echo $(hostname) >> hostfile
	2084	fi
	2085
	2086	else
	2087	cp $hostfile hostfile
	2088	fi
	2089	eval line=\"`head -n $ii hostfile`\"
	2090	printf "\n *** running on: $line"
	2091	fi
	2092
	2093
	2094
	2095	# SET THE NUMBER OF OPENMP-THREADS
	2096	if [[ $use_openmp = true ]]
	2097	then
	2098	export OMP_NUM_THREADS=$threads_per_task
	2099	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2100	else
	2101	export OMP_NUM_THREADS=1
	2102	fi
	2103
	2104
[2610]	2105	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2106	if [[ $run_coupled_model = false ]]
	2107	then
	2108	if [[ "$ocean_file_appendix" = true ]]
	2109	then
	2110	echo "precursor_ocean" > coupling_steering
	2111	else
	2112	echo "precursor_atmos" > coupling_steering
	2113	fi
	2114	else
	2115	(( iia = $cores_atmos / $threads_per_task ))
	2116	(( iio = $cores_ocean / $threads_per_task ))
	2117	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2118	printf "\n\n"
	2119	echo "coupled_run $iia $iio" > coupling_steering
	2120	fi
	2121
	2122	printf "\n *** execute command:"
	2123	printf "\n \"$execute_command\" \n\n"
	2124
	2125	$execute_command < coupling_steering
	2126
	2127	if [[ $? != 0 ]]
	2128	then
	2129
	2130	# ABORT IN CASE OF RUNTIME ERRORS
	2131	printf "\n +++ runtime error occured"
	2132	locat=execution
	2133	exit
	2134
	2135	else
	2136
	2137	printf "\n$dashes\n *** execution finished \n"
	2138
	2139	fi
	2140
	2141
	2142	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2143	# BY EACH CORE INTO ONE FILE
	2144	if [[ ! -f combine_plot_fields.x ]]
	2145	then
	2146
	2147	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2148	printf "\n 2d- and/or 3d-data may be incomplete!"
	2149	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2150
	2151	elif [[ "$combine_plot_fields" == true ]]
	2152	then
	2153
	2154	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2155	$execute_command_for_combine
	2156
	2157	else
	2158
	2159	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2160	# DATA OUTPUT
[2380]	2161	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2162	fi
	2163
	2164
	2165
	2166	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2167	(( i = 0 ))
	2168	while (( i < ioc ))
	2169	do
	2170	(( i = i + 1 ))
	2171	if (( i == 1 ))
	2172	then
	2173	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2174	fi
	2175	printf "\n >>> ${out_command[$i]}"
	2176	eval ${out_command[$i]}
	2177	if (( i == ioc ))
	2178	then
	2179	printf "\n$dashes\n"
	2180	fi
	2181	done
	2182
	2183
[2610]	2184	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2185	# WILDCARDS
[2380]	2186	(( i = 0 ))
[2610]	2187	(( nr_of_output_files = 0 ))
	2188
[2380]	2189	while (( i < iout ))
	2190	do
[2610]	2191
[2380]	2192	(( i = i + 1 ))
[2610]	2193
	2194	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2195	# CREATE A LIST FOR THE DETECTED ENDINGS
	2196	if [[ "${multout[$i]}" = true ]]
	2197	then
	2198	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2199	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2200	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2201
	2202	endings="DEFAULT"
	2203	while read line
	2204	do
	2205	# remove the local name from the beginning
	2206	localnamestring="${localout_pre[$i]}"
	2207	length_localname=${#localnamestring}
	2208	ending=${line:${length_localname}}
	2209
	2210	if [[ "$ending" != "" ]]
	2211	then
	2212	endings="$endings $ending"
	2213	fi
	2214
	2215	done <filelist
	2216
	2217	rm filelist
	2218
	2219	else
	2220
	2221	# SINGLE NAME
	2222	endings=DEFAULT
	2223
	2224	fi
	2225
	2226	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2227	for ending in $endings
	2228	do
	2229
	2230	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2231	if [[ $ending = DEFAULT ]]
	2232	then
	2233	ending=""
	2234	fi
	2235
	2236	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2237	(( nr_of_output_files = nr_of_output_files + 1 ))
	2238	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2239	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2240	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2241	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2242	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2243	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2244	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2245
	2246	done
	2247
	2248	done
	2249
	2250
	2251
	2252
	2253	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2254	(( i = 0 ))
	2255	while (( i < nr_of_output_files ))
	2256	do
	2257	(( i = i + 1 ))
[2380]	2258	if (( i == 1 ))
	2259	then
	2260	printf "\n\n *** saving OUTPUT-files:"
	2261
	2262	# GET RUN NUMBER ASSIGNED BY PALM
	2263	if [[ -f RUN_NUMBER ]]
	2264	then
	2265	read run_number < RUN_NUMBER
	2266	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2267	usecycle_option="-U $run_number"
	2268	else
	2269	run_number=0
	2270	usecycle_option=""
	2271	fi
	2272	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2273	then
[2404]	2274	printf "\n *** in case of SCP transfers to local host"
	2275	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2276	fi
	2277	printf "\n$dashes"
	2278	fi
	2279
	2280	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2281	then
	2282
[2610]	2283	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	2284
	2285	# DETERMINE THE CYCLE NUMBER
	2286	ls -1 -d $filename > filelist 2>/dev/null
	2287	ls -1 -d $filename.* >> filelist 2>/dev/null
	2288	while read line
	2289	do
	2290
	2291	# filename without path (i.e. after the last "/")
	2292	basefilename=$(basename ${line})
	2293
	2294	# check if there is an extension
	2295	extension=${basefilename##*.}
	2296	if [[ "$extension" = "${extout[$i]}" ]]
	2297	then
	2298	basefilename=${basefilename%.*}
	2299	fi
	2300
	2301	# check for an existing cycle number
	2302	cycle=${basefilename##*.}
	2303	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2304	then
[2669]	2305	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2306	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2307	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2308	else
	2309	(( icycle = 1 ))
	2310	fi
	2311
	2312	if (( icycle > maxcycle ))
	2313	then
	2314	(( maxcycle = icycle ))
	2315	fi
	2316
	2317	done <filelist
	2318	rm filelist
	2319
	2320
	2321	# SET THE CYCLE NUMBER
	2322	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2323	if [[ "${actionout[$i]}" = a ]]
	2324	then
	2325	(( maxcycle = maxcycle - 1 ))
	2326	fi
	2327
	2328	(( cycnum[$i] = maxcycle ))
	2329	pathout[$i]=$filename
	2330
	2331
	2332	# ADD CYCLE NUMBER TO FILENAME
	2333	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2334	if [[ "${actionout[$i]}" != "a" ]]
	2335	then
	2336	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2337	# WITH AN EXISTING CYCLE NUMBER
	2338	if (( run_number >= cycnum[$i] ))
	2339	then
	2340	(( cycnum[$i] = run_number ))
	2341	else
	2342	if (( run_number > 0 ))
	2343	then
	2344	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2345	fi
	2346	fi
	2347	fi
	2348	if (( cycnum[$i] > 0 ))
	2349	then
[2600]	2350	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2351	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2352	fi
	2353	fi
	2354
	2355	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2356	files_for_cores=false; filetype=file
	2357	link_local_output=false
	2358	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2359	then
	2360	files_for_cores=true; filetype=directory
	2361	actionout[$i]=""
	2362	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2363	then
	2364	actionout[$i]=""
	2365	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2366	then
	2367	files_for_cores=true; filetype=directory
	2368	link_local_output=true
	2369	actionout[$i]=""
	2370	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2371	then
	2372	link_local_output
	2373	actionout[$i]=""
	2374	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2375	then
	2376	files_for_cores=true; filetype=directory
	2377	actionout[$i]="tr"
	2378	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2379	then
	2380	actionout[$i]="tr"
	2381	fi
	2382
	2383	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2384	then
[2669]	2385	if [[ ${warnout[$i]} = true ]]
	2386	then
	2387	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2388	fi
[2380]	2389	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2390	then
[2669]	2391	if [[ ${warnout[$i]} = true ]]
	2392	then
	2393	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2394	fi
[2380]	2395	else
	2396
	2397
	2398	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2399	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2400	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2401	then
	2402	if [[ $running_on_remote = true ]]
	2403	then
	2404
	2405	# SET OPTIONS FOR TRANSFER
	2406	if [[ "${actionout[$i]}" = tr ]]
	2407	then
	2408	if [[ $files_for_cores = false ]]
	2409	then
	2410	catalog_option=""
	2411	catalog_string=""
	2412	else
	2413	catalog_option="-c"
	2414	catalog_string="/"
	2415	fi
	2416	append_option=""
	2417	append_string=""
	2418	else
	2419	append_option="-A"
	2420	append_string="append"
	2421	fi
	2422
	2423	transfer_failed=false
	2424	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2506]	2425	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2426
	2427	# TRANSFER VIA SCP
	2428	if [[ "$remote_loginnode" != "" ]]
	2429	then
[2566]	2430	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]}\" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
[2380]	2431	else
[2506]	2432	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}
[2380]	2433	fi
	2434	[[ $? != 0 ]] && transfer_failed=true
	2435
	2436
	2437	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2438	if [[ $transfer_failed = true ]]
	2439	then
	2440	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2506]	2441	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
[2380]	2442
	2443	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2444	eval local_catalog=${pathout[$i]}
	2445	if [[ ! -d $local_catalog ]]
	2446	then
	2447	printf " *** local directory does not exist. Trying to create:\n"
	2448	printf " $local_catalog \n"
	2449	mkdir -p $local_catalog
	2450	fi
[2506]	2451	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
[2380]	2452	transfer_problems=true
	2453	fi
	2454
	2455	else
	2456
	2457	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2458	# BE COPIED OR APPENDED ON THIS MACHINE
	2459	if [[ "${actionout[$i]}" = tr ]]
	2460	then
	2461	actionout[$i]=""
	2462	else
	2463	actionout[$i]="a"
	2464	fi
	2465	fi
	2466	fi
	2467
	2468
	2469	# APPEND ON THIS MACHINE
	2470	if [[ "${actionout[$i]}" = "a" ]]
	2471	then
	2472	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2473	then
	2474	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2475	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2476	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2477	else
	2478	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2479	printf "\n ${pathout[$i]}\n"
	2480	cat ${localout[$i]} >> ${pathout[$i]}
	2481	fi
	2482	fi
	2483
	2484	# COPY ON THIS MACHINE
	2485	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2486	# ON DIFFERENT FILE-SYSTEMS
	2487	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2488	then
	2489
	2490	# COPY IN CASE OF RUNS ON SINGLE CORES
	2491	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2492	then
	2493	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2494	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2495	if [[ $link_local_output = true ]]
	2496	then
	2497	printf " file will be linked\n"
	2498	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2499	fi
	2500	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2501	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2502	then
	2503	if [[ $link_local_output = true ]]
	2504	then
	2505	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2506	fi
	2507	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2508	else
	2509	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2510	fi
	2511	else
	2512	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2513	printf "\n ${pathout[$i]}\n"
	2514	if [[ $link_local_output = true ]]
	2515	then
	2516	printf " file will be linked\n"
	2517	ln -f ${localout[$i]} ${pathout[$i]}
	2518	fi
	2519	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2520	if [[ ! -f "${pathout[$i]}" ]]
	2521	then
	2522	if [[ $link_local_output = true ]]
	2523	then
	2524	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2525	fi
	2526	cp ${localout[$i]} ${pathout[$i]}
	2527	else
	2528	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2529	fi
	2530	fi
	2531
	2532	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2533	then
	2534
	2535	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2536	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2537	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2538	printf "\n ${pathout[$i]}\n"
	2539	if [[ $link_local_output = true ]]
	2540	then
	2541	printf " files will be linked\n"
[2396]	2542	mkdir -p ${pathout[$i]}
[2380]	2543	cd ${localout[$i]}
	2544	for file in $(ls *)
	2545	do
	2546	ln -f $file ${pathout[$i]}
	2547	done >\|/dev/null 2>&1
[2566]	2548	cd $tempdir
[2380]	2549	fi
	2550
	2551	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2552	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2553	then
	2554	if [[ $link_local_output = true ]]
	2555	then
	2556	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2557	fi
	2558	cp -r ${localout[$i]}/* ${pathout[$i]}
	2559	fi
	2560
	2561	fi
	2562	fi
	2563	done
	2564
	2565	if (( i != 0 ))
	2566	then
	2567	if [[ $transfer_problems = true ]]
	2568	then
	2569	printf "\n$dashes\n *** OUTPUT-files saved"
	2570	printf "\n +++ WARNING: some data transfers failed! \n"
	2571	else
	2572	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2573	fi
	2574	fi
	2575
	2576
	2577	# IF REQUIRED, START A RESTART-JOB
	2578	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2579	if [[ -f CONTINUE_RUN ]]
	2580	then
	2581
	2582	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2583	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2584	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2585	# -b START A BATCH JOB
	2586	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2587	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2588	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2589
	2590
	2591	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2592	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2593	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2594	then
[2381]	2595	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2596	fi
	2597
	2598
	2599	# START THE RESTART-JOB
	2600	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2601	echo " $prc"
	2602	printf "\n$dashes\n"
	2603	if [[ $running_on_remote = true ]]
	2604	then
	2605
	2606	echo "*** ssh will be used to initiate restart-runs!"
	2607	echo " return_address=\"$return_address\" "
	2608	echo " return_username=\"$local_username\" "
	2609
	2610	if [[ "$remote_loginnode" != "" ]]
	2611	then
[2420]	2612	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
[2380]	2613	else
[2420]	2614	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2615	fi
	2616
	2617	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2618	sleep 30
	2619
	2620	else
	2621
	2622	# START THE RESTART JOB ON THE LOCAL HOST
	2623	eval $prc # THE ' MUST BE EVALUATED
	2624	cd - > /dev/null
	2625
	2626	fi
	2627	printf "\n$dashes\n *** restart-run initiated \n"
	2628
	2629
	2630	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2631	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2632	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2633	# MAY BE VERY HUGE)
	2634	(( i = 0 ))
[2610]	2635	while (( i < nr_of_input_files ))
[2380]	2636	do
	2637	(( i = i + 1 ))
	2638	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2639	then
	2640	rm -r ${absnamein[$i]}
	2641	fi
	2642	done
	2643
	2644	fi
	2645
	2646
	2647	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2648	cd $HOME
[2566]	2649	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2650
	2651
	2652	else
	2653
	2654
	2655	# PREPARING ACTIONS,
	2656	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2657
	2658	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2506]	2659	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2660	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2661	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2662	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2663	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2664	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2665	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2666	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2667	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2668	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2669	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2670	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2671	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2672	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2673	if [[ $create_remote_batch_job = true ]]
	2674	then
	2675	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2676	if [[ $do_trace = true ]]
	2677	then
	2678	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2679	fi
[2380]	2680	elif [[ $create_batch_job = true ]]
	2681	then
	2682	palmrun_com=${palmrun_com}" -j"
[2420]	2683	if [[ $do_trace = true ]]
	2684	then
	2685	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2686	fi
[2380]	2687	fi
	2688
	2689
	2690	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2691	# REMOTE HOST
[2506]	2692	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2693	job_protocol_file=$job_protocol_file_local
	2694	if [[ $create_remote_batch_job = true ]]
	2695	then
[2506]	2696	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2697	job_protocol_file=$job_protocol_file_remote
	2698	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2699	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2700	fi
	2701
	2702
	2703	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2704	jobfile=jobfile.$run_id
	2705
	2706
	2707	# FIRST CREATE THE BATCH DIRECTIVES
	2708	(( i = 0 ))
	2709	while (( i < ibd ))
	2710	do
	2711	(( i = i + 1 ))
[2693]	2712	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2713	eval line=\"$line\"
	2714	echo "$line" >> $jobfile
	2715	done
	2716	echo " " >> $jobfile
	2717
	2718
	2719	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2720	# PROTOCOL
	2721	if [[ $create_remote_batch_job = true ]]
	2722	then
	2723	echo "set +vx" >> $jobfile
	2724	echo "trap '" >> $jobfile
	2725	echo "set +vx" >> $jobfile
	2726	echo "cd ${remote_jobcatalog}" >> $jobfile
	2727	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2728
	2729	# ADD THE BATCH DIRECTIVES
	2730	(( i = 0 ))
	2731	while (( i < ibdt ))
	2732	do
	2733	(( i = i + 1 ))
[2693]	2734	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2735	eval line=\"$line\"
	2736	echo "$line" >> $jobfile
	2737	done
	2738	echo " " >> $jobfile
	2739
	2740	echo "set -x" >> $jobfile
[2506]	2741	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${fname}" >> $jobfile
[2380]	2742	echo "%%END%%" >> $jobfile
	2743	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2744	echo "$submit_command $scpjob_file" >> $jobfile
	2745	echo "rm $scpjob_file" >> $jobfile
[2404]	2746	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2747	echo "set -x" >> $jobfile
	2748	echo " ' exit" >> $jobfile
	2749	fi
	2750
	2751
	2752	# ACTIVATE ERROR-TRACEBACK
	2753	if [[ $do_trace = true ]]
	2754	then
	2755	echo "set -x" >> $jobfile
	2756	else
	2757	echo "set +vx" >> $jobfile
	2758	fi
	2759
	2760
	2761	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2762	if [[ "$login_init_cmd" != "" ]]
	2763	then
	2764	echo "$login_init_cmd" >> $jobfile
	2765	fi
	2766	if [[ "$module_commands" != "" ]]
	2767	then
	2768	echo "$module_commands" >> $jobfile
	2769	fi
	2770
	2771
	2772	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2773	if [[ $create_remote_batch_job = true ]]
	2774	then
	2775	echo "mkdir $tempdir" >> $jobfile
	2776	echo "chmod go+rx $tempdir" >> $jobfile
	2777	else
	2778	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2779	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2780	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2781	mkdir $tempdir
	2782	chmod go+rx $tempdir
	2783	fi
	2784	echo "cd $tempdir" >> $jobfile
	2785	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2786	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2787	echo "export PATH=.:\$PATH" >> $jobfile
	2788	echo "export execute_palmrun=true" >> $jobfile
	2789
	2790
	2791	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2792	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2793	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2794	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2795	echo "export LOCAL_PWD" >> $jobfile
	2796
	2797
	2798	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2799	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2800	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2801
	2802
	2803	# CALL PALMRUN WITHIN THE JOB
	2804	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2805	echo "set -x" >> $jobfile
	2806	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2807
	2808
	2809	# TRANSFER JOBFILE TO THE TARGET HOST
	2810	if [[ $create_jobfile_only = false ]]
	2811	then
	2812
	2813	if [[ $create_remote_batch_job = true ]]
	2814	then
	2815
[2420]	2816	echo " "
[2566]	2817	echo " *** transfer of job to remote host via scp"
[2420]	2818	if [[ $do_trace = true ]]
	2819	then
[2506]	2820	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2821	fi
[2566]	2822	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2823
[2566]	2824	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2825	if [[ $do_trace = true ]]
	2826	then
[2506]	2827	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"
[2420]	2828	fi
[2506]	2829	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
[2380]	2830
	2831	elif [[ $create_batch_job = true ]]
	2832	then
	2833
[2385]	2834	eval local_jobcatalog=$local_jobcatalog
[2506]	2835	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2836	cd $local_jobcatalog
[2380]	2837	echo " "
[2420]	2838	echo " *** submit the job"
	2839	if [[ $do_trace = true ]]
	2840	then
[2506]	2841	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2842	fi
[2506]	2843	$submit_command ${host_configuration}_${job_id}
	2844	rm ${host_configuration}_${job_id}
[2380]	2845	cd - > /dev/null
	2846
	2847	fi
	2848
	2849	rm -rf $jobfile
	2850
	2851	else
	2852
	2853	printf "\n *** jobfile created under name \"$jobfile\" "
	2854	printf "\n no batch-job has been sent!"
	2855
	2856	fi
	2857
	2858	fi # END OF REMOTE-PART

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