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source: palm/trunk/SCRIPTS/palmrun @ 2769

Last change on this file since 2769 was 2762, checked in by raasch, 7 years ago
file connection file is taken by default from trunk/SCRIPTS
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 95.1 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 $
[2762]	29	# file connection file from trunk/SCRIPTS is taken by default
	30	#
	31	# 2718 2018-01-02 08:49:38Z maronga
[2716]	32	# Corrected "Former revisions" section
	33	#
	34	# 2696 2017-12-14 17:12:51Z kanani
	35	# Change in file header (GPL part)
	36	#
	37	# 2693 2017-12-13 12:33:49Z raasch
[2693]	38	# replacement of variables given by {{<variable>}} in configuration file is now
	39	# done in a more general way, variable names are written in small letters
	40	#
	41	# 2670 2017-12-06 16:32:19Z raasch
[2670]	42	# test printouts removed
	43	#
	44	# 2669 2017-12-06 16:03:27Z raasch
[2669]	45	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	46	# removed,
	47	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	48	# files,
	49	# informative messages in case of missing optional input files shortened
	50	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	51	#
	52	# 2638 2017-11-23 12:44:23Z raasch
[2610]	53	# use of wildcards in file connection statements enabled
	54	#
	55	# 2605 2017-11-09 15:31:46Z raasch
[2605]	56	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	57	# will not be sent with the job file any more, but copied into the
[2610]	58	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	59	#
	60	# 2600 2017-11-01 14:11:20Z raasch
[2600]	61	# cycle numbers are made three digits wide
	62	#
	63	# 2566 2017-10-20 08:50:47Z raasch
[2566]	64	# execute command for combine_plot_fields added
	65	# "TEMPDIR" renamed "tempdir"
	66	# temporary working directory for local batch jobs is created immediately within
	67	# the user's palmrun call, due to a requirement of the "grid engine" batch
	68	# system, where the working directory is given with batch directive -wd and must
	69	# already exist when the job is submitted,
	70	# informative messages in non-trace mode reduced and partly reformatted
	71	#
	72	# 2551 2017-10-18 07:25:11Z raasch
[2551]	73	# TEMPDIR added as replacement string to be used in batch directives
	74	#
	75	# 2512 2017-10-04 08:26:59Z raasch
[2507]	76	# bugfix for determining cycle numbers of NetCDF input files
	77	#
	78	# 2506 2017-09-29 08:30:37Z raasch
[2506]	79	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	80	# host configuration added to SOURCES_FOR_RUN_... folder name
	81	# host_identifier renamed host_configuration
	82	# option -W added to allow for job dependencies
	83	#
	84	# 2501 2017-09-26 11:41:55Z raasch
[2501]	85	# default value for number of cores (option -X) set to 1
	86	# bugfix for mechanism which overwrites configuration file settings with values
	87	# provided by palmrun options
	88	#
	89	# 2499 2017-09-22 16:47:58Z kanani
[2499]	90	# option -h named configuration identifier
	91	#
	92	# 2480 2017-09-19 06:24:14Z maronga
[2480]	93	# bugfix for last revision
	94	#
	95	# 2479 2017-09-19 06:12:16Z raasch
[2479]	96	# option -A (project account number) added
	97	#
	98	# 2422 2017-09-08 08:25:41Z raasch
[2410]	99	# initial revision
[2380]	100	#
	101	#--------------------------------------------------------------------------------#
	102	# palmrun - script for running PALM jobs on local and remote hosts
	103	#--------------------------------------------------------------------------------#
	104
	105
	106
	107	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	108
	109	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	110	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	111	# (TOO MANY ARGUMENTS - PROBLEM)
	112	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	113
[2610]	114	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	115	typeset -i nr_of_output_files=0
[2380]	116	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	117	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	118	# SCRIPT-OPTION ARGUMENTS
	119	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	120	typeset -i icycle inode ival maxcycle mpi_tasks
	121	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	122
	123	activation_string_list=""
	124	AddFilenames=""
	125	combine_plot_fields=true
	126	compiler_name=""
	127	compiler_name_ser=""
	128	compiler_options=""
[2501]	129	cores=1
[2380]	130	cores_atmos=0
	131	cores_ocean=0
	132	coupled_dist=""
	133	cpp_options=""
	134	cpumax=0
[2506]	135	create_batch_job=false
[2380]	136	create_jobfile_only=false
	137	create_remote_batch_job=false
	138	dashes=" ----------------------------------------------------------------------------"
	139	defaultqueue=""
[2506]	140	delete_temporary_catalog=true
[2380]	141	do_compile=true
	142	do_trace=false
	143	executable=""
	144	execute_command=""
	145	execution_error=false
[2762]	146	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	147	fname=test
	148	global_revision=""
[2506]	149	host_configuration="default"
[2380]	150	hostfile=""
	151	hp=""
	152	keep_data_from_previous_run=false
	153	link_local_input=false
	154	link_local_output=false
[2388]	155	linker_options=""
[2385]	156	local_jobcatalog=""
[2380]	157	locat=normal
	158	makefile=""
	159	max_par_io_str=""
	160	prc=$0
	161	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	162	do
	163	prc=`echo $prc \| cut -f2- -d"/"`
	164	done
	165	module_calls=""
[2506]	166	palmrun_memory=""
[2380]	167	palmrun_script_name=$prc
	168	openmp=false
[2506]	169	previous_job=""
[2479]	170	project_account=""
[2380]	171	queue=none
	172	restart_run=false
	173	return_address=""
[2385]	174	remote_jobcatalog=""
[2380]	175	remote_username=""
	176	running_in_batch_mode=false
	177	run_coupled_model=false
	178	run_id=""
	179	silent=false
	180	source_list=""
	181	source_path=""
[2501]	182	tasks_per_node=0
[2380]	183	threads_per_task=1
	184	transfer_problems=false
[2384]	185	user_source_path=""
[2506]	186	use_existing_sources_folder=""
[2380]	187	use_openmp=false
[2732]	188	version="palmrun 1.0 Rev$Rev: 2762 $"
[2380]	189	working_directory=`pwd`
	190	write_binary=""
	191	TOPT=""
	192
	193
	194	# ERROR HANDLING IN CASE OF EXIT
[2404]	195	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	196	then
	197
	198	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	199	(( i = 0 ))
	200	while (( i < iec ))
	201	do
	202	(( i = i + 1 ))
	203	printf "\n *** Execution of ERROR-command:\n"
	204	printf " >>> ${err_command[$i]}\n"
	205	eval ${err_command[$i]}
	206	done
[2566]	207	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	208	printf "\n\n+++ palmrun killed \n\n"
	209	elif [[ $locat != control_c ]]
	210	then
[2566]	211	printf "\n --> palmrun finished\n\n"
[2380]	212	fi' exit
	213
	214
	215	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	216	trap 'cd; rm -rf $tempdir
[2380]	217	printf "\n+++ palmrun killed by \"^C\" \n\n"
	218	locat=control_c
	219	exit
	220	' 2
	221
	222
	223	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	224	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	225	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]	226	do
	227	case $option in
	228	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	229	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	230	(b) create_batch_job=true; prc="$prc -b";;
	231	(B) delete_temporary_catalog=false; prc="$prc -B";;
	232	(C) restart_run=true; prc="$prc -C";;
	233	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	234	(F) create_jobfile_only=true;;
	235	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	236	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	237	(j) running_in_batch_mode=true;;
	238	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	239	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	240	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	241	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	242	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	243	(r) run_id=$OPTARG;;
	244	(R) return_address=$OPTARG;;
	245	(s) source_list=$OPTARG;;
[2501]	246	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	247	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	248	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	249	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	250	(v) silent=true; prc="$prc -v";;
[2506]	251	(V) use_existing_sources_folder="-V";;
[2380]	252	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	253	(W) previous_job=$OPTARG;;
[2380]	254	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	255	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	256	(y) ocean_file_appendix=true; prc="$prc -y";;
	257	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	258	(Z) combine_plot_fields=false; prc="$prc -Z";;
	259	(\?) printf "\n +++ unknown option $OPTARG \n"
	260	printf "\n --> type \"$0 ?\" for available options \n"
	261	locat=parameter;exit;;
	262	esac
	263	done
	264
	265
	266	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	267	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	268	(( to_shift = $OPTIND - 1 ))
	269	shift $to_shift
	270
	271	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	272	if [[ "$1" = "?" ]]
	273	then
	274	(printf "\n *** Description of available palmrun options:\n"
	275	printf "\n Option Description Default-Value"
	276	printf "\n -a activation string list \"\" "
[2479]	277	printf "\n -A project account number ---"
[2380]	278	printf "\n -b batch-job on local machine ---"
	279	printf "\n -B do not delete temporary directory at end ---"
	280	printf "\n -d base name of files attached to program test"
	281	printf "\n -F create batch job file only ---"
[2506]	282	printf "\n -h host configuration \"default\" "
[2380]	283	printf "\n -k keep data from previous run"
	284	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	285	printf "\n -M Makefile name Makefile"
	286	printf "\n -O threads per openMP task ---"
	287	printf "\n -q queue \"$queue\" "
	288	printf "\n -s filenames of routines to be compiled \"\" "
	289	printf "\n must end with .f, .f90, .F, or .c !"
	290	printf "\n use \"..\" for more than one file and wildcards"
	291	printf "\n -s LM compiles all locally modified files"
	292	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	293	printf "\n -T tasks per node ---"
[2380]	294	printf "\n -u username on remote machine \"\" "
	295	printf "\n -v no prompt for confirmation ---"
[2506]	296	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	297	printf "\n -w maximum parallel io streams as given by -X"
[2506]	298	printf "\n -W name of job to wait for ---"
[2380]	299	printf "\n -x tracing of palmrun for debug purposes ---"
	300	printf "\n -X # of processors (on parallel machines) 1"
	301	printf "\n -y add appendix \"_O\" to all local output"
	302	printf "\n files (ocean precursor runs followed by"
	303	printf "\n coupled atmosphere-ocean runs) ---"
	304	printf "\n -Y run coupled model, \"#1 #2\" with"
	305	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	306	printf "\n -Z skip combine_plot_fields at the end of "
	307	printf "\n the simulation ---"
	308	printf "\n "
	309	printf "\n Possible values of positional parameter <modus>:"
	310	printf "\n \"?\" - this outline \n\n") \| more
	311	exit
	312	elif [[ "$1" != "" ]]
	313	then
	314	printf "\n +++ positional parameter $1 unknown \n"
	315	locat=parameter; exit
	316	fi
	317
	318
	319
	320	# SHORT STARTING MESSAGE
	321	printf "\n*** $version "
	322	printf "\n will be executed. Please wait ..."
	323
	324
[2506]	325	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	326	config_file=.palm.config.$host_configuration
	327	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
[2380]	328
	329
	330	# CHECK, IF CONFIGURATION FILE EXISTS
	331	if [[ ! -f $config_file ]]
	332	then
	333	printf "\n\n +++ configuration file: "
	334	printf "\n $config_file"
	335	printf "\n does not exist"
	336	locat=connect; exit
	337	fi
	338
	339
[2762]	340	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	341	if [[ -f .palm.iofiles ]]
	342	then
	343	fileconnection_file=.palm.iofiles
	344	fi
	345
	346
[2380]	347	# CHECK, IF FILE CONNECTION FILE EXISTS
	348	if [[ ! -f $fileconnection_file ]]
	349	then
	350	printf "\n\n +++ file connection file: "
	351	printf "\n $fileconnection_file"
	352	printf "\n does not exist"
	353	locat=connect; exit
	354	fi
	355
	356
[2404]	357	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	358	if [[ "$activation_string_list" = "" ]]
	359	then
	360	printf "\n\n +++ no activation string list given: "
	361	printf "\n please set palmrun option \"-a\" "
	362	locat=palmrun_option; exit
	363	fi
	364
	365
	366	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	367	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	368	then
	369	write_binary=true
	370	else
	371	write_binary=false
	372	fi
	373
	374
[2380]	375	# READ AND EVALUATE THE CONFIGURATION-FILE
	376	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	377
	378	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	379	while read line
	380	do
	381
	382	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	383	eval line=\"$line\"
	384
	385
	386	# INTERPRET THE LINE
	387	if [[ "$(echo $line)" = "" ]]
	388	then
	389
	390	# EMPTY LINE, NO ACTION
	391	continue
	392
	393	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	394	then
	395
	396	# LINE IS A COMMENT LINE
	397	continue
	398
	399	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	400	then
	401
	402	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	403	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	404	value=`echo $line \| cut -d" " -s -f2-`
	405
	406
	407	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	408	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	409	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	410	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	411	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	412	# CONFIGURATION-FILE.
	413	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	414	then
	415	eval export $var="\$value"
	416
	417	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	418	if [[ $do_trace = true ]]
	419	then
	420	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	421	fi
	422	fi
	423
	424	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	425	then
	426
	427	# LINE DEFINES BATCH-DIRECTIVE
	428	(( ibd = ibd + 1 ))
	429	line=$(echo $line \| cut -c4-)
	430	batch_directive[$ibd]="$line"
	431
	432	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	433	then
	434
	435	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	436	# REMOTE TO A LOCAL HOST
	437	(( ibdt = ibdt + 1 ))
	438	line=$(echo $line \| cut -c5-)
	439	batch_directive_transfer[$ibdt]="$line"
	440
	441	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	442	then
	443
	444	# LINE DEFINES ERROR-COMMAND
	445	(( iec = iec + 1 ))
	446	line=$(echo $line \| cut -c4-)
	447	err_command[$iec]="$line"
	448
	449	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	450	then
	451
	452	# LINE DEFINES INPUT-COMMAND
	453	(( iic = iic + 1 ))
	454	line=$(echo $line \| cut -c4-)
	455	in_command[$iic]="$line"
	456
	457	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	458	then
	459
	460	# LINE DEFINES OUTPUT-COMMAND
	461	(( ioc = ioc + 1 ))
	462	line=$(echo $line \| cut -c4-)
	463	out_command[$ioc]="$line"
	464
	465	else
	466
	467	# SKIP ALL OTHER LINES
	468	continue
	469
	470	fi
	471
	472	done < $config_file
	473
	474
	475	# CHECK SETTING OF REQUIRED PARAMETERS
	476	if [[ "$compiler_name" = "" ]]
	477	then
	478	printf "\n +++ no compiler name found in $config_file"
	479	printf "\n Please add line \"compiler_name ...\" to that file."
	480	locat=config_file; exit
	481	fi
	482	if [[ "$compiler_name_ser" = "" ]]
	483	then
	484	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	485	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	486	locat=config_file; exit
	487	fi
	488	if [[ "$compiler_options" = "" ]]
	489	then
	490	printf "\n +++ no compiler options found in $config_file"
	491	printf "\n Please add line \"compiler_options ...\" to that file."
	492	locat=config_file; exit
	493	fi
[2388]	494	if [[ "$linker_options" = "" ]]
[2380]	495	then
[2388]	496	printf "\n +++ no linker options found in $config_file"
	497	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	498	locat=config_file; exit
	499	fi
	500	if [[ "$execute_command" = "" ]]
	501	then
	502	printf "\n +++ no execute command found in $config_file"
	503	printf "\n Please add line \"execute_command ...\" to that file."
	504	locat=config_file; exit
	505	fi
	506
	507	if [[ "$hostfile" != "" ]]
	508	then
	509	if [[ $hostfile != auto && ! -f $hostfile ]]
	510	then
	511	printf "\n +++ no hostfile \"$hostfile\" found"
	512	printf "\n Please check line \"hostfile ...\" in $config_file"
	513	locat=config_file; exit
	514	fi
	515	fi
	516
	517
	518	# DETERMINE THE CALL STATUS
	519	if [[ "$return_address" != "" ]]
	520	then
	521
	522	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	523	# BATCH MODE AND ...
	524	running_on_remote=true
	525
	526	else
	527
	528	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	529	if [[ "$remote_ip" != "" ]]
	530	then
	531
	532	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	533	create_remote_batch_job=true
	534
	535	fi
	536	running_on_remote=false
	537	fi
	538
	539
	540
	541	# READ AND EVALUATE THE I/O-FILE LIST
	542	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	543
	544	# READ THE FILE CONNECTION FILE LINE BY LINE
	545	while read line
	546	do
	547
[2669]	548	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	549	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	550
	551	# INTERPRET THE LINE
	552	if [[ "$(echo $line)" = "" ]]
	553	then
	554	# EMPTY LINE, NO ACTION
	555	continue
	556
	557	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	558	then
	559
	560	# LINE IS A COMMENT LINE
	561	true
	562
	563	else
	564
	565	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	566	# s2a: in/out - field
[2669]	567	# s2b: action - field (optional)
	568	s1=`echo "$line" \| cut -d" " -f1`
	569	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	570	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	571	then
[2669]	572	s2a=$s2
[2380]	573	s2b=""
	574	else
[2669]	575	s2a=`echo $s2 \| cut -d":" -f1`
	576	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	577	fi
[2669]	578	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	579	s4=`echo "$line" \| cut -d" " -s -f4`
	580	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	581	s5=`echo "$line" \| cut -d" " -s -f5`
	582	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	583
	584
	585	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	586	# INPUT- OR OUTPUT-LIST.
	587	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	588	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	589	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	590	# IS NOT CHECKED AND STORED.
[2610]	591	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	592	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	593	then
	594	found=false
	595	for actual in $activation_string_list
	596	do
	597	for formal in $s3
	598	do
	599	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	600	done
	601	done
	602	if [[ $found = true ]]
	603	then
	604	(( iin = iin + 1 ))
[2669]	605	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	606	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	607	if [[ "$s2a" = inopt ]]
	608	then
	609	optin_pre[$iin]=yes
	610	else
	611	optin_pre[$iin]=no
	612	fi
[2605]	613
	614	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	615	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	616	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	617	then
[2610]	618	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	619	fi
	620
[2610]	621	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	622	# THE WILDCARD FROM THE ENDING
	623	if [[ "${s5: -1}" = "*" ]]
	624	then
[2669]	625	if [[ "$s2b" = "di" ]]
[2610]	626	then
	627	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	628	printf "\n see file \"$fileconnection_file\", line"
	629	printf "\n$line"
	630	locat=iofiles_file; exit
	631	fi
	632	multin[$iin]=true
	633	string=${endin_pre[$iin]}
	634	endin_pre[$iin]="${string%?}"
	635	else
	636	multin[$iin]=false
	637	fi
[2380]	638	fi
[2669]	639	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	640	then
	641	found=false
	642	for actual in $activation_string_list
	643	do
	644	for formal in $s3
	645	do
[2670]	646	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	647	done
	648	done
	649	if [[ $found = true ]]
	650	then
	651	(( iout = iout + 1 ))
[2669]	652	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	653	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	654
[2669]	655	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	656	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	657	if [[ $formal = wildcard ]]
	658	then
	659	warnout_pre[$iout]=false
	660	else
	661	warnout_pre[$iout]=true
	662	fi
	663
[2610]	664	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	665	# THE WILDCARD FROM THE LOCAL FILENAME
	666	if [[ "${s1: -1}" = "*" ]]
	667	then
[2669]	668	if [[ "$s2b" = "di" ]]
[2610]	669	then
	670	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	671	printf "\n see file \"$fileconnection_file\", line"
	672	printf "\n$line"
	673	locat=iofiles_file; exit
	674	fi
	675	multout[$iout]=true
	676	string=${localout_pre[$iout]}
	677	localout_pre[$iout]="${string%?}"
	678	else
	679	multout[$iout]=false
	680	fi
[2380]	681	fi
[2669]	682	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	683	then
[2669]	684	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	685	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	686	locat=connect; exit
	687	fi
	688	IFS="$IFSALT"
	689	fi
	690
	691	done < $fileconnection_file
	692
	693
	694
[2501]	695	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	696	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	697	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	698	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	699	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	700	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	701
	702
	703
[2380]	704	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	705	if [[ $run_coupled_model = true ]]
	706	then
	707
	708	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	709	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	710
	711	if (( $cores_ocean + $cores_atmos != $cores ))
	712	then
	713
	714	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	715	printf "\n PEs (total) : $cores"
	716	printf "\n PEs (atmosphere): $cores_atmos"
	717	printf "\n PEs (ocean) : $cores_ocean"
	718	locat=coupling; exit
	719
	720	fi
	721
	722	fi
	723
	724
	725	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	726	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	727	# FOLDER
	728	if [[ $running_in_batch_mode = true ]]
	729	then
	730
[2506]	731	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	732	then
[2506]	733	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	734	printf "\n Please check the output of the palmrun-call"
	735	printf "\n that you did on your local host."
	736	locat=SOURCES_FOR_RUN; exit
	737	fi
	738
	739	else
	740
	741	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	742	# AUTOMATIC RESTART RUN
	743	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	744	if [[ $restart_run = false ]]
	745	then
	746
	747	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	748	# THE LOCAL HOST
	749	if [[ ! -d $source_path ]]
	750	then
	751	printf "\n\n +++ source path \"$source_path\" on local host"
	752	printf "\n \"$(hostname)\" does not exist"
	753	locat=source_path; exit
	754	fi
	755
[2506]	756	rm -rf $sources_for_run_catalog
	757	mkdir -p $sources_for_run_catalog
[2380]	758
	759	if [[ "$source_list" = LM ]]
	760	then
	761
	762	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	763	source_list=""
	764	cd $source_path
	765
	766
[2512]	767	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	768	if [[ ! -d ../.svn ]]
[2380]	769	then
	770	printf "\n\n +++ source directory"
	771	printf "\n \"$source_path\" "
	772	printf "\n is not under control of \"subversion\"."
[2512]	773	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	774	fi
	775
	776
	777	# LIST ALL MODIFIED SOURCE CODE FILES
	778	Filenames=""
[2404]	779	svn status > tmp_svnstatus
[2380]	780	while read line
	781	do
	782	firstc=`echo $line \| cut -c1`
	783	if [[ $firstc = M \|\| $firstc = "?" ]]
	784	then
	785	Name=`echo "$line" \| cut -c8-`
	786	extension=`echo $Name \| cut -d. -f2`
	787	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	788	then
	789	Filenames="$Filenames "$Name
	790	fi
	791	fi
[2404]	792	done < tmp_svnstatus
	793	rm -rf tmp_svnstatus
[2380]	794
	795
	796	# COPY FILES TO SOURCES_FOR_RUN_...
	797	for filename in $Filenames
	798	do
[2506]	799	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	800	source_list=$source_list"$filename "
	801	done
	802
	803	cd - > /dev/null
	804
	805
	806	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	807	elif [[ "$source_list" != "" ]]
	808	then
	809
	810	cd $source_path
	811
	812	for filename in $source_list
	813	do
	814
	815	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	816	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	817	then
	818	printf "\n +++ source code file: $filename"
	819	printf "\n must not contain (\"/\") "
	820	locat=source; exit
	821	fi
	822
	823	if [[ ! -f $filename ]]
	824	then
	825	printf "\n +++ source code file: $filename"
	826	printf "\n does not exist"
	827	locat=source; exit
	828	else
[2506]	829	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	830	fi
	831
	832	done
	833
	834	cd - > /dev/null
	835
	836	fi
	837
	838	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	839	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	840	if [[ ! -f $makefile ]]
	841	then
	842	printf "\n +++ file \"$makefile\" does not exist"
	843	locat=make; exit
	844	else
[2506]	845	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	846	fi
	847
	848
	849	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	850	if [[ "$user_source_path" != "" ]]
[2380]	851	then
	852
	853	# DOES THE DIRECTORY EXIST?
[2384]	854	if [[ ! -d $user_source_path ]]
[2380]	855	then
	856
	857	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	858	printf "\n \"$user_source_path\" "
[2380]	859	printf "\n does not exist or is not a directory."
	860	printf "\n No source code will be used from this directory!\n"
[2384]	861	user_source_path=""
[2380]	862	if [[ $silent == false ]]
	863	then
	864	sleep 2
	865	fi
	866
	867	else
	868
[2384]	869	cd $user_source_path
[2380]	870	found=false
	871
	872	Names=$(ls -1 *.f90 2>&1)
	873	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	874	Names=$(ls -1 *.F90 2>&1)
	875	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	876	Names=$(ls -1 *.F 2>&1)
	877	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	878	Names=$(ls -1 *.f 2>&1)
	879	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	880	Names=$(ls -1 *.c 2>&1)
	881	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	882
	883	cd - > /dev/null
[2506]	884	cd $sources_for_run_catalog
[2380]	885
	886	# COPY MAKEFILE IF EXISTING
[2384]	887	if [[ -f $user_source_path/Makefile ]]
[2380]	888	then
	889	printf "\n\n *** user Makefile from directory"
[2384]	890	printf "\n \"$user_source_path\" is used \n"
[2380]	891	if [[ $silent == false ]]
	892	then
	893	sleep 1
	894	fi
[2384]	895	cp $user_source_path/Makefile .
[2380]	896	fi
	897
	898	for filename in $AddFilenames
	899	do
	900	if [[ -f $filename ]]
	901	then
	902	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	903	printf "\n source code directory \"$user_source_path\" "
[2380]	904	printf "\n but was also given with option \"-s\" which means that it should be taken"
	905	printf "\n from directory \"$source_path\"."
	906	locat=source; exit
	907	fi
	908
[2384]	909	cp $user_source_path/$filename .
[2380]	910	source_list="$source_list $filename"
	911
	912	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	913	if [[ $(grep -c $filename Makefile) = 0 ]]
	914	then
	915	printf "\n\n +++ user file \"$filename\" "
	916	printf "\n is not listed in Makefile \n"
	917	locat=source; exit
	918	else
	919
	920	if [[ $found = false ]]
	921	then
	922	found=true
	923	printf "\n\n *** following user file(s) added to the"
	924	printf " files to be translated:\n "
	925	fi
	926	printf "$filename "
	927	if [[ $silent == false ]]
	928	then
	929	sleep 0.5
	930	fi
	931
	932	fi
	933	done
	934	[[ $found = true ]] && printf "\n"
	935	cd - > /dev/null
	936	fi
	937	fi
	938
	939	# COPY CONFIGURATION FILES
[2506]	940	cp $config_file $sources_for_run_catalog
	941	cp $fileconnection_file $sources_for_run_catalog
[2380]	942
	943	# COPY SHELLSCRIPTS
[2506]	944	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	945	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	946
	947	fi
	948
	949	fi
	950
[2605]	951
[2380]	952	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	953	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	954	if [[ "$global_revision" = "" ]]
	955	then
	956	global_revision=`svnversion $source_path 2>/dev/null`
	957	global_revision="Rev: $global_revision"
	958	fi
	959
	960
	961	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	962	if [[ -n $cores ]]
	963	then
	964
	965	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	966	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	967	if [[ $tasks_per_node = 0 ]]
[2380]	968	then
	969	printf "\n"
	970	printf "\n +++ option \"-T\" (tasks per node) is missing"
	971	printf "\n set -T option or define tasks_per_node in the config file"
	972	locat=tasks_per_node; (( iec = 0 )); exit
	973	fi
	974
	975	if (( cores < tasks_per_node ))
	976	then
	977	printf "\n"
	978	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	979	printf "\n given values: -T $tasks_per_node -X $cores"
	980	locat=tasks_per_node; (( iec = 0 )); exit
	981	fi
	982
	983	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	984	(( mpi_tasks = cores / threads_per_task ))
	985	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	986	(( ii = cores / tasks_per_node ))
	987	(( remaining_cores = cores - ii * tasks_per_node ))
	988	if (( remaining_cores > 0 ))
	989	then
	990	printf "\n"
	991	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	992	printf "\n divisor of the total number of cores (option \"-X\")"
	993	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	994	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	995	(( nodes = nodes + 1 ))
	996	fi
	997
	998	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	999	if [[ "$tasks_per_node" != "" ]]
	1000	then
	1001	TOPT="-T $tasks_per_node"
	1002	fi
	1003
	1004	fi
	1005
	1006
	1007	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1008	if [[ "$maximum_parallel_io_streams" = "" ]]
	1009	then
	1010	maximum_parallel_io_streams=$cores
	1011	fi
	1012
	1013
	1014	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1015	if [[ "$scp_port" != "" ]]
	1016	then
	1017	PORTOPT="-P $scp_port"
	1018	SSH_PORTOPT="-p $scp_port"
	1019	fi
	1020
	1021
	1022	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1023	# CONFIG-FILE
	1024	if [[ "$ssh_key" != "" ]]
	1025	then
	1026	ssh_key="-i $HOME/.ssh/$ssh_key"
	1027	fi
	1028
	1029
	1030	# SET QUEUE, IF NOT GIVEN
	1031	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1032	then
	1033
	1034	if [[ $queue = none && "$defaultqueue" = "" ]]
	1035	then
	1036	printf "\n"
	1037	printf "\n +++ no default queue given in configuration file and no queue"
	1038	printf "\n given with option -q"
	1039	fi
	1040	if [[ $queue = none ]]
	1041	then
	1042	queue=$defaultqueue
	1043	fi
	1044
	1045	fi
	1046
	1047
	1048	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1049	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1050	(( i = 0 ))
[2610]	1051	(( nr_of_input_files = 0 ))
[2380]	1052	while (( i < iin ))
	1053	do
	1054	(( i = i + 1 ))
	1055
	1056	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1057	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1058	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1059	then
[2610]	1060	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1061	else
[2610]	1062	eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]}
[2380]	1063	fi
	1064
[2610]	1065
[2380]	1066	# CHECK IF FILE EXISTS
	1067	if ! ls $filename* 1>/dev/null 2>&1
	1068	then
	1069
[2669]	1070	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1071	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1072	then
	1073	printf "\n\n +++ INPUT-file: "
[2610]	1074	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1075	then
	1076	printf "\n $filename"
	1077	else
[2610]	1078	printf "\n $filename.${extin_pre[$i]}"
[2380]	1079	fi
	1080	printf "\n does not exist\n"
	1081	locat=input; exit
	1082	else
[2610]	1083	(( nr_of_input_files = nr_of_input_files + 1 ))
	1084	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1085	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1086	actionin[$nr_of_input_files]="unavailable"
[2610]	1087	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1088	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1089	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1090	fi
[2605]	1091
[2380]	1092	else
	1093
[2610]	1094	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND
	1095	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
	1096	if [[ "${multin[$i]}" = true ]]
	1097	then
	1098	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1099	ls -1 -d ${filename} > filelist 2>/dev/null
	1100	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1101	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1102
[2610]	1103	endings=""
	1104	while read line
	1105	do
	1106	# filename without path (i.e. after the last "/")
	1107	basefilename=$(basename ${line})
[2380]	1108
[2610]	1109	# check if there is an extension and remove it
	1110	ext=${basefilename##*.}
	1111	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1112	then
	1113	basefilename=${basefilename%.*}
	1114	fi
[2380]	1115
[2610]	1116	# check for an existing cycle number and remove it
	1117	cycle=${basefilename##*.}
	1118	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1119	then
	1120	basefilename=${basefilename%.*}
	1121	fi
[2600]	1122
[2610]	1123	# remove the fname from the beginning
	1124	length_fname=${#fname}
	1125	ending=${basefilename:${length_fname}}
	1126
	1127	# remove the ending given in the .iofiles from the beginning
	1128	endingstring="${endin_pre[$i]}"
	1129	length_ending=${#endingstring}
	1130	ending=${ending:${length_ending}}
	1131
	1132	if [[ "$ending" = "" ]]
[2600]	1133	then
[2610]	1134	# standard ending as given in the .iofiles
	1135	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1136	then
	1137	endings="$endings DEFAULT"
	1138	fi
[2600]	1139	else
[2610]	1140	# ending must start with "_", otherwise its a different file
	1141	if [[ "${ending:0:1}" = "_" ]]
	1142	then
	1143	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1144	then
	1145	endings="$endings $ending"
	1146	fi
	1147	fi
[2600]	1148	fi
[2610]	1149
	1150	done <filelist
[2380]	1151
[2610]	1152	rm filelist
[2380]	1153
[2600]	1154	else
[2610]	1155
	1156	# SINGLE NAME
	1157	endings=DEFAULT
	1158
[2600]	1159	fi
	1160
[2610]	1161	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1162	for ending in $endings
	1163	do
	1164
	1165	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1166	if [[ $ending = DEFAULT ]]
[2380]	1167	then
[2610]	1168	ending=""
	1169	fi
	1170
	1171	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1172	(( nr_of_input_files = nr_of_input_files + 1 ))
	1173	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1174	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1175	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1176	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1177	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1178	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1179
	1180
	1181	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1182	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1183	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1184	then
	1185	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1186	else
[2610]	1187	eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]}
[2380]	1188	fi
[2610]	1189
	1190	# DETERMINE THE FILE'S CYCLE NUMBER
	1191	(( maxcycle = 0 ))
	1192	ls -1 -d $filename > filelist 2>/dev/null
	1193	ls -1 -d $filename.* >> filelist 2>/dev/null
	1194	while read line
	1195	do
	1196	# filename without path (i.e. after the last "/")
	1197	basefilename=$(basename ${line})
	1198
	1199	# check if there is an extension
	1200	extension=${basefilename##*.}
	1201	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1202	then
	1203	basefilename=${basefilename%.*}
	1204	fi
	1205
	1206	# check for an existing cycle number
	1207	cycle=${basefilename##*.}
	1208	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1209	then
[2669]	1210	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1211	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1212	(( icycle = $((10#$cycle)) ))
[2610]	1213	else
	1214	(( icycle = 0 ))
	1215	fi
	1216
	1217	if (( icycle > maxcycle ))
	1218	then
	1219	(( maxcycle = icycle ))
	1220
	1221	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1222	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1223	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1224	then
	1225	leading_zero=true
	1226	else
	1227	leading_zero=false
	1228	fi
	1229	fi
	1230
	1231	done <filelist
	1232	rm filelist
	1233
	1234	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1235	if [[ $leading_zero = true ]]
[2380]	1236	then
[2610]	1237	cyclestring=`printf "%03d" $maxcycle`
	1238	else
	1239	cyclestring=$maxcycle
[2380]	1240	fi
[2610]	1241
	1242	# APPEND CYCLE NUMBER TO FILENAME
	1243	if (( maxcycle > 0 ))
[2380]	1244	then
[2610]	1245	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1246	then
	1247	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1248	else
	1249	filename=${filename}.$cyclestring
	1250	fi
[2380]	1251	else
[2610]	1252	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1253	then
	1254	filename=${filename}.${extin[$nr_of_input_files]}
	1255	fi
[2380]	1256	fi
[2610]	1257
	1258	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1259	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1260	absnamein[$nr_of_input_files]=$filename
	1261	if (( maxcycle > 0 ))
[2380]	1262	then
[2610]	1263	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1264	then
	1265	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1266	else
	1267	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring
	1268	fi
[2380]	1269	else
[2610]	1270	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1271	then
	1272	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1273	else
	1274	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}
	1275	fi
[2380]	1276	fi
	1277
[2610]	1278	done
	1279
[2380]	1280	fi
[2610]	1281
[2380]	1282	done
	1283
[2610]	1284
[2380]	1285	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1286	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1287	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1288	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1289	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1290	# REMOTE HOST)
	1291	(( i = 0 ))
	1292	while (( i < iout ))
	1293	do
	1294	(( i = i + 1 ))
[2610]	1295	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1296	then
[2610]	1297	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1298	then
[2610]	1299	actionout_pre[$i]=""
	1300	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1301	then
[2610]	1302	actionout_pre[$i]=pe
	1303	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1304	then
[2610]	1305	actionout_pre[$i]=a
[2380]	1306	fi
	1307	(( maxcycle = 0 ))
[2610]	1308	eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]}
	1309	eval catalogname=${pathout_pre[$i]}
[2380]	1310	if ! ls $filename* 1>/dev/null 2>&1
	1311	then
	1312
	1313	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1314	if cat /dev/null > $filename
	1315	then
	1316	rm $filename
	1317	else
	1318
	1319	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1320	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1321	if [[ ! -d $catalogname ]]
	1322	then
	1323	if mkdir -p $catalogname
	1324	then
	1325	printf "\n\n *** directory:"
	1326	printf "\n $catalogname"
	1327	printf "\n was created\n"
	1328	else
	1329	printf "\n\n +++ OUTPUT-file:"
	1330	printf "\n $filename"
	1331	printf "\n cannot be created, because directory does not exist"
	1332	printf "\n and cannot be created either"
	1333	printf "\n"
	1334	locat=output ; exit
	1335	fi 2>/dev/null
	1336	else
	1337	printf "\n\n +++ OUTPUT-file:"
	1338	printf "\n $filename"
	1339	printf "\n cannot be created, although directory exists"
	1340	printf "\n"
	1341	locat=output ; exit
	1342	fi
	1343	fi 2>/dev/null
	1344
	1345	fi
	1346
	1347	fi
	1348	done
	1349
	1350
	1351	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1352	if [[ $running_in_batch_mode = false ]]
	1353	then
	1354	run_id=$RANDOM
	1355	job_id=${fname}.$run_id
	1356
[2566]	1357	tempdir=$fast_io_catalog/$job_id
[2380]	1358	fi
	1359
	1360
	1361	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1362	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1363	then
	1364
	1365	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1366	if [[ $ibd = 0 ]]
	1367	then
	1368	printf "\n"
	1369	printf "\n +++ no batch directives found in configuration file"
	1370	locat=config_file_batch_directives; (( iec = 0 )); exit
	1371	fi
	1372
	1373	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1374	done=false
[2384]	1375	cputime=$cpumax
[2380]	1376	while [[ $done = false ]]
	1377	do
[2384]	1378	if (( cputime == 0 ))
[2380]	1379	then
	1380	printf "\n +++ cpu-time is undefined"
	1381	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1382	printf "\n >>> "
[2384]	1383	read cputime 1>/dev/null 2>&1
[2380]	1384	else
	1385	done=true
	1386	fi
	1387	done
[2420]	1388	cpumax=$cputime
[2380]	1389
	1390	# CHECK THE MEMORY DEMAND
	1391	done=false
	1392	while [[ $done = false ]]
	1393	do
	1394	if (( memory == 0 ))
	1395	then
	1396	printf "\n +++ memory demand is undefined"
	1397	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1398	printf "\n >>> "
	1399	read memory 1>/dev/null 2>&1
	1400	else
	1401	done=true
	1402	fi
	1403	done
	1404
	1405	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1406	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1407	then
	1408	while [[ -z $remote_username ]]
	1409	do
[2420]	1410	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1411	printf "\n >>> Please type username:"
	1412	printf "\n >>> "
	1413	read remote_username
	1414	done
	1415	fi
	1416
	1417	else
	1418
[2420]	1419	if [[ $running_in_batch_mode = false ]]
	1420	then
	1421	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1422	cpumax=$cputime
	1423	else
	1424	cputime=$cpumax
	1425	fi
[2380]	1426
	1427	fi
	1428
	1429
	1430	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1431	(( cpu_hours = cputime / 3600 ))
	1432	(( resttime = cputime - cpu_hours * 3600 ))
	1433	(( cpu_minutes = resttime / 60 ))
	1434	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1435	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1436
	1437
	1438	# OUTPUT OF THE PALMRUN-HEADER
	1439	calltime=$(date)
	1440	printf "\n"
	1441	printf "#------------------------------------------------------------------------# \n"
	1442	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1443	printf "\| \| \n"
	1444	column1="called on:"; column2=$(hostname)
	1445	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1446	if [[ $create_remote_batch_job = true ]]
	1447	then
[2506]	1448	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1449	else
	1450	if [[ $running_on_remote = true ]]
	1451	then
[2506]	1452	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1453	else
[2506]	1454	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1455	fi
	1456	fi
	1457	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1458
	1459	column1="running in:"
	1460	if [[ $running_in_batch_mode = true ]]
	1461	then
	1462	column2="batch job mode"
	1463	else
	1464	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1465	then
	1466	column2="job creation mode"
	1467	else
	1468	column2="interactive run mode"
	1469	fi
	1470	fi
	1471	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1472
[2479]	1473	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1474	then
[2480]	1475	if [[ "$project_account" != "" ]]
[2479]	1476	then
	1477	column1="project account number:"
	1478	column2="$project_account"
	1479	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1480	fi
	1481	fi
	1482
[2380]	1483	if [[ -n $cores ]]
	1484	then
	1485	if [[ $run_coupled_model = false ]]
	1486	then
	1487	column1="number of cores:"; column2=$cores
	1488	else
	1489	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1490	fi
	1491	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1492	fi
	1493	if [[ -n $tasks_per_node ]]
	1494	then
	1495	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1496	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1497	if (( remaining_cores > 0 ))
	1498	then
	1499	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1500	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1501	fi
	1502	fi
	1503	if [[ $maximum_parallel_io_streams != $cores ]]
	1504	then
	1505	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1506	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1507	fi
	1508	if [[ $use_openmp = true ]]
	1509	then
	1510	column1="threads per task:"; column2="$threads_per_task"
	1511	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1512	fi
[2384]	1513	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1514	then
[2506]	1515	column1="memory demand / PE":; column2="$memory MB"
	1516	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1517	column1="job cpu time (h:m:s):"; column2="$timestring"
	1518	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1519	fi
[2380]	1520	printf "\| \| \n"
	1521	if [[ "$source_list" != "" ]]
	1522	then
	1523	if [[ "$make_options" != "" ]]
	1524	then
	1525	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1526	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1527	line=$(echo "$make_options" \| cut -c46-)
	1528	while [[ "$line" != "" ]]
	1529	do
	1530	column1=""
	1531	column2=$(echo "$line" \| cut -c-45)
	1532	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1533	line=$(echo "$line" \| cut -c46-)
	1534	done
	1535	fi
	1536	fi
	1537
	1538	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1539	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1540	line=$(echo "$cpp_options" \| cut -c46-)
	1541	while [[ "$line" != "" ]]
	1542	do
	1543	column1=""
	1544	column2=$(echo "$line" \| cut -c-45)
	1545	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1546	line=$(echo "$line" \| cut -c46-)
	1547	done
	1548
	1549	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1550	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1551	line=$(echo "$compiler_options" \| cut -c46-)
	1552	while [[ "$line" != "" ]]
	1553	do
	1554	column1=""
	1555	column2=$(echo "$line" \| cut -c-45)
	1556	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1557	line=$(echo "$line" \| cut -c46-)
	1558	done
	1559
[2388]	1560	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1561	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1562	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1563	while [[ "$line" != "" ]]
	1564	do
	1565	column1=""
	1566	column2=$(echo "$line" \| cut -c-45)
	1567	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1568	line=$(echo "$line" \| cut -c46-)
	1569	done
	1570
	1571	if [[ "$login_init_cmd" != "" ]]
	1572	then
	1573	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1574	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1575	line=$(echo "$login_init_cmd" \| cut -c46-)
	1576	while [[ "$line" != "" ]]
	1577	do
	1578	column1=""
	1579	column2=$(echo "$line" \| cut -c-45)
	1580	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1581	line=$(echo "$line" \| cut -c46-)
	1582	done
	1583	fi
	1584
	1585	if [[ "$module_commands" != "" ]]
	1586	then
	1587	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1588	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1589	line=$(echo "$module_commands" \| cut -c46-)
	1590	while [[ "$line" != "" ]]
	1591	do
	1592	column1=""
	1593	column2=$(echo "$line" \| cut -c-45)
	1594	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1595	line=$(echo "$line" \| cut -c46-)
	1596	done
	1597	fi
	1598	printf "\| \| \n"
	1599	column1="base name of files:"; column2=$fname
	1600	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1601	column1="activation string list:"; column2=$(echo $activation_string_list)
	1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1603
	1604	if [[ "$ocean_file_appendix" = true ]]
	1605	then
	1606	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1607	fi
	1608
	1609	if [[ "$source_list" != "" ]]
	1610	then
	1611	printf "\| \| \n"
	1612	printf "\| Files to be compiled: \| \n"
	1613	line=$source_list
	1614	while [[ "$line" != "" ]]
	1615	do
	1616	linestart=$(echo $line \| cut -c-70)
	1617	printf "\| %-70s \| \n" "$linestart"
	1618	line=$(echo "$line" \| cut -c71-)
	1619	done
	1620	fi
	1621	printf "#------------------------------------------------------------------------#"
	1622
	1623
	1624
	1625	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1626	if [[ $do_trace = true ]]
	1627	then
	1628	(( i = 0 ))
[2610]	1629	while (( i < nr_of_input_files ))
[2380]	1630	do
	1631	(( i = i + 1 ))
	1632	if (( i == 1 ))
	1633	then
	1634	printf "\n\n >>> INPUT-file assignments:\n"
	1635	fi
	1636	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1637	done
	1638	(( i = 0 ))
	1639	while (( i < iout ))
	1640	do
	1641	(( i = i + 1 ))
	1642	if (( i == 1 ))
	1643	then
	1644	printf "\n\n >>> OUTPUT-file assignments:\n"
	1645	fi
	1646	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1647	done
	1648	(( i = 0 ))
	1649	while (( i < iic ))
	1650	do
	1651	(( i = i + 1 ))
	1652	if (( i == 1 ))
	1653	then
	1654	printf "\n\n >>> INPUT-commands:\n"
	1655	fi
	1656	printf "\n ${in_command[$i]}"
	1657	done
	1658	(( i = 0 ))
	1659	while (( i < ioc ))
	1660	do
	1661	(( i = i + 1 ))
	1662	if (( i == 1 ))
	1663	then
	1664	printf "\n\n >>> OUTPUT-commands:\n"
	1665	fi
	1666	printf "\n ${out_command[$i]}"
	1667	done
	1668	fi
	1669
	1670	# QUERY FOR CONTINUE
	1671	if [[ $silent = false && $running_in_batch_mode = false ]]
	1672	then
	1673	antwort=dummy
	1674	printf "\n\n"
	1675	printf " >>> everything o.k. (y/n) ? "
	1676	while read antwort
	1677	do
	1678	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1679	then
	1680	printf " >>> everything o.k. (y/n) ? "
	1681	else
	1682	break
	1683	fi
	1684	done
	1685	if [[ $antwort = n \|\| $antwort = N ]]
	1686	then
	1687	locat=user_abort; (( iec = 0 )); exit
	1688	fi
	1689	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1690	then
[2566]	1691	printf "\n *** batch-job will be created and submitted"
[2380]	1692	else
[2566]	1693	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1694	fi
	1695	fi
	1696
	1697
	1698
	1699	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1700	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1701	then
	1702
	1703	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1704	then
[2566]	1705	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1706	else
[2566]	1707	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1708	fi
	1709
[2422]	1710	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1711	# IT SHALL BE CREATED
	1712	ask_for_make_depository=false
	1713	if [[ $create_remote_batch_job = true ]]
	1714	then
	1715
	1716	line=`grep %base_directory $config_file`
[2506]	1717	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1718	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]	1719
[2506]	1720	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1721	then
	1722	printf "\n\n +++ make depository \"${make_depository}\""
	1723	printf "\n on remote host not found!"
	1724	ask_for_make_depository=true
	1725	fi
[2506]	1726	rm ${host_configuration}_last_make_protokoll
[2422]	1727
	1728	else
	1729
	1730	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1731	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1732	if [[ ! -d ${make_depository} ]]
	1733	then
	1734	printf "\n\n +++ make depository \"${make_depository}\""
	1735	printf "\n on local host not found!"
	1736	ask_for_make_depository=true
	1737	fi
	1738
	1739	fi
	1740
	1741	if [[ $ask_for_make_depository = true ]]
	1742	then
	1743
	1744	antwort=dummy
	1745	printf "\n\n"
	1746	printf " >>> Create a new one (y/n) ? "
	1747	while read antwort
	1748	do
	1749	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1750	then
	1751	printf " >>> Create a new one (y/n) ? "
	1752	else
	1753	break
	1754	fi
	1755	done
	1756	if [[ $antwort = n \|\| $antwort = N ]]
	1757	then
	1758	locat=user_abort; (( iec = 0 )); exit
	1759	fi
	1760
[2566]	1761	if [[ $do_trace = true ]]
	1762	then
	1763	palmbuild -h $host_configuration
	1764	else
	1765	palmbuild -v -h $host_configuration
	1766	fi
[2422]	1767
	1768	if [[ $? != 0 ]]
	1769	then
	1770
	1771	# ABORT IN CASE OF COMPILATION PROBLEMS
	1772	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1773	locat=make_depository
	1774	exit
	1775	else
	1776	echo " *** now continue with creating executable and other sources"
	1777	fi
	1778
	1779	fi
	1780
[2566]	1781	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2506]	1782	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
[2380]	1783
	1784	if [[ $? != 0 ]]
	1785	then
	1786
	1787	# ABORT IN CASE OF COMPILATION PROBLEMS
	1788	printf "\n +++ error while creating executable and/or other sources"
	1789	locat=execution
[2506]	1790	rm -rf $sources_for_run_catalog
[2380]	1791	exit
	1792
	1793	else
	1794
[2566]	1795	printf " *** executable and other sources created\n"
[2506]	1796	rm -rf $sources_for_run_catalog
[2380]	1797
	1798	fi
	1799
	1800	fi
	1801
	1802
[2669]	1803	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1804	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1805	if [[ $create_remote_batch_job = true ]]
	1806	then
	1807	(( i = 0 ))
[2610]	1808	while (( i < nr_of_input_files ))
[2605]	1809	do
	1810	(( i = i + 1 ))
[2669]	1811	if [[ "${actionin[$i]}" = tr ]]
[2605]	1812	then
	1813	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1814	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1815	fi
	1816	done
	1817	if (( i > 0 ))
	1818	then
	1819	printf " *** input files have been copied to the remote host\n"
	1820	fi
	1821	fi
	1822
	1823
[2380]	1824	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1825	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1826	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1827	then
	1828
	1829	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1830	if [[ $running_in_batch_mode = false ]]
	1831	then
	1832	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1833	# FOLDER
[2566]	1834	mkdir -p $tempdir
	1835	chmod go+rx $tempdir
	1836	cd $tempdir
	1837	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1838	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1839
	1840	else
	1841
	1842	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1843	printf "\n *** running in temporary directory: $tempdir"
[2380]	1844
	1845	fi
	1846
	1847
	1848	# PROVIDE THE INPUT FILES
	1849	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1850	optional_files_missing=false
[2380]	1851	(( i = 0 ))
[2610]	1852	while (( i < nr_of_input_files ))
[2380]	1853	do
	1854	(( i = i + 1 ))
	1855	if (( i == 1 ))
	1856	then
	1857	printf "\n\n *** providing INPUT-files:\n$dashes"
	1858	fi
	1859
	1860
	1861	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1862	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1863	then
[2669]	1864	optional_files_missing=true
[2380]	1865	continue
	1866	fi
	1867
	1868	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1869	files_for_cores=false; filetype=file
	1870	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1871	then
	1872	files_for_cores=true; filetype=files
	1873	actionin[$i]=""
	1874	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1875	then
	1876	actionin[$i]=""
	1877	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1878	then
	1879	files_for_cores=true; filetype=files
	1880	actionin[$i]="ln"
	1881	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1882	then
	1883	actionin[$i]="ln"
	1884	fi
	1885
	1886	if [[ $files_for_cores = true ]]
	1887	then
	1888	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1889	else
	1890	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1891	fi
	1892
	1893	# INPUT-FILES TO BE LINKED
	1894	if [[ "${actionin[$i]}" = ln ]]
	1895	then
	1896
	1897	printf "\n $filetype will be linked"
	1898	if [[ $files_for_cores = false ]]
	1899	then
	1900	if [[ -f "${absnamein[$i]}" ]]
	1901	then
	1902	ln ${absnamein[$i]} ${localin[$i]}
	1903	got_tmp[$i]=true
	1904	fi
	1905	else
	1906	if [[ -d "${absnamein[$i]}" ]]
	1907	then
[2396]	1908	mkdir -p ${localin[$i]}
[2380]	1909	cd ${absnamein[$i]}
	1910	for file in $(ls *)
	1911	do
[2566]	1912	ln $file $tempdir/${localin[$i]}
[2380]	1913	done >\|/dev/null 2>&1
[2566]	1914	cd $tempdir
[2380]	1915	fi
	1916
	1917	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1918	if [[ ! -f "${localin[$i]}/_000000" ]]
	1919	then
	1920	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1921	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1922	fi
	1923
	1924	got_tmp[$i]=true
	1925	fi
	1926	fi
	1927
	1928	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	1929	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	1930	then
	1931
	1932	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1933	then
	1934
	1935	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1936	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1937	printf "\n file will be provided for $cores processors"
[2396]	1938	mkdir -p ${localin[$i]}
[2380]	1939	ival=$cores
	1940	(( ii = 0 ))
	1941	while (( ii <= ival-1 ))
	1942	do
	1943	if (( ii < 10 ))
	1944	then
	1945	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1946	elif (( ii < 100 ))
	1947	then
	1948	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1949	elif (( ii < 1000 ))
	1950	then
	1951	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1952	else
	1953	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1954	fi
	1955	(( ii = ii + 1 ))
	1956	done
	1957
	1958	else
	1959
	1960	if [[ $files_for_cores = true ]]
	1961	then
	1962
	1963	# PROVIDE FILES FOR EACH CORE
	1964	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1965	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1966	printf "\n providing $cores files for the respective cores"
[2396]	1967	mkdir -p ${localin[$i]}
[2380]	1968	if [[ $link_local_input = true ]]
	1969	then
	1970	printf " files will be linked\n"
	1971	cd ${absnamein[$i]}
	1972	for file in $(ls *)
	1973	do
	1974	ln -f $file ${localin[$i]}
	1975	done
[2566]	1976	cd $tempdir
[2380]	1977	fi
	1978
	1979	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1980	if [[ ! -f "${localin[$i]}/_000000" ]]
	1981	then
	1982	if [[ $link_local_input = true ]]
	1983	then
	1984	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1985	fi
	1986	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1987	fi
	1988
	1989	else
	1990
	1991	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1992	if [[ $link_local_input = true ]]
	1993	then
	1994	printf " file will be linked\n"
	1995	ln -f ${absnamein[$i]} ${localin[$i]}
	1996	fi
[2605]	1997	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	1998	if [[ ! -f "${localin[$i]}" ]]
	1999	then
	2000	if [[ $link_local_input = true ]]
	2001	then
	2002	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2003	fi
[2669]	2004	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2005	then
	2006	mv ${absnamein[$i]} ${localin[$i]}
	2007	else
	2008	cp ${absnamein[$i]} ${localin[$i]}
	2009	fi
[2380]	2010	fi
	2011	fi
	2012	fi
	2013	fi
	2014
	2015	done
	2016	if (( i != 0 ))
	2017	then
[2669]	2018	if [[ $optional_files_missing = true ]]
	2019	then
	2020	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2021	fi
[2380]	2022	printf "\n$dashes\n *** all INPUT-files provided \n"
	2023	fi
	2024
	2025
	2026	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2027	(( i = 0 ))
	2028	while (( i < iic ))
	2029	do
	2030	(( i = i + 1 ))
	2031	if (( i == 1 ))
	2032	then
	2033	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2034	fi
	2035	printf "\n >>> ${in_command[$i]}"
	2036	eval ${in_command[$i]}
	2037	if (( i == iic ))
	2038	then
	2039	printf "\n$dashes\n"
	2040	fi
	2041	done
	2042
	2043
	2044	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2045	# (FILE ENVPAR WILL BE READ BY PALM)
	2046	cat > ENVPAR << EOF
[2506]	2047	&envpar run_identifier = '$fname', host = '$host_configuration',
[2380]	2048	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	2049	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2050	maximum_cpu_time_allowed = ${cpumax}.,
	2051	revision = '$global_revision',
	2052	batch_job = .${running_in_batch_mode}. /
	2053
	2054	EOF
	2055
	2056
	2057	# STARTING THE EXECUTABLE
	2058	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2059	PATH=$PATH:$tempdir
[2380]	2060
	2061
	2062	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2063	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2064	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2065	eval line=\"$line\"
	2066	execute_command="$line"
	2067
	2068
	2069	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2070	if [[ "$execute_command_for_combine" = "" ]]
	2071	then
	2072	eval line2=\"$line2\"
	2073	execute_command_for_combine="$line2"
	2074	fi
	2075
[2380]	2076
	2077
	2078	# PROVIDE A HOSTFILE, IF REQUIRED
	2079	if [[ "$hostfile" != "" ]]
	2080	then
	2081
	2082	if [[ $hostfile = auto ]]
	2083	then
	2084	# CREATE A NEW HOSTFILE
	2085	(( ii = 1 ))
	2086	while (( ii <= cores / threads_per_task ))
	2087	do
	2088	echo $(hostname) >> hostfile
	2089	(( ii = ii + 1 ))
	2090	done
	2091	if (( cores / threads_per_task == 0 ))
	2092	then
	2093	echo $(hostname) >> hostfile
	2094	fi
	2095
	2096	else
	2097	cp $hostfile hostfile
	2098	fi
	2099	eval line=\"`head -n $ii hostfile`\"
	2100	printf "\n *** running on: $line"
	2101	fi
	2102
	2103
	2104
	2105	# SET THE NUMBER OF OPENMP-THREADS
	2106	if [[ $use_openmp = true ]]
	2107	then
	2108	export OMP_NUM_THREADS=$threads_per_task
	2109	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2110	else
	2111	export OMP_NUM_THREADS=1
	2112	fi
	2113
	2114
[2610]	2115	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2116	if [[ $run_coupled_model = false ]]
	2117	then
	2118	if [[ "$ocean_file_appendix" = true ]]
	2119	then
	2120	echo "precursor_ocean" > coupling_steering
	2121	else
	2122	echo "precursor_atmos" > coupling_steering
	2123	fi
	2124	else
	2125	(( iia = $cores_atmos / $threads_per_task ))
	2126	(( iio = $cores_ocean / $threads_per_task ))
	2127	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2128	printf "\n\n"
	2129	echo "coupled_run $iia $iio" > coupling_steering
	2130	fi
	2131
	2132	printf "\n *** execute command:"
	2133	printf "\n \"$execute_command\" \n\n"
	2134
	2135	$execute_command < coupling_steering
	2136
	2137	if [[ $? != 0 ]]
	2138	then
	2139
	2140	# ABORT IN CASE OF RUNTIME ERRORS
	2141	printf "\n +++ runtime error occured"
	2142	locat=execution
	2143	exit
	2144
	2145	else
	2146
	2147	printf "\n$dashes\n *** execution finished \n"
	2148
	2149	fi
	2150
	2151
	2152	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2153	# BY EACH CORE INTO ONE FILE
	2154	if [[ ! -f combine_plot_fields.x ]]
	2155	then
	2156
	2157	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2158	printf "\n 2d- and/or 3d-data may be incomplete!"
	2159	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2160
	2161	elif [[ "$combine_plot_fields" == true ]]
	2162	then
	2163
	2164	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2165	$execute_command_for_combine
	2166
	2167	else
	2168
	2169	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2170	# DATA OUTPUT
[2380]	2171	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2172	fi
	2173
	2174
	2175
	2176	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2177	(( i = 0 ))
	2178	while (( i < ioc ))
	2179	do
	2180	(( i = i + 1 ))
	2181	if (( i == 1 ))
	2182	then
	2183	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2184	fi
	2185	printf "\n >>> ${out_command[$i]}"
	2186	eval ${out_command[$i]}
	2187	if (( i == ioc ))
	2188	then
	2189	printf "\n$dashes\n"
	2190	fi
	2191	done
	2192
	2193
[2610]	2194	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2195	# WILDCARDS
[2380]	2196	(( i = 0 ))
[2610]	2197	(( nr_of_output_files = 0 ))
	2198
[2380]	2199	while (( i < iout ))
	2200	do
[2610]	2201
[2380]	2202	(( i = i + 1 ))
[2610]	2203
	2204	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2205	# CREATE A LIST FOR THE DETECTED ENDINGS
	2206	if [[ "${multout[$i]}" = true ]]
	2207	then
	2208	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2209	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2210	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2211
	2212	endings="DEFAULT"
	2213	while read line
	2214	do
	2215	# remove the local name from the beginning
	2216	localnamestring="${localout_pre[$i]}"
	2217	length_localname=${#localnamestring}
	2218	ending=${line:${length_localname}}
	2219
	2220	if [[ "$ending" != "" ]]
	2221	then
	2222	endings="$endings $ending"
	2223	fi
	2224
	2225	done <filelist
	2226
	2227	rm filelist
	2228
	2229	else
	2230
	2231	# SINGLE NAME
	2232	endings=DEFAULT
	2233
	2234	fi
	2235
	2236	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2237	for ending in $endings
	2238	do
	2239
	2240	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2241	if [[ $ending = DEFAULT ]]
	2242	then
	2243	ending=""
	2244	fi
	2245
	2246	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2247	(( nr_of_output_files = nr_of_output_files + 1 ))
	2248	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2249	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2250	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2251	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2252	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2253	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2254	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2255
	2256	done
	2257
	2258	done
	2259
	2260
	2261
	2262
	2263	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2264	(( i = 0 ))
	2265	while (( i < nr_of_output_files ))
	2266	do
	2267	(( i = i + 1 ))
[2380]	2268	if (( i == 1 ))
	2269	then
	2270	printf "\n\n *** saving OUTPUT-files:"
	2271
	2272	# GET RUN NUMBER ASSIGNED BY PALM
	2273	if [[ -f RUN_NUMBER ]]
	2274	then
	2275	read run_number < RUN_NUMBER
	2276	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2277	usecycle_option="-U $run_number"
	2278	else
	2279	run_number=0
	2280	usecycle_option=""
	2281	fi
	2282	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2283	then
[2404]	2284	printf "\n *** in case of SCP transfers to local host"
	2285	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2286	fi
	2287	printf "\n$dashes"
	2288	fi
	2289
	2290	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2291	then
	2292
[2610]	2293	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	2294
	2295	# DETERMINE THE CYCLE NUMBER
	2296	ls -1 -d $filename > filelist 2>/dev/null
	2297	ls -1 -d $filename.* >> filelist 2>/dev/null
	2298	while read line
	2299	do
	2300
	2301	# filename without path (i.e. after the last "/")
	2302	basefilename=$(basename ${line})
	2303
	2304	# check if there is an extension
	2305	extension=${basefilename##*.}
	2306	if [[ "$extension" = "${extout[$i]}" ]]
	2307	then
	2308	basefilename=${basefilename%.*}
	2309	fi
	2310
	2311	# check for an existing cycle number
	2312	cycle=${basefilename##*.}
	2313	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2314	then
[2669]	2315	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2316	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2317	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2318	else
	2319	(( icycle = 1 ))
	2320	fi
	2321
	2322	if (( icycle > maxcycle ))
	2323	then
	2324	(( maxcycle = icycle ))
	2325	fi
	2326
	2327	done <filelist
	2328	rm filelist
	2329
	2330
	2331	# SET THE CYCLE NUMBER
	2332	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2333	if [[ "${actionout[$i]}" = a ]]
	2334	then
	2335	(( maxcycle = maxcycle - 1 ))
	2336	fi
	2337
	2338	(( cycnum[$i] = maxcycle ))
	2339	pathout[$i]=$filename
	2340
	2341
	2342	# ADD CYCLE NUMBER TO FILENAME
	2343	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2344	if [[ "${actionout[$i]}" != "a" ]]
	2345	then
	2346	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2347	# WITH AN EXISTING CYCLE NUMBER
	2348	if (( run_number >= cycnum[$i] ))
	2349	then
	2350	(( cycnum[$i] = run_number ))
	2351	else
	2352	if (( run_number > 0 ))
	2353	then
	2354	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2355	fi
	2356	fi
	2357	fi
	2358	if (( cycnum[$i] > 0 ))
	2359	then
[2600]	2360	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2361	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2362	fi
	2363	fi
	2364
	2365	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2366	files_for_cores=false; filetype=file
	2367	link_local_output=false
	2368	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2369	then
	2370	files_for_cores=true; filetype=directory
	2371	actionout[$i]=""
	2372	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2373	then
	2374	actionout[$i]=""
	2375	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2376	then
	2377	files_for_cores=true; filetype=directory
	2378	link_local_output=true
	2379	actionout[$i]=""
	2380	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2381	then
	2382	link_local_output
	2383	actionout[$i]=""
	2384	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2385	then
	2386	files_for_cores=true; filetype=directory
	2387	actionout[$i]="tr"
	2388	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2389	then
	2390	actionout[$i]="tr"
	2391	fi
	2392
	2393	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2394	then
[2669]	2395	if [[ ${warnout[$i]} = true ]]
	2396	then
	2397	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2398	fi
[2380]	2399	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2400	then
[2669]	2401	if [[ ${warnout[$i]} = true ]]
	2402	then
	2403	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2404	fi
[2380]	2405	else
	2406
	2407
	2408	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2409	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2410	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2411	then
	2412	if [[ $running_on_remote = true ]]
	2413	then
	2414
	2415	# SET OPTIONS FOR TRANSFER
	2416	if [[ "${actionout[$i]}" = tr ]]
	2417	then
	2418	if [[ $files_for_cores = false ]]
	2419	then
	2420	catalog_option=""
	2421	catalog_string=""
	2422	else
	2423	catalog_option="-c"
	2424	catalog_string="/"
	2425	fi
	2426	append_option=""
	2427	append_string=""
	2428	else
	2429	append_option="-A"
	2430	append_string="append"
	2431	fi
	2432
	2433	transfer_failed=false
	2434	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2506]	2435	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2436
	2437	# TRANSFER VIA SCP
	2438	if [[ "$remote_loginnode" != "" ]]
	2439	then
[2566]	2440	echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
[2380]	2441	else
[2506]	2442	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}
[2380]	2443	fi
	2444	[[ $? != 0 ]] && transfer_failed=true
	2445
	2446
	2447	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2448	if [[ $transfer_failed = true ]]
	2449	then
	2450	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2506]	2451	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
[2380]	2452
	2453	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2454	eval local_catalog=${pathout[$i]}
	2455	if [[ ! -d $local_catalog ]]
	2456	then
	2457	printf " *** local directory does not exist. Trying to create:\n"
	2458	printf " $local_catalog \n"
	2459	mkdir -p $local_catalog
	2460	fi
[2506]	2461	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
[2380]	2462	transfer_problems=true
	2463	fi
	2464
	2465	else
	2466
	2467	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2468	# BE COPIED OR APPENDED ON THIS MACHINE
	2469	if [[ "${actionout[$i]}" = tr ]]
	2470	then
	2471	actionout[$i]=""
	2472	else
	2473	actionout[$i]="a"
	2474	fi
	2475	fi
	2476	fi
	2477
	2478
	2479	# APPEND ON THIS MACHINE
	2480	if [[ "${actionout[$i]}" = "a" ]]
	2481	then
	2482	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2483	then
	2484	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2485	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2486	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2487	else
	2488	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2489	printf "\n ${pathout[$i]}\n"
	2490	cat ${localout[$i]} >> ${pathout[$i]}
	2491	fi
	2492	fi
	2493
	2494	# COPY ON THIS MACHINE
	2495	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2496	# ON DIFFERENT FILE-SYSTEMS
	2497	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2498	then
	2499
	2500	# COPY IN CASE OF RUNS ON SINGLE CORES
	2501	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2502	then
	2503	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2504	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2505	if [[ $link_local_output = true ]]
	2506	then
	2507	printf " file will be linked\n"
	2508	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2509	fi
	2510	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2511	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2512	then
	2513	if [[ $link_local_output = true ]]
	2514	then
	2515	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2516	fi
	2517	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2518	else
	2519	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2520	fi
	2521	else
	2522	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2523	printf "\n ${pathout[$i]}\n"
	2524	if [[ $link_local_output = true ]]
	2525	then
	2526	printf " file will be linked\n"
	2527	ln -f ${localout[$i]} ${pathout[$i]}
	2528	fi
	2529	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2530	if [[ ! -f "${pathout[$i]}" ]]
	2531	then
	2532	if [[ $link_local_output = true ]]
	2533	then
	2534	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2535	fi
	2536	cp ${localout[$i]} ${pathout[$i]}
	2537	else
	2538	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2539	fi
	2540	fi
	2541
	2542	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2543	then
	2544
	2545	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2546	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2547	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2548	printf "\n ${pathout[$i]}\n"
	2549	if [[ $link_local_output = true ]]
	2550	then
	2551	printf " files will be linked\n"
[2396]	2552	mkdir -p ${pathout[$i]}
[2380]	2553	cd ${localout[$i]}
	2554	for file in $(ls *)
	2555	do
	2556	ln -f $file ${pathout[$i]}
	2557	done >\|/dev/null 2>&1
[2566]	2558	cd $tempdir
[2380]	2559	fi
	2560
	2561	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2562	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2563	then
	2564	if [[ $link_local_output = true ]]
	2565	then
	2566	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2567	fi
	2568	cp -r ${localout[$i]}/* ${pathout[$i]}
	2569	fi
	2570
	2571	fi
	2572	fi
	2573	done
	2574
	2575	if (( i != 0 ))
	2576	then
	2577	if [[ $transfer_problems = true ]]
	2578	then
	2579	printf "\n$dashes\n *** OUTPUT-files saved"
	2580	printf "\n +++ WARNING: some data transfers failed! \n"
	2581	else
	2582	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2583	fi
	2584	fi
	2585
	2586
	2587	# IF REQUIRED, START A RESTART-JOB
	2588	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2589	if [[ -f CONTINUE_RUN ]]
	2590	then
	2591
	2592	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2593	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2594	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2595	# -b START A BATCH JOB
	2596	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2597	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2598	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2599
	2600
	2601	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2602	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2603	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2604	then
[2381]	2605	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2606	fi
	2607
	2608
	2609	# START THE RESTART-JOB
	2610	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2611	echo " $prc"
	2612	printf "\n$dashes\n"
	2613	if [[ $running_on_remote = true ]]
	2614	then
	2615
	2616	echo "*** ssh will be used to initiate restart-runs!"
	2617	echo " return_address=\"$return_address\" "
	2618	echo " return_username=\"$local_username\" "
	2619
	2620	if [[ "$remote_loginnode" != "" ]]
	2621	then
[2420]	2622	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]	2623	else
[2420]	2624	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2625	fi
	2626
	2627	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2628	sleep 30
	2629
	2630	else
	2631
	2632	# START THE RESTART JOB ON THE LOCAL HOST
	2633	eval $prc # THE ' MUST BE EVALUATED
	2634	cd - > /dev/null
	2635
	2636	fi
	2637	printf "\n$dashes\n *** restart-run initiated \n"
	2638
	2639
	2640	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2641	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2642	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2643	# MAY BE VERY HUGE)
	2644	(( i = 0 ))
[2610]	2645	while (( i < nr_of_input_files ))
[2380]	2646	do
	2647	(( i = i + 1 ))
	2648	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2649	then
	2650	rm -r ${absnamein[$i]}
	2651	fi
	2652	done
	2653
	2654	fi
	2655
	2656
	2657	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2658	cd $HOME
[2566]	2659	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2660
	2661
	2662	else
	2663
	2664
	2665	# PREPARING ACTIONS,
	2666	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2667
	2668	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2506]	2669	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2670	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2671	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2672	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2673	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2674	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2675	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2676	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2677	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2678	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2679	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2680	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2681	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2682	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2683	if [[ $create_remote_batch_job = true ]]
	2684	then
	2685	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2686	if [[ $do_trace = true ]]
	2687	then
	2688	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2689	fi
[2380]	2690	elif [[ $create_batch_job = true ]]
	2691	then
	2692	palmrun_com=${palmrun_com}" -j"
[2420]	2693	if [[ $do_trace = true ]]
	2694	then
	2695	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2696	fi
[2380]	2697	fi
	2698
	2699
	2700	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2701	# REMOTE HOST
[2506]	2702	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2703	job_protocol_file=$job_protocol_file_local
	2704	if [[ $create_remote_batch_job = true ]]
	2705	then
[2506]	2706	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2707	job_protocol_file=$job_protocol_file_remote
	2708	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2709	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2710	fi
	2711
	2712
	2713	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2714	jobfile=jobfile.$run_id
	2715
	2716
	2717	# FIRST CREATE THE BATCH DIRECTIVES
	2718	(( i = 0 ))
	2719	while (( i < ibd ))
	2720	do
	2721	(( i = i + 1 ))
[2693]	2722	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2723	eval line=\"$line\"
	2724	echo "$line" >> $jobfile
	2725	done
	2726	echo " " >> $jobfile
	2727
	2728
	2729	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2730	# PROTOCOL
	2731	if [[ $create_remote_batch_job = true ]]
	2732	then
	2733	echo "set +vx" >> $jobfile
	2734	echo "trap '" >> $jobfile
	2735	echo "set +vx" >> $jobfile
	2736	echo "cd ${remote_jobcatalog}" >> $jobfile
	2737	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2738
	2739	# ADD THE BATCH DIRECTIVES
	2740	(( i = 0 ))
	2741	while (( i < ibdt ))
	2742	do
	2743	(( i = i + 1 ))
[2693]	2744	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2745	eval line=\"$line\"
	2746	echo "$line" >> $jobfile
	2747	done
	2748	echo " " >> $jobfile
	2749
	2750	echo "set -x" >> $jobfile
[2506]	2751	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${fname}" >> $jobfile
[2380]	2752	echo "%%END%%" >> $jobfile
	2753	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2754	echo "$submit_command $scpjob_file" >> $jobfile
	2755	echo "rm $scpjob_file" >> $jobfile
[2404]	2756	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2757	echo "set -x" >> $jobfile
	2758	echo " ' exit" >> $jobfile
	2759	fi
	2760
	2761
	2762	# ACTIVATE ERROR-TRACEBACK
	2763	if [[ $do_trace = true ]]
	2764	then
	2765	echo "set -x" >> $jobfile
	2766	else
	2767	echo "set +vx" >> $jobfile
	2768	fi
	2769
	2770
	2771	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2772	if [[ "$login_init_cmd" != "" ]]
	2773	then
	2774	echo "$login_init_cmd" >> $jobfile
	2775	fi
	2776	if [[ "$module_commands" != "" ]]
	2777	then
	2778	echo "$module_commands" >> $jobfile
	2779	fi
	2780
	2781
	2782	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2783	if [[ $create_remote_batch_job = true ]]
	2784	then
	2785	echo "mkdir $tempdir" >> $jobfile
	2786	echo "chmod go+rx $tempdir" >> $jobfile
	2787	else
	2788	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2789	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2790	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2791	mkdir $tempdir
	2792	chmod go+rx $tempdir
	2793	fi
	2794	echo "cd $tempdir" >> $jobfile
	2795	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2796	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2797	echo "export PATH=.:\$PATH" >> $jobfile
	2798	echo "export execute_palmrun=true" >> $jobfile
	2799
	2800
	2801	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2802	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2803	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2804	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2805	echo "export LOCAL_PWD" >> $jobfile
	2806
	2807
	2808	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2809	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2810	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2811
	2812
	2813	# CALL PALMRUN WITHIN THE JOB
	2814	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2815	echo "set -x" >> $jobfile
	2816	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2817
	2818
	2819	# TRANSFER JOBFILE TO THE TARGET HOST
	2820	if [[ $create_jobfile_only = false ]]
	2821	then
	2822
	2823	if [[ $create_remote_batch_job = true ]]
	2824	then
	2825
[2420]	2826	echo " "
[2566]	2827	echo " *** transfer of job to remote host via scp"
[2420]	2828	if [[ $do_trace = true ]]
	2829	then
[2506]	2830	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2831	fi
[2566]	2832	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2833
[2566]	2834	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2835	if [[ $do_trace = true ]]
	2836	then
[2506]	2837	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]	2838	fi
[2506]	2839	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]	2840
	2841	elif [[ $create_batch_job = true ]]
	2842	then
	2843
[2385]	2844	eval local_jobcatalog=$local_jobcatalog
[2506]	2845	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2846	cd $local_jobcatalog
[2380]	2847	echo " "
[2420]	2848	echo " *** submit the job"
	2849	if [[ $do_trace = true ]]
	2850	then
[2506]	2851	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2852	fi
[2506]	2853	$submit_command ${host_configuration}_${job_id}
	2854	rm ${host_configuration}_${job_id}
[2380]	2855	cd - > /dev/null
	2856
	2857	fi
	2858
	2859	rm -rf $jobfile
	2860
	2861	else
	2862
	2863	printf "\n *** jobfile created under name \"$jobfile\" "
	2864	printf "\n no batch-job has been sent!"
	2865
	2866	fi
	2867
	2868	fi # END OF REMOTE-PART

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