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source: palm/trunk/SCRIPTS/palmrun @ 2965

Last change on this file since 2965 was 2957, checked in by Giersch, 7 years ago
Sky view factors will always be read from file now in case of automatic restarts, corrected error message in case of writing sky view factors
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 96.7 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 $
[2957]	29	# svfout in the activation string will be replaced now by svfin in case of
	30	# automatic restarts
	31	#
	32	# 2718 2018-01-02 08:49:38Z maronga
[2906]	33	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	34	# the possible output or input of sky view factors
	35	#
	36	# 2718 2018-01-02 08:49:38Z maronga
[2834]	37	# "fname" renamed to "jobname"
	38	#
	39	# 2718 2018-01-02 08:49:38Z maronga
[2799]	40	# parameters are allowed in output commands (OC:)
	41	#
	42	# 2718 2018-01-02 08:49:38Z maronga
[2789]	43	# bugfix: exit if no queue has been given neither with option -q nor in the
	44	# configuration file
	45	#
	46	# 2718 2018-01-02 08:49:38Z maronga
[2762]	47	# file connection file from trunk/SCRIPTS is taken by default
	48	#
	49	# 2718 2018-01-02 08:49:38Z maronga
[2716]	50	# Corrected "Former revisions" section
	51	#
	52	# 2696 2017-12-14 17:12:51Z kanani
	53	# Change in file header (GPL part)
	54	#
	55	# 2693 2017-12-13 12:33:49Z raasch
[2693]	56	# replacement of variables given by {{<variable>}} in configuration file is now
	57	# done in a more general way, variable names are written in small letters
	58	#
	59	# 2670 2017-12-06 16:32:19Z raasch
[2670]	60	# test printouts removed
	61	#
	62	# 2669 2017-12-06 16:03:27Z raasch
[2669]	63	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	64	# removed,
	65	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	66	# files,
	67	# informative messages in case of missing optional input files shortened
	68	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	69	#
	70	# 2638 2017-11-23 12:44:23Z raasch
[2610]	71	# use of wildcards in file connection statements enabled
	72	#
	73	# 2605 2017-11-09 15:31:46Z raasch
[2605]	74	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	75	# will not be sent with the job file any more, but copied into the
[2610]	76	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	77	#
	78	# 2600 2017-11-01 14:11:20Z raasch
[2600]	79	# cycle numbers are made three digits wide
	80	#
	81	# 2566 2017-10-20 08:50:47Z raasch
[2566]	82	# execute command for combine_plot_fields added
	83	# "TEMPDIR" renamed "tempdir"
	84	# temporary working directory for local batch jobs is created immediately within
	85	# the user's palmrun call, due to a requirement of the "grid engine" batch
	86	# system, where the working directory is given with batch directive -wd and must
	87	# already exist when the job is submitted,
	88	# informative messages in non-trace mode reduced and partly reformatted
	89	#
	90	# 2551 2017-10-18 07:25:11Z raasch
[2551]	91	# TEMPDIR added as replacement string to be used in batch directives
	92	#
	93	# 2512 2017-10-04 08:26:59Z raasch
[2507]	94	# bugfix for determining cycle numbers of NetCDF input files
	95	#
	96	# 2506 2017-09-29 08:30:37Z raasch
[2506]	97	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	98	# host configuration added to SOURCES_FOR_RUN_... folder name
	99	# host_identifier renamed host_configuration
	100	# option -W added to allow for job dependencies
	101	#
	102	# 2501 2017-09-26 11:41:55Z raasch
[2501]	103	# default value for number of cores (option -X) set to 1
	104	# bugfix for mechanism which overwrites configuration file settings with values
	105	# provided by palmrun options
	106	#
	107	# 2499 2017-09-22 16:47:58Z kanani
[2499]	108	# option -h named configuration identifier
	109	#
	110	# 2480 2017-09-19 06:24:14Z maronga
[2480]	111	# bugfix for last revision
	112	#
	113	# 2479 2017-09-19 06:12:16Z raasch
[2479]	114	# option -A (project account number) added
	115	#
	116	# 2422 2017-09-08 08:25:41Z raasch
[2410]	117	# initial revision
[2380]	118	#
	119	#--------------------------------------------------------------------------------#
	120	# palmrun - script for running PALM jobs on local and remote hosts
	121	#--------------------------------------------------------------------------------#
	122
	123
	124
	125	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	126
	127	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	128	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	129	# (TOO MANY ARGUMENTS - PROBLEM)
	130	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	131
[2610]	132	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	133	typeset -i nr_of_output_files=0
[2380]	134	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	135	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	136	# SCRIPT-OPTION ARGUMENTS
	137	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	138	typeset -i icycle inode ival maxcycle mpi_tasks
	139	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	140
	141	activation_string_list=""
	142	AddFilenames=""
	143	combine_plot_fields=true
	144	compiler_name=""
	145	compiler_name_ser=""
	146	compiler_options=""
[2501]	147	cores=1
[2380]	148	cores_atmos=0
	149	cores_ocean=0
	150	coupled_dist=""
	151	cpp_options=""
	152	cpumax=0
[2506]	153	create_batch_job=false
[2380]	154	create_jobfile_only=false
	155	create_remote_batch_job=false
	156	dashes=" ----------------------------------------------------------------------------"
	157	defaultqueue=""
[2506]	158	delete_temporary_catalog=true
[2380]	159	do_compile=true
	160	do_trace=false
	161	executable=""
	162	execute_command=""
	163	execution_error=false
[2762]	164	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2834]	165	jobname=test
[2380]	166	global_revision=""
[2506]	167	host_configuration="default"
[2380]	168	hostfile=""
	169	hp=""
	170	keep_data_from_previous_run=false
	171	link_local_input=false
	172	link_local_output=false
[2388]	173	linker_options=""
[2385]	174	local_jobcatalog=""
[2380]	175	locat=normal
	176	makefile=""
	177	max_par_io_str=""
	178	prc=$0
	179	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	180	do
	181	prc=`echo $prc \| cut -f2- -d"/"`
	182	done
	183	module_calls=""
[2506]	184	palmrun_memory=""
[2380]	185	palmrun_script_name=$prc
	186	openmp=false
[2506]	187	previous_job=""
[2479]	188	project_account=""
[2380]	189	queue=none
[2906]	190	read_svf=""
[2380]	191	restart_run=false
	192	return_address=""
[2385]	193	remote_jobcatalog=""
[2380]	194	remote_username=""
	195	running_in_batch_mode=false
	196	run_coupled_model=false
	197	run_id=""
	198	silent=false
	199	source_list=""
	200	source_path=""
[2501]	201	tasks_per_node=0
[2380]	202	threads_per_task=1
	203	transfer_problems=false
[2384]	204	user_source_path=""
[2506]	205	use_existing_sources_folder=""
[2380]	206	use_openmp=false
[2732]	207	version="palmrun 1.0 Rev$Rev: 2957 $"
[2380]	208	working_directory=`pwd`
	209	write_binary=""
[2906]	210	write_svf=""
[2380]	211	TOPT=""
	212
	213
	214	# ERROR HANDLING IN CASE OF EXIT
[2404]	215	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	216	then
	217
	218	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	219	(( i = 0 ))
	220	while (( i < iec ))
	221	do
	222	(( i = i + 1 ))
	223	printf "\n *** Execution of ERROR-command:\n"
	224	printf " >>> ${err_command[$i]}\n"
	225	eval ${err_command[$i]}
	226	done
[2566]	227	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	228	printf "\n\n+++ palmrun killed \n\n"
	229	elif [[ $locat != control_c ]]
	230	then
[2566]	231	printf "\n --> palmrun finished\n\n"
[2380]	232	fi' exit
	233
	234
	235	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	236	trap 'cd; rm -rf $tempdir
[2380]	237	printf "\n+++ palmrun killed by \"^C\" \n\n"
	238	locat=control_c
	239	exit
	240	' 2
	241
	242
	243	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	244	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	245	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]	246	do
	247	case $option in
	248	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	249	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	250	(b) create_batch_job=true; prc="$prc -b";;
	251	(B) delete_temporary_catalog=false; prc="$prc -B";;
	252	(C) restart_run=true; prc="$prc -C";;
[2834]	253	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
[2380]	254	(F) create_jobfile_only=true;;
	255	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	256	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	257	(j) running_in_batch_mode=true;;
	258	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	259	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	260	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	261	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	262	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	263	(r) run_id=$OPTARG;;
	264	(R) return_address=$OPTARG;;
	265	(s) source_list=$OPTARG;;
[2501]	266	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	267	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	268	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	269	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	270	(v) silent=true; prc="$prc -v";;
[2506]	271	(V) use_existing_sources_folder="-V";;
[2380]	272	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	273	(W) previous_job=$OPTARG;;
[2380]	274	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	275	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	276	(y) ocean_file_appendix=true; prc="$prc -y";;
	277	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	278	(Z) combine_plot_fields=false; prc="$prc -Z";;
	279	(\?) printf "\n +++ unknown option $OPTARG \n"
	280	printf "\n --> type \"$0 ?\" for available options \n"
	281	locat=parameter;exit;;
	282	esac
	283	done
	284
	285
	286	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	287	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	288	(( to_shift = $OPTIND - 1 ))
	289	shift $to_shift
	290
	291	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	292	if [[ "$1" = "?" ]]
	293	then
	294	(printf "\n *** Description of available palmrun options:\n"
	295	printf "\n Option Description Default-Value"
	296	printf "\n -a activation string list \"\" "
[2479]	297	printf "\n -A project account number ---"
[2380]	298	printf "\n -b batch-job on local machine ---"
	299	printf "\n -B do not delete temporary directory at end ---"
	300	printf "\n -d base name of files attached to program test"
	301	printf "\n -F create batch job file only ---"
[2506]	302	printf "\n -h host configuration \"default\" "
[2380]	303	printf "\n -k keep data from previous run"
	304	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	305	printf "\n -M Makefile name Makefile"
	306	printf "\n -O threads per openMP task ---"
	307	printf "\n -q queue \"$queue\" "
	308	printf "\n -s filenames of routines to be compiled \"\" "
	309	printf "\n must end with .f, .f90, .F, or .c !"
	310	printf "\n use \"..\" for more than one file and wildcards"
	311	printf "\n -s LM compiles all locally modified files"
	312	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	313	printf "\n -T tasks per node ---"
[2380]	314	printf "\n -u username on remote machine \"\" "
	315	printf "\n -v no prompt for confirmation ---"
[2506]	316	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	317	printf "\n -w maximum parallel io streams as given by -X"
[2506]	318	printf "\n -W name of job to wait for ---"
[2380]	319	printf "\n -x tracing of palmrun for debug purposes ---"
	320	printf "\n -X # of processors (on parallel machines) 1"
	321	printf "\n -y add appendix \"_O\" to all local output"
	322	printf "\n files (ocean precursor runs followed by"
	323	printf "\n coupled atmosphere-ocean runs) ---"
	324	printf "\n -Y run coupled model, \"#1 #2\" with"
	325	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	326	printf "\n -Z skip combine_plot_fields at the end of "
	327	printf "\n the simulation ---"
	328	printf "\n "
	329	printf "\n Possible values of positional parameter <modus>:"
	330	printf "\n \"?\" - this outline \n\n") \| more
	331	exit
	332	elif [[ "$1" != "" ]]
	333	then
	334	printf "\n +++ positional parameter $1 unknown \n"
	335	locat=parameter; exit
	336	fi
	337
	338
	339
	340	# SHORT STARTING MESSAGE
	341	printf "\n*** $version "
	342	printf "\n will be executed. Please wait ..."
	343
	344
[2834]	345	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
	346	export fname=$jobname
	347
	348
[2506]	349	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	350	config_file=.palm.config.$host_configuration
[2834]	351	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
[2380]	352
	353
	354	# CHECK, IF CONFIGURATION FILE EXISTS
	355	if [[ ! -f $config_file ]]
	356	then
	357	printf "\n\n +++ configuration file: "
	358	printf "\n $config_file"
	359	printf "\n does not exist"
	360	locat=connect; exit
	361	fi
	362
	363
[2762]	364	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	365	if [[ -f .palm.iofiles ]]
	366	then
	367	fileconnection_file=.palm.iofiles
	368	fi
	369
	370
[2380]	371	# CHECK, IF FILE CONNECTION FILE EXISTS
	372	if [[ ! -f $fileconnection_file ]]
	373	then
	374	printf "\n\n +++ file connection file: "
	375	printf "\n $fileconnection_file"
	376	printf "\n does not exist"
	377	locat=connect; exit
	378	fi
	379
	380
[2404]	381	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	382	if [[ "$activation_string_list" = "" ]]
	383	then
	384	printf "\n\n +++ no activation string list given: "
	385	printf "\n please set palmrun option \"-a\" "
	386	locat=palmrun_option; exit
	387	fi
	388
	389
	390	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	391	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	392	then
	393	write_binary=true
	394	else
	395	write_binary=false
	396	fi
	397
[2906]	398	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	399	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	400	then
	401	write_svf=true
	402	else
	403	write_svf=false
	404	fi
[2404]	405
[2906]	406	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	407	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	408	then
	409	read_svf=true
	410	else
	411	read_svf=false
	412	fi
	413
	414
[2380]	415	# READ AND EVALUATE THE CONFIGURATION-FILE
	416	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	417
	418	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	419	while read line
	420	do
	421
	422	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	423	eval line=\"$line\"
	424
	425
	426	# INTERPRET THE LINE
	427	if [[ "$(echo $line)" = "" ]]
	428	then
	429
	430	# EMPTY LINE, NO ACTION
	431	continue
	432
	433	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	434	then
	435
	436	# LINE IS A COMMENT LINE
	437	continue
	438
	439	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	440	then
	441
	442	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	443	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	444	value=`echo $line \| cut -d" " -s -f2-`
	445
	446
	447	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	448	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	449	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	450	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	451	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	452	# CONFIGURATION-FILE.
	453	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	454	then
	455	eval export $var="\$value"
	456
	457	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	458	if [[ $do_trace = true ]]
	459	then
	460	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	461	fi
	462	fi
	463
	464	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	465	then
	466
	467	# LINE DEFINES BATCH-DIRECTIVE
	468	(( ibd = ibd + 1 ))
	469	line=$(echo $line \| cut -c4-)
	470	batch_directive[$ibd]="$line"
	471
	472	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	473	then
	474
	475	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	476	# REMOTE TO A LOCAL HOST
	477	(( ibdt = ibdt + 1 ))
	478	line=$(echo $line \| cut -c5-)
	479	batch_directive_transfer[$ibdt]="$line"
	480
	481	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	482	then
	483
	484	# LINE DEFINES ERROR-COMMAND
	485	(( iec = iec + 1 ))
	486	line=$(echo $line \| cut -c4-)
	487	err_command[$iec]="$line"
	488
	489	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	490	then
	491
	492	# LINE DEFINES INPUT-COMMAND
	493	(( iic = iic + 1 ))
	494	line=$(echo $line \| cut -c4-)
	495	in_command[$iic]="$line"
	496
	497	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	498	then
	499
	500	# LINE DEFINES OUTPUT-COMMAND
	501	(( ioc = ioc + 1 ))
	502	line=$(echo $line \| cut -c4-)
	503	out_command[$ioc]="$line"
	504
	505	else
	506
	507	# SKIP ALL OTHER LINES
	508	continue
	509
	510	fi
	511
	512	done < $config_file
	513
	514
	515	# CHECK SETTING OF REQUIRED PARAMETERS
	516	if [[ "$compiler_name" = "" ]]
	517	then
	518	printf "\n +++ no compiler name found in $config_file"
	519	printf "\n Please add line \"compiler_name ...\" to that file."
	520	locat=config_file; exit
	521	fi
	522	if [[ "$compiler_name_ser" = "" ]]
	523	then
	524	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	525	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	526	locat=config_file; exit
	527	fi
	528	if [[ "$compiler_options" = "" ]]
	529	then
	530	printf "\n +++ no compiler options found in $config_file"
	531	printf "\n Please add line \"compiler_options ...\" to that file."
	532	locat=config_file; exit
	533	fi
[2388]	534	if [[ "$linker_options" = "" ]]
[2380]	535	then
[2388]	536	printf "\n +++ no linker options found in $config_file"
	537	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	538	locat=config_file; exit
	539	fi
	540	if [[ "$execute_command" = "" ]]
	541	then
	542	printf "\n +++ no execute command found in $config_file"
	543	printf "\n Please add line \"execute_command ...\" to that file."
	544	locat=config_file; exit
	545	fi
	546
	547	if [[ "$hostfile" != "" ]]
	548	then
	549	if [[ $hostfile != auto && ! -f $hostfile ]]
	550	then
	551	printf "\n +++ no hostfile \"$hostfile\" found"
	552	printf "\n Please check line \"hostfile ...\" in $config_file"
	553	locat=config_file; exit
	554	fi
	555	fi
	556
	557
	558	# DETERMINE THE CALL STATUS
	559	if [[ "$return_address" != "" ]]
	560	then
	561
	562	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	563	# BATCH MODE AND ...
	564	running_on_remote=true
	565
	566	else
	567
	568	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	569	if [[ "$remote_ip" != "" ]]
	570	then
	571
	572	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	573	create_remote_batch_job=true
	574
	575	fi
	576	running_on_remote=false
	577	fi
	578
	579
	580
	581	# READ AND EVALUATE THE I/O-FILE LIST
	582	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	583
	584	# READ THE FILE CONNECTION FILE LINE BY LINE
	585	while read line
	586	do
	587
[2669]	588	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	589	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	590
	591	# INTERPRET THE LINE
	592	if [[ "$(echo $line)" = "" ]]
	593	then
	594	# EMPTY LINE, NO ACTION
	595	continue
	596
	597	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	598	then
	599
	600	# LINE IS A COMMENT LINE
	601	true
	602
	603	else
	604
	605	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	606	# s2a: in/out - field
[2669]	607	# s2b: action - field (optional)
	608	s1=`echo "$line" \| cut -d" " -f1`
	609	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	610	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	611	then
[2669]	612	s2a=$s2
[2380]	613	s2b=""
	614	else
[2669]	615	s2a=`echo $s2 \| cut -d":" -f1`
	616	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	617	fi
[2669]	618	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	619	s4=`echo "$line" \| cut -d" " -s -f4`
	620	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	621	s5=`echo "$line" \| cut -d" " -s -f5`
	622	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	623
	624
	625	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	626	# INPUT- OR OUTPUT-LIST.
	627	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	628	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	629	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	630	# IS NOT CHECKED AND STORED.
[2610]	631	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	632	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	633	then
	634	found=false
	635	for actual in $activation_string_list
	636	do
	637	for formal in $s3
	638	do
	639	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	640	done
	641	done
	642	if [[ $found = true ]]
	643	then
	644	(( iin = iin + 1 ))
[2669]	645	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	646	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	647	if [[ "$s2a" = inopt ]]
	648	then
	649	optin_pre[$iin]=yes
	650	else
	651	optin_pre[$iin]=no
	652	fi
[2605]	653
	654	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	655	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	656	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	657	then
[2610]	658	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	659	fi
	660
[2610]	661	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	662	# THE WILDCARD FROM THE ENDING
	663	if [[ "${s5: -1}" = "*" ]]
	664	then
[2669]	665	if [[ "$s2b" = "di" ]]
[2610]	666	then
	667	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	668	printf "\n see file \"$fileconnection_file\", line"
	669	printf "\n$line"
	670	locat=iofiles_file; exit
	671	fi
	672	multin[$iin]=true
	673	string=${endin_pre[$iin]}
	674	endin_pre[$iin]="${string%?}"
	675	else
	676	multin[$iin]=false
	677	fi
[2380]	678	fi
[2669]	679	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	680	then
	681	found=false
	682	for actual in $activation_string_list
	683	do
	684	for formal in $s3
	685	do
[2670]	686	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	687	done
	688	done
	689	if [[ $found = true ]]
	690	then
	691	(( iout = iout + 1 ))
[2669]	692	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	693	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	694
[2669]	695	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	696	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	697	if [[ $formal = wildcard ]]
	698	then
	699	warnout_pre[$iout]=false
	700	else
	701	warnout_pre[$iout]=true
	702	fi
	703
[2610]	704	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	705	# THE WILDCARD FROM THE LOCAL FILENAME
	706	if [[ "${s1: -1}" = "*" ]]
	707	then
[2669]	708	if [[ "$s2b" = "di" ]]
[2610]	709	then
	710	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	711	printf "\n see file \"$fileconnection_file\", line"
	712	printf "\n$line"
	713	locat=iofiles_file; exit
	714	fi
	715	multout[$iout]=true
	716	string=${localout_pre[$iout]}
	717	localout_pre[$iout]="${string%?}"
	718	else
	719	multout[$iout]=false
	720	fi
[2380]	721	fi
[2669]	722	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	723	then
[2669]	724	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	725	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	726	locat=connect; exit
	727	fi
	728	IFS="$IFSALT"
	729	fi
	730
	731	done < $fileconnection_file
	732
	733
	734
[2501]	735	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	736	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	737	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	738	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	739	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	740	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	741
	742
	743
[2380]	744	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	745	if [[ $run_coupled_model = true ]]
	746	then
	747
	748	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	749	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	750
	751	if (( $cores_ocean + $cores_atmos != $cores ))
	752	then
	753
	754	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	755	printf "\n PEs (total) : $cores"
	756	printf "\n PEs (atmosphere): $cores_atmos"
	757	printf "\n PEs (ocean) : $cores_ocean"
	758	locat=coupling; exit
	759
	760	fi
	761
	762	fi
	763
	764
	765	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	766	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	767	# FOLDER
	768	if [[ $running_in_batch_mode = true ]]
	769	then
	770
[2506]	771	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	772	then
[2506]	773	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	774	printf "\n Please check the output of the palmrun-call"
	775	printf "\n that you did on your local host."
	776	locat=SOURCES_FOR_RUN; exit
	777	fi
	778
	779	else
	780
	781	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	782	# AUTOMATIC RESTART RUN
	783	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	784	if [[ $restart_run = false ]]
	785	then
	786
	787	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	788	# THE LOCAL HOST
	789	if [[ ! -d $source_path ]]
	790	then
	791	printf "\n\n +++ source path \"$source_path\" on local host"
	792	printf "\n \"$(hostname)\" does not exist"
	793	locat=source_path; exit
	794	fi
	795
[2506]	796	rm -rf $sources_for_run_catalog
	797	mkdir -p $sources_for_run_catalog
[2380]	798
	799	if [[ "$source_list" = LM ]]
	800	then
	801
	802	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	803	source_list=""
	804	cd $source_path
	805
	806
[2512]	807	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	808	if [[ ! -d ../.svn ]]
[2380]	809	then
	810	printf "\n\n +++ source directory"
	811	printf "\n \"$source_path\" "
	812	printf "\n is not under control of \"subversion\"."
[2512]	813	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	814	fi
	815
	816
	817	# LIST ALL MODIFIED SOURCE CODE FILES
	818	Filenames=""
[2404]	819	svn status > tmp_svnstatus
[2380]	820	while read line
	821	do
	822	firstc=`echo $line \| cut -c1`
	823	if [[ $firstc = M \|\| $firstc = "?" ]]
	824	then
	825	Name=`echo "$line" \| cut -c8-`
	826	extension=`echo $Name \| cut -d. -f2`
	827	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	828	then
	829	Filenames="$Filenames "$Name
	830	fi
	831	fi
[2404]	832	done < tmp_svnstatus
	833	rm -rf tmp_svnstatus
[2380]	834
	835
	836	# COPY FILES TO SOURCES_FOR_RUN_...
	837	for filename in $Filenames
	838	do
[2506]	839	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	840	source_list=$source_list"$filename "
	841	done
	842
	843	cd - > /dev/null
	844
	845
	846	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	847	elif [[ "$source_list" != "" ]]
	848	then
	849
	850	cd $source_path
	851
	852	for filename in $source_list
	853	do
	854
	855	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	856	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	857	then
	858	printf "\n +++ source code file: $filename"
	859	printf "\n must not contain (\"/\") "
	860	locat=source; exit
	861	fi
	862
	863	if [[ ! -f $filename ]]
	864	then
	865	printf "\n +++ source code file: $filename"
	866	printf "\n does not exist"
	867	locat=source; exit
	868	else
[2506]	869	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	870	fi
	871
	872	done
	873
	874	cd - > /dev/null
	875
	876	fi
	877
	878	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	879	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	880	if [[ ! -f $makefile ]]
	881	then
	882	printf "\n +++ file \"$makefile\" does not exist"
	883	locat=make; exit
	884	else
[2506]	885	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	886	fi
	887
	888
	889	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	890	if [[ "$user_source_path" != "" ]]
[2380]	891	then
	892
	893	# DOES THE DIRECTORY EXIST?
[2384]	894	if [[ ! -d $user_source_path ]]
[2380]	895	then
	896
	897	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	898	printf "\n \"$user_source_path\" "
[2380]	899	printf "\n does not exist or is not a directory."
	900	printf "\n No source code will be used from this directory!\n"
[2384]	901	user_source_path=""
[2380]	902	if [[ $silent == false ]]
	903	then
	904	sleep 2
	905	fi
	906
	907	else
	908
[2384]	909	cd $user_source_path
[2380]	910	found=false
	911
	912	Names=$(ls -1 *.f90 2>&1)
	913	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	914	Names=$(ls -1 *.F90 2>&1)
	915	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	916	Names=$(ls -1 *.F 2>&1)
	917	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	918	Names=$(ls -1 *.f 2>&1)
	919	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	920	Names=$(ls -1 *.c 2>&1)
	921	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	922
	923	cd - > /dev/null
[2506]	924	cd $sources_for_run_catalog
[2380]	925
	926	# COPY MAKEFILE IF EXISTING
[2384]	927	if [[ -f $user_source_path/Makefile ]]
[2380]	928	then
	929	printf "\n\n *** user Makefile from directory"
[2384]	930	printf "\n \"$user_source_path\" is used \n"
[2380]	931	if [[ $silent == false ]]
	932	then
	933	sleep 1
	934	fi
[2384]	935	cp $user_source_path/Makefile .
[2380]	936	fi
	937
	938	for filename in $AddFilenames
	939	do
	940	if [[ -f $filename ]]
	941	then
	942	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	943	printf "\n source code directory \"$user_source_path\" "
[2380]	944	printf "\n but was also given with option \"-s\" which means that it should be taken"
	945	printf "\n from directory \"$source_path\"."
	946	locat=source; exit
	947	fi
	948
[2384]	949	cp $user_source_path/$filename .
[2380]	950	source_list="$source_list $filename"
	951
	952	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	953	if [[ $(grep -c $filename Makefile) = 0 ]]
	954	then
	955	printf "\n\n +++ user file \"$filename\" "
	956	printf "\n is not listed in Makefile \n"
	957	locat=source; exit
	958	else
	959
	960	if [[ $found = false ]]
	961	then
	962	found=true
	963	printf "\n\n *** following user file(s) added to the"
	964	printf " files to be translated:\n "
	965	fi
	966	printf "$filename "
	967	if [[ $silent == false ]]
	968	then
	969	sleep 0.5
	970	fi
	971
	972	fi
	973	done
	974	[[ $found = true ]] && printf "\n"
	975	cd - > /dev/null
	976	fi
	977	fi
	978
	979	# COPY CONFIGURATION FILES
[2506]	980	cp $config_file $sources_for_run_catalog
	981	cp $fileconnection_file $sources_for_run_catalog
[2380]	982
	983	# COPY SHELLSCRIPTS
[2506]	984	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	985	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	986
	987	fi
	988
	989	fi
	990
[2605]	991
[2380]	992	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	993	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	994	if [[ "$global_revision" = "" ]]
	995	then
	996	global_revision=`svnversion $source_path 2>/dev/null`
	997	global_revision="Rev: $global_revision"
	998	fi
	999
	1000
	1001	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1002	if [[ -n $cores ]]
	1003	then
	1004
	1005	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1006	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1007	if [[ $tasks_per_node = 0 ]]
[2380]	1008	then
	1009	printf "\n"
	1010	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1011	printf "\n set -T option or define tasks_per_node in the config file"
	1012	locat=tasks_per_node; (( iec = 0 )); exit
	1013	fi
	1014
	1015	if (( cores < tasks_per_node ))
	1016	then
	1017	printf "\n"
	1018	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1019	printf "\n given values: -T $tasks_per_node -X $cores"
	1020	locat=tasks_per_node; (( iec = 0 )); exit
	1021	fi
	1022
	1023	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1024	(( mpi_tasks = cores / threads_per_task ))
	1025	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1026	(( ii = cores / tasks_per_node ))
	1027	(( remaining_cores = cores - ii * tasks_per_node ))
	1028	if (( remaining_cores > 0 ))
	1029	then
	1030	printf "\n"
	1031	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1032	printf "\n divisor of the total number of cores (option \"-X\")"
	1033	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1034	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1035	(( nodes = nodes + 1 ))
	1036	fi
	1037
	1038	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	1039	if [[ "$tasks_per_node" != "" ]]
	1040	then
	1041	TOPT="-T $tasks_per_node"
	1042	fi
	1043
	1044	fi
	1045
	1046
	1047	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1048	if [[ "$maximum_parallel_io_streams" = "" ]]
	1049	then
	1050	maximum_parallel_io_streams=$cores
	1051	fi
	1052
	1053
	1054	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1055	if [[ "$scp_port" != "" ]]
	1056	then
	1057	PORTOPT="-P $scp_port"
	1058	SSH_PORTOPT="-p $scp_port"
	1059	fi
	1060
	1061
	1062	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1063	# CONFIG-FILE
	1064	if [[ "$ssh_key" != "" ]]
	1065	then
	1066	ssh_key="-i $HOME/.ssh/$ssh_key"
	1067	fi
	1068
	1069
	1070	# SET QUEUE, IF NOT GIVEN
	1071	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1072	then
	1073
	1074	if [[ $queue = none && "$defaultqueue" = "" ]]
	1075	then
	1076	printf "\n"
	1077	printf "\n +++ no default queue given in configuration file and no queue"
	1078	printf "\n given with option -q"
[2789]	1079	locat=queue; exit
[2380]	1080	fi
	1081	if [[ $queue = none ]]
	1082	then
	1083	queue=$defaultqueue
	1084	fi
	1085
	1086	fi
	1087
	1088
	1089	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1090	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1091	(( i = 0 ))
[2610]	1092	(( nr_of_input_files = 0 ))
[2380]	1093	while (( i < iin ))
	1094	do
	1095	(( i = i + 1 ))
	1096
	1097	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1098	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1099	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1100	then
[2610]	1101	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1102	else
[2834]	1103	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
[2380]	1104	fi
	1105
[2610]	1106
[2380]	1107	# CHECK IF FILE EXISTS
	1108	if ! ls $filename* 1>/dev/null 2>&1
	1109	then
	1110
[2669]	1111	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1112	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1113	then
	1114	printf "\n\n +++ INPUT-file: "
[2610]	1115	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1116	then
	1117	printf "\n $filename"
	1118	else
[2610]	1119	printf "\n $filename.${extin_pre[$i]}"
[2380]	1120	fi
	1121	printf "\n does not exist\n"
	1122	locat=input; exit
	1123	else
[2610]	1124	(( nr_of_input_files = nr_of_input_files + 1 ))
	1125	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1126	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1127	actionin[$nr_of_input_files]="unavailable"
[2610]	1128	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1129	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1130	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1131	fi
[2605]	1132
[2380]	1133	else
	1134
[2834]	1135	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
[2610]	1136	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
	1137	if [[ "${multin[$i]}" = true ]]
	1138	then
	1139	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1140	ls -1 -d ${filename} > filelist 2>/dev/null
	1141	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1142	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1143
[2610]	1144	endings=""
	1145	while read line
	1146	do
	1147	# filename without path (i.e. after the last "/")
	1148	basefilename=$(basename ${line})
[2380]	1149
[2610]	1150	# check if there is an extension and remove it
	1151	ext=${basefilename##*.}
	1152	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1153	then
	1154	basefilename=${basefilename%.*}
	1155	fi
[2380]	1156
[2610]	1157	# check for an existing cycle number and remove it
	1158	cycle=${basefilename##*.}
	1159	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1160	then
	1161	basefilename=${basefilename%.*}
	1162	fi
[2600]	1163
[2834]	1164	# remove the jobname from the beginning
	1165	length_jobname=${#jobname}
	1166	ending=${basefilename:${length_jobname}}
[2610]	1167
	1168	# remove the ending given in the .iofiles from the beginning
	1169	endingstring="${endin_pre[$i]}"
	1170	length_ending=${#endingstring}
	1171	ending=${ending:${length_ending}}
	1172
	1173	if [[ "$ending" = "" ]]
[2600]	1174	then
[2610]	1175	# standard ending as given in the .iofiles
	1176	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1177	then
	1178	endings="$endings DEFAULT"
	1179	fi
[2600]	1180	else
[2610]	1181	# ending must start with "_", otherwise its a different file
	1182	if [[ "${ending:0:1}" = "_" ]]
	1183	then
	1184	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1185	then
	1186	endings="$endings $ending"
	1187	fi
	1188	fi
[2600]	1189	fi
[2610]	1190
	1191	done <filelist
[2380]	1192
[2610]	1193	rm filelist
[2380]	1194
[2600]	1195	else
[2610]	1196
	1197	# SINGLE NAME
	1198	endings=DEFAULT
	1199
[2600]	1200	fi
	1201
[2610]	1202	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1203	for ending in $endings
	1204	do
	1205
	1206	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1207	if [[ $ending = DEFAULT ]]
[2380]	1208	then
[2610]	1209	ending=""
	1210	fi
	1211
	1212	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1213	(( nr_of_input_files = nr_of_input_files + 1 ))
	1214	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1215	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1216	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1217	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1218	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1219	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1220
	1221
	1222	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1223	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1224	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1225	then
	1226	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1227	else
[2834]	1228	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
[2380]	1229	fi
[2610]	1230
	1231	# DETERMINE THE FILE'S CYCLE NUMBER
	1232	(( maxcycle = 0 ))
	1233	ls -1 -d $filename > filelist 2>/dev/null
	1234	ls -1 -d $filename.* >> filelist 2>/dev/null
	1235	while read line
	1236	do
	1237	# filename without path (i.e. after the last "/")
	1238	basefilename=$(basename ${line})
	1239
	1240	# check if there is an extension
	1241	extension=${basefilename##*.}
	1242	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1243	then
	1244	basefilename=${basefilename%.*}
	1245	fi
	1246
	1247	# check for an existing cycle number
	1248	cycle=${basefilename##*.}
	1249	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1250	then
[2669]	1251	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1252	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1253	(( icycle = $((10#$cycle)) ))
[2610]	1254	else
	1255	(( icycle = 0 ))
	1256	fi
	1257
	1258	if (( icycle > maxcycle ))
	1259	then
	1260	(( maxcycle = icycle ))
	1261
	1262	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1263	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1264	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1265	then
	1266	leading_zero=true
	1267	else
	1268	leading_zero=false
	1269	fi
	1270	fi
	1271
	1272	done <filelist
	1273	rm filelist
	1274
	1275	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1276	if [[ $leading_zero = true ]]
[2380]	1277	then
[2610]	1278	cyclestring=`printf "%03d" $maxcycle`
	1279	else
	1280	cyclestring=$maxcycle
[2380]	1281	fi
[2610]	1282
	1283	# APPEND CYCLE NUMBER TO FILENAME
	1284	if (( maxcycle > 0 ))
[2380]	1285	then
[2610]	1286	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1287	then
	1288	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1289	else
	1290	filename=${filename}.$cyclestring
	1291	fi
[2380]	1292	else
[2610]	1293	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1294	then
	1295	filename=${filename}.${extin[$nr_of_input_files]}
	1296	fi
[2380]	1297	fi
[2610]	1298
	1299	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1300	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1301	absnamein[$nr_of_input_files]=$filename
	1302	if (( maxcycle > 0 ))
[2380]	1303	then
[2610]	1304	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1305	then
	1306	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1307	else
[2834]	1308	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1309	fi
[2380]	1310	else
[2610]	1311	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1312	then
	1313	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1314	else
[2834]	1315	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
[2610]	1316	fi
[2380]	1317	fi
	1318
[2610]	1319	done
	1320
[2380]	1321	fi
[2610]	1322
[2380]	1323	done
	1324
[2610]	1325
[2380]	1326	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1327	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1328	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1329	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1330	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1331	# REMOTE HOST)
	1332	(( i = 0 ))
	1333	while (( i < iout ))
	1334	do
	1335	(( i = i + 1 ))
[2610]	1336	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1337	then
[2610]	1338	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1339	then
[2610]	1340	actionout_pre[$i]=""
	1341	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1342	then
[2610]	1343	actionout_pre[$i]=pe
	1344	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1345	then
[2610]	1346	actionout_pre[$i]=a
[2380]	1347	fi
	1348	(( maxcycle = 0 ))
[2834]	1349	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
[2610]	1350	eval catalogname=${pathout_pre[$i]}
[2380]	1351	if ! ls $filename* 1>/dev/null 2>&1
	1352	then
	1353
	1354	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1355	if cat /dev/null > $filename
	1356	then
	1357	rm $filename
	1358	else
	1359
	1360	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1361	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1362	if [[ ! -d $catalogname ]]
	1363	then
	1364	if mkdir -p $catalogname
	1365	then
	1366	printf "\n\n *** directory:"
	1367	printf "\n $catalogname"
	1368	printf "\n was created\n"
	1369	else
	1370	printf "\n\n +++ OUTPUT-file:"
	1371	printf "\n $filename"
	1372	printf "\n cannot be created, because directory does not exist"
	1373	printf "\n and cannot be created either"
	1374	printf "\n"
	1375	locat=output ; exit
	1376	fi 2>/dev/null
	1377	else
	1378	printf "\n\n +++ OUTPUT-file:"
	1379	printf "\n $filename"
	1380	printf "\n cannot be created, although directory exists"
	1381	printf "\n"
	1382	locat=output ; exit
	1383	fi
	1384	fi 2>/dev/null
	1385
	1386	fi
	1387
	1388	fi
	1389	done
	1390
	1391
	1392	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1393	if [[ $running_in_batch_mode = false ]]
	1394	then
	1395	run_id=$RANDOM
[2834]	1396	job_id=${jobname}.$run_id
[2380]	1397
[2566]	1398	tempdir=$fast_io_catalog/$job_id
[2380]	1399	fi
	1400
	1401
	1402	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1403	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1404	then
	1405
	1406	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1407	if [[ $ibd = 0 ]]
	1408	then
	1409	printf "\n"
	1410	printf "\n +++ no batch directives found in configuration file"
	1411	locat=config_file_batch_directives; (( iec = 0 )); exit
	1412	fi
	1413
	1414	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1415	done=false
[2384]	1416	cputime=$cpumax
[2380]	1417	while [[ $done = false ]]
	1418	do
[2384]	1419	if (( cputime == 0 ))
[2380]	1420	then
	1421	printf "\n +++ cpu-time is undefined"
	1422	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1423	printf "\n >>> "
[2384]	1424	read cputime 1>/dev/null 2>&1
[2380]	1425	else
	1426	done=true
	1427	fi
	1428	done
[2420]	1429	cpumax=$cputime
[2380]	1430
	1431	# CHECK THE MEMORY DEMAND
	1432	done=false
	1433	while [[ $done = false ]]
	1434	do
	1435	if (( memory == 0 ))
	1436	then
	1437	printf "\n +++ memory demand is undefined"
	1438	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1439	printf "\n >>> "
	1440	read memory 1>/dev/null 2>&1
	1441	else
	1442	done=true
	1443	fi
	1444	done
	1445
	1446	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1447	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1448	then
	1449	while [[ -z $remote_username ]]
	1450	do
[2420]	1451	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1452	printf "\n >>> Please type username:"
	1453	printf "\n >>> "
	1454	read remote_username
	1455	done
	1456	fi
	1457
	1458	else
	1459
[2420]	1460	if [[ $running_in_batch_mode = false ]]
	1461	then
	1462	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1463	cpumax=$cputime
	1464	else
	1465	cputime=$cpumax
	1466	fi
[2380]	1467
	1468	fi
	1469
	1470
	1471	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1472	(( cpu_hours = cputime / 3600 ))
	1473	(( resttime = cputime - cpu_hours * 3600 ))
	1474	(( cpu_minutes = resttime / 60 ))
	1475	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1476	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1477
	1478
	1479	# OUTPUT OF THE PALMRUN-HEADER
	1480	calltime=$(date)
	1481	printf "\n"
	1482	printf "#------------------------------------------------------------------------# \n"
	1483	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1484	printf "\| \| \n"
	1485	column1="called on:"; column2=$(hostname)
	1486	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1487	if [[ $create_remote_batch_job = true ]]
	1488	then
[2506]	1489	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1490	else
	1491	if [[ $running_on_remote = true ]]
	1492	then
[2506]	1493	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1494	else
[2506]	1495	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1496	fi
	1497	fi
	1498	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1499
	1500	column1="running in:"
	1501	if [[ $running_in_batch_mode = true ]]
	1502	then
	1503	column2="batch job mode"
	1504	else
	1505	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1506	then
	1507	column2="job creation mode"
	1508	else
	1509	column2="interactive run mode"
	1510	fi
	1511	fi
	1512	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1513
[2479]	1514	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1515	then
[2480]	1516	if [[ "$project_account" != "" ]]
[2479]	1517	then
	1518	column1="project account number:"
	1519	column2="$project_account"
	1520	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1521	fi
	1522	fi
	1523
[2380]	1524	if [[ -n $cores ]]
	1525	then
	1526	if [[ $run_coupled_model = false ]]
	1527	then
	1528	column1="number of cores:"; column2=$cores
	1529	else
	1530	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1531	fi
	1532	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1533	fi
	1534	if [[ -n $tasks_per_node ]]
	1535	then
	1536	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1537	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1538	if (( remaining_cores > 0 ))
	1539	then
	1540	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1541	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1542	fi
	1543	fi
	1544	if [[ $maximum_parallel_io_streams != $cores ]]
	1545	then
	1546	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1547	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1548	fi
	1549	if [[ $use_openmp = true ]]
	1550	then
	1551	column1="threads per task:"; column2="$threads_per_task"
	1552	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1553	fi
[2384]	1554	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1555	then
[2506]	1556	column1="memory demand / PE":; column2="$memory MB"
	1557	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1558	column1="job cpu time (h:m:s):"; column2="$timestring"
	1559	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1560	fi
[2380]	1561	printf "\| \| \n"
	1562	if [[ "$source_list" != "" ]]
	1563	then
	1564	if [[ "$make_options" != "" ]]
	1565	then
	1566	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1567	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1568	line=$(echo "$make_options" \| cut -c46-)
	1569	while [[ "$line" != "" ]]
	1570	do
	1571	column1=""
	1572	column2=$(echo "$line" \| cut -c-45)
	1573	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1574	line=$(echo "$line" \| cut -c46-)
	1575	done
	1576	fi
	1577	fi
	1578
	1579	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1580	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1581	line=$(echo "$cpp_options" \| cut -c46-)
	1582	while [[ "$line" != "" ]]
	1583	do
	1584	column1=""
	1585	column2=$(echo "$line" \| cut -c-45)
	1586	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1587	line=$(echo "$line" \| cut -c46-)
	1588	done
	1589
	1590	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1591	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1592	line=$(echo "$compiler_options" \| cut -c46-)
	1593	while [[ "$line" != "" ]]
	1594	do
	1595	column1=""
	1596	column2=$(echo "$line" \| cut -c-45)
	1597	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1598	line=$(echo "$line" \| cut -c46-)
	1599	done
	1600
[2388]	1601	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1603	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1604	while [[ "$line" != "" ]]
	1605	do
	1606	column1=""
	1607	column2=$(echo "$line" \| cut -c-45)
	1608	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1609	line=$(echo "$line" \| cut -c46-)
	1610	done
	1611
	1612	if [[ "$login_init_cmd" != "" ]]
	1613	then
	1614	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1616	line=$(echo "$login_init_cmd" \| cut -c46-)
	1617	while [[ "$line" != "" ]]
	1618	do
	1619	column1=""
	1620	column2=$(echo "$line" \| cut -c-45)
	1621	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1622	line=$(echo "$line" \| cut -c46-)
	1623	done
	1624	fi
	1625
	1626	if [[ "$module_commands" != "" ]]
	1627	then
	1628	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1629	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1630	line=$(echo "$module_commands" \| cut -c46-)
	1631	while [[ "$line" != "" ]]
	1632	do
	1633	column1=""
	1634	column2=$(echo "$line" \| cut -c-45)
	1635	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1636	line=$(echo "$line" \| cut -c46-)
	1637	done
	1638	fi
	1639	printf "\| \| \n"
[2834]	1640	column1="base name of files:"; column2=$jobname
[2380]	1641	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1642	column1="activation string list:"; column2=$(echo $activation_string_list)
	1643	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1644
	1645	if [[ "$ocean_file_appendix" = true ]]
	1646	then
	1647	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1648	fi
	1649
	1650	if [[ "$source_list" != "" ]]
	1651	then
	1652	printf "\| \| \n"
	1653	printf "\| Files to be compiled: \| \n"
	1654	line=$source_list
	1655	while [[ "$line" != "" ]]
	1656	do
	1657	linestart=$(echo $line \| cut -c-70)
	1658	printf "\| %-70s \| \n" "$linestart"
	1659	line=$(echo "$line" \| cut -c71-)
	1660	done
	1661	fi
	1662	printf "#------------------------------------------------------------------------#"
	1663
	1664
	1665
	1666	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1667	if [[ $do_trace = true ]]
	1668	then
	1669	(( i = 0 ))
[2610]	1670	while (( i < nr_of_input_files ))
[2380]	1671	do
	1672	(( i = i + 1 ))
	1673	if (( i == 1 ))
	1674	then
	1675	printf "\n\n >>> INPUT-file assignments:\n"
	1676	fi
	1677	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1678	done
	1679	(( i = 0 ))
	1680	while (( i < iout ))
	1681	do
	1682	(( i = i + 1 ))
	1683	if (( i == 1 ))
	1684	then
	1685	printf "\n\n >>> OUTPUT-file assignments:\n"
	1686	fi
	1687	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1688	done
	1689	(( i = 0 ))
	1690	while (( i < iic ))
	1691	do
	1692	(( i = i + 1 ))
	1693	if (( i == 1 ))
	1694	then
	1695	printf "\n\n >>> INPUT-commands:\n"
	1696	fi
	1697	printf "\n ${in_command[$i]}"
	1698	done
	1699	(( i = 0 ))
	1700	while (( i < ioc ))
	1701	do
	1702	(( i = i + 1 ))
	1703	if (( i == 1 ))
	1704	then
	1705	printf "\n\n >>> OUTPUT-commands:\n"
	1706	fi
	1707	printf "\n ${out_command[$i]}"
	1708	done
	1709	fi
	1710
	1711	# QUERY FOR CONTINUE
	1712	if [[ $silent = false && $running_in_batch_mode = false ]]
	1713	then
	1714	antwort=dummy
	1715	printf "\n\n"
	1716	printf " >>> everything o.k. (y/n) ? "
	1717	while read antwort
	1718	do
	1719	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1720	then
	1721	printf " >>> everything o.k. (y/n) ? "
	1722	else
	1723	break
	1724	fi
	1725	done
	1726	if [[ $antwort = n \|\| $antwort = N ]]
	1727	then
	1728	locat=user_abort; (( iec = 0 )); exit
	1729	fi
	1730	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1731	then
[2566]	1732	printf "\n *** batch-job will be created and submitted"
[2380]	1733	else
[2566]	1734	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1735	fi
	1736	fi
	1737
	1738
	1739
	1740	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1741	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1742	then
	1743
	1744	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1745	then
[2566]	1746	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1747	else
[2566]	1748	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1749	fi
	1750
[2422]	1751	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1752	# IT SHALL BE CREATED
	1753	ask_for_make_depository=false
	1754	if [[ $create_remote_batch_job = true ]]
	1755	then
	1756
	1757	line=`grep %base_directory $config_file`
[2506]	1758	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1759	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]	1760
[2506]	1761	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1762	then
	1763	printf "\n\n +++ make depository \"${make_depository}\""
	1764	printf "\n on remote host not found!"
	1765	ask_for_make_depository=true
	1766	fi
[2506]	1767	rm ${host_configuration}_last_make_protokoll
[2422]	1768
	1769	else
	1770
	1771	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1772	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1773	if [[ ! -d ${make_depository} ]]
	1774	then
	1775	printf "\n\n +++ make depository \"${make_depository}\""
	1776	printf "\n on local host not found!"
	1777	ask_for_make_depository=true
	1778	fi
	1779
	1780	fi
	1781
	1782	if [[ $ask_for_make_depository = true ]]
	1783	then
	1784
	1785	antwort=dummy
	1786	printf "\n\n"
	1787	printf " >>> Create a new one (y/n) ? "
	1788	while read antwort
	1789	do
	1790	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1791	then
	1792	printf " >>> Create a new one (y/n) ? "
	1793	else
	1794	break
	1795	fi
	1796	done
	1797	if [[ $antwort = n \|\| $antwort = N ]]
	1798	then
	1799	locat=user_abort; (( iec = 0 )); exit
	1800	fi
	1801
[2566]	1802	if [[ $do_trace = true ]]
	1803	then
	1804	palmbuild -h $host_configuration
	1805	else
	1806	palmbuild -v -h $host_configuration
	1807	fi
[2422]	1808
	1809	if [[ $? != 0 ]]
	1810	then
	1811
	1812	# ABORT IN CASE OF COMPILATION PROBLEMS
	1813	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1814	locat=make_depository
	1815	exit
	1816	else
	1817	echo " *** now continue with creating executable and other sources"
	1818	fi
	1819
	1820	fi
	1821
[2566]	1822	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2834]	1823	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
[2380]	1824
	1825	if [[ $? != 0 ]]
	1826	then
	1827
	1828	# ABORT IN CASE OF COMPILATION PROBLEMS
	1829	printf "\n +++ error while creating executable and/or other sources"
	1830	locat=execution
[2506]	1831	rm -rf $sources_for_run_catalog
[2380]	1832	exit
	1833
	1834	else
	1835
[2566]	1836	printf " *** executable and other sources created\n"
[2506]	1837	rm -rf $sources_for_run_catalog
[2380]	1838
	1839	fi
	1840
	1841	fi
	1842
	1843
[2669]	1844	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1845	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1846	if [[ $create_remote_batch_job = true ]]
	1847	then
	1848	(( i = 0 ))
[2610]	1849	while (( i < nr_of_input_files ))
[2605]	1850	do
	1851	(( i = i + 1 ))
[2669]	1852	if [[ "${actionin[$i]}" = tr ]]
[2605]	1853	then
	1854	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1855	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1856	fi
	1857	done
	1858	if (( i > 0 ))
	1859	then
	1860	printf " *** input files have been copied to the remote host\n"
	1861	fi
	1862	fi
	1863
	1864
[2380]	1865	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1866	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1867	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1868	then
	1869
	1870	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1871	if [[ $running_in_batch_mode = false ]]
	1872	then
	1873	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1874	# FOLDER
[2566]	1875	mkdir -p $tempdir
	1876	chmod go+rx $tempdir
	1877	cd $tempdir
	1878	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1879	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1880
	1881	else
	1882
	1883	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1884	printf "\n *** running in temporary directory: $tempdir"
[2380]	1885
	1886	fi
	1887
	1888
	1889	# PROVIDE THE INPUT FILES
	1890	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1891	optional_files_missing=false
[2380]	1892	(( i = 0 ))
[2610]	1893	while (( i < nr_of_input_files ))
[2380]	1894	do
	1895	(( i = i + 1 ))
	1896	if (( i == 1 ))
	1897	then
	1898	printf "\n\n *** providing INPUT-files:\n$dashes"
	1899	fi
	1900
	1901
	1902	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1903	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1904	then
[2669]	1905	optional_files_missing=true
[2380]	1906	continue
	1907	fi
	1908
	1909	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1910	files_for_cores=false; filetype=file
	1911	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1912	then
	1913	files_for_cores=true; filetype=files
	1914	actionin[$i]=""
	1915	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1916	then
	1917	actionin[$i]=""
	1918	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1919	then
	1920	files_for_cores=true; filetype=files
	1921	actionin[$i]="ln"
	1922	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1923	then
	1924	actionin[$i]="ln"
	1925	fi
	1926
	1927	if [[ $files_for_cores = true ]]
	1928	then
	1929	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1930	else
	1931	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1932	fi
	1933
	1934	# INPUT-FILES TO BE LINKED
	1935	if [[ "${actionin[$i]}" = ln ]]
	1936	then
	1937
	1938	printf "\n $filetype will be linked"
	1939	if [[ $files_for_cores = false ]]
	1940	then
	1941	if [[ -f "${absnamein[$i]}" ]]
	1942	then
	1943	ln ${absnamein[$i]} ${localin[$i]}
	1944	got_tmp[$i]=true
	1945	fi
	1946	else
	1947	if [[ -d "${absnamein[$i]}" ]]
	1948	then
[2396]	1949	mkdir -p ${localin[$i]}
[2380]	1950	cd ${absnamein[$i]}
	1951	for file in $(ls *)
	1952	do
[2566]	1953	ln $file $tempdir/${localin[$i]}
[2380]	1954	done >\|/dev/null 2>&1
[2566]	1955	cd $tempdir
[2380]	1956	fi
	1957
	1958	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1959	if [[ ! -f "${localin[$i]}/_000000" ]]
	1960	then
	1961	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1962	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1963	fi
	1964
	1965	got_tmp[$i]=true
	1966	fi
	1967	fi
	1968
	1969	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	1970	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	1971	then
	1972
	1973	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1974	then
	1975
	1976	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1977	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1978	printf "\n file will be provided for $cores processors"
[2396]	1979	mkdir -p ${localin[$i]}
[2380]	1980	ival=$cores
	1981	(( ii = 0 ))
	1982	while (( ii <= ival-1 ))
	1983	do
	1984	if (( ii < 10 ))
	1985	then
	1986	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1987	elif (( ii < 100 ))
	1988	then
	1989	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1990	elif (( ii < 1000 ))
	1991	then
	1992	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1993	else
	1994	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1995	fi
	1996	(( ii = ii + 1 ))
	1997	done
	1998
	1999	else
	2000
	2001	if [[ $files_for_cores = true ]]
	2002	then
	2003
	2004	# PROVIDE FILES FOR EACH CORE
	2005	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2006	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2007	printf "\n providing $cores files for the respective cores"
[2396]	2008	mkdir -p ${localin[$i]}
[2380]	2009	if [[ $link_local_input = true ]]
	2010	then
	2011	printf " files will be linked\n"
	2012	cd ${absnamein[$i]}
	2013	for file in $(ls *)
	2014	do
	2015	ln -f $file ${localin[$i]}
	2016	done
[2566]	2017	cd $tempdir
[2380]	2018	fi
	2019
	2020	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2021	if [[ ! -f "${localin[$i]}/_000000" ]]
	2022	then
	2023	if [[ $link_local_input = true ]]
	2024	then
	2025	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2026	fi
	2027	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2028	fi
	2029
	2030	else
	2031
	2032	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2033	if [[ $link_local_input = true ]]
	2034	then
	2035	printf " file will be linked\n"
	2036	ln -f ${absnamein[$i]} ${localin[$i]}
	2037	fi
[2605]	2038	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2039	if [[ ! -f "${localin[$i]}" ]]
	2040	then
	2041	if [[ $link_local_input = true ]]
	2042	then
	2043	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2044	fi
[2669]	2045	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2046	then
	2047	mv ${absnamein[$i]} ${localin[$i]}
	2048	else
	2049	cp ${absnamein[$i]} ${localin[$i]}
	2050	fi
[2380]	2051	fi
	2052	fi
	2053	fi
	2054	fi
	2055
	2056	done
	2057	if (( i != 0 ))
	2058	then
[2669]	2059	if [[ $optional_files_missing = true ]]
	2060	then
	2061	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2062	fi
[2380]	2063	printf "\n$dashes\n *** all INPUT-files provided \n"
	2064	fi
	2065
	2066
	2067	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2068	(( i = 0 ))
	2069	while (( i < iic ))
	2070	do
	2071	(( i = i + 1 ))
	2072	if (( i == 1 ))
	2073	then
	2074	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2075	fi
	2076	printf "\n >>> ${in_command[$i]}"
	2077	eval ${in_command[$i]}
	2078	if (( i == iic ))
	2079	then
	2080	printf "\n$dashes\n"
	2081	fi
	2082	done
	2083
	2084
	2085	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2086	# (FILE ENVPAR WILL BE READ BY PALM)
	2087	cat > ENVPAR << EOF
[2834]	2088	&envpar run_identifier = '$jobname', host = '$host_configuration',
[2906]	2089	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2090	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2091	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2092	maximum_cpu_time_allowed = ${cpumax}.,
	2093	revision = '$global_revision',
	2094	batch_job = .${running_in_batch_mode}. /
	2095
	2096	EOF
	2097
	2098
	2099	# STARTING THE EXECUTABLE
	2100	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2101	PATH=$PATH:$tempdir
[2380]	2102
	2103
	2104	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2105	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2106	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2107	eval line=\"$line\"
	2108	execute_command="$line"
	2109
	2110
	2111	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2112	if [[ "$execute_command_for_combine" = "" ]]
	2113	then
	2114	eval line2=\"$line2\"
	2115	execute_command_for_combine="$line2"
	2116	fi
	2117
[2380]	2118
	2119
	2120	# PROVIDE A HOSTFILE, IF REQUIRED
	2121	if [[ "$hostfile" != "" ]]
	2122	then
	2123
	2124	if [[ $hostfile = auto ]]
	2125	then
	2126	# CREATE A NEW HOSTFILE
	2127	(( ii = 1 ))
	2128	while (( ii <= cores / threads_per_task ))
	2129	do
	2130	echo $(hostname) >> hostfile
	2131	(( ii = ii + 1 ))
	2132	done
	2133	if (( cores / threads_per_task == 0 ))
	2134	then
	2135	echo $(hostname) >> hostfile
	2136	fi
	2137
	2138	else
	2139	cp $hostfile hostfile
	2140	fi
	2141	eval line=\"`head -n $ii hostfile`\"
	2142	printf "\n *** running on: $line"
	2143	fi
	2144
	2145
	2146
	2147	# SET THE NUMBER OF OPENMP-THREADS
	2148	if [[ $use_openmp = true ]]
	2149	then
	2150	export OMP_NUM_THREADS=$threads_per_task
	2151	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2152	else
	2153	export OMP_NUM_THREADS=1
	2154	fi
	2155
	2156
[2610]	2157	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2158	if [[ $run_coupled_model = false ]]
	2159	then
	2160	if [[ "$ocean_file_appendix" = true ]]
	2161	then
	2162	echo "precursor_ocean" > coupling_steering
	2163	else
	2164	echo "precursor_atmos" > coupling_steering
	2165	fi
	2166	else
	2167	(( iia = $cores_atmos / $threads_per_task ))
	2168	(( iio = $cores_ocean / $threads_per_task ))
	2169	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2170	printf "\n\n"
	2171	echo "coupled_run $iia $iio" > coupling_steering
	2172	fi
	2173
	2174	printf "\n *** execute command:"
	2175	printf "\n \"$execute_command\" \n\n"
	2176
	2177	$execute_command < coupling_steering
	2178
	2179	if [[ $? != 0 ]]
	2180	then
	2181
	2182	# ABORT IN CASE OF RUNTIME ERRORS
	2183	printf "\n +++ runtime error occured"
	2184	locat=execution
	2185	exit
	2186
	2187	else
	2188
	2189	printf "\n$dashes\n *** execution finished \n"
	2190
	2191	fi
	2192
	2193
	2194	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2195	# BY EACH CORE INTO ONE FILE
	2196	if [[ ! -f combine_plot_fields.x ]]
	2197	then
	2198
	2199	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2200	printf "\n 2d- and/or 3d-data may be incomplete!"
	2201	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2202
	2203	elif [[ "$combine_plot_fields" == true ]]
	2204	then
	2205
	2206	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2207	$execute_command_for_combine
	2208
	2209	else
	2210
	2211	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2212	# DATA OUTPUT
[2380]	2213	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2214	fi
	2215
	2216
	2217
	2218	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2219	(( i = 0 ))
	2220	while (( i < ioc ))
	2221	do
	2222	(( i = i + 1 ))
	2223	if (( i == 1 ))
	2224	then
	2225	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2226	fi
[2799]	2227
	2228	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2229	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2230
[2380]	2231	printf "\n >>> ${out_command[$i]}"
	2232	eval ${out_command[$i]}
	2233	if (( i == ioc ))
	2234	then
	2235	printf "\n$dashes\n"
	2236	fi
	2237	done
	2238
	2239
[2610]	2240	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2241	# WILDCARDS
[2380]	2242	(( i = 0 ))
[2610]	2243	(( nr_of_output_files = 0 ))
	2244
[2380]	2245	while (( i < iout ))
	2246	do
[2610]	2247
[2380]	2248	(( i = i + 1 ))
[2610]	2249
	2250	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2251	# CREATE A LIST FOR THE DETECTED ENDINGS
	2252	if [[ "${multout[$i]}" = true ]]
	2253	then
	2254	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2255	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2256	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2257
	2258	endings="DEFAULT"
	2259	while read line
	2260	do
	2261	# remove the local name from the beginning
	2262	localnamestring="${localout_pre[$i]}"
	2263	length_localname=${#localnamestring}
	2264	ending=${line:${length_localname}}
	2265
	2266	if [[ "$ending" != "" ]]
	2267	then
	2268	endings="$endings $ending"
	2269	fi
	2270
	2271	done <filelist
	2272
	2273	rm filelist
	2274
	2275	else
	2276
	2277	# SINGLE NAME
	2278	endings=DEFAULT
	2279
	2280	fi
	2281
	2282	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2283	for ending in $endings
	2284	do
	2285
	2286	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2287	if [[ $ending = DEFAULT ]]
	2288	then
	2289	ending=""
	2290	fi
	2291
	2292	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2293	(( nr_of_output_files = nr_of_output_files + 1 ))
	2294	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2295	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2296	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2297	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2298	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2299	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2300	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2301
	2302	done
	2303
	2304	done
	2305
	2306
	2307
	2308
	2309	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2310	(( i = 0 ))
	2311	while (( i < nr_of_output_files ))
	2312	do
	2313	(( i = i + 1 ))
[2380]	2314	if (( i == 1 ))
	2315	then
	2316	printf "\n\n *** saving OUTPUT-files:"
	2317
	2318	# GET RUN NUMBER ASSIGNED BY PALM
	2319	if [[ -f RUN_NUMBER ]]
	2320	then
	2321	read run_number < RUN_NUMBER
	2322	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2323	usecycle_option="-U $run_number"
	2324	else
	2325	run_number=0
	2326	usecycle_option=""
	2327	fi
	2328	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2329	then
[2404]	2330	printf "\n *** in case of SCP transfers to local host"
	2331	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2332	fi
	2333	printf "\n$dashes"
	2334	fi
	2335
	2336	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2337	then
	2338
[2834]	2339	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
[2610]	2340
	2341	# DETERMINE THE CYCLE NUMBER
	2342	ls -1 -d $filename > filelist 2>/dev/null
	2343	ls -1 -d $filename.* >> filelist 2>/dev/null
	2344	while read line
	2345	do
	2346
	2347	# filename without path (i.e. after the last "/")
	2348	basefilename=$(basename ${line})
	2349
	2350	# check if there is an extension
	2351	extension=${basefilename##*.}
	2352	if [[ "$extension" = "${extout[$i]}" ]]
	2353	then
	2354	basefilename=${basefilename%.*}
	2355	fi
	2356
	2357	# check for an existing cycle number
	2358	cycle=${basefilename##*.}
	2359	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2360	then
[2669]	2361	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2362	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2363	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2364	else
	2365	(( icycle = 1 ))
	2366	fi
	2367
	2368	if (( icycle > maxcycle ))
	2369	then
	2370	(( maxcycle = icycle ))
	2371	fi
	2372
	2373	done <filelist
	2374	rm filelist
	2375
	2376
	2377	# SET THE CYCLE NUMBER
	2378	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2379	if [[ "${actionout[$i]}" = a ]]
	2380	then
	2381	(( maxcycle = maxcycle - 1 ))
	2382	fi
	2383
	2384	(( cycnum[$i] = maxcycle ))
	2385	pathout[$i]=$filename
	2386
	2387
	2388	# ADD CYCLE NUMBER TO FILENAME
	2389	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2390	if [[ "${actionout[$i]}" != "a" ]]
	2391	then
	2392	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2393	# WITH AN EXISTING CYCLE NUMBER
	2394	if (( run_number >= cycnum[$i] ))
	2395	then
	2396	(( cycnum[$i] = run_number ))
	2397	else
	2398	if (( run_number > 0 ))
	2399	then
	2400	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2401	fi
	2402	fi
	2403	fi
	2404	if (( cycnum[$i] > 0 ))
	2405	then
[2600]	2406	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2407	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2408	fi
	2409	fi
	2410
	2411	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2412	files_for_cores=false; filetype=file
	2413	link_local_output=false
	2414	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2415	then
	2416	files_for_cores=true; filetype=directory
	2417	actionout[$i]=""
	2418	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2419	then
	2420	actionout[$i]=""
	2421	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2422	then
	2423	files_for_cores=true; filetype=directory
	2424	link_local_output=true
	2425	actionout[$i]=""
	2426	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2427	then
	2428	link_local_output
	2429	actionout[$i]=""
	2430	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2431	then
	2432	files_for_cores=true; filetype=directory
	2433	actionout[$i]="tr"
	2434	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2435	then
	2436	actionout[$i]="tr"
	2437	fi
	2438
	2439	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2440	then
[2669]	2441	if [[ ${warnout[$i]} = true ]]
	2442	then
	2443	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2444	fi
[2380]	2445	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2446	then
[2669]	2447	if [[ ${warnout[$i]} = true ]]
	2448	then
	2449	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2450	fi
[2380]	2451	else
	2452
	2453
	2454	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2455	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2456	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2457	then
	2458	if [[ $running_on_remote = true ]]
	2459	then
	2460
	2461	# SET OPTIONS FOR TRANSFER
	2462	if [[ "${actionout[$i]}" = tr ]]
	2463	then
	2464	if [[ $files_for_cores = false ]]
	2465	then
	2466	catalog_option=""
	2467	catalog_string=""
	2468	else
	2469	catalog_option="-c"
	2470	catalog_string="/"
	2471	fi
	2472	append_option=""
	2473	append_string=""
	2474	else
	2475	append_option="-A"
	2476	append_string="append"
	2477	fi
	2478
	2479	transfer_failed=false
	2480	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2834]	2481	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
[2380]	2482
	2483	# TRANSFER VIA SCP
	2484	if [[ "$remote_loginnode" != "" ]]
	2485	then
[2834]	2486	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]	2487	else
[2834]	2488	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]	2489	fi
	2490	[[ $? != 0 ]] && transfer_failed=true
	2491
	2492
	2493	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2494	if [[ $transfer_failed = true ]]
	2495	then
	2496	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2834]	2497	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
[2380]	2498
	2499	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2500	eval local_catalog=${pathout[$i]}
	2501	if [[ ! -d $local_catalog ]]
	2502	then
	2503	printf " *** local directory does not exist. Trying to create:\n"
	2504	printf " $local_catalog \n"
	2505	mkdir -p $local_catalog
	2506	fi
[2834]	2507	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
[2380]	2508	transfer_problems=true
	2509	fi
	2510
	2511	else
	2512
	2513	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2514	# BE COPIED OR APPENDED ON THIS MACHINE
	2515	if [[ "${actionout[$i]}" = tr ]]
	2516	then
	2517	actionout[$i]=""
	2518	else
	2519	actionout[$i]="a"
	2520	fi
	2521	fi
	2522	fi
	2523
	2524
	2525	# APPEND ON THIS MACHINE
	2526	if [[ "${actionout[$i]}" = "a" ]]
	2527	then
	2528	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2529	then
	2530	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2531	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2532	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2533	else
	2534	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2535	printf "\n ${pathout[$i]}\n"
	2536	cat ${localout[$i]} >> ${pathout[$i]}
	2537	fi
	2538	fi
	2539
	2540	# COPY ON THIS MACHINE
	2541	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2542	# ON DIFFERENT FILE-SYSTEMS
	2543	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2544	then
	2545
	2546	# COPY IN CASE OF RUNS ON SINGLE CORES
	2547	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2548	then
	2549	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2550	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2551	if [[ $link_local_output = true ]]
	2552	then
	2553	printf " file will be linked\n"
	2554	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2555	fi
	2556	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2557	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2558	then
	2559	if [[ $link_local_output = true ]]
	2560	then
	2561	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2562	fi
	2563	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2564	else
	2565	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2566	fi
	2567	else
	2568	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2569	printf "\n ${pathout[$i]}\n"
	2570	if [[ $link_local_output = true ]]
	2571	then
	2572	printf " file will be linked\n"
	2573	ln -f ${localout[$i]} ${pathout[$i]}
	2574	fi
	2575	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2576	if [[ ! -f "${pathout[$i]}" ]]
	2577	then
	2578	if [[ $link_local_output = true ]]
	2579	then
	2580	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2581	fi
	2582	cp ${localout[$i]} ${pathout[$i]}
	2583	else
	2584	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2585	fi
	2586	fi
	2587
	2588	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2589	then
	2590
	2591	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2592	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2593	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2594	printf "\n ${pathout[$i]}\n"
	2595	if [[ $link_local_output = true ]]
	2596	then
	2597	printf " files will be linked\n"
[2396]	2598	mkdir -p ${pathout[$i]}
[2380]	2599	cd ${localout[$i]}
	2600	for file in $(ls *)
	2601	do
	2602	ln -f $file ${pathout[$i]}
	2603	done >\|/dev/null 2>&1
[2566]	2604	cd $tempdir
[2380]	2605	fi
	2606
	2607	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2608	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2609	then
	2610	if [[ $link_local_output = true ]]
	2611	then
	2612	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2613	fi
	2614	cp -r ${localout[$i]}/* ${pathout[$i]}
	2615	fi
	2616
	2617	fi
	2618	fi
	2619	done
	2620
	2621	if (( i != 0 ))
	2622	then
	2623	if [[ $transfer_problems = true ]]
	2624	then
	2625	printf "\n$dashes\n *** OUTPUT-files saved"
	2626	printf "\n +++ WARNING: some data transfers failed! \n"
	2627	else
	2628	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2629	fi
	2630	fi
	2631
	2632
	2633	# IF REQUIRED, START A RESTART-JOB
	2634	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2635	if [[ -f CONTINUE_RUN ]]
	2636	then
	2637
	2638	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2639	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2640	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2641	# -b START A BATCH JOB
	2642	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2643	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2644	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2645
[2957]	2646	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2647	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2648	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2649	then
	2650	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2651	fi
[2380]	2652
	2653	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2654	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2655	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2656	then
[2381]	2657	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2658	fi
	2659
	2660
	2661	# START THE RESTART-JOB
	2662	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2663	echo " $prc"
	2664	printf "\n$dashes\n"
	2665	if [[ $running_on_remote = true ]]
	2666	then
	2667
	2668	echo "*** ssh will be used to initiate restart-runs!"
	2669	echo " return_address=\"$return_address\" "
	2670	echo " return_username=\"$local_username\" "
	2671
	2672	if [[ "$remote_loginnode" != "" ]]
	2673	then
[2420]	2674	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]	2675	else
[2420]	2676	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2677	fi
	2678
	2679	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2680	sleep 30
	2681
	2682	else
	2683
	2684	# START THE RESTART JOB ON THE LOCAL HOST
	2685	eval $prc # THE ' MUST BE EVALUATED
	2686	cd - > /dev/null
	2687
	2688	fi
	2689	printf "\n$dashes\n *** restart-run initiated \n"
	2690
	2691
	2692	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2693	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2694	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2695	# MAY BE VERY HUGE)
	2696	(( i = 0 ))
[2610]	2697	while (( i < nr_of_input_files ))
[2380]	2698	do
	2699	(( i = i + 1 ))
	2700	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2701	then
	2702	rm -r ${absnamein[$i]}
	2703	fi
	2704	done
	2705
	2706	fi
	2707
	2708
	2709	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2710	cd $HOME
[2566]	2711	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2712
	2713
	2714	else
	2715
	2716
	2717	# PREPARING ACTIONS,
	2718	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2719
	2720	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2834]	2721	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2722	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2723	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2724	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2725	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2726	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2727	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2728	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2729	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2730	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2731	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2732	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2733	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2734	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2735	if [[ $create_remote_batch_job = true ]]
	2736	then
	2737	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2738	if [[ $do_trace = true ]]
	2739	then
	2740	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2741	fi
[2380]	2742	elif [[ $create_batch_job = true ]]
	2743	then
	2744	palmrun_com=${palmrun_com}" -j"
[2420]	2745	if [[ $do_trace = true ]]
	2746	then
	2747	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2748	fi
[2380]	2749	fi
	2750
	2751
	2752	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2753	# REMOTE HOST
[2506]	2754	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2755	job_protocol_file=$job_protocol_file_local
	2756	if [[ $create_remote_batch_job = true ]]
	2757	then
[2506]	2758	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2759	job_protocol_file=$job_protocol_file_remote
	2760	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2761	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2762	fi
	2763
	2764
	2765	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2766	jobfile=jobfile.$run_id
	2767
	2768
	2769	# FIRST CREATE THE BATCH DIRECTIVES
	2770	(( i = 0 ))
	2771	while (( i < ibd ))
	2772	do
	2773	(( i = i + 1 ))
[2693]	2774	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2775	eval line=\"$line\"
	2776	echo "$line" >> $jobfile
	2777	done
	2778	echo " " >> $jobfile
	2779
	2780
	2781	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2782	# PROTOCOL
	2783	if [[ $create_remote_batch_job = true ]]
	2784	then
	2785	echo "set +vx" >> $jobfile
	2786	echo "trap '" >> $jobfile
	2787	echo "set +vx" >> $jobfile
	2788	echo "cd ${remote_jobcatalog}" >> $jobfile
	2789	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2790
	2791	# ADD THE BATCH DIRECTIVES
	2792	(( i = 0 ))
	2793	while (( i < ibdt ))
	2794	do
	2795	(( i = i + 1 ))
[2693]	2796	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2797	eval line=\"$line\"
	2798	echo "$line" >> $jobfile
	2799	done
	2800	echo " " >> $jobfile
	2801
	2802	echo "set -x" >> $jobfile
[2834]	2803	echo "${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]	2804	echo "%%END%%" >> $jobfile
	2805	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2806	echo "$submit_command $scpjob_file" >> $jobfile
	2807	echo "rm $scpjob_file" >> $jobfile
[2404]	2808	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2809	echo "set -x" >> $jobfile
	2810	echo " ' exit" >> $jobfile
	2811	fi
	2812
	2813
	2814	# ACTIVATE ERROR-TRACEBACK
	2815	if [[ $do_trace = true ]]
	2816	then
	2817	echo "set -x" >> $jobfile
	2818	else
	2819	echo "set +vx" >> $jobfile
	2820	fi
	2821
	2822
	2823	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2824	if [[ "$login_init_cmd" != "" ]]
	2825	then
	2826	echo "$login_init_cmd" >> $jobfile
	2827	fi
	2828	if [[ "$module_commands" != "" ]]
	2829	then
	2830	echo "$module_commands" >> $jobfile
	2831	fi
	2832
	2833
	2834	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2835	if [[ $create_remote_batch_job = true ]]
	2836	then
	2837	echo "mkdir $tempdir" >> $jobfile
	2838	echo "chmod go+rx $tempdir" >> $jobfile
	2839	else
	2840	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2841	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2842	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2843	mkdir $tempdir
	2844	chmod go+rx $tempdir
	2845	fi
	2846	echo "cd $tempdir" >> $jobfile
	2847	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2848	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2849	echo "export PATH=.:\$PATH" >> $jobfile
	2850	echo "export execute_palmrun=true" >> $jobfile
	2851
	2852
	2853	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2854	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2855	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2856	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2857	echo "export LOCAL_PWD" >> $jobfile
	2858
	2859
	2860	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2861	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2862	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2863
	2864
	2865	# CALL PALMRUN WITHIN THE JOB
	2866	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2867	echo "set -x" >> $jobfile
	2868	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2869
	2870
	2871	# TRANSFER JOBFILE TO THE TARGET HOST
	2872	if [[ $create_jobfile_only = false ]]
	2873	then
	2874
	2875	if [[ $create_remote_batch_job = true ]]
	2876	then
	2877
[2420]	2878	echo " "
[2566]	2879	echo " *** transfer of job to remote host via scp"
[2420]	2880	if [[ $do_trace = true ]]
	2881	then
[2506]	2882	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2883	fi
[2566]	2884	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2885
[2566]	2886	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2887	if [[ $do_trace = true ]]
	2888	then
[2506]	2889	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]	2890	fi
[2506]	2891	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]	2892
	2893	elif [[ $create_batch_job = true ]]
	2894	then
	2895
[2385]	2896	eval local_jobcatalog=$local_jobcatalog
[2506]	2897	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2898	cd $local_jobcatalog
[2380]	2899	echo " "
[2420]	2900	echo " *** submit the job"
	2901	if [[ $do_trace = true ]]
	2902	then
[2506]	2903	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2904	fi
[2506]	2905	$submit_command ${host_configuration}_${job_id}
	2906	rm ${host_configuration}_${job_id}
[2380]	2907	cd - > /dev/null
	2908
	2909	fi
	2910
	2911	rm -rf $jobfile
	2912
	2913	else
	2914
	2915	printf "\n *** jobfile created under name \"$jobfile\" "
	2916	printf "\n no batch-job has been sent!"
	2917
	2918	fi
	2919
	2920	fi # END OF REMOTE-PART

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