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source: palm/trunk/SCRIPTS/palmrun @ 2675

Last change on this file since 2675 was 2670, checked in by raasch, 7 years ago
test printouts removed
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 95.5 KB

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

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