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source: palm/trunk/SCRIPTS/palmrun @ 3004

Last change on this file since 3004 was 2993, checked in by raasch, 7 years ago
bugfix of r2990
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 97.2 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 $
[2993]	29	# bugfix of r2990
	30	#
	31	# 2718 2018-01-02 08:49:38Z maronga
[2990]	32	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	33	# not in the working directory from where palmrun is called
	34	#
	35	# 2718 2018-01-02 08:49:38Z maronga
[2957]	36	# svfout in the activation string will be replaced now by svfin in case of
	37	# automatic restarts
	38	#
	39	# 2718 2018-01-02 08:49:38Z maronga
[2906]	40	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	41	# the possible output or input of sky view factors
	42	#
	43	# 2718 2018-01-02 08:49:38Z maronga
[2834]	44	# "fname" renamed to "jobname"
	45	#
	46	# 2718 2018-01-02 08:49:38Z maronga
[2799]	47	# parameters are allowed in output commands (OC:)
	48	#
	49	# 2718 2018-01-02 08:49:38Z maronga
[2789]	50	# bugfix: exit if no queue has been given neither with option -q nor in the
	51	# configuration file
	52	#
	53	# 2718 2018-01-02 08:49:38Z maronga
[2762]	54	# file connection file from trunk/SCRIPTS is taken by default
	55	#
	56	# 2718 2018-01-02 08:49:38Z maronga
[2716]	57	# Corrected "Former revisions" section
	58	#
	59	# 2696 2017-12-14 17:12:51Z kanani
	60	# Change in file header (GPL part)
	61	#
	62	# 2693 2017-12-13 12:33:49Z raasch
[2693]	63	# replacement of variables given by {{<variable>}} in configuration file is now
	64	# done in a more general way, variable names are written in small letters
	65	#
	66	# 2670 2017-12-06 16:32:19Z raasch
[2670]	67	# test printouts removed
	68	#
	69	# 2669 2017-12-06 16:03:27Z raasch
[2669]	70	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	71	# removed,
	72	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	73	# files,
	74	# informative messages in case of missing optional input files shortened
	75	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	76	#
	77	# 2638 2017-11-23 12:44:23Z raasch
[2610]	78	# use of wildcards in file connection statements enabled
	79	#
	80	# 2605 2017-11-09 15:31:46Z raasch
[2605]	81	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	82	# will not be sent with the job file any more, but copied into the
[2610]	83	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	84	#
	85	# 2600 2017-11-01 14:11:20Z raasch
[2600]	86	# cycle numbers are made three digits wide
	87	#
	88	# 2566 2017-10-20 08:50:47Z raasch
[2566]	89	# execute command for combine_plot_fields added
	90	# "TEMPDIR" renamed "tempdir"
	91	# temporary working directory for local batch jobs is created immediately within
	92	# the user's palmrun call, due to a requirement of the "grid engine" batch
	93	# system, where the working directory is given with batch directive -wd and must
	94	# already exist when the job is submitted,
	95	# informative messages in non-trace mode reduced and partly reformatted
	96	#
	97	# 2551 2017-10-18 07:25:11Z raasch
[2551]	98	# TEMPDIR added as replacement string to be used in batch directives
	99	#
	100	# 2512 2017-10-04 08:26:59Z raasch
[2507]	101	# bugfix for determining cycle numbers of NetCDF input files
	102	#
	103	# 2506 2017-09-29 08:30:37Z raasch
[2506]	104	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	105	# host configuration added to SOURCES_FOR_RUN_... folder name
	106	# host_identifier renamed host_configuration
	107	# option -W added to allow for job dependencies
	108	#
	109	# 2501 2017-09-26 11:41:55Z raasch
[2501]	110	# default value for number of cores (option -X) set to 1
	111	# bugfix for mechanism which overwrites configuration file settings with values
	112	# provided by palmrun options
	113	#
	114	# 2499 2017-09-22 16:47:58Z kanani
[2499]	115	# option -h named configuration identifier
	116	#
	117	# 2480 2017-09-19 06:24:14Z maronga
[2480]	118	# bugfix for last revision
	119	#
	120	# 2479 2017-09-19 06:12:16Z raasch
[2479]	121	# option -A (project account number) added
	122	#
	123	# 2422 2017-09-08 08:25:41Z raasch
[2410]	124	# initial revision
[2380]	125	#
	126	#--------------------------------------------------------------------------------#
	127	# palmrun - script for running PALM jobs on local and remote hosts
	128	#--------------------------------------------------------------------------------#
	129
	130
	131
	132	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	133
	134	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	135	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	136	# (TOO MANY ARGUMENTS - PROBLEM)
	137	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	138
[2610]	139	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	140	typeset -i nr_of_output_files=0
[2380]	141	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	142	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	143	# SCRIPT-OPTION ARGUMENTS
	144	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	145	typeset -i icycle inode ival maxcycle mpi_tasks
	146	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	147
	148	activation_string_list=""
	149	AddFilenames=""
	150	combine_plot_fields=true
	151	compiler_name=""
	152	compiler_name_ser=""
	153	compiler_options=""
[2501]	154	cores=1
[2380]	155	cores_atmos=0
	156	cores_ocean=0
	157	coupled_dist=""
	158	cpp_options=""
	159	cpumax=0
[2506]	160	create_batch_job=false
[2380]	161	create_jobfile_only=false
	162	create_remote_batch_job=false
	163	dashes=" ----------------------------------------------------------------------------"
	164	defaultqueue=""
[2506]	165	delete_temporary_catalog=true
[2380]	166	do_compile=true
	167	do_trace=false
	168	executable=""
	169	execute_command=""
	170	execution_error=false
[2762]	171	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2834]	172	jobname=test
[2380]	173	global_revision=""
[2506]	174	host_configuration="default"
[2380]	175	hostfile=""
	176	hp=""
	177	keep_data_from_previous_run=false
	178	link_local_input=false
	179	link_local_output=false
[2388]	180	linker_options=""
[2385]	181	local_jobcatalog=""
[2380]	182	locat=normal
	183	makefile=""
	184	max_par_io_str=""
	185	prc=$0
	186	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	187	do
	188	prc=`echo $prc \| cut -f2- -d"/"`
	189	done
	190	module_calls=""
[2506]	191	palmrun_memory=""
[2380]	192	palmrun_script_name=$prc
	193	openmp=false
[2506]	194	previous_job=""
[2479]	195	project_account=""
[2380]	196	queue=none
[2906]	197	read_svf=""
[2380]	198	restart_run=false
	199	return_address=""
[2385]	200	remote_jobcatalog=""
[2380]	201	remote_username=""
	202	running_in_batch_mode=false
	203	run_coupled_model=false
	204	run_id=""
	205	silent=false
	206	source_list=""
	207	source_path=""
[2501]	208	tasks_per_node=0
[2380]	209	threads_per_task=1
	210	transfer_problems=false
[2384]	211	user_source_path=""
[2506]	212	use_existing_sources_folder=""
[2380]	213	use_openmp=false
[2732]	214	version="palmrun 1.0 Rev$Rev: 2993 $"
[2380]	215	working_directory=`pwd`
	216	write_binary=""
[2906]	217	write_svf=""
[2380]	218	TOPT=""
	219
	220
	221	# ERROR HANDLING IN CASE OF EXIT
[2404]	222	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	223	then
	224
	225	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	226	(( i = 0 ))
	227	while (( i < iec ))
	228	do
	229	(( i = i + 1 ))
	230	printf "\n *** Execution of ERROR-command:\n"
	231	printf " >>> ${err_command[$i]}\n"
	232	eval ${err_command[$i]}
	233	done
[2566]	234	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	235	printf "\n\n+++ palmrun killed \n\n"
	236	elif [[ $locat != control_c ]]
	237	then
[2566]	238	printf "\n --> palmrun finished\n\n"
[2380]	239	fi' exit
	240
	241
	242	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	243	trap 'cd; rm -rf $tempdir
[2380]	244	printf "\n+++ palmrun killed by \"^C\" \n\n"
	245	locat=control_c
	246	exit
	247	' 2
	248
	249
	250	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	251	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	252	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]	253	do
	254	case $option in
	255	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	256	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	257	(b) create_batch_job=true; prc="$prc -b";;
	258	(B) delete_temporary_catalog=false; prc="$prc -B";;
	259	(C) restart_run=true; prc="$prc -C";;
[2834]	260	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
[2380]	261	(F) create_jobfile_only=true;;
	262	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	263	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	264	(j) running_in_batch_mode=true;;
	265	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	266	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	267	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	268	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	269	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	270	(r) run_id=$OPTARG;;
	271	(R) return_address=$OPTARG;;
	272	(s) source_list=$OPTARG;;
[2501]	273	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	274	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	275	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	276	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	277	(v) silent=true; prc="$prc -v";;
[2506]	278	(V) use_existing_sources_folder="-V";;
[2380]	279	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	280	(W) previous_job=$OPTARG;;
[2380]	281	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	282	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	283	(y) ocean_file_appendix=true; prc="$prc -y";;
	284	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	285	(Z) combine_plot_fields=false; prc="$prc -Z";;
	286	(\?) printf "\n +++ unknown option $OPTARG \n"
	287	printf "\n --> type \"$0 ?\" for available options \n"
	288	locat=parameter;exit;;
	289	esac
	290	done
	291
	292
	293	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	294	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	295	(( to_shift = $OPTIND - 1 ))
	296	shift $to_shift
	297
	298	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	299	if [[ "$1" = "?" ]]
	300	then
	301	(printf "\n *** Description of available palmrun options:\n"
	302	printf "\n Option Description Default-Value"
	303	printf "\n -a activation string list \"\" "
[2479]	304	printf "\n -A project account number ---"
[2380]	305	printf "\n -b batch-job on local machine ---"
	306	printf "\n -B do not delete temporary directory at end ---"
	307	printf "\n -d base name of files attached to program test"
	308	printf "\n -F create batch job file only ---"
[2506]	309	printf "\n -h host configuration \"default\" "
[2380]	310	printf "\n -k keep data from previous run"
	311	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	312	printf "\n -M Makefile name Makefile"
	313	printf "\n -O threads per openMP task ---"
	314	printf "\n -q queue \"$queue\" "
	315	printf "\n -s filenames of routines to be compiled \"\" "
	316	printf "\n must end with .f, .f90, .F, or .c !"
	317	printf "\n use \"..\" for more than one file and wildcards"
	318	printf "\n -s LM compiles all locally modified files"
	319	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	320	printf "\n -T tasks per node ---"
[2380]	321	printf "\n -u username on remote machine \"\" "
	322	printf "\n -v no prompt for confirmation ---"
[2506]	323	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	324	printf "\n -w maximum parallel io streams as given by -X"
[2506]	325	printf "\n -W name of job to wait for ---"
[2380]	326	printf "\n -x tracing of palmrun for debug purposes ---"
	327	printf "\n -X # of processors (on parallel machines) 1"
	328	printf "\n -y add appendix \"_O\" to all local output"
	329	printf "\n files (ocean precursor runs followed by"
	330	printf "\n coupled atmosphere-ocean runs) ---"
	331	printf "\n -Y run coupled model, \"#1 #2\" with"
	332	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	333	printf "\n -Z skip combine_plot_fields at the end of "
	334	printf "\n the simulation ---"
	335	printf "\n "
	336	printf "\n Possible values of positional parameter <modus>:"
	337	printf "\n \"?\" - this outline \n\n") \| more
	338	exit
	339	elif [[ "$1" != "" ]]
	340	then
	341	printf "\n +++ positional parameter $1 unknown \n"
	342	locat=parameter; exit
	343	fi
	344
	345
	346
	347	# SHORT STARTING MESSAGE
	348	printf "\n*** $version "
	349	printf "\n will be executed. Please wait ..."
	350
	351
[2834]	352	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
	353	export fname=$jobname
	354
	355
[2506]	356	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	357	config_file=.palm.config.$host_configuration
[2834]	358	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
[2380]	359
	360
	361	# CHECK, IF CONFIGURATION FILE EXISTS
	362	if [[ ! -f $config_file ]]
	363	then
	364	printf "\n\n +++ configuration file: "
	365	printf "\n $config_file"
	366	printf "\n does not exist"
	367	locat=connect; exit
	368	fi
	369
	370
[2762]	371	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	372	if [[ -f .palm.iofiles ]]
	373	then
	374	fileconnection_file=.palm.iofiles
	375	fi
	376
	377
[2380]	378	# CHECK, IF FILE CONNECTION FILE EXISTS
	379	if [[ ! -f $fileconnection_file ]]
	380	then
	381	printf "\n\n +++ file connection file: "
	382	printf "\n $fileconnection_file"
	383	printf "\n does not exist"
	384	locat=connect; exit
	385	fi
	386
	387
[2404]	388	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	389	if [[ "$activation_string_list" = "" ]]
	390	then
	391	printf "\n\n +++ no activation string list given: "
	392	printf "\n please set palmrun option \"-a\" "
	393	locat=palmrun_option; exit
	394	fi
	395
	396
	397	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	398	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	399	then
	400	write_binary=true
	401	else
	402	write_binary=false
	403	fi
	404
[2906]	405	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	406	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	407	then
	408	write_svf=true
	409	else
	410	write_svf=false
	411	fi
[2404]	412
[2906]	413	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	414	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	415	then
	416	read_svf=true
	417	else
	418	read_svf=false
	419	fi
	420
	421
[2380]	422	# READ AND EVALUATE THE CONFIGURATION-FILE
	423	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	424
	425	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	426	while read line
	427	do
	428
	429	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	430	eval line=\"$line\"
	431
	432
	433	# INTERPRET THE LINE
	434	if [[ "$(echo $line)" = "" ]]
	435	then
	436
	437	# EMPTY LINE, NO ACTION
	438	continue
	439
	440	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	441	then
	442
	443	# LINE IS A COMMENT LINE
	444	continue
	445
	446	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	447	then
	448
	449	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	450	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	451	value=`echo $line \| cut -d" " -s -f2-`
	452
	453
	454	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	455	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	456	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	457	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	458	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	459	# CONFIGURATION-FILE.
	460	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	461	then
	462	eval export $var="\$value"
	463
	464	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	465	if [[ $do_trace = true ]]
	466	then
	467	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	468	fi
	469	fi
	470
	471	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	472	then
	473
	474	# LINE DEFINES BATCH-DIRECTIVE
	475	(( ibd = ibd + 1 ))
	476	line=$(echo $line \| cut -c4-)
	477	batch_directive[$ibd]="$line"
	478
	479	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	480	then
	481
	482	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	483	# REMOTE TO A LOCAL HOST
	484	(( ibdt = ibdt + 1 ))
	485	line=$(echo $line \| cut -c5-)
	486	batch_directive_transfer[$ibdt]="$line"
	487
	488	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	489	then
	490
	491	# LINE DEFINES ERROR-COMMAND
	492	(( iec = iec + 1 ))
	493	line=$(echo $line \| cut -c4-)
	494	err_command[$iec]="$line"
	495
	496	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	497	then
	498
	499	# LINE DEFINES INPUT-COMMAND
	500	(( iic = iic + 1 ))
	501	line=$(echo $line \| cut -c4-)
	502	in_command[$iic]="$line"
	503
	504	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	505	then
	506
	507	# LINE DEFINES OUTPUT-COMMAND
	508	(( ioc = ioc + 1 ))
	509	line=$(echo $line \| cut -c4-)
	510	out_command[$ioc]="$line"
	511
	512	else
	513
	514	# SKIP ALL OTHER LINES
	515	continue
	516
	517	fi
	518
	519	done < $config_file
	520
	521
	522	# CHECK SETTING OF REQUIRED PARAMETERS
	523	if [[ "$compiler_name" = "" ]]
	524	then
	525	printf "\n +++ no compiler name found in $config_file"
	526	printf "\n Please add line \"compiler_name ...\" to that file."
	527	locat=config_file; exit
	528	fi
	529	if [[ "$compiler_name_ser" = "" ]]
	530	then
	531	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	532	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	533	locat=config_file; exit
	534	fi
	535	if [[ "$compiler_options" = "" ]]
	536	then
	537	printf "\n +++ no compiler options found in $config_file"
	538	printf "\n Please add line \"compiler_options ...\" to that file."
	539	locat=config_file; exit
	540	fi
[2388]	541	if [[ "$linker_options" = "" ]]
[2380]	542	then
[2388]	543	printf "\n +++ no linker options found in $config_file"
	544	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	545	locat=config_file; exit
	546	fi
	547	if [[ "$execute_command" = "" ]]
	548	then
	549	printf "\n +++ no execute command found in $config_file"
	550	printf "\n Please add line \"execute_command ...\" to that file."
	551	locat=config_file; exit
	552	fi
	553
	554	if [[ "$hostfile" != "" ]]
	555	then
	556	if [[ $hostfile != auto && ! -f $hostfile ]]
	557	then
	558	printf "\n +++ no hostfile \"$hostfile\" found"
	559	printf "\n Please check line \"hostfile ...\" in $config_file"
	560	locat=config_file; exit
	561	fi
	562	fi
	563
	564
	565	# DETERMINE THE CALL STATUS
	566	if [[ "$return_address" != "" ]]
	567	then
	568
	569	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	570	# BATCH MODE AND ...
	571	running_on_remote=true
	572
	573	else
	574
	575	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	576	if [[ "$remote_ip" != "" ]]
	577	then
	578
	579	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	580	create_remote_batch_job=true
	581
	582	fi
	583	running_on_remote=false
	584	fi
	585
	586
	587
	588	# READ AND EVALUATE THE I/O-FILE LIST
	589	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	590
	591	# READ THE FILE CONNECTION FILE LINE BY LINE
	592	while read line
	593	do
	594
[2669]	595	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	596	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	597
	598	# INTERPRET THE LINE
	599	if [[ "$(echo $line)" = "" ]]
	600	then
	601	# EMPTY LINE, NO ACTION
	602	continue
	603
	604	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	605	then
	606
	607	# LINE IS A COMMENT LINE
	608	true
	609
	610	else
	611
	612	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	613	# s2a: in/out - field
[2669]	614	# s2b: action - field (optional)
	615	s1=`echo "$line" \| cut -d" " -f1`
	616	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	617	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	618	then
[2669]	619	s2a=$s2
[2380]	620	s2b=""
	621	else
[2669]	622	s2a=`echo $s2 \| cut -d":" -f1`
	623	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	624	fi
[2669]	625	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	626	s4=`echo "$line" \| cut -d" " -s -f4`
	627	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	628	s5=`echo "$line" \| cut -d" " -s -f5`
	629	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	630
	631
	632	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	633	# INPUT- OR OUTPUT-LIST.
	634	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	635	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	636	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	637	# IS NOT CHECKED AND STORED.
[2610]	638	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	639	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	640	then
	641	found=false
	642	for actual in $activation_string_list
	643	do
	644	for formal in $s3
	645	do
	646	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	647	done
	648	done
	649	if [[ $found = true ]]
	650	then
	651	(( iin = iin + 1 ))
[2669]	652	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	653	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	654	if [[ "$s2a" = inopt ]]
	655	then
	656	optin_pre[$iin]=yes
	657	else
	658	optin_pre[$iin]=no
	659	fi
[2605]	660
	661	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	662	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	663	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	664	then
[2610]	665	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	666	fi
	667
[2610]	668	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	669	# THE WILDCARD FROM THE ENDING
	670	if [[ "${s5: -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$line"
	677	locat=iofiles_file; exit
	678	fi
	679	multin[$iin]=true
	680	string=${endin_pre[$iin]}
	681	endin_pre[$iin]="${string%?}"
	682	else
	683	multin[$iin]=false
	684	fi
[2380]	685	fi
[2669]	686	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	687	then
	688	found=false
	689	for actual in $activation_string_list
	690	do
	691	for formal in $s3
	692	do
[2670]	693	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	694	done
	695	done
	696	if [[ $found = true ]]
	697	then
	698	(( iout = iout + 1 ))
[2669]	699	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	700	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	701
[2669]	702	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	703	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	704	if [[ $formal = wildcard ]]
	705	then
	706	warnout_pre[$iout]=false
	707	else
	708	warnout_pre[$iout]=true
	709	fi
	710
[2610]	711	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	712	# THE WILDCARD FROM THE LOCAL FILENAME
	713	if [[ "${s1: -1}" = "*" ]]
	714	then
[2669]	715	if [[ "$s2b" = "di" ]]
[2610]	716	then
	717	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	718	printf "\n see file \"$fileconnection_file\", line"
	719	printf "\n$line"
	720	locat=iofiles_file; exit
	721	fi
	722	multout[$iout]=true
	723	string=${localout_pre[$iout]}
	724	localout_pre[$iout]="${string%?}"
	725	else
	726	multout[$iout]=false
	727	fi
[2380]	728	fi
[2669]	729	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	730	then
[2669]	731	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	732	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	733	locat=connect; exit
	734	fi
	735	IFS="$IFSALT"
	736	fi
	737
	738	done < $fileconnection_file
	739
	740
	741
[2501]	742	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	743	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	744	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	745	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	746	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	747	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	748
	749
	750
[2380]	751	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	752	if [[ $run_coupled_model = true ]]
	753	then
	754
	755	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	756	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	757
	758	if (( $cores_ocean + $cores_atmos != $cores ))
	759	then
	760
	761	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	762	printf "\n PEs (total) : $cores"
	763	printf "\n PEs (atmosphere): $cores_atmos"
	764	printf "\n PEs (ocean) : $cores_ocean"
	765	locat=coupling; exit
	766
	767	fi
	768
	769	fi
	770
	771
	772	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	773	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	774	# FOLDER
	775	if [[ $running_in_batch_mode = true ]]
	776	then
	777
[2506]	778	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	779	then
[2506]	780	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	781	printf "\n Please check the output of the palmrun-call"
	782	printf "\n that you did on your local host."
	783	locat=SOURCES_FOR_RUN; exit
	784	fi
	785
	786	else
	787
	788	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	789	# AUTOMATIC RESTART RUN
	790	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	791	if [[ $restart_run = false ]]
	792	then
	793
	794	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	795	# THE LOCAL HOST
	796	if [[ ! -d $source_path ]]
	797	then
	798	printf "\n\n +++ source path \"$source_path\" on local host"
	799	printf "\n \"$(hostname)\" does not exist"
	800	locat=source_path; exit
	801	fi
	802
[2990]	803	rm -rf ${base_directory}/${sources_for_run_catalog}
	804	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	805
	806	if [[ "$source_list" = LM ]]
	807	then
	808
	809	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	810	source_list=""
	811	cd $source_path
	812
	813
[2512]	814	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	815	if [[ ! -d ../.svn ]]
[2380]	816	then
	817	printf "\n\n +++ source directory"
	818	printf "\n \"$source_path\" "
	819	printf "\n is not under control of \"subversion\"."
[2512]	820	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	821	fi
	822
	823
	824	# LIST ALL MODIFIED SOURCE CODE FILES
	825	Filenames=""
[2404]	826	svn status > tmp_svnstatus
[2380]	827	while read line
	828	do
	829	firstc=`echo $line \| cut -c1`
	830	if [[ $firstc = M \|\| $firstc = "?" ]]
	831	then
	832	Name=`echo "$line" \| cut -c8-`
	833	extension=`echo $Name \| cut -d. -f2`
	834	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	835	then
	836	Filenames="$Filenames "$Name
	837	fi
	838	fi
[2404]	839	done < tmp_svnstatus
	840	rm -rf tmp_svnstatus
[2380]	841
	842
	843	# COPY FILES TO SOURCES_FOR_RUN_...
	844	for filename in $Filenames
	845	do
[2990]	846	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	847	source_list=$source_list"$filename "
	848	done
	849
	850	cd - > /dev/null
	851
	852
	853	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	854	elif [[ "$source_list" != "" ]]
	855	then
	856
	857	cd $source_path
	858
	859	for filename in $source_list
	860	do
	861
	862	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	863	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	864	then
	865	printf "\n +++ source code file: $filename"
	866	printf "\n must not contain (\"/\") "
	867	locat=source; exit
	868	fi
	869
	870	if [[ ! -f $filename ]]
	871	then
	872	printf "\n +++ source code file: $filename"
	873	printf "\n does not exist"
	874	locat=source; exit
	875	else
[2990]	876	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	877	fi
	878
	879	done
	880
	881	cd - > /dev/null
	882
	883	fi
	884
	885	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	886	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	887	if [[ ! -f $makefile ]]
	888	then
	889	printf "\n +++ file \"$makefile\" does not exist"
	890	locat=make; exit
	891	else
[2990]	892	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	893	fi
	894
	895
	896	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	897	if [[ "$user_source_path" != "" ]]
[2380]	898	then
	899
	900	# DOES THE DIRECTORY EXIST?
[2384]	901	if [[ ! -d $user_source_path ]]
[2380]	902	then
	903
	904	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	905	printf "\n \"$user_source_path\" "
[2380]	906	printf "\n does not exist or is not a directory."
	907	printf "\n No source code will be used from this directory!\n"
[2384]	908	user_source_path=""
[2380]	909	if [[ $silent == false ]]
	910	then
	911	sleep 2
	912	fi
	913
	914	else
	915
[2384]	916	cd $user_source_path
[2380]	917	found=false
	918
	919	Names=$(ls -1 *.f90 2>&1)
	920	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	921	Names=$(ls -1 *.F90 2>&1)
	922	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	923	Names=$(ls -1 *.F 2>&1)
	924	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	925	Names=$(ls -1 *.f 2>&1)
	926	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	927	Names=$(ls -1 *.c 2>&1)
	928	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	929
	930	cd - > /dev/null
[2990]	931	cd ${base_directory}/${sources_for_run_catalog}
[2380]	932
	933	# COPY MAKEFILE IF EXISTING
[2384]	934	if [[ -f $user_source_path/Makefile ]]
[2380]	935	then
	936	printf "\n\n *** user Makefile from directory"
[2384]	937	printf "\n \"$user_source_path\" is used \n"
[2380]	938	if [[ $silent == false ]]
	939	then
	940	sleep 1
	941	fi
[2384]	942	cp $user_source_path/Makefile .
[2380]	943	fi
	944
	945	for filename in $AddFilenames
	946	do
	947	if [[ -f $filename ]]
	948	then
	949	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	950	printf "\n source code directory \"$user_source_path\" "
[2380]	951	printf "\n but was also given with option \"-s\" which means that it should be taken"
	952	printf "\n from directory \"$source_path\"."
	953	locat=source; exit
	954	fi
	955
[2384]	956	cp $user_source_path/$filename .
[2380]	957	source_list="$source_list $filename"
	958
	959	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	960	if [[ $(grep -c $filename Makefile) = 0 ]]
	961	then
	962	printf "\n\n +++ user file \"$filename\" "
	963	printf "\n is not listed in Makefile \n"
	964	locat=source; exit
	965	else
	966
	967	if [[ $found = false ]]
	968	then
	969	found=true
	970	printf "\n\n *** following user file(s) added to the"
	971	printf " files to be translated:\n "
	972	fi
	973	printf "$filename "
	974	if [[ $silent == false ]]
	975	then
	976	sleep 0.5
	977	fi
	978
	979	fi
	980	done
	981	[[ $found = true ]] && printf "\n"
	982	cd - > /dev/null
	983	fi
	984	fi
	985
	986	# COPY CONFIGURATION FILES
[2990]	987	cp $config_file ${base_directory}/${sources_for_run_catalog}
	988	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	989
	990	# COPY SHELLSCRIPTS
[2990]	991	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	992	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	993
	994	fi
	995
	996	fi
	997
[2605]	998
[2380]	999	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1000	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1001	if [[ "$global_revision" = "" ]]
	1002	then
	1003	global_revision=`svnversion $source_path 2>/dev/null`
	1004	global_revision="Rev: $global_revision"
	1005	fi
	1006
	1007
	1008	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1009	if [[ -n $cores ]]
	1010	then
	1011
	1012	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1013	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1014	if [[ $tasks_per_node = 0 ]]
[2380]	1015	then
	1016	printf "\n"
	1017	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1018	printf "\n set -T option or define tasks_per_node in the config file"
	1019	locat=tasks_per_node; (( iec = 0 )); exit
	1020	fi
	1021
	1022	if (( cores < tasks_per_node ))
	1023	then
	1024	printf "\n"
	1025	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1026	printf "\n given values: -T $tasks_per_node -X $cores"
	1027	locat=tasks_per_node; (( iec = 0 )); exit
	1028	fi
	1029
	1030	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1031	(( mpi_tasks = cores / threads_per_task ))
	1032	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1033	(( ii = cores / tasks_per_node ))
	1034	(( remaining_cores = cores - ii * tasks_per_node ))
	1035	if (( remaining_cores > 0 ))
	1036	then
	1037	printf "\n"
	1038	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1039	printf "\n divisor of the total number of cores (option \"-X\")"
	1040	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1041	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1042	(( nodes = nodes + 1 ))
	1043	fi
	1044
	1045	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	1046	if [[ "$tasks_per_node" != "" ]]
	1047	then
	1048	TOPT="-T $tasks_per_node"
	1049	fi
	1050
	1051	fi
	1052
	1053
	1054	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1055	if [[ "$maximum_parallel_io_streams" = "" ]]
	1056	then
	1057	maximum_parallel_io_streams=$cores
	1058	fi
	1059
	1060
	1061	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1062	if [[ "$scp_port" != "" ]]
	1063	then
	1064	PORTOPT="-P $scp_port"
	1065	SSH_PORTOPT="-p $scp_port"
	1066	fi
	1067
	1068
	1069	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1070	# CONFIG-FILE
	1071	if [[ "$ssh_key" != "" ]]
	1072	then
	1073	ssh_key="-i $HOME/.ssh/$ssh_key"
	1074	fi
	1075
	1076
	1077	# SET QUEUE, IF NOT GIVEN
	1078	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1079	then
	1080
	1081	if [[ $queue = none && "$defaultqueue" = "" ]]
	1082	then
	1083	printf "\n"
	1084	printf "\n +++ no default queue given in configuration file and no queue"
	1085	printf "\n given with option -q"
[2789]	1086	locat=queue; exit
[2380]	1087	fi
	1088	if [[ $queue = none ]]
	1089	then
	1090	queue=$defaultqueue
	1091	fi
	1092
	1093	fi
	1094
	1095
	1096	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1097	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1098	(( i = 0 ))
[2610]	1099	(( nr_of_input_files = 0 ))
[2380]	1100	while (( i < iin ))
	1101	do
	1102	(( i = i + 1 ))
	1103
	1104	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1105	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1106	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1107	then
[2610]	1108	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1109	else
[2834]	1110	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
[2380]	1111	fi
	1112
[2610]	1113
[2380]	1114	# CHECK IF FILE EXISTS
	1115	if ! ls $filename* 1>/dev/null 2>&1
	1116	then
	1117
[2669]	1118	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1119	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1120	then
	1121	printf "\n\n +++ INPUT-file: "
[2610]	1122	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1123	then
	1124	printf "\n $filename"
	1125	else
[2610]	1126	printf "\n $filename.${extin_pre[$i]}"
[2380]	1127	fi
	1128	printf "\n does not exist\n"
	1129	locat=input; exit
	1130	else
[2610]	1131	(( nr_of_input_files = nr_of_input_files + 1 ))
	1132	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1133	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1134	actionin[$nr_of_input_files]="unavailable"
[2610]	1135	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1136	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1137	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1138	fi
[2605]	1139
[2380]	1140	else
	1141
[2834]	1142	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
[2610]	1143	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
	1144	if [[ "${multin[$i]}" = true ]]
	1145	then
	1146	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1147	ls -1 -d ${filename} > filelist 2>/dev/null
	1148	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1149	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1150
[2610]	1151	endings=""
	1152	while read line
	1153	do
	1154	# filename without path (i.e. after the last "/")
	1155	basefilename=$(basename ${line})
[2380]	1156
[2610]	1157	# check if there is an extension and remove it
	1158	ext=${basefilename##*.}
	1159	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1160	then
	1161	basefilename=${basefilename%.*}
	1162	fi
[2380]	1163
[2610]	1164	# check for an existing cycle number and remove it
	1165	cycle=${basefilename##*.}
	1166	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1167	then
	1168	basefilename=${basefilename%.*}
	1169	fi
[2600]	1170
[2834]	1171	# remove the jobname from the beginning
	1172	length_jobname=${#jobname}
	1173	ending=${basefilename:${length_jobname}}
[2610]	1174
	1175	# remove the ending given in the .iofiles from the beginning
	1176	endingstring="${endin_pre[$i]}"
	1177	length_ending=${#endingstring}
	1178	ending=${ending:${length_ending}}
	1179
	1180	if [[ "$ending" = "" ]]
[2600]	1181	then
[2610]	1182	# standard ending as given in the .iofiles
	1183	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1184	then
	1185	endings="$endings DEFAULT"
	1186	fi
[2600]	1187	else
[2610]	1188	# ending must start with "_", otherwise its a different file
	1189	if [[ "${ending:0:1}" = "_" ]]
	1190	then
	1191	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1192	then
	1193	endings="$endings $ending"
	1194	fi
	1195	fi
[2600]	1196	fi
[2610]	1197
	1198	done <filelist
[2380]	1199
[2610]	1200	rm filelist
[2380]	1201
[2600]	1202	else
[2610]	1203
	1204	# SINGLE NAME
	1205	endings=DEFAULT
	1206
[2600]	1207	fi
	1208
[2610]	1209	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1210	for ending in $endings
	1211	do
	1212
	1213	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1214	if [[ $ending = DEFAULT ]]
[2380]	1215	then
[2610]	1216	ending=""
	1217	fi
	1218
	1219	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1220	(( nr_of_input_files = nr_of_input_files + 1 ))
	1221	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1222	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1223	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1224	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1225	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1226	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1227
	1228
	1229	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1230	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1231	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1232	then
	1233	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1234	else
[2834]	1235	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
[2380]	1236	fi
[2610]	1237
	1238	# DETERMINE THE FILE'S CYCLE NUMBER
	1239	(( maxcycle = 0 ))
	1240	ls -1 -d $filename > filelist 2>/dev/null
	1241	ls -1 -d $filename.* >> filelist 2>/dev/null
	1242	while read line
	1243	do
	1244	# filename without path (i.e. after the last "/")
	1245	basefilename=$(basename ${line})
	1246
	1247	# check if there is an extension
	1248	extension=${basefilename##*.}
	1249	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1250	then
	1251	basefilename=${basefilename%.*}
	1252	fi
	1253
	1254	# check for an existing cycle number
	1255	cycle=${basefilename##*.}
	1256	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1257	then
[2669]	1258	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1259	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1260	(( icycle = $((10#$cycle)) ))
[2610]	1261	else
	1262	(( icycle = 0 ))
	1263	fi
	1264
	1265	if (( icycle > maxcycle ))
	1266	then
	1267	(( maxcycle = icycle ))
	1268
	1269	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1270	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1271	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1272	then
	1273	leading_zero=true
	1274	else
	1275	leading_zero=false
	1276	fi
	1277	fi
	1278
	1279	done <filelist
	1280	rm filelist
	1281
	1282	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1283	if [[ $leading_zero = true ]]
[2380]	1284	then
[2610]	1285	cyclestring=`printf "%03d" $maxcycle`
	1286	else
	1287	cyclestring=$maxcycle
[2380]	1288	fi
[2610]	1289
	1290	# APPEND CYCLE NUMBER TO FILENAME
	1291	if (( maxcycle > 0 ))
[2380]	1292	then
[2610]	1293	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1294	then
	1295	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1296	else
	1297	filename=${filename}.$cyclestring
	1298	fi
[2380]	1299	else
[2610]	1300	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1301	then
	1302	filename=${filename}.${extin[$nr_of_input_files]}
	1303	fi
[2380]	1304	fi
[2610]	1305
	1306	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1307	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1308	absnamein[$nr_of_input_files]=$filename
	1309	if (( maxcycle > 0 ))
[2380]	1310	then
[2610]	1311	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1312	then
	1313	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1314	else
[2834]	1315	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1316	fi
[2380]	1317	else
[2610]	1318	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1319	then
	1320	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1321	else
[2834]	1322	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
[2610]	1323	fi
[2380]	1324	fi
	1325
[2610]	1326	done
	1327
[2380]	1328	fi
[2610]	1329
[2380]	1330	done
	1331
[2610]	1332
[2380]	1333	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1334	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1335	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1336	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1337	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1338	# REMOTE HOST)
	1339	(( i = 0 ))
	1340	while (( i < iout ))
	1341	do
	1342	(( i = i + 1 ))
[2610]	1343	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1344	then
[2610]	1345	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1346	then
[2610]	1347	actionout_pre[$i]=""
	1348	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1349	then
[2610]	1350	actionout_pre[$i]=pe
	1351	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1352	then
[2610]	1353	actionout_pre[$i]=a
[2380]	1354	fi
	1355	(( maxcycle = 0 ))
[2834]	1356	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
[2610]	1357	eval catalogname=${pathout_pre[$i]}
[2380]	1358	if ! ls $filename* 1>/dev/null 2>&1
	1359	then
	1360
	1361	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1362	if cat /dev/null > $filename
	1363	then
	1364	rm $filename
	1365	else
	1366
	1367	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1368	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1369	if [[ ! -d $catalogname ]]
	1370	then
	1371	if mkdir -p $catalogname
	1372	then
	1373	printf "\n\n *** directory:"
	1374	printf "\n $catalogname"
	1375	printf "\n was created\n"
	1376	else
	1377	printf "\n\n +++ OUTPUT-file:"
	1378	printf "\n $filename"
	1379	printf "\n cannot be created, because directory does not exist"
	1380	printf "\n and cannot be created either"
	1381	printf "\n"
	1382	locat=output ; exit
	1383	fi 2>/dev/null
	1384	else
	1385	printf "\n\n +++ OUTPUT-file:"
	1386	printf "\n $filename"
	1387	printf "\n cannot be created, although directory exists"
	1388	printf "\n"
	1389	locat=output ; exit
	1390	fi
	1391	fi 2>/dev/null
	1392
	1393	fi
	1394
	1395	fi
	1396	done
	1397
	1398
	1399	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1400	if [[ $running_in_batch_mode = false ]]
	1401	then
	1402	run_id=$RANDOM
[2834]	1403	job_id=${jobname}.$run_id
[2380]	1404
[2566]	1405	tempdir=$fast_io_catalog/$job_id
[2380]	1406	fi
	1407
	1408
	1409	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1410	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1411	then
	1412
	1413	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1414	if [[ $ibd = 0 ]]
	1415	then
	1416	printf "\n"
	1417	printf "\n +++ no batch directives found in configuration file"
	1418	locat=config_file_batch_directives; (( iec = 0 )); exit
	1419	fi
	1420
	1421	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1422	done=false
[2384]	1423	cputime=$cpumax
[2380]	1424	while [[ $done = false ]]
	1425	do
[2384]	1426	if (( cputime == 0 ))
[2380]	1427	then
	1428	printf "\n +++ cpu-time is undefined"
	1429	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1430	printf "\n >>> "
[2384]	1431	read cputime 1>/dev/null 2>&1
[2380]	1432	else
	1433	done=true
	1434	fi
	1435	done
[2420]	1436	cpumax=$cputime
[2380]	1437
	1438	# CHECK THE MEMORY DEMAND
	1439	done=false
	1440	while [[ $done = false ]]
	1441	do
	1442	if (( memory == 0 ))
	1443	then
	1444	printf "\n +++ memory demand is undefined"
	1445	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1446	printf "\n >>> "
	1447	read memory 1>/dev/null 2>&1
	1448	else
	1449	done=true
	1450	fi
	1451	done
	1452
	1453	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1454	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1455	then
	1456	while [[ -z $remote_username ]]
	1457	do
[2420]	1458	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1459	printf "\n >>> Please type username:"
	1460	printf "\n >>> "
	1461	read remote_username
	1462	done
	1463	fi
	1464
	1465	else
	1466
[2420]	1467	if [[ $running_in_batch_mode = false ]]
	1468	then
	1469	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1470	cpumax=$cputime
	1471	else
	1472	cputime=$cpumax
	1473	fi
[2380]	1474
	1475	fi
	1476
	1477
	1478	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1479	(( cpu_hours = cputime / 3600 ))
	1480	(( resttime = cputime - cpu_hours * 3600 ))
	1481	(( cpu_minutes = resttime / 60 ))
	1482	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1483	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1484
	1485
	1486	# OUTPUT OF THE PALMRUN-HEADER
	1487	calltime=$(date)
	1488	printf "\n"
	1489	printf "#------------------------------------------------------------------------# \n"
	1490	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1491	printf "\| \| \n"
	1492	column1="called on:"; column2=$(hostname)
	1493	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1494	if [[ $create_remote_batch_job = true ]]
	1495	then
[2506]	1496	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1497	else
	1498	if [[ $running_on_remote = true ]]
	1499	then
[2506]	1500	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1501	else
[2506]	1502	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1503	fi
	1504	fi
	1505	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1506
	1507	column1="running in:"
	1508	if [[ $running_in_batch_mode = true ]]
	1509	then
	1510	column2="batch job mode"
	1511	else
	1512	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1513	then
	1514	column2="job creation mode"
	1515	else
	1516	column2="interactive run mode"
	1517	fi
	1518	fi
	1519	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1520
[2479]	1521	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1522	then
[2480]	1523	if [[ "$project_account" != "" ]]
[2479]	1524	then
	1525	column1="project account number:"
	1526	column2="$project_account"
	1527	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1528	fi
	1529	fi
	1530
[2380]	1531	if [[ -n $cores ]]
	1532	then
	1533	if [[ $run_coupled_model = false ]]
	1534	then
	1535	column1="number of cores:"; column2=$cores
	1536	else
	1537	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1538	fi
	1539	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1540	fi
	1541	if [[ -n $tasks_per_node ]]
	1542	then
	1543	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1544	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1545	if (( remaining_cores > 0 ))
	1546	then
	1547	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1548	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1549	fi
	1550	fi
	1551	if [[ $maximum_parallel_io_streams != $cores ]]
	1552	then
	1553	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1554	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1555	fi
	1556	if [[ $use_openmp = true ]]
	1557	then
	1558	column1="threads per task:"; column2="$threads_per_task"
	1559	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1560	fi
[2384]	1561	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1562	then
[2506]	1563	column1="memory demand / PE":; column2="$memory MB"
	1564	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1565	column1="job cpu time (h:m:s):"; column2="$timestring"
	1566	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1567	fi
[2380]	1568	printf "\| \| \n"
	1569	if [[ "$source_list" != "" ]]
	1570	then
	1571	if [[ "$make_options" != "" ]]
	1572	then
	1573	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1574	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1575	line=$(echo "$make_options" \| cut -c46-)
	1576	while [[ "$line" != "" ]]
	1577	do
	1578	column1=""
	1579	column2=$(echo "$line" \| cut -c-45)
	1580	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1581	line=$(echo "$line" \| cut -c46-)
	1582	done
	1583	fi
	1584	fi
	1585
	1586	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1587	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1588	line=$(echo "$cpp_options" \| cut -c46-)
	1589	while [[ "$line" != "" ]]
	1590	do
	1591	column1=""
	1592	column2=$(echo "$line" \| cut -c-45)
	1593	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1594	line=$(echo "$line" \| cut -c46-)
	1595	done
	1596
	1597	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1598	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1599	line=$(echo "$compiler_options" \| cut -c46-)
	1600	while [[ "$line" != "" ]]
	1601	do
	1602	column1=""
	1603	column2=$(echo "$line" \| cut -c-45)
	1604	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1605	line=$(echo "$line" \| cut -c46-)
	1606	done
	1607
[2388]	1608	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1609	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1610	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1611	while [[ "$line" != "" ]]
	1612	do
	1613	column1=""
	1614	column2=$(echo "$line" \| cut -c-45)
	1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1616	line=$(echo "$line" \| cut -c46-)
	1617	done
	1618
	1619	if [[ "$login_init_cmd" != "" ]]
	1620	then
	1621	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1622	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1623	line=$(echo "$login_init_cmd" \| cut -c46-)
	1624	while [[ "$line" != "" ]]
	1625	do
	1626	column1=""
	1627	column2=$(echo "$line" \| cut -c-45)
	1628	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1629	line=$(echo "$line" \| cut -c46-)
	1630	done
	1631	fi
	1632
	1633	if [[ "$module_commands" != "" ]]
	1634	then
	1635	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1636	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1637	line=$(echo "$module_commands" \| cut -c46-)
	1638	while [[ "$line" != "" ]]
	1639	do
	1640	column1=""
	1641	column2=$(echo "$line" \| cut -c-45)
	1642	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1643	line=$(echo "$line" \| cut -c46-)
	1644	done
	1645	fi
	1646	printf "\| \| \n"
[2834]	1647	column1="base name of files:"; column2=$jobname
[2380]	1648	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1649	column1="activation string list:"; column2=$(echo $activation_string_list)
	1650	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1651
	1652	if [[ "$ocean_file_appendix" = true ]]
	1653	then
	1654	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1655	fi
	1656
	1657	if [[ "$source_list" != "" ]]
	1658	then
	1659	printf "\| \| \n"
	1660	printf "\| Files to be compiled: \| \n"
	1661	line=$source_list
	1662	while [[ "$line" != "" ]]
	1663	do
	1664	linestart=$(echo $line \| cut -c-70)
	1665	printf "\| %-70s \| \n" "$linestart"
	1666	line=$(echo "$line" \| cut -c71-)
	1667	done
	1668	fi
	1669	printf "#------------------------------------------------------------------------#"
	1670
	1671
	1672
	1673	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1674	if [[ $do_trace = true ]]
	1675	then
	1676	(( i = 0 ))
[2610]	1677	while (( i < nr_of_input_files ))
[2380]	1678	do
	1679	(( i = i + 1 ))
	1680	if (( i == 1 ))
	1681	then
	1682	printf "\n\n >>> INPUT-file assignments:\n"
	1683	fi
	1684	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1685	done
	1686	(( i = 0 ))
	1687	while (( i < iout ))
	1688	do
	1689	(( i = i + 1 ))
	1690	if (( i == 1 ))
	1691	then
	1692	printf "\n\n >>> OUTPUT-file assignments:\n"
	1693	fi
	1694	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1695	done
	1696	(( i = 0 ))
	1697	while (( i < iic ))
	1698	do
	1699	(( i = i + 1 ))
	1700	if (( i == 1 ))
	1701	then
	1702	printf "\n\n >>> INPUT-commands:\n"
	1703	fi
	1704	printf "\n ${in_command[$i]}"
	1705	done
	1706	(( i = 0 ))
	1707	while (( i < ioc ))
	1708	do
	1709	(( i = i + 1 ))
	1710	if (( i == 1 ))
	1711	then
	1712	printf "\n\n >>> OUTPUT-commands:\n"
	1713	fi
	1714	printf "\n ${out_command[$i]}"
	1715	done
	1716	fi
	1717
	1718	# QUERY FOR CONTINUE
	1719	if [[ $silent = false && $running_in_batch_mode = false ]]
	1720	then
	1721	antwort=dummy
	1722	printf "\n\n"
	1723	printf " >>> everything o.k. (y/n) ? "
	1724	while read antwort
	1725	do
	1726	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1727	then
	1728	printf " >>> everything o.k. (y/n) ? "
	1729	else
	1730	break
	1731	fi
	1732	done
	1733	if [[ $antwort = n \|\| $antwort = N ]]
	1734	then
	1735	locat=user_abort; (( iec = 0 )); exit
	1736	fi
	1737	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1738	then
[2566]	1739	printf "\n *** batch-job will be created and submitted"
[2380]	1740	else
[2566]	1741	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1742	fi
	1743	fi
	1744
	1745
	1746
	1747	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1748	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1749	then
	1750
	1751	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1752	then
[2566]	1753	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1754	else
[2566]	1755	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1756	fi
	1757
[2422]	1758	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1759	# IT SHALL BE CREATED
	1760	ask_for_make_depository=false
	1761	if [[ $create_remote_batch_job = true ]]
	1762	then
	1763
	1764	line=`grep %base_directory $config_file`
[2506]	1765	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1766	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]	1767
[2506]	1768	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1769	then
	1770	printf "\n\n +++ make depository \"${make_depository}\""
	1771	printf "\n on remote host not found!"
	1772	ask_for_make_depository=true
	1773	fi
[2506]	1774	rm ${host_configuration}_last_make_protokoll
[2422]	1775
	1776	else
	1777
	1778	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1779	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1780	if [[ ! -d ${make_depository} ]]
	1781	then
	1782	printf "\n\n +++ make depository \"${make_depository}\""
	1783	printf "\n on local host not found!"
	1784	ask_for_make_depository=true
	1785	fi
	1786
	1787	fi
	1788
	1789	if [[ $ask_for_make_depository = true ]]
	1790	then
	1791
	1792	antwort=dummy
	1793	printf "\n\n"
	1794	printf " >>> Create a new one (y/n) ? "
	1795	while read antwort
	1796	do
	1797	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1798	then
	1799	printf " >>> Create a new one (y/n) ? "
	1800	else
	1801	break
	1802	fi
	1803	done
	1804	if [[ $antwort = n \|\| $antwort = N ]]
	1805	then
	1806	locat=user_abort; (( iec = 0 )); exit
	1807	fi
	1808
[2566]	1809	if [[ $do_trace = true ]]
	1810	then
	1811	palmbuild -h $host_configuration
	1812	else
	1813	palmbuild -v -h $host_configuration
	1814	fi
[2422]	1815
	1816	if [[ $? != 0 ]]
	1817	then
	1818
	1819	# ABORT IN CASE OF COMPILATION PROBLEMS
	1820	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1821	locat=make_depository
	1822	exit
	1823	else
	1824	echo " *** now continue with creating executable and other sources"
	1825	fi
	1826
	1827	fi
	1828
[2566]	1829	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2993]	1830	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
[2380]	1831
	1832	if [[ $? != 0 ]]
	1833	then
	1834
	1835	# ABORT IN CASE OF COMPILATION PROBLEMS
	1836	printf "\n +++ error while creating executable and/or other sources"
	1837	locat=execution
[2990]	1838	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1839	exit
	1840
	1841	else
	1842
[2566]	1843	printf " *** executable and other sources created\n"
[2990]	1844	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1845
	1846	fi
	1847
	1848	fi
	1849
	1850
[2669]	1851	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1852	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1853	if [[ $create_remote_batch_job = true ]]
	1854	then
	1855	(( i = 0 ))
[2610]	1856	while (( i < nr_of_input_files ))
[2605]	1857	do
	1858	(( i = i + 1 ))
[2669]	1859	if [[ "${actionin[$i]}" = tr ]]
[2605]	1860	then
	1861	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1862	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1863	fi
	1864	done
	1865	if (( i > 0 ))
	1866	then
	1867	printf " *** input files have been copied to the remote host\n"
	1868	fi
	1869	fi
	1870
	1871
[2380]	1872	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1873	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1874	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1875	then
	1876
	1877	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1878	if [[ $running_in_batch_mode = false ]]
	1879	then
	1880	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1881	# FOLDER
[2566]	1882	mkdir -p $tempdir
	1883	chmod go+rx $tempdir
	1884	cd $tempdir
	1885	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1886	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1887
	1888	else
	1889
	1890	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1891	printf "\n *** running in temporary directory: $tempdir"
[2380]	1892
	1893	fi
	1894
	1895
	1896	# PROVIDE THE INPUT FILES
	1897	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1898	optional_files_missing=false
[2380]	1899	(( i = 0 ))
[2610]	1900	while (( i < nr_of_input_files ))
[2380]	1901	do
	1902	(( i = i + 1 ))
	1903	if (( i == 1 ))
	1904	then
	1905	printf "\n\n *** providing INPUT-files:\n$dashes"
	1906	fi
	1907
	1908
	1909	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1910	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1911	then
[2669]	1912	optional_files_missing=true
[2380]	1913	continue
	1914	fi
	1915
	1916	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1917	files_for_cores=false; filetype=file
	1918	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1919	then
	1920	files_for_cores=true; filetype=files
	1921	actionin[$i]=""
	1922	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1923	then
	1924	actionin[$i]=""
	1925	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1926	then
	1927	files_for_cores=true; filetype=files
	1928	actionin[$i]="ln"
	1929	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1930	then
	1931	actionin[$i]="ln"
	1932	fi
	1933
	1934	if [[ $files_for_cores = true ]]
	1935	then
	1936	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1937	else
	1938	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1939	fi
	1940
	1941	# INPUT-FILES TO BE LINKED
	1942	if [[ "${actionin[$i]}" = ln ]]
	1943	then
	1944
	1945	printf "\n $filetype will be linked"
	1946	if [[ $files_for_cores = false ]]
	1947	then
	1948	if [[ -f "${absnamein[$i]}" ]]
	1949	then
	1950	ln ${absnamein[$i]} ${localin[$i]}
	1951	got_tmp[$i]=true
	1952	fi
	1953	else
	1954	if [[ -d "${absnamein[$i]}" ]]
	1955	then
[2396]	1956	mkdir -p ${localin[$i]}
[2380]	1957	cd ${absnamein[$i]}
	1958	for file in $(ls *)
	1959	do
[2566]	1960	ln $file $tempdir/${localin[$i]}
[2380]	1961	done >\|/dev/null 2>&1
[2566]	1962	cd $tempdir
[2380]	1963	fi
	1964
	1965	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1966	if [[ ! -f "${localin[$i]}/_000000" ]]
	1967	then
	1968	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1969	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1970	fi
	1971
	1972	got_tmp[$i]=true
	1973	fi
	1974	fi
	1975
	1976	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	1977	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	1978	then
	1979
	1980	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1981	then
	1982
	1983	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1984	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1985	printf "\n file will be provided for $cores processors"
[2396]	1986	mkdir -p ${localin[$i]}
[2380]	1987	ival=$cores
	1988	(( ii = 0 ))
	1989	while (( ii <= ival-1 ))
	1990	do
	1991	if (( ii < 10 ))
	1992	then
	1993	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1994	elif (( ii < 100 ))
	1995	then
	1996	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1997	elif (( ii < 1000 ))
	1998	then
	1999	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2000	else
	2001	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2002	fi
	2003	(( ii = ii + 1 ))
	2004	done
	2005
	2006	else
	2007
	2008	if [[ $files_for_cores = true ]]
	2009	then
	2010
	2011	# PROVIDE FILES FOR EACH CORE
	2012	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2013	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2014	printf "\n providing $cores files for the respective cores"
[2396]	2015	mkdir -p ${localin[$i]}
[2380]	2016	if [[ $link_local_input = true ]]
	2017	then
	2018	printf " files will be linked\n"
	2019	cd ${absnamein[$i]}
	2020	for file in $(ls *)
	2021	do
	2022	ln -f $file ${localin[$i]}
	2023	done
[2566]	2024	cd $tempdir
[2380]	2025	fi
	2026
	2027	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2028	if [[ ! -f "${localin[$i]}/_000000" ]]
	2029	then
	2030	if [[ $link_local_input = true ]]
	2031	then
	2032	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2033	fi
	2034	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2035	fi
	2036
	2037	else
	2038
	2039	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2040	if [[ $link_local_input = true ]]
	2041	then
	2042	printf " file will be linked\n"
	2043	ln -f ${absnamein[$i]} ${localin[$i]}
	2044	fi
[2605]	2045	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2046	if [[ ! -f "${localin[$i]}" ]]
	2047	then
	2048	if [[ $link_local_input = true ]]
	2049	then
	2050	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2051	fi
[2669]	2052	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2053	then
	2054	mv ${absnamein[$i]} ${localin[$i]}
	2055	else
	2056	cp ${absnamein[$i]} ${localin[$i]}
	2057	fi
[2380]	2058	fi
	2059	fi
	2060	fi
	2061	fi
	2062
	2063	done
	2064	if (( i != 0 ))
	2065	then
[2669]	2066	if [[ $optional_files_missing = true ]]
	2067	then
	2068	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2069	fi
[2380]	2070	printf "\n$dashes\n *** all INPUT-files provided \n"
	2071	fi
	2072
	2073
	2074	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2075	(( i = 0 ))
	2076	while (( i < iic ))
	2077	do
	2078	(( i = i + 1 ))
	2079	if (( i == 1 ))
	2080	then
	2081	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2082	fi
	2083	printf "\n >>> ${in_command[$i]}"
	2084	eval ${in_command[$i]}
	2085	if (( i == iic ))
	2086	then
	2087	printf "\n$dashes\n"
	2088	fi
	2089	done
	2090
	2091
	2092	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2093	# (FILE ENVPAR WILL BE READ BY PALM)
	2094	cat > ENVPAR << EOF
[2834]	2095	&envpar run_identifier = '$jobname', host = '$host_configuration',
[2906]	2096	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2097	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2098	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2099	maximum_cpu_time_allowed = ${cpumax}.,
	2100	revision = '$global_revision',
	2101	batch_job = .${running_in_batch_mode}. /
	2102
	2103	EOF
	2104
	2105
	2106	# STARTING THE EXECUTABLE
	2107	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2108	PATH=$PATH:$tempdir
[2380]	2109
	2110
	2111	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2112	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2113	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2114	eval line=\"$line\"
	2115	execute_command="$line"
	2116
	2117
	2118	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2119	if [[ "$execute_command_for_combine" = "" ]]
	2120	then
	2121	eval line2=\"$line2\"
	2122	execute_command_for_combine="$line2"
	2123	fi
	2124
[2380]	2125
	2126
	2127	# PROVIDE A HOSTFILE, IF REQUIRED
	2128	if [[ "$hostfile" != "" ]]
	2129	then
	2130
	2131	if [[ $hostfile = auto ]]
	2132	then
	2133	# CREATE A NEW HOSTFILE
	2134	(( ii = 1 ))
	2135	while (( ii <= cores / threads_per_task ))
	2136	do
	2137	echo $(hostname) >> hostfile
	2138	(( ii = ii + 1 ))
	2139	done
	2140	if (( cores / threads_per_task == 0 ))
	2141	then
	2142	echo $(hostname) >> hostfile
	2143	fi
	2144
	2145	else
	2146	cp $hostfile hostfile
	2147	fi
	2148	eval line=\"`head -n $ii hostfile`\"
	2149	printf "\n *** running on: $line"
	2150	fi
	2151
	2152
	2153
	2154	# SET THE NUMBER OF OPENMP-THREADS
	2155	if [[ $use_openmp = true ]]
	2156	then
	2157	export OMP_NUM_THREADS=$threads_per_task
	2158	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2159	else
	2160	export OMP_NUM_THREADS=1
	2161	fi
	2162
	2163
[2610]	2164	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2165	if [[ $run_coupled_model = false ]]
	2166	then
	2167	if [[ "$ocean_file_appendix" = true ]]
	2168	then
	2169	echo "precursor_ocean" > coupling_steering
	2170	else
	2171	echo "precursor_atmos" > coupling_steering
	2172	fi
	2173	else
	2174	(( iia = $cores_atmos / $threads_per_task ))
	2175	(( iio = $cores_ocean / $threads_per_task ))
	2176	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2177	printf "\n\n"
	2178	echo "coupled_run $iia $iio" > coupling_steering
	2179	fi
	2180
	2181	printf "\n *** execute command:"
	2182	printf "\n \"$execute_command\" \n\n"
	2183
	2184	$execute_command < coupling_steering
	2185
	2186	if [[ $? != 0 ]]
	2187	then
	2188
	2189	# ABORT IN CASE OF RUNTIME ERRORS
	2190	printf "\n +++ runtime error occured"
	2191	locat=execution
	2192	exit
	2193
	2194	else
	2195
	2196	printf "\n$dashes\n *** execution finished \n"
	2197
	2198	fi
	2199
	2200
	2201	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2202	# BY EACH CORE INTO ONE FILE
	2203	if [[ ! -f combine_plot_fields.x ]]
	2204	then
	2205
	2206	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2207	printf "\n 2d- and/or 3d-data may be incomplete!"
	2208	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2209
	2210	elif [[ "$combine_plot_fields" == true ]]
	2211	then
	2212
	2213	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2214	$execute_command_for_combine
	2215
	2216	else
	2217
	2218	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2219	# DATA OUTPUT
[2380]	2220	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2221	fi
	2222
	2223
	2224
	2225	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2226	(( i = 0 ))
	2227	while (( i < ioc ))
	2228	do
	2229	(( i = i + 1 ))
	2230	if (( i == 1 ))
	2231	then
	2232	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2233	fi
[2799]	2234
	2235	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2236	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2237
[2380]	2238	printf "\n >>> ${out_command[$i]}"
	2239	eval ${out_command[$i]}
	2240	if (( i == ioc ))
	2241	then
	2242	printf "\n$dashes\n"
	2243	fi
	2244	done
	2245
	2246
[2610]	2247	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2248	# WILDCARDS
[2380]	2249	(( i = 0 ))
[2610]	2250	(( nr_of_output_files = 0 ))
	2251
[2380]	2252	while (( i < iout ))
	2253	do
[2610]	2254
[2380]	2255	(( i = i + 1 ))
[2610]	2256
	2257	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2258	# CREATE A LIST FOR THE DETECTED ENDINGS
	2259	if [[ "${multout[$i]}" = true ]]
	2260	then
	2261	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2262	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2263	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2264
	2265	endings="DEFAULT"
	2266	while read line
	2267	do
	2268	# remove the local name from the beginning
	2269	localnamestring="${localout_pre[$i]}"
	2270	length_localname=${#localnamestring}
	2271	ending=${line:${length_localname}}
	2272
	2273	if [[ "$ending" != "" ]]
	2274	then
	2275	endings="$endings $ending"
	2276	fi
	2277
	2278	done <filelist
	2279
	2280	rm filelist
	2281
	2282	else
	2283
	2284	# SINGLE NAME
	2285	endings=DEFAULT
	2286
	2287	fi
	2288
	2289	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2290	for ending in $endings
	2291	do
	2292
	2293	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2294	if [[ $ending = DEFAULT ]]
	2295	then
	2296	ending=""
	2297	fi
	2298
	2299	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2300	(( nr_of_output_files = nr_of_output_files + 1 ))
	2301	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2302	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2303	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2304	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2305	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2306	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2307	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2308
	2309	done
	2310
	2311	done
	2312
	2313
	2314
	2315
	2316	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2317	(( i = 0 ))
	2318	while (( i < nr_of_output_files ))
	2319	do
	2320	(( i = i + 1 ))
[2380]	2321	if (( i == 1 ))
	2322	then
	2323	printf "\n\n *** saving OUTPUT-files:"
	2324
	2325	# GET RUN NUMBER ASSIGNED BY PALM
	2326	if [[ -f RUN_NUMBER ]]
	2327	then
	2328	read run_number < RUN_NUMBER
	2329	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2330	usecycle_option="-U $run_number"
	2331	else
	2332	run_number=0
	2333	usecycle_option=""
	2334	fi
	2335	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2336	then
[2404]	2337	printf "\n *** in case of SCP transfers to local host"
	2338	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2339	fi
	2340	printf "\n$dashes"
	2341	fi
	2342
	2343	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2344	then
	2345
[2834]	2346	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
[2610]	2347
	2348	# DETERMINE THE CYCLE NUMBER
	2349	ls -1 -d $filename > filelist 2>/dev/null
	2350	ls -1 -d $filename.* >> filelist 2>/dev/null
	2351	while read line
	2352	do
	2353
	2354	# filename without path (i.e. after the last "/")
	2355	basefilename=$(basename ${line})
	2356
	2357	# check if there is an extension
	2358	extension=${basefilename##*.}
	2359	if [[ "$extension" = "${extout[$i]}" ]]
	2360	then
	2361	basefilename=${basefilename%.*}
	2362	fi
	2363
	2364	# check for an existing cycle number
	2365	cycle=${basefilename##*.}
	2366	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2367	then
[2669]	2368	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2369	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2370	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2371	else
	2372	(( icycle = 1 ))
	2373	fi
	2374
	2375	if (( icycle > maxcycle ))
	2376	then
	2377	(( maxcycle = icycle ))
	2378	fi
	2379
	2380	done <filelist
	2381	rm filelist
	2382
	2383
	2384	# SET THE CYCLE NUMBER
	2385	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2386	if [[ "${actionout[$i]}" = a ]]
	2387	then
	2388	(( maxcycle = maxcycle - 1 ))
	2389	fi
	2390
	2391	(( cycnum[$i] = maxcycle ))
	2392	pathout[$i]=$filename
	2393
	2394
	2395	# ADD CYCLE NUMBER TO FILENAME
	2396	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2397	if [[ "${actionout[$i]}" != "a" ]]
	2398	then
	2399	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2400	# WITH AN EXISTING CYCLE NUMBER
	2401	if (( run_number >= cycnum[$i] ))
	2402	then
	2403	(( cycnum[$i] = run_number ))
	2404	else
	2405	if (( run_number > 0 ))
	2406	then
	2407	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2408	fi
	2409	fi
	2410	fi
	2411	if (( cycnum[$i] > 0 ))
	2412	then
[2600]	2413	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2414	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2415	fi
	2416	fi
	2417
	2418	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2419	files_for_cores=false; filetype=file
	2420	link_local_output=false
	2421	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2422	then
	2423	files_for_cores=true; filetype=directory
	2424	actionout[$i]=""
	2425	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2426	then
	2427	actionout[$i]=""
	2428	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2429	then
	2430	files_for_cores=true; filetype=directory
	2431	link_local_output=true
	2432	actionout[$i]=""
	2433	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2434	then
	2435	link_local_output
	2436	actionout[$i]=""
	2437	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2438	then
	2439	files_for_cores=true; filetype=directory
	2440	actionout[$i]="tr"
	2441	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2442	then
	2443	actionout[$i]="tr"
	2444	fi
	2445
	2446	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2447	then
[2669]	2448	if [[ ${warnout[$i]} = true ]]
	2449	then
	2450	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2451	fi
[2380]	2452	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2453	then
[2669]	2454	if [[ ${warnout[$i]} = true ]]
	2455	then
	2456	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2457	fi
[2380]	2458	else
	2459
	2460
	2461	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2462	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2463	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2464	then
	2465	if [[ $running_on_remote = true ]]
	2466	then
	2467
	2468	# SET OPTIONS FOR TRANSFER
	2469	if [[ "${actionout[$i]}" = tr ]]
	2470	then
	2471	if [[ $files_for_cores = false ]]
	2472	then
	2473	catalog_option=""
	2474	catalog_string=""
	2475	else
	2476	catalog_option="-c"
	2477	catalog_string="/"
	2478	fi
	2479	append_option=""
	2480	append_string=""
	2481	else
	2482	append_option="-A"
	2483	append_string="append"
	2484	fi
	2485
	2486	transfer_failed=false
	2487	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2834]	2488	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
[2380]	2489
	2490	# TRANSFER VIA SCP
	2491	if [[ "$remote_loginnode" != "" ]]
	2492	then
[2834]	2493	echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${jobname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
[2380]	2494	else
[2834]	2495	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${jobname}${endout[$i]} ${extout[$i]}
[2380]	2496	fi
	2497	[[ $? != 0 ]] && transfer_failed=true
	2498
	2499
	2500	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2501	if [[ $transfer_failed = true ]]
	2502	then
	2503	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2834]	2504	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
[2380]	2505
	2506	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2507	eval local_catalog=${pathout[$i]}
	2508	if [[ ! -d $local_catalog ]]
	2509	then
	2510	printf " *** local directory does not exist. Trying to create:\n"
	2511	printf " $local_catalog \n"
	2512	mkdir -p $local_catalog
	2513	fi
[2834]	2514	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
[2380]	2515	transfer_problems=true
	2516	fi
	2517
	2518	else
	2519
	2520	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2521	# BE COPIED OR APPENDED ON THIS MACHINE
	2522	if [[ "${actionout[$i]}" = tr ]]
	2523	then
	2524	actionout[$i]=""
	2525	else
	2526	actionout[$i]="a"
	2527	fi
	2528	fi
	2529	fi
	2530
	2531
	2532	# APPEND ON THIS MACHINE
	2533	if [[ "${actionout[$i]}" = "a" ]]
	2534	then
	2535	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2536	then
	2537	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2538	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2539	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2540	else
	2541	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2542	printf "\n ${pathout[$i]}\n"
	2543	cat ${localout[$i]} >> ${pathout[$i]}
	2544	fi
	2545	fi
	2546
	2547	# COPY ON THIS MACHINE
	2548	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2549	# ON DIFFERENT FILE-SYSTEMS
	2550	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2551	then
	2552
	2553	# COPY IN CASE OF RUNS ON SINGLE CORES
	2554	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2555	then
	2556	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2557	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2558	if [[ $link_local_output = true ]]
	2559	then
	2560	printf " file will be linked\n"
	2561	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2562	fi
	2563	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2564	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2565	then
	2566	if [[ $link_local_output = true ]]
	2567	then
	2568	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2569	fi
	2570	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2571	else
	2572	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2573	fi
	2574	else
	2575	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2576	printf "\n ${pathout[$i]}\n"
	2577	if [[ $link_local_output = true ]]
	2578	then
	2579	printf " file will be linked\n"
	2580	ln -f ${localout[$i]} ${pathout[$i]}
	2581	fi
	2582	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2583	if [[ ! -f "${pathout[$i]}" ]]
	2584	then
	2585	if [[ $link_local_output = true ]]
	2586	then
	2587	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2588	fi
	2589	cp ${localout[$i]} ${pathout[$i]}
	2590	else
	2591	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2592	fi
	2593	fi
	2594
	2595	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2596	then
	2597
	2598	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2599	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2600	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2601	printf "\n ${pathout[$i]}\n"
	2602	if [[ $link_local_output = true ]]
	2603	then
	2604	printf " files will be linked\n"
[2396]	2605	mkdir -p ${pathout[$i]}
[2380]	2606	cd ${localout[$i]}
	2607	for file in $(ls *)
	2608	do
	2609	ln -f $file ${pathout[$i]}
	2610	done >\|/dev/null 2>&1
[2566]	2611	cd $tempdir
[2380]	2612	fi
	2613
	2614	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2615	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2616	then
	2617	if [[ $link_local_output = true ]]
	2618	then
	2619	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2620	fi
	2621	cp -r ${localout[$i]}/* ${pathout[$i]}
	2622	fi
	2623
	2624	fi
	2625	fi
	2626	done
	2627
	2628	if (( i != 0 ))
	2629	then
	2630	if [[ $transfer_problems = true ]]
	2631	then
	2632	printf "\n$dashes\n *** OUTPUT-files saved"
	2633	printf "\n +++ WARNING: some data transfers failed! \n"
	2634	else
	2635	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2636	fi
	2637	fi
	2638
	2639
	2640	# IF REQUIRED, START A RESTART-JOB
	2641	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2642	if [[ -f CONTINUE_RUN ]]
	2643	then
	2644
	2645	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2646	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2647	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2648	# -b START A BATCH JOB
	2649	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2650	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2651	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2652
[2957]	2653	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2654	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2655	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2656	then
	2657	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2658	fi
[2380]	2659
	2660	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2661	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2662	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2663	then
[2381]	2664	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2665	fi
	2666
	2667
	2668	# START THE RESTART-JOB
	2669	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2670	echo " $prc"
	2671	printf "\n$dashes\n"
	2672	if [[ $running_on_remote = true ]]
	2673	then
	2674
	2675	echo "*** ssh will be used to initiate restart-runs!"
	2676	echo " return_address=\"$return_address\" "
	2677	echo " return_username=\"$local_username\" "
	2678
	2679	if [[ "$remote_loginnode" != "" ]]
	2680	then
[2420]	2681	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]	2682	else
[2420]	2683	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2684	fi
	2685
	2686	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2687	sleep 30
	2688
	2689	else
	2690
	2691	# START THE RESTART JOB ON THE LOCAL HOST
	2692	eval $prc # THE ' MUST BE EVALUATED
	2693	cd - > /dev/null
	2694
	2695	fi
	2696	printf "\n$dashes\n *** restart-run initiated \n"
	2697
	2698
	2699	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2700	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2701	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2702	# MAY BE VERY HUGE)
	2703	(( i = 0 ))
[2610]	2704	while (( i < nr_of_input_files ))
[2380]	2705	do
	2706	(( i = i + 1 ))
	2707	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2708	then
	2709	rm -r ${absnamein[$i]}
	2710	fi
	2711	done
	2712
	2713	fi
	2714
	2715
	2716	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2717	cd $HOME
[2566]	2718	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2719
	2720
	2721	else
	2722
	2723
	2724	# PREPARING ACTIONS,
	2725	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2726
	2727	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2834]	2728	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2729	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2730	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2731	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2732	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2733	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2734	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2735	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2736	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2737	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2738	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2739	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2740	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2741	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2742	if [[ $create_remote_batch_job = true ]]
	2743	then
	2744	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2745	if [[ $do_trace = true ]]
	2746	then
	2747	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2748	fi
[2380]	2749	elif [[ $create_batch_job = true ]]
	2750	then
	2751	palmrun_com=${palmrun_com}" -j"
[2420]	2752	if [[ $do_trace = true ]]
	2753	then
	2754	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2755	fi
[2380]	2756	fi
	2757
	2758
	2759	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2760	# REMOTE HOST
[2506]	2761	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2762	job_protocol_file=$job_protocol_file_local
	2763	if [[ $create_remote_batch_job = true ]]
	2764	then
[2506]	2765	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2766	job_protocol_file=$job_protocol_file_remote
	2767	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2768	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2769	fi
	2770
	2771
	2772	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2773	jobfile=jobfile.$run_id
	2774
	2775
	2776	# FIRST CREATE THE BATCH DIRECTIVES
	2777	(( i = 0 ))
	2778	while (( i < ibd ))
	2779	do
	2780	(( i = i + 1 ))
[2693]	2781	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2782	eval line=\"$line\"
	2783	echo "$line" >> $jobfile
	2784	done
	2785	echo " " >> $jobfile
	2786
	2787
	2788	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2789	# PROTOCOL
	2790	if [[ $create_remote_batch_job = true ]]
	2791	then
	2792	echo "set +vx" >> $jobfile
	2793	echo "trap '" >> $jobfile
	2794	echo "set +vx" >> $jobfile
	2795	echo "cd ${remote_jobcatalog}" >> $jobfile
	2796	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2797
	2798	# ADD THE BATCH DIRECTIVES
	2799	(( i = 0 ))
	2800	while (( i < ibdt ))
	2801	do
	2802	(( i = i + 1 ))
[2693]	2803	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2804	eval line=\"$line\"
	2805	echo "$line" >> $jobfile
	2806	done
	2807	echo " " >> $jobfile
	2808
	2809	echo "set -x" >> $jobfile
[2834]	2810	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${jobname}" >> $jobfile
[2380]	2811	echo "%%END%%" >> $jobfile
	2812	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2813	echo "$submit_command $scpjob_file" >> $jobfile
	2814	echo "rm $scpjob_file" >> $jobfile
[2404]	2815	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2816	echo "set -x" >> $jobfile
	2817	echo " ' exit" >> $jobfile
	2818	fi
	2819
	2820
	2821	# ACTIVATE ERROR-TRACEBACK
	2822	if [[ $do_trace = true ]]
	2823	then
	2824	echo "set -x" >> $jobfile
	2825	else
	2826	echo "set +vx" >> $jobfile
	2827	fi
	2828
	2829
	2830	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2831	if [[ "$login_init_cmd" != "" ]]
	2832	then
	2833	echo "$login_init_cmd" >> $jobfile
	2834	fi
	2835	if [[ "$module_commands" != "" ]]
	2836	then
	2837	echo "$module_commands" >> $jobfile
	2838	fi
	2839
	2840
	2841	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2842	if [[ $create_remote_batch_job = true ]]
	2843	then
	2844	echo "mkdir $tempdir" >> $jobfile
	2845	echo "chmod go+rx $tempdir" >> $jobfile
	2846	else
	2847	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2848	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2849	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2850	mkdir $tempdir
	2851	chmod go+rx $tempdir
	2852	fi
	2853	echo "cd $tempdir" >> $jobfile
	2854	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2855	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2856	echo "export PATH=.:\$PATH" >> $jobfile
	2857	echo "export execute_palmrun=true" >> $jobfile
	2858
	2859
	2860	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2861	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2862	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2863	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2864	echo "export LOCAL_PWD" >> $jobfile
	2865
	2866
	2867	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2868	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2869	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2870
	2871
	2872	# CALL PALMRUN WITHIN THE JOB
	2873	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2874	echo "set -x" >> $jobfile
	2875	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2876
	2877
	2878	# TRANSFER JOBFILE TO THE TARGET HOST
	2879	if [[ $create_jobfile_only = false ]]
	2880	then
	2881
	2882	if [[ $create_remote_batch_job = true ]]
	2883	then
	2884
[2420]	2885	echo " "
[2566]	2886	echo " *** transfer of job to remote host via scp"
[2420]	2887	if [[ $do_trace = true ]]
	2888	then
[2506]	2889	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2890	fi
[2566]	2891	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2892
[2566]	2893	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2894	if [[ $do_trace = true ]]
	2895	then
[2506]	2896	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]	2897	fi
[2506]	2898	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]	2899
	2900	elif [[ $create_batch_job = true ]]
	2901	then
	2902
[2385]	2903	eval local_jobcatalog=$local_jobcatalog
[2506]	2904	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2905	cd $local_jobcatalog
[2380]	2906	echo " "
[2420]	2907	echo " *** submit the job"
	2908	if [[ $do_trace = true ]]
	2909	then
[2506]	2910	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2911	fi
[2506]	2912	$submit_command ${host_configuration}_${job_id}
	2913	rm ${host_configuration}_${job_id}
[2380]	2914	cd - > /dev/null
	2915
	2916	fi
	2917
	2918	rm -rf $jobfile
	2919
	2920	else
	2921
	2922	printf "\n *** jobfile created under name \"$jobfile\" "
	2923	printf "\n no batch-job has been sent!"
	2924
	2925	fi
	2926
	2927	fi # END OF REMOTE-PART

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