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source: palm/trunk/SCRIPTS/palmrun @ 2794

Last change on this file since 2794 was 2789, checked in by raasch, 7 years ago
bugfix: exit if no queue has been given neither with option -q nor in the configuration file
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 95.3 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	# -----------------
[2732]	28	# $Id: palmrun 2718 2018-01-02 08:49:38Z maronga $
[2789]	29	# bugfix: exit if no queue has been given neither with option -q nor in the
	30	# configuration file
	31	#
	32	# 2718 2018-01-02 08:49:38Z maronga
[2762]	33	# file connection file from trunk/SCRIPTS is taken by default
	34	#
	35	# 2718 2018-01-02 08:49:38Z maronga
[2716]	36	# Corrected "Former revisions" section
	37	#
	38	# 2696 2017-12-14 17:12:51Z kanani
	39	# Change in file header (GPL part)
	40	#
	41	# 2693 2017-12-13 12:33:49Z raasch
[2693]	42	# replacement of variables given by {{<variable>}} in configuration file is now
	43	# done in a more general way, variable names are written in small letters
	44	#
	45	# 2670 2017-12-06 16:32:19Z raasch
[2670]	46	# test printouts removed
	47	#
	48	# 2669 2017-12-06 16:03:27Z raasch
[2669]	49	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	50	# removed,
	51	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	52	# files,
	53	# informative messages in case of missing optional input files shortened
	54	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	55	#
	56	# 2638 2017-11-23 12:44:23Z raasch
[2610]	57	# use of wildcards in file connection statements enabled
	58	#
	59	# 2605 2017-11-09 15:31:46Z raasch
[2605]	60	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	61	# will not be sent with the job file any more, but copied into the
[2610]	62	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	63	#
	64	# 2600 2017-11-01 14:11:20Z raasch
[2600]	65	# cycle numbers are made three digits wide
	66	#
	67	# 2566 2017-10-20 08:50:47Z raasch
[2566]	68	# execute command for combine_plot_fields added
	69	# "TEMPDIR" renamed "tempdir"
	70	# temporary working directory for local batch jobs is created immediately within
	71	# the user's palmrun call, due to a requirement of the "grid engine" batch
	72	# system, where the working directory is given with batch directive -wd and must
	73	# already exist when the job is submitted,
	74	# informative messages in non-trace mode reduced and partly reformatted
	75	#
	76	# 2551 2017-10-18 07:25:11Z raasch
[2551]	77	# TEMPDIR added as replacement string to be used in batch directives
	78	#
	79	# 2512 2017-10-04 08:26:59Z raasch
[2507]	80	# bugfix for determining cycle numbers of NetCDF input files
	81	#
	82	# 2506 2017-09-29 08:30:37Z raasch
[2506]	83	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	84	# host configuration added to SOURCES_FOR_RUN_... folder name
	85	# host_identifier renamed host_configuration
	86	# option -W added to allow for job dependencies
	87	#
	88	# 2501 2017-09-26 11:41:55Z raasch
[2501]	89	# default value for number of cores (option -X) set to 1
	90	# bugfix for mechanism which overwrites configuration file settings with values
	91	# provided by palmrun options
	92	#
	93	# 2499 2017-09-22 16:47:58Z kanani
[2499]	94	# option -h named configuration identifier
	95	#
	96	# 2480 2017-09-19 06:24:14Z maronga
[2480]	97	# bugfix for last revision
	98	#
	99	# 2479 2017-09-19 06:12:16Z raasch
[2479]	100	# option -A (project account number) added
	101	#
	102	# 2422 2017-09-08 08:25:41Z raasch
[2410]	103	# initial revision
[2380]	104	#
	105	#--------------------------------------------------------------------------------#
	106	# palmrun - script for running PALM jobs on local and remote hosts
	107	#--------------------------------------------------------------------------------#
	108
	109
	110
	111	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	112
	113	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	114	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	115	# (TOO MANY ARGUMENTS - PROBLEM)
	116	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	117
[2610]	118	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	119	typeset -i nr_of_output_files=0
[2380]	120	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	121	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	122	# SCRIPT-OPTION ARGUMENTS
	123	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	124	typeset -i icycle inode ival maxcycle mpi_tasks
	125	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	126
	127	activation_string_list=""
	128	AddFilenames=""
	129	combine_plot_fields=true
	130	compiler_name=""
	131	compiler_name_ser=""
	132	compiler_options=""
[2501]	133	cores=1
[2380]	134	cores_atmos=0
	135	cores_ocean=0
	136	coupled_dist=""
	137	cpp_options=""
	138	cpumax=0
[2506]	139	create_batch_job=false
[2380]	140	create_jobfile_only=false
	141	create_remote_batch_job=false
	142	dashes=" ----------------------------------------------------------------------------"
	143	defaultqueue=""
[2506]	144	delete_temporary_catalog=true
[2380]	145	do_compile=true
	146	do_trace=false
	147	executable=""
	148	execute_command=""
	149	execution_error=false
[2762]	150	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	151	fname=test
	152	global_revision=""
[2506]	153	host_configuration="default"
[2380]	154	hostfile=""
	155	hp=""
	156	keep_data_from_previous_run=false
	157	link_local_input=false
	158	link_local_output=false
[2388]	159	linker_options=""
[2385]	160	local_jobcatalog=""
[2380]	161	locat=normal
	162	makefile=""
	163	max_par_io_str=""
	164	prc=$0
	165	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	166	do
	167	prc=`echo $prc \| cut -f2- -d"/"`
	168	done
	169	module_calls=""
[2506]	170	palmrun_memory=""
[2380]	171	palmrun_script_name=$prc
	172	openmp=false
[2506]	173	previous_job=""
[2479]	174	project_account=""
[2380]	175	queue=none
	176	restart_run=false
	177	return_address=""
[2385]	178	remote_jobcatalog=""
[2380]	179	remote_username=""
	180	running_in_batch_mode=false
	181	run_coupled_model=false
	182	run_id=""
	183	silent=false
	184	source_list=""
	185	source_path=""
[2501]	186	tasks_per_node=0
[2380]	187	threads_per_task=1
	188	transfer_problems=false
[2384]	189	user_source_path=""
[2506]	190	use_existing_sources_folder=""
[2380]	191	use_openmp=false
[2732]	192	version="palmrun 1.0 Rev$Rev: 2789 $"
[2380]	193	working_directory=`pwd`
	194	write_binary=""
	195	TOPT=""
	196
	197
	198	# ERROR HANDLING IN CASE OF EXIT
[2404]	199	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	200	then
	201
	202	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	203	(( i = 0 ))
	204	while (( i < iec ))
	205	do
	206	(( i = i + 1 ))
	207	printf "\n *** Execution of ERROR-command:\n"
	208	printf " >>> ${err_command[$i]}\n"
	209	eval ${err_command[$i]}
	210	done
[2566]	211	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	212	printf "\n\n+++ palmrun killed \n\n"
	213	elif [[ $locat != control_c ]]
	214	then
[2566]	215	printf "\n --> palmrun finished\n\n"
[2380]	216	fi' exit
	217
	218
	219	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	220	trap 'cd; rm -rf $tempdir
[2380]	221	printf "\n+++ palmrun killed by \"^C\" \n\n"
	222	locat=control_c
	223	exit
	224	' 2
	225
	226
	227	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	228	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	229	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]	230	do
	231	case $option in
	232	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	233	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	234	(b) create_batch_job=true; prc="$prc -b";;
	235	(B) delete_temporary_catalog=false; prc="$prc -B";;
	236	(C) restart_run=true; prc="$prc -C";;
	237	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	238	(F) create_jobfile_only=true;;
	239	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	240	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	241	(j) running_in_batch_mode=true;;
	242	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	243	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	244	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	245	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	246	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	247	(r) run_id=$OPTARG;;
	248	(R) return_address=$OPTARG;;
	249	(s) source_list=$OPTARG;;
[2501]	250	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	251	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	252	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	253	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	254	(v) silent=true; prc="$prc -v";;
[2506]	255	(V) use_existing_sources_folder="-V";;
[2380]	256	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	257	(W) previous_job=$OPTARG;;
[2380]	258	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	259	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	260	(y) ocean_file_appendix=true; prc="$prc -y";;
	261	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	262	(Z) combine_plot_fields=false; prc="$prc -Z";;
	263	(\?) printf "\n +++ unknown option $OPTARG \n"
	264	printf "\n --> type \"$0 ?\" for available options \n"
	265	locat=parameter;exit;;
	266	esac
	267	done
	268
	269
	270	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	271	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	272	(( to_shift = $OPTIND - 1 ))
	273	shift $to_shift
	274
	275	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	276	if [[ "$1" = "?" ]]
	277	then
	278	(printf "\n *** Description of available palmrun options:\n"
	279	printf "\n Option Description Default-Value"
	280	printf "\n -a activation string list \"\" "
[2479]	281	printf "\n -A project account number ---"
[2380]	282	printf "\n -b batch-job on local machine ---"
	283	printf "\n -B do not delete temporary directory at end ---"
	284	printf "\n -d base name of files attached to program test"
	285	printf "\n -F create batch job file only ---"
[2506]	286	printf "\n -h host configuration \"default\" "
[2380]	287	printf "\n -k keep data from previous run"
	288	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	289	printf "\n -M Makefile name Makefile"
	290	printf "\n -O threads per openMP task ---"
	291	printf "\n -q queue \"$queue\" "
	292	printf "\n -s filenames of routines to be compiled \"\" "
	293	printf "\n must end with .f, .f90, .F, or .c !"
	294	printf "\n use \"..\" for more than one file and wildcards"
	295	printf "\n -s LM compiles all locally modified files"
	296	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	297	printf "\n -T tasks per node ---"
[2380]	298	printf "\n -u username on remote machine \"\" "
	299	printf "\n -v no prompt for confirmation ---"
[2506]	300	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	301	printf "\n -w maximum parallel io streams as given by -X"
[2506]	302	printf "\n -W name of job to wait for ---"
[2380]	303	printf "\n -x tracing of palmrun for debug purposes ---"
	304	printf "\n -X # of processors (on parallel machines) 1"
	305	printf "\n -y add appendix \"_O\" to all local output"
	306	printf "\n files (ocean precursor runs followed by"
	307	printf "\n coupled atmosphere-ocean runs) ---"
	308	printf "\n -Y run coupled model, \"#1 #2\" with"
	309	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	310	printf "\n -Z skip combine_plot_fields at the end of "
	311	printf "\n the simulation ---"
	312	printf "\n "
	313	printf "\n Possible values of positional parameter <modus>:"
	314	printf "\n \"?\" - this outline \n\n") \| more
	315	exit
	316	elif [[ "$1" != "" ]]
	317	then
	318	printf "\n +++ positional parameter $1 unknown \n"
	319	locat=parameter; exit
	320	fi
	321
	322
	323
	324	# SHORT STARTING MESSAGE
	325	printf "\n*** $version "
	326	printf "\n will be executed. Please wait ..."
	327
	328
[2506]	329	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	330	config_file=.palm.config.$host_configuration
	331	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
[2380]	332
	333
	334	# CHECK, IF CONFIGURATION FILE EXISTS
	335	if [[ ! -f $config_file ]]
	336	then
	337	printf "\n\n +++ configuration file: "
	338	printf "\n $config_file"
	339	printf "\n does not exist"
	340	locat=connect; exit
	341	fi
	342
	343
[2762]	344	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	345	if [[ -f .palm.iofiles ]]
	346	then
	347	fileconnection_file=.palm.iofiles
	348	fi
	349
	350
[2380]	351	# CHECK, IF FILE CONNECTION FILE EXISTS
	352	if [[ ! -f $fileconnection_file ]]
	353	then
	354	printf "\n\n +++ file connection file: "
	355	printf "\n $fileconnection_file"
	356	printf "\n does not exist"
	357	locat=connect; exit
	358	fi
	359
	360
[2404]	361	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	362	if [[ "$activation_string_list" = "" ]]
	363	then
	364	printf "\n\n +++ no activation string list given: "
	365	printf "\n please set palmrun option \"-a\" "
	366	locat=palmrun_option; exit
	367	fi
	368
	369
	370	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	371	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	372	then
	373	write_binary=true
	374	else
	375	write_binary=false
	376	fi
	377
	378
[2380]	379	# READ AND EVALUATE THE CONFIGURATION-FILE
	380	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	381
	382	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	383	while read line
	384	do
	385
	386	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	387	eval line=\"$line\"
	388
	389
	390	# INTERPRET THE LINE
	391	if [[ "$(echo $line)" = "" ]]
	392	then
	393
	394	# EMPTY LINE, NO ACTION
	395	continue
	396
	397	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	398	then
	399
	400	# LINE IS A COMMENT LINE
	401	continue
	402
	403	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	404	then
	405
	406	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	407	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	408	value=`echo $line \| cut -d" " -s -f2-`
	409
	410
	411	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	412	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	413	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	414	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	415	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	416	# CONFIGURATION-FILE.
	417	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	418	then
	419	eval export $var="\$value"
	420
	421	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	422	if [[ $do_trace = true ]]
	423	then
	424	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	425	fi
	426	fi
	427
	428	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	429	then
	430
	431	# LINE DEFINES BATCH-DIRECTIVE
	432	(( ibd = ibd + 1 ))
	433	line=$(echo $line \| cut -c4-)
	434	batch_directive[$ibd]="$line"
	435
	436	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	437	then
	438
	439	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	440	# REMOTE TO A LOCAL HOST
	441	(( ibdt = ibdt + 1 ))
	442	line=$(echo $line \| cut -c5-)
	443	batch_directive_transfer[$ibdt]="$line"
	444
	445	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	446	then
	447
	448	# LINE DEFINES ERROR-COMMAND
	449	(( iec = iec + 1 ))
	450	line=$(echo $line \| cut -c4-)
	451	err_command[$iec]="$line"
	452
	453	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	454	then
	455
	456	# LINE DEFINES INPUT-COMMAND
	457	(( iic = iic + 1 ))
	458	line=$(echo $line \| cut -c4-)
	459	in_command[$iic]="$line"
	460
	461	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	462	then
	463
	464	# LINE DEFINES OUTPUT-COMMAND
	465	(( ioc = ioc + 1 ))
	466	line=$(echo $line \| cut -c4-)
	467	out_command[$ioc]="$line"
	468
	469	else
	470
	471	# SKIP ALL OTHER LINES
	472	continue
	473
	474	fi
	475
	476	done < $config_file
	477
	478
	479	# CHECK SETTING OF REQUIRED PARAMETERS
	480	if [[ "$compiler_name" = "" ]]
	481	then
	482	printf "\n +++ no compiler name found in $config_file"
	483	printf "\n Please add line \"compiler_name ...\" to that file."
	484	locat=config_file; exit
	485	fi
	486	if [[ "$compiler_name_ser" = "" ]]
	487	then
	488	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	489	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	490	locat=config_file; exit
	491	fi
	492	if [[ "$compiler_options" = "" ]]
	493	then
	494	printf "\n +++ no compiler options found in $config_file"
	495	printf "\n Please add line \"compiler_options ...\" to that file."
	496	locat=config_file; exit
	497	fi
[2388]	498	if [[ "$linker_options" = "" ]]
[2380]	499	then
[2388]	500	printf "\n +++ no linker options found in $config_file"
	501	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	502	locat=config_file; exit
	503	fi
	504	if [[ "$execute_command" = "" ]]
	505	then
	506	printf "\n +++ no execute command found in $config_file"
	507	printf "\n Please add line \"execute_command ...\" to that file."
	508	locat=config_file; exit
	509	fi
	510
	511	if [[ "$hostfile" != "" ]]
	512	then
	513	if [[ $hostfile != auto && ! -f $hostfile ]]
	514	then
	515	printf "\n +++ no hostfile \"$hostfile\" found"
	516	printf "\n Please check line \"hostfile ...\" in $config_file"
	517	locat=config_file; exit
	518	fi
	519	fi
	520
	521
	522	# DETERMINE THE CALL STATUS
	523	if [[ "$return_address" != "" ]]
	524	then
	525
	526	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	527	# BATCH MODE AND ...
	528	running_on_remote=true
	529
	530	else
	531
	532	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	533	if [[ "$remote_ip" != "" ]]
	534	then
	535
	536	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	537	create_remote_batch_job=true
	538
	539	fi
	540	running_on_remote=false
	541	fi
	542
	543
	544
	545	# READ AND EVALUATE THE I/O-FILE LIST
	546	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	547
	548	# READ THE FILE CONNECTION FILE LINE BY LINE
	549	while read line
	550	do
	551
[2669]	552	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	553	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	554
	555	# INTERPRET THE LINE
	556	if [[ "$(echo $line)" = "" ]]
	557	then
	558	# EMPTY LINE, NO ACTION
	559	continue
	560
	561	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	562	then
	563
	564	# LINE IS A COMMENT LINE
	565	true
	566
	567	else
	568
	569	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	570	# s2a: in/out - field
[2669]	571	# s2b: action - field (optional)
	572	s1=`echo "$line" \| cut -d" " -f1`
	573	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	574	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	575	then
[2669]	576	s2a=$s2
[2380]	577	s2b=""
	578	else
[2669]	579	s2a=`echo $s2 \| cut -d":" -f1`
	580	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	581	fi
[2669]	582	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	583	s4=`echo "$line" \| cut -d" " -s -f4`
	584	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	585	s5=`echo "$line" \| cut -d" " -s -f5`
	586	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	587
	588
	589	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	590	# INPUT- OR OUTPUT-LIST.
	591	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	592	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	593	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	594	# IS NOT CHECKED AND STORED.
[2610]	595	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	596	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	597	then
	598	found=false
	599	for actual in $activation_string_list
	600	do
	601	for formal in $s3
	602	do
	603	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	604	done
	605	done
	606	if [[ $found = true ]]
	607	then
	608	(( iin = iin + 1 ))
[2669]	609	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	610	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	611	if [[ "$s2a" = inopt ]]
	612	then
	613	optin_pre[$iin]=yes
	614	else
	615	optin_pre[$iin]=no
	616	fi
[2605]	617
	618	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	619	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	620	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	621	then
[2610]	622	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	623	fi
	624
[2610]	625	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	626	# THE WILDCARD FROM THE ENDING
	627	if [[ "${s5: -1}" = "*" ]]
	628	then
[2669]	629	if [[ "$s2b" = "di" ]]
[2610]	630	then
	631	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	632	printf "\n see file \"$fileconnection_file\", line"
	633	printf "\n$line"
	634	locat=iofiles_file; exit
	635	fi
	636	multin[$iin]=true
	637	string=${endin_pre[$iin]}
	638	endin_pre[$iin]="${string%?}"
	639	else
	640	multin[$iin]=false
	641	fi
[2380]	642	fi
[2669]	643	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	644	then
	645	found=false
	646	for actual in $activation_string_list
	647	do
	648	for formal in $s3
	649	do
[2670]	650	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	651	done
	652	done
	653	if [[ $found = true ]]
	654	then
	655	(( iout = iout + 1 ))
[2669]	656	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	657	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	658
[2669]	659	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	660	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	661	if [[ $formal = wildcard ]]
	662	then
	663	warnout_pre[$iout]=false
	664	else
	665	warnout_pre[$iout]=true
	666	fi
	667
[2610]	668	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	669	# THE WILDCARD FROM THE LOCAL FILENAME
	670	if [[ "${s1: -1}" = "*" ]]
	671	then
[2669]	672	if [[ "$s2b" = "di" ]]
[2610]	673	then
	674	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	675	printf "\n see file \"$fileconnection_file\", line"
	676	printf "\n$line"
	677	locat=iofiles_file; exit
	678	fi
	679	multout[$iout]=true
	680	string=${localout_pre[$iout]}
	681	localout_pre[$iout]="${string%?}"
	682	else
	683	multout[$iout]=false
	684	fi
[2380]	685	fi
[2669]	686	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	687	then
[2669]	688	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	689	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	690	locat=connect; exit
	691	fi
	692	IFS="$IFSALT"
	693	fi
	694
	695	done < $fileconnection_file
	696
	697
	698
[2501]	699	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	700	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	701	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	702	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	703	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	704	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	705
	706
	707
[2380]	708	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	709	if [[ $run_coupled_model = true ]]
	710	then
	711
	712	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	713	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	714
	715	if (( $cores_ocean + $cores_atmos != $cores ))
	716	then
	717
	718	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	719	printf "\n PEs (total) : $cores"
	720	printf "\n PEs (atmosphere): $cores_atmos"
	721	printf "\n PEs (ocean) : $cores_ocean"
	722	locat=coupling; exit
	723
	724	fi
	725
	726	fi
	727
	728
	729	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	730	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	731	# FOLDER
	732	if [[ $running_in_batch_mode = true ]]
	733	then
	734
[2506]	735	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	736	then
[2506]	737	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	738	printf "\n Please check the output of the palmrun-call"
	739	printf "\n that you did on your local host."
	740	locat=SOURCES_FOR_RUN; exit
	741	fi
	742
	743	else
	744
	745	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	746	# AUTOMATIC RESTART RUN
	747	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	748	if [[ $restart_run = false ]]
	749	then
	750
	751	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	752	# THE LOCAL HOST
	753	if [[ ! -d $source_path ]]
	754	then
	755	printf "\n\n +++ source path \"$source_path\" on local host"
	756	printf "\n \"$(hostname)\" does not exist"
	757	locat=source_path; exit
	758	fi
	759
[2506]	760	rm -rf $sources_for_run_catalog
	761	mkdir -p $sources_for_run_catalog
[2380]	762
	763	if [[ "$source_list" = LM ]]
	764	then
	765
	766	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	767	source_list=""
	768	cd $source_path
	769
	770
[2512]	771	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	772	if [[ ! -d ../.svn ]]
[2380]	773	then
	774	printf "\n\n +++ source directory"
	775	printf "\n \"$source_path\" "
	776	printf "\n is not under control of \"subversion\"."
[2512]	777	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	778	fi
	779
	780
	781	# LIST ALL MODIFIED SOURCE CODE FILES
	782	Filenames=""
[2404]	783	svn status > tmp_svnstatus
[2380]	784	while read line
	785	do
	786	firstc=`echo $line \| cut -c1`
	787	if [[ $firstc = M \|\| $firstc = "?" ]]
	788	then
	789	Name=`echo "$line" \| cut -c8-`
	790	extension=`echo $Name \| cut -d. -f2`
	791	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	792	then
	793	Filenames="$Filenames "$Name
	794	fi
	795	fi
[2404]	796	done < tmp_svnstatus
	797	rm -rf tmp_svnstatus
[2380]	798
	799
	800	# COPY FILES TO SOURCES_FOR_RUN_...
	801	for filename in $Filenames
	802	do
[2506]	803	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	804	source_list=$source_list"$filename "
	805	done
	806
	807	cd - > /dev/null
	808
	809
	810	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	811	elif [[ "$source_list" != "" ]]
	812	then
	813
	814	cd $source_path
	815
	816	for filename in $source_list
	817	do
	818
	819	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	820	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	821	then
	822	printf "\n +++ source code file: $filename"
	823	printf "\n must not contain (\"/\") "
	824	locat=source; exit
	825	fi
	826
	827	if [[ ! -f $filename ]]
	828	then
	829	printf "\n +++ source code file: $filename"
	830	printf "\n does not exist"
	831	locat=source; exit
	832	else
[2506]	833	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	834	fi
	835
	836	done
	837
	838	cd - > /dev/null
	839
	840	fi
	841
	842	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	843	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	844	if [[ ! -f $makefile ]]
	845	then
	846	printf "\n +++ file \"$makefile\" does not exist"
	847	locat=make; exit
	848	else
[2506]	849	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	850	fi
	851
	852
	853	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	854	if [[ "$user_source_path" != "" ]]
[2380]	855	then
	856
	857	# DOES THE DIRECTORY EXIST?
[2384]	858	if [[ ! -d $user_source_path ]]
[2380]	859	then
	860
	861	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	862	printf "\n \"$user_source_path\" "
[2380]	863	printf "\n does not exist or is not a directory."
	864	printf "\n No source code will be used from this directory!\n"
[2384]	865	user_source_path=""
[2380]	866	if [[ $silent == false ]]
	867	then
	868	sleep 2
	869	fi
	870
	871	else
	872
[2384]	873	cd $user_source_path
[2380]	874	found=false
	875
	876	Names=$(ls -1 *.f90 2>&1)
	877	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	878	Names=$(ls -1 *.F90 2>&1)
	879	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	880	Names=$(ls -1 *.F 2>&1)
	881	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	882	Names=$(ls -1 *.f 2>&1)
	883	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	884	Names=$(ls -1 *.c 2>&1)
	885	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	886
	887	cd - > /dev/null
[2506]	888	cd $sources_for_run_catalog
[2380]	889
	890	# COPY MAKEFILE IF EXISTING
[2384]	891	if [[ -f $user_source_path/Makefile ]]
[2380]	892	then
	893	printf "\n\n *** user Makefile from directory"
[2384]	894	printf "\n \"$user_source_path\" is used \n"
[2380]	895	if [[ $silent == false ]]
	896	then
	897	sleep 1
	898	fi
[2384]	899	cp $user_source_path/Makefile .
[2380]	900	fi
	901
	902	for filename in $AddFilenames
	903	do
	904	if [[ -f $filename ]]
	905	then
	906	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	907	printf "\n source code directory \"$user_source_path\" "
[2380]	908	printf "\n but was also given with option \"-s\" which means that it should be taken"
	909	printf "\n from directory \"$source_path\"."
	910	locat=source; exit
	911	fi
	912
[2384]	913	cp $user_source_path/$filename .
[2380]	914	source_list="$source_list $filename"
	915
	916	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	917	if [[ $(grep -c $filename Makefile) = 0 ]]
	918	then
	919	printf "\n\n +++ user file \"$filename\" "
	920	printf "\n is not listed in Makefile \n"
	921	locat=source; exit
	922	else
	923
	924	if [[ $found = false ]]
	925	then
	926	found=true
	927	printf "\n\n *** following user file(s) added to the"
	928	printf " files to be translated:\n "
	929	fi
	930	printf "$filename "
	931	if [[ $silent == false ]]
	932	then
	933	sleep 0.5
	934	fi
	935
	936	fi
	937	done
	938	[[ $found = true ]] && printf "\n"
	939	cd - > /dev/null
	940	fi
	941	fi
	942
	943	# COPY CONFIGURATION FILES
[2506]	944	cp $config_file $sources_for_run_catalog
	945	cp $fileconnection_file $sources_for_run_catalog
[2380]	946
	947	# COPY SHELLSCRIPTS
[2506]	948	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	949	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	950
	951	fi
	952
	953	fi
	954
[2605]	955
[2380]	956	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	957	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	958	if [[ "$global_revision" = "" ]]
	959	then
	960	global_revision=`svnversion $source_path 2>/dev/null`
	961	global_revision="Rev: $global_revision"
	962	fi
	963
	964
	965	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	966	if [[ -n $cores ]]
	967	then
	968
	969	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	970	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	971	if [[ $tasks_per_node = 0 ]]
[2380]	972	then
	973	printf "\n"
	974	printf "\n +++ option \"-T\" (tasks per node) is missing"
	975	printf "\n set -T option or define tasks_per_node in the config file"
	976	locat=tasks_per_node; (( iec = 0 )); exit
	977	fi
	978
	979	if (( cores < tasks_per_node ))
	980	then
	981	printf "\n"
	982	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	983	printf "\n given values: -T $tasks_per_node -X $cores"
	984	locat=tasks_per_node; (( iec = 0 )); exit
	985	fi
	986
	987	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	988	(( mpi_tasks = cores / threads_per_task ))
	989	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	990	(( ii = cores / tasks_per_node ))
	991	(( remaining_cores = cores - ii * tasks_per_node ))
	992	if (( remaining_cores > 0 ))
	993	then
	994	printf "\n"
	995	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	996	printf "\n divisor of the total number of cores (option \"-X\")"
	997	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	998	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	999	(( nodes = nodes + 1 ))
	1000	fi
	1001
	1002	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	1003	if [[ "$tasks_per_node" != "" ]]
	1004	then
	1005	TOPT="-T $tasks_per_node"
	1006	fi
	1007
	1008	fi
	1009
	1010
	1011	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1012	if [[ "$maximum_parallel_io_streams" = "" ]]
	1013	then
	1014	maximum_parallel_io_streams=$cores
	1015	fi
	1016
	1017
	1018	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1019	if [[ "$scp_port" != "" ]]
	1020	then
	1021	PORTOPT="-P $scp_port"
	1022	SSH_PORTOPT="-p $scp_port"
	1023	fi
	1024
	1025
	1026	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1027	# CONFIG-FILE
	1028	if [[ "$ssh_key" != "" ]]
	1029	then
	1030	ssh_key="-i $HOME/.ssh/$ssh_key"
	1031	fi
	1032
	1033
	1034	# SET QUEUE, IF NOT GIVEN
	1035	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1036	then
	1037
	1038	if [[ $queue = none && "$defaultqueue" = "" ]]
	1039	then
	1040	printf "\n"
	1041	printf "\n +++ no default queue given in configuration file and no queue"
	1042	printf "\n given with option -q"
[2789]	1043	locat=queue; exit
[2380]	1044	fi
	1045	if [[ $queue = none ]]
	1046	then
	1047	queue=$defaultqueue
	1048	fi
	1049
	1050	fi
	1051
	1052
	1053	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1054	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1055	(( i = 0 ))
[2610]	1056	(( nr_of_input_files = 0 ))
[2380]	1057	while (( i < iin ))
	1058	do
	1059	(( i = i + 1 ))
	1060
	1061	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1062	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1063	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1064	then
[2610]	1065	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1066	else
[2610]	1067	eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]}
[2380]	1068	fi
	1069
[2610]	1070
[2380]	1071	# CHECK IF FILE EXISTS
	1072	if ! ls $filename* 1>/dev/null 2>&1
	1073	then
	1074
[2669]	1075	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1076	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1077	then
	1078	printf "\n\n +++ INPUT-file: "
[2610]	1079	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1080	then
	1081	printf "\n $filename"
	1082	else
[2610]	1083	printf "\n $filename.${extin_pre[$i]}"
[2380]	1084	fi
	1085	printf "\n does not exist\n"
	1086	locat=input; exit
	1087	else
[2610]	1088	(( nr_of_input_files = nr_of_input_files + 1 ))
	1089	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1090	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1091	actionin[$nr_of_input_files]="unavailable"
[2610]	1092	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1093	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1094	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1095	fi
[2605]	1096
[2380]	1097	else
	1098
[2610]	1099	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND
	1100	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
	1101	if [[ "${multin[$i]}" = true ]]
	1102	then
	1103	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1104	ls -1 -d ${filename} > filelist 2>/dev/null
	1105	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1106	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1107
[2610]	1108	endings=""
	1109	while read line
	1110	do
	1111	# filename without path (i.e. after the last "/")
	1112	basefilename=$(basename ${line})
[2380]	1113
[2610]	1114	# check if there is an extension and remove it
	1115	ext=${basefilename##*.}
	1116	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1117	then
	1118	basefilename=${basefilename%.*}
	1119	fi
[2380]	1120
[2610]	1121	# check for an existing cycle number and remove it
	1122	cycle=${basefilename##*.}
	1123	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1124	then
	1125	basefilename=${basefilename%.*}
	1126	fi
[2600]	1127
[2610]	1128	# remove the fname from the beginning
	1129	length_fname=${#fname}
	1130	ending=${basefilename:${length_fname}}
	1131
	1132	# remove the ending given in the .iofiles from the beginning
	1133	endingstring="${endin_pre[$i]}"
	1134	length_ending=${#endingstring}
	1135	ending=${ending:${length_ending}}
	1136
	1137	if [[ "$ending" = "" ]]
[2600]	1138	then
[2610]	1139	# standard ending as given in the .iofiles
	1140	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1141	then
	1142	endings="$endings DEFAULT"
	1143	fi
[2600]	1144	else
[2610]	1145	# ending must start with "_", otherwise its a different file
	1146	if [[ "${ending:0:1}" = "_" ]]
	1147	then
	1148	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1149	then
	1150	endings="$endings $ending"
	1151	fi
	1152	fi
[2600]	1153	fi
[2610]	1154
	1155	done <filelist
[2380]	1156
[2610]	1157	rm filelist
[2380]	1158
[2600]	1159	else
[2610]	1160
	1161	# SINGLE NAME
	1162	endings=DEFAULT
	1163
[2600]	1164	fi
	1165
[2610]	1166	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1167	for ending in $endings
	1168	do
	1169
	1170	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1171	if [[ $ending = DEFAULT ]]
[2380]	1172	then
[2610]	1173	ending=""
	1174	fi
	1175
	1176	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1177	(( nr_of_input_files = nr_of_input_files + 1 ))
	1178	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1179	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1180	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1181	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1182	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1183	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1184
	1185
	1186	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1187	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1188	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1189	then
	1190	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1191	else
[2610]	1192	eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]}
[2380]	1193	fi
[2610]	1194
	1195	# DETERMINE THE FILE'S CYCLE NUMBER
	1196	(( maxcycle = 0 ))
	1197	ls -1 -d $filename > filelist 2>/dev/null
	1198	ls -1 -d $filename.* >> filelist 2>/dev/null
	1199	while read line
	1200	do
	1201	# filename without path (i.e. after the last "/")
	1202	basefilename=$(basename ${line})
	1203
	1204	# check if there is an extension
	1205	extension=${basefilename##*.}
	1206	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1207	then
	1208	basefilename=${basefilename%.*}
	1209	fi
	1210
	1211	# check for an existing cycle number
	1212	cycle=${basefilename##*.}
	1213	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1214	then
[2669]	1215	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1216	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1217	(( icycle = $((10#$cycle)) ))
[2610]	1218	else
	1219	(( icycle = 0 ))
	1220	fi
	1221
	1222	if (( icycle > maxcycle ))
	1223	then
	1224	(( maxcycle = icycle ))
	1225
	1226	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1227	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1228	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1229	then
	1230	leading_zero=true
	1231	else
	1232	leading_zero=false
	1233	fi
	1234	fi
	1235
	1236	done <filelist
	1237	rm filelist
	1238
	1239	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1240	if [[ $leading_zero = true ]]
[2380]	1241	then
[2610]	1242	cyclestring=`printf "%03d" $maxcycle`
	1243	else
	1244	cyclestring=$maxcycle
[2380]	1245	fi
[2610]	1246
	1247	# APPEND CYCLE NUMBER TO FILENAME
	1248	if (( maxcycle > 0 ))
[2380]	1249	then
[2610]	1250	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1251	then
	1252	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1253	else
	1254	filename=${filename}.$cyclestring
	1255	fi
[2380]	1256	else
[2610]	1257	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1258	then
	1259	filename=${filename}.${extin[$nr_of_input_files]}
	1260	fi
[2380]	1261	fi
[2610]	1262
	1263	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1264	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1265	absnamein[$nr_of_input_files]=$filename
	1266	if (( maxcycle > 0 ))
[2380]	1267	then
[2610]	1268	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1269	then
	1270	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1271	else
	1272	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring
	1273	fi
[2380]	1274	else
[2610]	1275	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1276	then
	1277	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1278	else
	1279	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}
	1280	fi
[2380]	1281	fi
	1282
[2610]	1283	done
	1284
[2380]	1285	fi
[2610]	1286
[2380]	1287	done
	1288
[2610]	1289
[2380]	1290	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1291	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1292	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1293	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1294	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1295	# REMOTE HOST)
	1296	(( i = 0 ))
	1297	while (( i < iout ))
	1298	do
	1299	(( i = i + 1 ))
[2610]	1300	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1301	then
[2610]	1302	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1303	then
[2610]	1304	actionout_pre[$i]=""
	1305	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1306	then
[2610]	1307	actionout_pre[$i]=pe
	1308	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1309	then
[2610]	1310	actionout_pre[$i]=a
[2380]	1311	fi
	1312	(( maxcycle = 0 ))
[2610]	1313	eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]}
	1314	eval catalogname=${pathout_pre[$i]}
[2380]	1315	if ! ls $filename* 1>/dev/null 2>&1
	1316	then
	1317
	1318	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1319	if cat /dev/null > $filename
	1320	then
	1321	rm $filename
	1322	else
	1323
	1324	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1325	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1326	if [[ ! -d $catalogname ]]
	1327	then
	1328	if mkdir -p $catalogname
	1329	then
	1330	printf "\n\n *** directory:"
	1331	printf "\n $catalogname"
	1332	printf "\n was created\n"
	1333	else
	1334	printf "\n\n +++ OUTPUT-file:"
	1335	printf "\n $filename"
	1336	printf "\n cannot be created, because directory does not exist"
	1337	printf "\n and cannot be created either"
	1338	printf "\n"
	1339	locat=output ; exit
	1340	fi 2>/dev/null
	1341	else
	1342	printf "\n\n +++ OUTPUT-file:"
	1343	printf "\n $filename"
	1344	printf "\n cannot be created, although directory exists"
	1345	printf "\n"
	1346	locat=output ; exit
	1347	fi
	1348	fi 2>/dev/null
	1349
	1350	fi
	1351
	1352	fi
	1353	done
	1354
	1355
	1356	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1357	if [[ $running_in_batch_mode = false ]]
	1358	then
	1359	run_id=$RANDOM
	1360	job_id=${fname}.$run_id
	1361
[2566]	1362	tempdir=$fast_io_catalog/$job_id
[2380]	1363	fi
	1364
	1365
	1366	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1367	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1368	then
	1369
	1370	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1371	if [[ $ibd = 0 ]]
	1372	then
	1373	printf "\n"
	1374	printf "\n +++ no batch directives found in configuration file"
	1375	locat=config_file_batch_directives; (( iec = 0 )); exit
	1376	fi
	1377
	1378	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1379	done=false
[2384]	1380	cputime=$cpumax
[2380]	1381	while [[ $done = false ]]
	1382	do
[2384]	1383	if (( cputime == 0 ))
[2380]	1384	then
	1385	printf "\n +++ cpu-time is undefined"
	1386	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1387	printf "\n >>> "
[2384]	1388	read cputime 1>/dev/null 2>&1
[2380]	1389	else
	1390	done=true
	1391	fi
	1392	done
[2420]	1393	cpumax=$cputime
[2380]	1394
	1395	# CHECK THE MEMORY DEMAND
	1396	done=false
	1397	while [[ $done = false ]]
	1398	do
	1399	if (( memory == 0 ))
	1400	then
	1401	printf "\n +++ memory demand is undefined"
	1402	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1403	printf "\n >>> "
	1404	read memory 1>/dev/null 2>&1
	1405	else
	1406	done=true
	1407	fi
	1408	done
	1409
	1410	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1411	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1412	then
	1413	while [[ -z $remote_username ]]
	1414	do
[2420]	1415	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1416	printf "\n >>> Please type username:"
	1417	printf "\n >>> "
	1418	read remote_username
	1419	done
	1420	fi
	1421
	1422	else
	1423
[2420]	1424	if [[ $running_in_batch_mode = false ]]
	1425	then
	1426	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1427	cpumax=$cputime
	1428	else
	1429	cputime=$cpumax
	1430	fi
[2380]	1431
	1432	fi
	1433
	1434
	1435	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1436	(( cpu_hours = cputime / 3600 ))
	1437	(( resttime = cputime - cpu_hours * 3600 ))
	1438	(( cpu_minutes = resttime / 60 ))
	1439	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1440	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1441
	1442
	1443	# OUTPUT OF THE PALMRUN-HEADER
	1444	calltime=$(date)
	1445	printf "\n"
	1446	printf "#------------------------------------------------------------------------# \n"
	1447	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1448	printf "\| \| \n"
	1449	column1="called on:"; column2=$(hostname)
	1450	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1451	if [[ $create_remote_batch_job = true ]]
	1452	then
[2506]	1453	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1454	else
	1455	if [[ $running_on_remote = true ]]
	1456	then
[2506]	1457	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1458	else
[2506]	1459	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1460	fi
	1461	fi
	1462	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1463
	1464	column1="running in:"
	1465	if [[ $running_in_batch_mode = true ]]
	1466	then
	1467	column2="batch job mode"
	1468	else
	1469	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1470	then
	1471	column2="job creation mode"
	1472	else
	1473	column2="interactive run mode"
	1474	fi
	1475	fi
	1476	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1477
[2479]	1478	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1479	then
[2480]	1480	if [[ "$project_account" != "" ]]
[2479]	1481	then
	1482	column1="project account number:"
	1483	column2="$project_account"
	1484	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1485	fi
	1486	fi
	1487
[2380]	1488	if [[ -n $cores ]]
	1489	then
	1490	if [[ $run_coupled_model = false ]]
	1491	then
	1492	column1="number of cores:"; column2=$cores
	1493	else
	1494	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1495	fi
	1496	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1497	fi
	1498	if [[ -n $tasks_per_node ]]
	1499	then
	1500	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1501	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1502	if (( remaining_cores > 0 ))
	1503	then
	1504	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1505	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1506	fi
	1507	fi
	1508	if [[ $maximum_parallel_io_streams != $cores ]]
	1509	then
	1510	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1511	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1512	fi
	1513	if [[ $use_openmp = true ]]
	1514	then
	1515	column1="threads per task:"; column2="$threads_per_task"
	1516	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1517	fi
[2384]	1518	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1519	then
[2506]	1520	column1="memory demand / PE":; column2="$memory MB"
	1521	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1522	column1="job cpu time (h:m:s):"; column2="$timestring"
	1523	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1524	fi
[2380]	1525	printf "\| \| \n"
	1526	if [[ "$source_list" != "" ]]
	1527	then
	1528	if [[ "$make_options" != "" ]]
	1529	then
	1530	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1531	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1532	line=$(echo "$make_options" \| cut -c46-)
	1533	while [[ "$line" != "" ]]
	1534	do
	1535	column1=""
	1536	column2=$(echo "$line" \| cut -c-45)
	1537	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1538	line=$(echo "$line" \| cut -c46-)
	1539	done
	1540	fi
	1541	fi
	1542
	1543	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1544	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1545	line=$(echo "$cpp_options" \| cut -c46-)
	1546	while [[ "$line" != "" ]]
	1547	do
	1548	column1=""
	1549	column2=$(echo "$line" \| cut -c-45)
	1550	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1551	line=$(echo "$line" \| cut -c46-)
	1552	done
	1553
	1554	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1555	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1556	line=$(echo "$compiler_options" \| cut -c46-)
	1557	while [[ "$line" != "" ]]
	1558	do
	1559	column1=""
	1560	column2=$(echo "$line" \| cut -c-45)
	1561	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1562	line=$(echo "$line" \| cut -c46-)
	1563	done
	1564
[2388]	1565	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1566	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1567	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1568	while [[ "$line" != "" ]]
	1569	do
	1570	column1=""
	1571	column2=$(echo "$line" \| cut -c-45)
	1572	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1573	line=$(echo "$line" \| cut -c46-)
	1574	done
	1575
	1576	if [[ "$login_init_cmd" != "" ]]
	1577	then
	1578	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1579	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1580	line=$(echo "$login_init_cmd" \| cut -c46-)
	1581	while [[ "$line" != "" ]]
	1582	do
	1583	column1=""
	1584	column2=$(echo "$line" \| cut -c-45)
	1585	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1586	line=$(echo "$line" \| cut -c46-)
	1587	done
	1588	fi
	1589
	1590	if [[ "$module_commands" != "" ]]
	1591	then
	1592	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1593	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1594	line=$(echo "$module_commands" \| cut -c46-)
	1595	while [[ "$line" != "" ]]
	1596	do
	1597	column1=""
	1598	column2=$(echo "$line" \| cut -c-45)
	1599	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1600	line=$(echo "$line" \| cut -c46-)
	1601	done
	1602	fi
	1603	printf "\| \| \n"
	1604	column1="base name of files:"; column2=$fname
	1605	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1606	column1="activation string list:"; column2=$(echo $activation_string_list)
	1607	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1608
	1609	if [[ "$ocean_file_appendix" = true ]]
	1610	then
	1611	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1612	fi
	1613
	1614	if [[ "$source_list" != "" ]]
	1615	then
	1616	printf "\| \| \n"
	1617	printf "\| Files to be compiled: \| \n"
	1618	line=$source_list
	1619	while [[ "$line" != "" ]]
	1620	do
	1621	linestart=$(echo $line \| cut -c-70)
	1622	printf "\| %-70s \| \n" "$linestart"
	1623	line=$(echo "$line" \| cut -c71-)
	1624	done
	1625	fi
	1626	printf "#------------------------------------------------------------------------#"
	1627
	1628
	1629
	1630	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1631	if [[ $do_trace = true ]]
	1632	then
	1633	(( i = 0 ))
[2610]	1634	while (( i < nr_of_input_files ))
[2380]	1635	do
	1636	(( i = i + 1 ))
	1637	if (( i == 1 ))
	1638	then
	1639	printf "\n\n >>> INPUT-file assignments:\n"
	1640	fi
	1641	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1642	done
	1643	(( i = 0 ))
	1644	while (( i < iout ))
	1645	do
	1646	(( i = i + 1 ))
	1647	if (( i == 1 ))
	1648	then
	1649	printf "\n\n >>> OUTPUT-file assignments:\n"
	1650	fi
	1651	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1652	done
	1653	(( i = 0 ))
	1654	while (( i < iic ))
	1655	do
	1656	(( i = i + 1 ))
	1657	if (( i == 1 ))
	1658	then
	1659	printf "\n\n >>> INPUT-commands:\n"
	1660	fi
	1661	printf "\n ${in_command[$i]}"
	1662	done
	1663	(( i = 0 ))
	1664	while (( i < ioc ))
	1665	do
	1666	(( i = i + 1 ))
	1667	if (( i == 1 ))
	1668	then
	1669	printf "\n\n >>> OUTPUT-commands:\n"
	1670	fi
	1671	printf "\n ${out_command[$i]}"
	1672	done
	1673	fi
	1674
	1675	# QUERY FOR CONTINUE
	1676	if [[ $silent = false && $running_in_batch_mode = false ]]
	1677	then
	1678	antwort=dummy
	1679	printf "\n\n"
	1680	printf " >>> everything o.k. (y/n) ? "
	1681	while read antwort
	1682	do
	1683	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1684	then
	1685	printf " >>> everything o.k. (y/n) ? "
	1686	else
	1687	break
	1688	fi
	1689	done
	1690	if [[ $antwort = n \|\| $antwort = N ]]
	1691	then
	1692	locat=user_abort; (( iec = 0 )); exit
	1693	fi
	1694	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1695	then
[2566]	1696	printf "\n *** batch-job will be created and submitted"
[2380]	1697	else
[2566]	1698	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1699	fi
	1700	fi
	1701
	1702
	1703
	1704	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1705	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1706	then
	1707
	1708	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1709	then
[2566]	1710	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1711	else
[2566]	1712	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1713	fi
	1714
[2422]	1715	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1716	# IT SHALL BE CREATED
	1717	ask_for_make_depository=false
	1718	if [[ $create_remote_batch_job = true ]]
	1719	then
	1720
	1721	line=`grep %base_directory $config_file`
[2506]	1722	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1723	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]	1724
[2506]	1725	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1726	then
	1727	printf "\n\n +++ make depository \"${make_depository}\""
	1728	printf "\n on remote host not found!"
	1729	ask_for_make_depository=true
	1730	fi
[2506]	1731	rm ${host_configuration}_last_make_protokoll
[2422]	1732
	1733	else
	1734
	1735	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1736	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1737	if [[ ! -d ${make_depository} ]]
	1738	then
	1739	printf "\n\n +++ make depository \"${make_depository}\""
	1740	printf "\n on local host not found!"
	1741	ask_for_make_depository=true
	1742	fi
	1743
	1744	fi
	1745
	1746	if [[ $ask_for_make_depository = true ]]
	1747	then
	1748
	1749	antwort=dummy
	1750	printf "\n\n"
	1751	printf " >>> Create a new one (y/n) ? "
	1752	while read antwort
	1753	do
	1754	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1755	then
	1756	printf " >>> Create a new one (y/n) ? "
	1757	else
	1758	break
	1759	fi
	1760	done
	1761	if [[ $antwort = n \|\| $antwort = N ]]
	1762	then
	1763	locat=user_abort; (( iec = 0 )); exit
	1764	fi
	1765
[2566]	1766	if [[ $do_trace = true ]]
	1767	then
	1768	palmbuild -h $host_configuration
	1769	else
	1770	palmbuild -v -h $host_configuration
	1771	fi
[2422]	1772
	1773	if [[ $? != 0 ]]
	1774	then
	1775
	1776	# ABORT IN CASE OF COMPILATION PROBLEMS
	1777	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1778	locat=make_depository
	1779	exit
	1780	else
	1781	echo " *** now continue with creating executable and other sources"
	1782	fi
	1783
	1784	fi
	1785
[2566]	1786	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2506]	1787	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
[2380]	1788
	1789	if [[ $? != 0 ]]
	1790	then
	1791
	1792	# ABORT IN CASE OF COMPILATION PROBLEMS
	1793	printf "\n +++ error while creating executable and/or other sources"
	1794	locat=execution
[2506]	1795	rm -rf $sources_for_run_catalog
[2380]	1796	exit
	1797
	1798	else
	1799
[2566]	1800	printf " *** executable and other sources created\n"
[2506]	1801	rm -rf $sources_for_run_catalog
[2380]	1802
	1803	fi
	1804
	1805	fi
	1806
	1807
[2669]	1808	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1809	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1810	if [[ $create_remote_batch_job = true ]]
	1811	then
	1812	(( i = 0 ))
[2610]	1813	while (( i < nr_of_input_files ))
[2605]	1814	do
	1815	(( i = i + 1 ))
[2669]	1816	if [[ "${actionin[$i]}" = tr ]]
[2605]	1817	then
	1818	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1819	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1820	fi
	1821	done
	1822	if (( i > 0 ))
	1823	then
	1824	printf " *** input files have been copied to the remote host\n"
	1825	fi
	1826	fi
	1827
	1828
[2380]	1829	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1830	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1831	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1832	then
	1833
	1834	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1835	if [[ $running_in_batch_mode = false ]]
	1836	then
	1837	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1838	# FOLDER
[2566]	1839	mkdir -p $tempdir
	1840	chmod go+rx $tempdir
	1841	cd $tempdir
	1842	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1843	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1844
	1845	else
	1846
	1847	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1848	printf "\n *** running in temporary directory: $tempdir"
[2380]	1849
	1850	fi
	1851
	1852
	1853	# PROVIDE THE INPUT FILES
	1854	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1855	optional_files_missing=false
[2380]	1856	(( i = 0 ))
[2610]	1857	while (( i < nr_of_input_files ))
[2380]	1858	do
	1859	(( i = i + 1 ))
	1860	if (( i == 1 ))
	1861	then
	1862	printf "\n\n *** providing INPUT-files:\n$dashes"
	1863	fi
	1864
	1865
	1866	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1867	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1868	then
[2669]	1869	optional_files_missing=true
[2380]	1870	continue
	1871	fi
	1872
	1873	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1874	files_for_cores=false; filetype=file
	1875	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1876	then
	1877	files_for_cores=true; filetype=files
	1878	actionin[$i]=""
	1879	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1880	then
	1881	actionin[$i]=""
	1882	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1883	then
	1884	files_for_cores=true; filetype=files
	1885	actionin[$i]="ln"
	1886	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1887	then
	1888	actionin[$i]="ln"
	1889	fi
	1890
	1891	if [[ $files_for_cores = true ]]
	1892	then
	1893	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1894	else
	1895	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1896	fi
	1897
	1898	# INPUT-FILES TO BE LINKED
	1899	if [[ "${actionin[$i]}" = ln ]]
	1900	then
	1901
	1902	printf "\n $filetype will be linked"
	1903	if [[ $files_for_cores = false ]]
	1904	then
	1905	if [[ -f "${absnamein[$i]}" ]]
	1906	then
	1907	ln ${absnamein[$i]} ${localin[$i]}
	1908	got_tmp[$i]=true
	1909	fi
	1910	else
	1911	if [[ -d "${absnamein[$i]}" ]]
	1912	then
[2396]	1913	mkdir -p ${localin[$i]}
[2380]	1914	cd ${absnamein[$i]}
	1915	for file in $(ls *)
	1916	do
[2566]	1917	ln $file $tempdir/${localin[$i]}
[2380]	1918	done >\|/dev/null 2>&1
[2566]	1919	cd $tempdir
[2380]	1920	fi
	1921
	1922	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1923	if [[ ! -f "${localin[$i]}/_000000" ]]
	1924	then
	1925	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1926	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1927	fi
	1928
	1929	got_tmp[$i]=true
	1930	fi
	1931	fi
	1932
	1933	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	1934	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	1935	then
	1936
	1937	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1938	then
	1939
	1940	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1941	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1942	printf "\n file will be provided for $cores processors"
[2396]	1943	mkdir -p ${localin[$i]}
[2380]	1944	ival=$cores
	1945	(( ii = 0 ))
	1946	while (( ii <= ival-1 ))
	1947	do
	1948	if (( ii < 10 ))
	1949	then
	1950	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1951	elif (( ii < 100 ))
	1952	then
	1953	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1954	elif (( ii < 1000 ))
	1955	then
	1956	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1957	else
	1958	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1959	fi
	1960	(( ii = ii + 1 ))
	1961	done
	1962
	1963	else
	1964
	1965	if [[ $files_for_cores = true ]]
	1966	then
	1967
	1968	# PROVIDE FILES FOR EACH CORE
	1969	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1970	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1971	printf "\n providing $cores files for the respective cores"
[2396]	1972	mkdir -p ${localin[$i]}
[2380]	1973	if [[ $link_local_input = true ]]
	1974	then
	1975	printf " files will be linked\n"
	1976	cd ${absnamein[$i]}
	1977	for file in $(ls *)
	1978	do
	1979	ln -f $file ${localin[$i]}
	1980	done
[2566]	1981	cd $tempdir
[2380]	1982	fi
	1983
	1984	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1985	if [[ ! -f "${localin[$i]}/_000000" ]]
	1986	then
	1987	if [[ $link_local_input = true ]]
	1988	then
	1989	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1990	fi
	1991	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1992	fi
	1993
	1994	else
	1995
	1996	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1997	if [[ $link_local_input = true ]]
	1998	then
	1999	printf " file will be linked\n"
	2000	ln -f ${absnamein[$i]} ${localin[$i]}
	2001	fi
[2605]	2002	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2003	if [[ ! -f "${localin[$i]}" ]]
	2004	then
	2005	if [[ $link_local_input = true ]]
	2006	then
	2007	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2008	fi
[2669]	2009	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2010	then
	2011	mv ${absnamein[$i]} ${localin[$i]}
	2012	else
	2013	cp ${absnamein[$i]} ${localin[$i]}
	2014	fi
[2380]	2015	fi
	2016	fi
	2017	fi
	2018	fi
	2019
	2020	done
	2021	if (( i != 0 ))
	2022	then
[2669]	2023	if [[ $optional_files_missing = true ]]
	2024	then
	2025	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2026	fi
[2380]	2027	printf "\n$dashes\n *** all INPUT-files provided \n"
	2028	fi
	2029
	2030
	2031	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2032	(( i = 0 ))
	2033	while (( i < iic ))
	2034	do
	2035	(( i = i + 1 ))
	2036	if (( i == 1 ))
	2037	then
	2038	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2039	fi
	2040	printf "\n >>> ${in_command[$i]}"
	2041	eval ${in_command[$i]}
	2042	if (( i == iic ))
	2043	then
	2044	printf "\n$dashes\n"
	2045	fi
	2046	done
	2047
	2048
	2049	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2050	# (FILE ENVPAR WILL BE READ BY PALM)
	2051	cat > ENVPAR << EOF
[2506]	2052	&envpar run_identifier = '$fname', host = '$host_configuration',
[2380]	2053	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	2054	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2055	maximum_cpu_time_allowed = ${cpumax}.,
	2056	revision = '$global_revision',
	2057	batch_job = .${running_in_batch_mode}. /
	2058
	2059	EOF
	2060
	2061
	2062	# STARTING THE EXECUTABLE
	2063	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2064	PATH=$PATH:$tempdir
[2380]	2065
	2066
	2067	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2068	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2069	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2070	eval line=\"$line\"
	2071	execute_command="$line"
	2072
	2073
	2074	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2075	if [[ "$execute_command_for_combine" = "" ]]
	2076	then
	2077	eval line2=\"$line2\"
	2078	execute_command_for_combine="$line2"
	2079	fi
	2080
[2380]	2081
	2082
	2083	# PROVIDE A HOSTFILE, IF REQUIRED
	2084	if [[ "$hostfile" != "" ]]
	2085	then
	2086
	2087	if [[ $hostfile = auto ]]
	2088	then
	2089	# CREATE A NEW HOSTFILE
	2090	(( ii = 1 ))
	2091	while (( ii <= cores / threads_per_task ))
	2092	do
	2093	echo $(hostname) >> hostfile
	2094	(( ii = ii + 1 ))
	2095	done
	2096	if (( cores / threads_per_task == 0 ))
	2097	then
	2098	echo $(hostname) >> hostfile
	2099	fi
	2100
	2101	else
	2102	cp $hostfile hostfile
	2103	fi
	2104	eval line=\"`head -n $ii hostfile`\"
	2105	printf "\n *** running on: $line"
	2106	fi
	2107
	2108
	2109
	2110	# SET THE NUMBER OF OPENMP-THREADS
	2111	if [[ $use_openmp = true ]]
	2112	then
	2113	export OMP_NUM_THREADS=$threads_per_task
	2114	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2115	else
	2116	export OMP_NUM_THREADS=1
	2117	fi
	2118
	2119
[2610]	2120	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2121	if [[ $run_coupled_model = false ]]
	2122	then
	2123	if [[ "$ocean_file_appendix" = true ]]
	2124	then
	2125	echo "precursor_ocean" > coupling_steering
	2126	else
	2127	echo "precursor_atmos" > coupling_steering
	2128	fi
	2129	else
	2130	(( iia = $cores_atmos / $threads_per_task ))
	2131	(( iio = $cores_ocean / $threads_per_task ))
	2132	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2133	printf "\n\n"
	2134	echo "coupled_run $iia $iio" > coupling_steering
	2135	fi
	2136
	2137	printf "\n *** execute command:"
	2138	printf "\n \"$execute_command\" \n\n"
	2139
	2140	$execute_command < coupling_steering
	2141
	2142	if [[ $? != 0 ]]
	2143	then
	2144
	2145	# ABORT IN CASE OF RUNTIME ERRORS
	2146	printf "\n +++ runtime error occured"
	2147	locat=execution
	2148	exit
	2149
	2150	else
	2151
	2152	printf "\n$dashes\n *** execution finished \n"
	2153
	2154	fi
	2155
	2156
	2157	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2158	# BY EACH CORE INTO ONE FILE
	2159	if [[ ! -f combine_plot_fields.x ]]
	2160	then
	2161
	2162	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2163	printf "\n 2d- and/or 3d-data may be incomplete!"
	2164	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2165
	2166	elif [[ "$combine_plot_fields" == true ]]
	2167	then
	2168
	2169	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2170	$execute_command_for_combine
	2171
	2172	else
	2173
	2174	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2175	# DATA OUTPUT
[2380]	2176	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2177	fi
	2178
	2179
	2180
	2181	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2182	(( i = 0 ))
	2183	while (( i < ioc ))
	2184	do
	2185	(( i = i + 1 ))
	2186	if (( i == 1 ))
	2187	then
	2188	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2189	fi
	2190	printf "\n >>> ${out_command[$i]}"
	2191	eval ${out_command[$i]}
	2192	if (( i == ioc ))
	2193	then
	2194	printf "\n$dashes\n"
	2195	fi
	2196	done
	2197
	2198
[2610]	2199	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2200	# WILDCARDS
[2380]	2201	(( i = 0 ))
[2610]	2202	(( nr_of_output_files = 0 ))
	2203
[2380]	2204	while (( i < iout ))
	2205	do
[2610]	2206
[2380]	2207	(( i = i + 1 ))
[2610]	2208
	2209	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2210	# CREATE A LIST FOR THE DETECTED ENDINGS
	2211	if [[ "${multout[$i]}" = true ]]
	2212	then
	2213	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2214	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2215	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2216
	2217	endings="DEFAULT"
	2218	while read line
	2219	do
	2220	# remove the local name from the beginning
	2221	localnamestring="${localout_pre[$i]}"
	2222	length_localname=${#localnamestring}
	2223	ending=${line:${length_localname}}
	2224
	2225	if [[ "$ending" != "" ]]
	2226	then
	2227	endings="$endings $ending"
	2228	fi
	2229
	2230	done <filelist
	2231
	2232	rm filelist
	2233
	2234	else
	2235
	2236	# SINGLE NAME
	2237	endings=DEFAULT
	2238
	2239	fi
	2240
	2241	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2242	for ending in $endings
	2243	do
	2244
	2245	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2246	if [[ $ending = DEFAULT ]]
	2247	then
	2248	ending=""
	2249	fi
	2250
	2251	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2252	(( nr_of_output_files = nr_of_output_files + 1 ))
	2253	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2254	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2255	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2256	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2257	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2258	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2259	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2260
	2261	done
	2262
	2263	done
	2264
	2265
	2266
	2267
	2268	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2269	(( i = 0 ))
	2270	while (( i < nr_of_output_files ))
	2271	do
	2272	(( i = i + 1 ))
[2380]	2273	if (( i == 1 ))
	2274	then
	2275	printf "\n\n *** saving OUTPUT-files:"
	2276
	2277	# GET RUN NUMBER ASSIGNED BY PALM
	2278	if [[ -f RUN_NUMBER ]]
	2279	then
	2280	read run_number < RUN_NUMBER
	2281	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2282	usecycle_option="-U $run_number"
	2283	else
	2284	run_number=0
	2285	usecycle_option=""
	2286	fi
	2287	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2288	then
[2404]	2289	printf "\n *** in case of SCP transfers to local host"
	2290	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2291	fi
	2292	printf "\n$dashes"
	2293	fi
	2294
	2295	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2296	then
	2297
[2610]	2298	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	2299
	2300	# DETERMINE THE CYCLE NUMBER
	2301	ls -1 -d $filename > filelist 2>/dev/null
	2302	ls -1 -d $filename.* >> filelist 2>/dev/null
	2303	while read line
	2304	do
	2305
	2306	# filename without path (i.e. after the last "/")
	2307	basefilename=$(basename ${line})
	2308
	2309	# check if there is an extension
	2310	extension=${basefilename##*.}
	2311	if [[ "$extension" = "${extout[$i]}" ]]
	2312	then
	2313	basefilename=${basefilename%.*}
	2314	fi
	2315
	2316	# check for an existing cycle number
	2317	cycle=${basefilename##*.}
	2318	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2319	then
[2669]	2320	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2321	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2322	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2323	else
	2324	(( icycle = 1 ))
	2325	fi
	2326
	2327	if (( icycle > maxcycle ))
	2328	then
	2329	(( maxcycle = icycle ))
	2330	fi
	2331
	2332	done <filelist
	2333	rm filelist
	2334
	2335
	2336	# SET THE CYCLE NUMBER
	2337	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2338	if [[ "${actionout[$i]}" = a ]]
	2339	then
	2340	(( maxcycle = maxcycle - 1 ))
	2341	fi
	2342
	2343	(( cycnum[$i] = maxcycle ))
	2344	pathout[$i]=$filename
	2345
	2346
	2347	# ADD CYCLE NUMBER TO FILENAME
	2348	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2349	if [[ "${actionout[$i]}" != "a" ]]
	2350	then
	2351	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2352	# WITH AN EXISTING CYCLE NUMBER
	2353	if (( run_number >= cycnum[$i] ))
	2354	then
	2355	(( cycnum[$i] = run_number ))
	2356	else
	2357	if (( run_number > 0 ))
	2358	then
	2359	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2360	fi
	2361	fi
	2362	fi
	2363	if (( cycnum[$i] > 0 ))
	2364	then
[2600]	2365	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2366	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2367	fi
	2368	fi
	2369
	2370	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2371	files_for_cores=false; filetype=file
	2372	link_local_output=false
	2373	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2374	then
	2375	files_for_cores=true; filetype=directory
	2376	actionout[$i]=""
	2377	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2378	then
	2379	actionout[$i]=""
	2380	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2381	then
	2382	files_for_cores=true; filetype=directory
	2383	link_local_output=true
	2384	actionout[$i]=""
	2385	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2386	then
	2387	link_local_output
	2388	actionout[$i]=""
	2389	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2390	then
	2391	files_for_cores=true; filetype=directory
	2392	actionout[$i]="tr"
	2393	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2394	then
	2395	actionout[$i]="tr"
	2396	fi
	2397
	2398	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2399	then
[2669]	2400	if [[ ${warnout[$i]} = true ]]
	2401	then
	2402	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2403	fi
[2380]	2404	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2405	then
[2669]	2406	if [[ ${warnout[$i]} = true ]]
	2407	then
	2408	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2409	fi
[2380]	2410	else
	2411
	2412
	2413	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2414	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2415	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2416	then
	2417	if [[ $running_on_remote = true ]]
	2418	then
	2419
	2420	# SET OPTIONS FOR TRANSFER
	2421	if [[ "${actionout[$i]}" = tr ]]
	2422	then
	2423	if [[ $files_for_cores = false ]]
	2424	then
	2425	catalog_option=""
	2426	catalog_string=""
	2427	else
	2428	catalog_option="-c"
	2429	catalog_string="/"
	2430	fi
	2431	append_option=""
	2432	append_string=""
	2433	else
	2434	append_option="-A"
	2435	append_string="append"
	2436	fi
	2437
	2438	transfer_failed=false
	2439	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2506]	2440	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2441
	2442	# TRANSFER VIA SCP
	2443	if [[ "$remote_loginnode" != "" ]]
	2444	then
[2566]	2445	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]	2446	else
[2506]	2447	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]	2448	fi
	2449	[[ $? != 0 ]] && transfer_failed=true
	2450
	2451
	2452	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2453	if [[ $transfer_failed = true ]]
	2454	then
	2455	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2506]	2456	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
[2380]	2457
	2458	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2459	eval local_catalog=${pathout[$i]}
	2460	if [[ ! -d $local_catalog ]]
	2461	then
	2462	printf " *** local directory does not exist. Trying to create:\n"
	2463	printf " $local_catalog \n"
	2464	mkdir -p $local_catalog
	2465	fi
[2506]	2466	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
[2380]	2467	transfer_problems=true
	2468	fi
	2469
	2470	else
	2471
	2472	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2473	# BE COPIED OR APPENDED ON THIS MACHINE
	2474	if [[ "${actionout[$i]}" = tr ]]
	2475	then
	2476	actionout[$i]=""
	2477	else
	2478	actionout[$i]="a"
	2479	fi
	2480	fi
	2481	fi
	2482
	2483
	2484	# APPEND ON THIS MACHINE
	2485	if [[ "${actionout[$i]}" = "a" ]]
	2486	then
	2487	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2488	then
	2489	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2490	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2491	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2492	else
	2493	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2494	printf "\n ${pathout[$i]}\n"
	2495	cat ${localout[$i]} >> ${pathout[$i]}
	2496	fi
	2497	fi
	2498
	2499	# COPY ON THIS MACHINE
	2500	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2501	# ON DIFFERENT FILE-SYSTEMS
	2502	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2503	then
	2504
	2505	# COPY IN CASE OF RUNS ON SINGLE CORES
	2506	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2507	then
	2508	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2509	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2510	if [[ $link_local_output = true ]]
	2511	then
	2512	printf " file will be linked\n"
	2513	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2514	fi
	2515	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2516	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2517	then
	2518	if [[ $link_local_output = true ]]
	2519	then
	2520	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2521	fi
	2522	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2523	else
	2524	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2525	fi
	2526	else
	2527	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2528	printf "\n ${pathout[$i]}\n"
	2529	if [[ $link_local_output = true ]]
	2530	then
	2531	printf " file will be linked\n"
	2532	ln -f ${localout[$i]} ${pathout[$i]}
	2533	fi
	2534	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2535	if [[ ! -f "${pathout[$i]}" ]]
	2536	then
	2537	if [[ $link_local_output = true ]]
	2538	then
	2539	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2540	fi
	2541	cp ${localout[$i]} ${pathout[$i]}
	2542	else
	2543	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2544	fi
	2545	fi
	2546
	2547	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2548	then
	2549
	2550	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2551	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2552	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2553	printf "\n ${pathout[$i]}\n"
	2554	if [[ $link_local_output = true ]]
	2555	then
	2556	printf " files will be linked\n"
[2396]	2557	mkdir -p ${pathout[$i]}
[2380]	2558	cd ${localout[$i]}
	2559	for file in $(ls *)
	2560	do
	2561	ln -f $file ${pathout[$i]}
	2562	done >\|/dev/null 2>&1
[2566]	2563	cd $tempdir
[2380]	2564	fi
	2565
	2566	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2567	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2568	then
	2569	if [[ $link_local_output = true ]]
	2570	then
	2571	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2572	fi
	2573	cp -r ${localout[$i]}/* ${pathout[$i]}
	2574	fi
	2575
	2576	fi
	2577	fi
	2578	done
	2579
	2580	if (( i != 0 ))
	2581	then
	2582	if [[ $transfer_problems = true ]]
	2583	then
	2584	printf "\n$dashes\n *** OUTPUT-files saved"
	2585	printf "\n +++ WARNING: some data transfers failed! \n"
	2586	else
	2587	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2588	fi
	2589	fi
	2590
	2591
	2592	# IF REQUIRED, START A RESTART-JOB
	2593	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2594	if [[ -f CONTINUE_RUN ]]
	2595	then
	2596
	2597	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2598	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2599	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2600	# -b START A BATCH JOB
	2601	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2602	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2603	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2604
	2605
	2606	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2607	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2608	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2609	then
[2381]	2610	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2611	fi
	2612
	2613
	2614	# START THE RESTART-JOB
	2615	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2616	echo " $prc"
	2617	printf "\n$dashes\n"
	2618	if [[ $running_on_remote = true ]]
	2619	then
	2620
	2621	echo "*** ssh will be used to initiate restart-runs!"
	2622	echo " return_address=\"$return_address\" "
	2623	echo " return_username=\"$local_username\" "
	2624
	2625	if [[ "$remote_loginnode" != "" ]]
	2626	then
[2420]	2627	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]	2628	else
[2420]	2629	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2630	fi
	2631
	2632	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2633	sleep 30
	2634
	2635	else
	2636
	2637	# START THE RESTART JOB ON THE LOCAL HOST
	2638	eval $prc # THE ' MUST BE EVALUATED
	2639	cd - > /dev/null
	2640
	2641	fi
	2642	printf "\n$dashes\n *** restart-run initiated \n"
	2643
	2644
	2645	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2646	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2647	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2648	# MAY BE VERY HUGE)
	2649	(( i = 0 ))
[2610]	2650	while (( i < nr_of_input_files ))
[2380]	2651	do
	2652	(( i = i + 1 ))
	2653	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2654	then
	2655	rm -r ${absnamein[$i]}
	2656	fi
	2657	done
	2658
	2659	fi
	2660
	2661
	2662	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2663	cd $HOME
[2566]	2664	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2665
	2666
	2667	else
	2668
	2669
	2670	# PREPARING ACTIONS,
	2671	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2672
	2673	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2506]	2674	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2675	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2676	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2677	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2678	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2679	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2680	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2681	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2682	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2683	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2684	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2685	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2686	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2687	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2688	if [[ $create_remote_batch_job = true ]]
	2689	then
	2690	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2691	if [[ $do_trace = true ]]
	2692	then
	2693	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2694	fi
[2380]	2695	elif [[ $create_batch_job = true ]]
	2696	then
	2697	palmrun_com=${palmrun_com}" -j"
[2420]	2698	if [[ $do_trace = true ]]
	2699	then
	2700	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2701	fi
[2380]	2702	fi
	2703
	2704
	2705	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2706	# REMOTE HOST
[2506]	2707	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2708	job_protocol_file=$job_protocol_file_local
	2709	if [[ $create_remote_batch_job = true ]]
	2710	then
[2506]	2711	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2712	job_protocol_file=$job_protocol_file_remote
	2713	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2714	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2715	fi
	2716
	2717
	2718	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2719	jobfile=jobfile.$run_id
	2720
	2721
	2722	# FIRST CREATE THE BATCH DIRECTIVES
	2723	(( i = 0 ))
	2724	while (( i < ibd ))
	2725	do
	2726	(( i = i + 1 ))
[2693]	2727	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2728	eval line=\"$line\"
	2729	echo "$line" >> $jobfile
	2730	done
	2731	echo " " >> $jobfile
	2732
	2733
	2734	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2735	# PROTOCOL
	2736	if [[ $create_remote_batch_job = true ]]
	2737	then
	2738	echo "set +vx" >> $jobfile
	2739	echo "trap '" >> $jobfile
	2740	echo "set +vx" >> $jobfile
	2741	echo "cd ${remote_jobcatalog}" >> $jobfile
	2742	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2743
	2744	# ADD THE BATCH DIRECTIVES
	2745	(( i = 0 ))
	2746	while (( i < ibdt ))
	2747	do
	2748	(( i = i + 1 ))
[2693]	2749	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2750	eval line=\"$line\"
	2751	echo "$line" >> $jobfile
	2752	done
	2753	echo " " >> $jobfile
	2754
	2755	echo "set -x" >> $jobfile
[2506]	2756	echo "${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]	2757	echo "%%END%%" >> $jobfile
	2758	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2759	echo "$submit_command $scpjob_file" >> $jobfile
	2760	echo "rm $scpjob_file" >> $jobfile
[2404]	2761	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2762	echo "set -x" >> $jobfile
	2763	echo " ' exit" >> $jobfile
	2764	fi
	2765
	2766
	2767	# ACTIVATE ERROR-TRACEBACK
	2768	if [[ $do_trace = true ]]
	2769	then
	2770	echo "set -x" >> $jobfile
	2771	else
	2772	echo "set +vx" >> $jobfile
	2773	fi
	2774
	2775
	2776	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2777	if [[ "$login_init_cmd" != "" ]]
	2778	then
	2779	echo "$login_init_cmd" >> $jobfile
	2780	fi
	2781	if [[ "$module_commands" != "" ]]
	2782	then
	2783	echo "$module_commands" >> $jobfile
	2784	fi
	2785
	2786
	2787	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2788	if [[ $create_remote_batch_job = true ]]
	2789	then
	2790	echo "mkdir $tempdir" >> $jobfile
	2791	echo "chmod go+rx $tempdir" >> $jobfile
	2792	else
	2793	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2794	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2795	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2796	mkdir $tempdir
	2797	chmod go+rx $tempdir
	2798	fi
	2799	echo "cd $tempdir" >> $jobfile
	2800	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2801	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2802	echo "export PATH=.:\$PATH" >> $jobfile
	2803	echo "export execute_palmrun=true" >> $jobfile
	2804
	2805
	2806	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2807	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2808	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2809	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2810	echo "export LOCAL_PWD" >> $jobfile
	2811
	2812
	2813	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2814	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2815	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2816
	2817
	2818	# CALL PALMRUN WITHIN THE JOB
	2819	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2820	echo "set -x" >> $jobfile
	2821	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2822
	2823
	2824	# TRANSFER JOBFILE TO THE TARGET HOST
	2825	if [[ $create_jobfile_only = false ]]
	2826	then
	2827
	2828	if [[ $create_remote_batch_job = true ]]
	2829	then
	2830
[2420]	2831	echo " "
[2566]	2832	echo " *** transfer of job to remote host via scp"
[2420]	2833	if [[ $do_trace = true ]]
	2834	then
[2506]	2835	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2836	fi
[2566]	2837	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2838
[2566]	2839	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2840	if [[ $do_trace = true ]]
	2841	then
[2506]	2842	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]	2843	fi
[2506]	2844	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]	2845
	2846	elif [[ $create_batch_job = true ]]
	2847	then
	2848
[2385]	2849	eval local_jobcatalog=$local_jobcatalog
[2506]	2850	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2851	cd $local_jobcatalog
[2380]	2852	echo " "
[2420]	2853	echo " *** submit the job"
	2854	if [[ $do_trace = true ]]
	2855	then
[2506]	2856	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2857	fi
[2506]	2858	$submit_command ${host_configuration}_${job_id}
	2859	rm ${host_configuration}_${job_id}
[2380]	2860	cd - > /dev/null
	2861
	2862	fi
	2863
	2864	rm -rf $jobfile
	2865
	2866	else
	2867
	2868	printf "\n *** jobfile created under name \"$jobfile\" "
	2869	printf "\n no batch-job has been sent!"
	2870
	2871	fi
	2872
	2873	fi # END OF REMOTE-PART

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