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source: palm/trunk/SCRIPTS/palmrun @ 2610

Last change on this file since 2610 was 2610, checked in by raasch, 7 years ago
use of wildcards in file connection statements enabled, bugfix in logarithmic interpolation of v-component for particles (usws was used by mistake)
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 94.4 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 2610 2017-11-15 08:24:11Z raasch $
[2610]	29	# use of wildcards in file connection statements enabled
	30	#
	31	# 2605 2017-11-09 15:31:46Z raasch
[2605]	32	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	33	# will not be sent with the job file any more, but copied into the
[2610]	34	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	35	#
	36	# 2600 2017-11-01 14:11:20Z raasch
[2600]	37	# cycle numbers are made three digits wide
	38	#
	39	# 2566 2017-10-20 08:50:47Z raasch
[2566]	40	# execute command for combine_plot_fields added
	41	# "TEMPDIR" renamed "tempdir"
	42	# temporary working directory for local batch jobs is created immediately within
	43	# the user's palmrun call, due to a requirement of the "grid engine" batch
	44	# system, where the working directory is given with batch directive -wd and must
	45	# already exist when the job is submitted,
	46	# informative messages in non-trace mode reduced and partly reformatted
	47	#
	48	# 2551 2017-10-18 07:25:11Z raasch
[2551]	49	# TEMPDIR added as replacement string to be used in batch directives
	50	#
	51	# 2512 2017-10-04 08:26:59Z raasch
[2507]	52	# bugfix for determining cycle numbers of NetCDF input files
	53	#
	54	# 2506 2017-09-29 08:30:37Z raasch
[2506]	55	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	56	# host configuration added to SOURCES_FOR_RUN_... folder name
	57	# host_identifier renamed host_configuration
	58	# option -W added to allow for job dependencies
	59	#
	60	# 2501 2017-09-26 11:41:55Z raasch
[2501]	61	# default value for number of cores (option -X) set to 1
	62	# bugfix for mechanism which overwrites configuration file settings with values
	63	# provided by palmrun options
	64	#
	65	# 2499 2017-09-22 16:47:58Z kanani
[2499]	66	# option -h named configuration identifier
	67	#
	68	# 2480 2017-09-19 06:24:14Z maronga
[2480]	69	# bugfix for last revision
	70	#
	71	# 2479 2017-09-19 06:12:16Z raasch
[2479]	72	# option -A (project account number) added
	73	#
	74	# 2422 2017-09-08 08:25:41Z raasch
[2410]	75	# initial revision
[2380]	76	#
	77	#--------------------------------------------------------------------------------#
	78	# palmrun - script for running PALM jobs on local and remote hosts
	79	#--------------------------------------------------------------------------------#
	80
	81
	82
	83	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	84
	85	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	86	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	87	# (TOO MANY ARGUMENTS - PROBLEM)
	88	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	89
[2610]	90	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	91	typeset -i nr_of_output_files=0
[2380]	92	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	93	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	94	# SCRIPT-OPTION ARGUMENTS
	95	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	96	typeset -i icycle inode ival maxcycle mpi_tasks
	97	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	98
	99	activation_string_list=""
	100	AddFilenames=""
	101	combine_plot_fields=true
	102	compiler_name=""
	103	compiler_name_ser=""
	104	compiler_options=""
[2501]	105	cores=1
[2380]	106	cores_atmos=0
	107	cores_ocean=0
	108	coupled_dist=""
	109	cpp_options=""
	110	cpumax=0
[2506]	111	create_batch_job=false
[2380]	112	create_jobfile_only=false
	113	create_remote_batch_job=false
	114	dashes=" ----------------------------------------------------------------------------"
	115	defaultqueue=""
[2506]	116	delete_temporary_catalog=true
[2380]	117	do_compile=true
	118	do_trace=false
	119	executable=""
	120	execute_command=""
	121	execution_error=false
	122	fileconnection_file=.palm.iofiles
	123	fname=test
	124	global_revision=""
[2506]	125	host_configuration="default"
[2380]	126	hostfile=""
	127	hp=""
	128	keep_data_from_previous_run=false
	129	link_local_input=false
	130	link_local_output=false
[2388]	131	linker_options=""
[2385]	132	local_jobcatalog=""
[2380]	133	locat=normal
	134	makefile=""
	135	max_par_io_str=""
	136	prc=$0
	137	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	138	do
	139	prc=`echo $prc \| cut -f2- -d"/"`
	140	done
	141	module_calls=""
[2506]	142	palmrun_memory=""
[2380]	143	palmrun_script_name=$prc
	144	openmp=false
[2506]	145	previous_job=""
[2479]	146	project_account=""
[2380]	147	queue=none
	148	restart_run=false
	149	return_address=""
[2385]	150	remote_jobcatalog=""
[2380]	151	remote_username=""
	152	running_in_batch_mode=false
	153	run_coupled_model=false
	154	run_id=""
	155	silent=false
	156	source_list=""
	157	source_path=""
[2501]	158	tasks_per_node=0
[2380]	159	threads_per_task=1
	160	transfer_problems=false
[2384]	161	user_source_path=""
[2506]	162	use_existing_sources_folder=""
[2380]	163	use_openmp=false
[2422]	164	version="palmrun 1.0 Rev$Rev: 2303 $"
[2380]	165	working_directory=`pwd`
	166	write_binary=""
	167	TOPT=""
	168
	169
	170	# ERROR HANDLING IN CASE OF EXIT
[2404]	171	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	172	then
	173
	174	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	175	(( i = 0 ))
	176	while (( i < iec ))
	177	do
	178	(( i = i + 1 ))
	179	printf "\n *** Execution of ERROR-command:\n"
	180	printf " >>> ${err_command[$i]}\n"
	181	eval ${err_command[$i]}
	182	done
[2566]	183	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	184	printf "\n\n+++ palmrun killed \n\n"
	185	elif [[ $locat != control_c ]]
	186	then
[2566]	187	printf "\n --> palmrun finished\n\n"
[2380]	188	fi' exit
	189
	190
	191	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	192	trap 'cd; rm -rf $tempdir
[2380]	193	printf "\n+++ palmrun killed by \"^C\" \n\n"
	194	locat=control_c
	195	exit
	196	' 2
	197
	198
	199	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	200	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	201	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]	202	do
	203	case $option in
	204	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	205	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	206	(b) create_batch_job=true; prc="$prc -b";;
	207	(B) delete_temporary_catalog=false; prc="$prc -B";;
	208	(C) restart_run=true; prc="$prc -C";;
	209	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	210	(F) create_jobfile_only=true;;
	211	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	212	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	213	(j) running_in_batch_mode=true;;
	214	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	215	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	216	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	217	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	218	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	219	(r) run_id=$OPTARG;;
	220	(R) return_address=$OPTARG;;
	221	(s) source_list=$OPTARG;;
[2501]	222	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	223	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	224	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	225	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	226	(v) silent=true; prc="$prc -v";;
[2506]	227	(V) use_existing_sources_folder="-V";;
[2380]	228	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	229	(W) previous_job=$OPTARG;;
[2380]	230	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	231	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	232	(y) ocean_file_appendix=true; prc="$prc -y";;
	233	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	234	(Z) combine_plot_fields=false; prc="$prc -Z";;
	235	(\?) printf "\n +++ unknown option $OPTARG \n"
	236	printf "\n --> type \"$0 ?\" for available options \n"
	237	locat=parameter;exit;;
	238	esac
	239	done
	240
	241
	242	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	243	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	244	(( to_shift = $OPTIND - 1 ))
	245	shift $to_shift
	246
	247	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	248	if [[ "$1" = "?" ]]
	249	then
	250	(printf "\n *** Description of available palmrun options:\n"
	251	printf "\n Option Description Default-Value"
	252	printf "\n -a activation string list \"\" "
[2479]	253	printf "\n -A project account number ---"
[2380]	254	printf "\n -b batch-job on local machine ---"
	255	printf "\n -B do not delete temporary directory at end ---"
	256	printf "\n -d base name of files attached to program test"
	257	printf "\n -F create batch job file only ---"
[2506]	258	printf "\n -h host configuration \"default\" "
[2380]	259	printf "\n -k keep data from previous run"
	260	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	261	printf "\n -M Makefile name Makefile"
	262	printf "\n -O threads per openMP task ---"
	263	printf "\n -q queue \"$queue\" "
	264	printf "\n -s filenames of routines to be compiled \"\" "
	265	printf "\n must end with .f, .f90, .F, or .c !"
	266	printf "\n use \"..\" for more than one file and wildcards"
	267	printf "\n -s LM compiles all locally modified files"
	268	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	269	printf "\n -T tasks per node ---"
[2380]	270	printf "\n -u username on remote machine \"\" "
	271	printf "\n -v no prompt for confirmation ---"
[2506]	272	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	273	printf "\n -w maximum parallel io streams as given by -X"
[2506]	274	printf "\n -W name of job to wait for ---"
[2380]	275	printf "\n -x tracing of palmrun for debug purposes ---"
	276	printf "\n -X # of processors (on parallel machines) 1"
	277	printf "\n -y add appendix \"_O\" to all local output"
	278	printf "\n files (ocean precursor runs followed by"
	279	printf "\n coupled atmosphere-ocean runs) ---"
	280	printf "\n -Y run coupled model, \"#1 #2\" with"
	281	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	282	printf "\n -Z skip combine_plot_fields at the end of "
	283	printf "\n the simulation ---"
	284	printf "\n "
	285	printf "\n Possible values of positional parameter <modus>:"
	286	printf "\n \"?\" - this outline \n\n") \| more
	287	exit
	288	elif [[ "$1" != "" ]]
	289	then
	290	printf "\n +++ positional parameter $1 unknown \n"
	291	locat=parameter; exit
	292	fi
	293
	294
	295
	296	# SHORT STARTING MESSAGE
	297	printf "\n*** $version "
	298	printf "\n will be executed. Please wait ..."
	299
	300
[2506]	301	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	302	config_file=.palm.config.$host_configuration
	303	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
[2380]	304
	305
	306	# CHECK, IF CONFIGURATION FILE EXISTS
	307	if [[ ! -f $config_file ]]
	308	then
	309	printf "\n\n +++ configuration file: "
	310	printf "\n $config_file"
	311	printf "\n does not exist"
	312	locat=connect; exit
	313	fi
	314
	315
	316	# CHECK, IF FILE CONNECTION FILE EXISTS
	317	if [[ ! -f $fileconnection_file ]]
	318	then
	319	printf "\n\n +++ file connection file: "
	320	printf "\n $fileconnection_file"
	321	printf "\n does not exist"
	322	locat=connect; exit
	323	fi
	324
	325
[2404]	326	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	327	if [[ "$activation_string_list" = "" ]]
	328	then
	329	printf "\n\n +++ no activation string list given: "
	330	printf "\n please set palmrun option \"-a\" "
	331	locat=palmrun_option; exit
	332	fi
	333
	334
	335	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	336	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	337	then
	338	write_binary=true
	339	else
	340	write_binary=false
	341	fi
	342
	343
[2380]	344	# READ AND EVALUATE THE CONFIGURATION-FILE
	345	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	346
	347	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	348	while read line
	349	do
	350
	351	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	352	eval line=\"$line\"
	353
	354
	355	# INTERPRET THE LINE
	356	if [[ "$(echo $line)" = "" ]]
	357	then
	358
	359	# EMPTY LINE, NO ACTION
	360	continue
	361
	362	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	363	then
	364
	365	# LINE IS A COMMENT LINE
	366	continue
	367
	368	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	369	then
	370
	371	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	372	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	373	value=`echo $line \| cut -d" " -s -f2-`
	374
	375
	376	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	377	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	378	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	379	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	380	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	381	# CONFIGURATION-FILE.
	382	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	383	then
	384	eval export $var="\$value"
	385
	386	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	387	if [[ $do_trace = true ]]
	388	then
	389	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	390	fi
	391	fi
	392
	393	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	394	then
	395
	396	# LINE DEFINES BATCH-DIRECTIVE
	397	(( ibd = ibd + 1 ))
	398	line=$(echo $line \| cut -c4-)
	399	batch_directive[$ibd]="$line"
	400
	401	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	402	then
	403
	404	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	405	# REMOTE TO A LOCAL HOST
	406	(( ibdt = ibdt + 1 ))
	407	line=$(echo $line \| cut -c5-)
	408	batch_directive_transfer[$ibdt]="$line"
	409
	410	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	411	then
	412
	413	# LINE DEFINES ERROR-COMMAND
	414	(( iec = iec + 1 ))
	415	line=$(echo $line \| cut -c4-)
	416	err_command[$iec]="$line"
	417
	418	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	419	then
	420
	421	# LINE DEFINES INPUT-COMMAND
	422	(( iic = iic + 1 ))
	423	line=$(echo $line \| cut -c4-)
	424	in_command[$iic]="$line"
	425
	426	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	427	then
	428
	429	# LINE DEFINES OUTPUT-COMMAND
	430	(( ioc = ioc + 1 ))
	431	line=$(echo $line \| cut -c4-)
	432	out_command[$ioc]="$line"
	433
	434	else
	435
	436	# SKIP ALL OTHER LINES
	437	continue
	438
	439	fi
	440
	441	done < $config_file
	442
	443
	444	# CHECK SETTING OF REQUIRED PARAMETERS
	445	if [[ "$compiler_name" = "" ]]
	446	then
	447	printf "\n +++ no compiler name found in $config_file"
	448	printf "\n Please add line \"compiler_name ...\" to that file."
	449	locat=config_file; exit
	450	fi
	451	if [[ "$compiler_name_ser" = "" ]]
	452	then
	453	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	454	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	455	locat=config_file; exit
	456	fi
	457	if [[ "$compiler_options" = "" ]]
	458	then
	459	printf "\n +++ no compiler options found in $config_file"
	460	printf "\n Please add line \"compiler_options ...\" to that file."
	461	locat=config_file; exit
	462	fi
[2388]	463	if [[ "$linker_options" = "" ]]
[2380]	464	then
[2388]	465	printf "\n +++ no linker options found in $config_file"
	466	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	467	locat=config_file; exit
	468	fi
	469	if [[ "$execute_command" = "" ]]
	470	then
	471	printf "\n +++ no execute command found in $config_file"
	472	printf "\n Please add line \"execute_command ...\" to that file."
	473	locat=config_file; exit
	474	fi
	475
	476	if [[ "$hostfile" != "" ]]
	477	then
	478	if [[ $hostfile != auto && ! -f $hostfile ]]
	479	then
	480	printf "\n +++ no hostfile \"$hostfile\" found"
	481	printf "\n Please check line \"hostfile ...\" in $config_file"
	482	locat=config_file; exit
	483	fi
	484	fi
	485
	486
	487	# DETERMINE THE CALL STATUS
	488	if [[ "$return_address" != "" ]]
	489	then
	490
	491	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	492	# BATCH MODE AND ...
	493	running_on_remote=true
	494
	495	else
	496
	497	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	498	if [[ "$remote_ip" != "" ]]
	499	then
	500
	501	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	502	create_remote_batch_job=true
	503
	504	fi
	505	running_on_remote=false
	506	fi
	507
	508
	509
	510	# READ AND EVALUATE THE I/O-FILE LIST
	511	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	512
	513	# READ THE FILE CONNECTION FILE LINE BY LINE
	514	while read line
	515	do
	516
	517	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	518	eval line=\"$line\"
	519
	520
	521	# INTERPRET THE LINE
	522	if [[ "$(echo $line)" = "" ]]
	523	then
	524	# EMPTY LINE, NO ACTION
	525	continue
	526
	527	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	528	then
	529
	530	# LINE IS A COMMENT LINE
	531	true
	532
	533	else
	534
	535	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	536	# s2a: in/out - field
	537	# s2b: loc - field (optional)
	538	# s2c: tr/ar - field (optional)
	539	s1=`echo $line \| cut -d" " -f1`
	540	s2=`echo $line \| cut -d" " -s -f2`
	541	s2a=$(echo $s2 \| cut -d":" -f1)
	542	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	543	then
	544	s2b=""
	545	s2c=""
	546	else
	547	s2b=`echo $s2 \| cut -d":" -f2 \| sed 's/:/ /g'`
	548	s2c=`echo $s2 \| cut -d":" -s -f3 \| sed 's/:/ /g'`
	549	fi
	550	s3=`echo $line \| cut -d" " -f3`
	551	s4=`echo $line \| cut -d" " -s -f4`
	552	s5=`echo $line \| cut -d" " -s -f5`
	553	s6=`echo $line \| cut -d" " -s -f6`
	554
	555
	556	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	557	# INPUT- OR OUTPUT-LIST.
	558	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	559	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
	560	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b = loc), THE FILE CONNECTION
	561	# IS NOT CHECKED AND STORED.
[2610]	562	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2380]	563	if [[ "$s2a" = in && ! ( $create_remote_batch_job = true && ( "$s2b" = loc \|\| "$s2b" = locopt ) ) ]]
	564	then
	565	found=false
	566	for actual in $activation_string_list
	567	do
	568	for formal in $s3
	569	do
	570	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	571	done
	572	done
	573	if [[ $found = true ]]
	574	then
	575	(( iin = iin + 1 ))
[2610]	576	localin_pre[$iin]=$s1; transin_pre[$iin]=$s2b; actionin_pre[$iin]=$s2c;
	577	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2605]	578
	579	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	580	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
	581	if [[ $running_on_remote = true && ( "$s2b" = job \|\| "$s2b" = jobopt ) ]]
	582	then
[2610]	583	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	584	fi
	585
[2610]	586	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	587	# THE WILDCARD FROM THE ENDING
	588	if [[ "${s5: -1}" = "*" ]]
	589	then
	590	if [[ "$s2c" = "di" ]]
	591	then
	592	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	593	printf "\n see file \"$fileconnection_file\", line"
	594	printf "\n$line"
	595	locat=iofiles_file; exit
	596	fi
	597	multin[$iin]=true
	598	string=${endin_pre[$iin]}
	599	endin_pre[$iin]="${string%?}"
	600	else
	601	multin[$iin]=false
	602	fi
[2380]	603	fi
	604	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true && "$s2b" = loc ) ]]
	605	then
	606	found=false
	607	for actual in $activation_string_list
	608	do
	609	for formal in $s3
	610	do
	611	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	612	done
	613	done
	614	if [[ $found = true ]]
	615	then
	616	(( iout = iout + 1 ))
[2610]	617	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2c; typeout_pre[$iout]=$s3;
	618	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	619
	620	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	621	# THE WILDCARD FROM THE LOCAL FILENAME
	622	if [[ "${s1: -1}" = "*" ]]
	623	then
	624	if [[ "$s2c" = "di" ]]
	625	then
	626	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	627	printf "\n see file \"$fileconnection_file\", line"
	628	printf "\n$line"
	629	locat=iofiles_file; exit
	630	fi
	631	multout[$iout]=true
	632	string=${localout_pre[$iout]}
	633	localout_pre[$iout]="${string%?}"
	634	else
	635	multout[$iout]=false
	636	fi
[2380]	637	fi
	638	elif [[ "$s2a" != in && "$s2a" != out ]]
	639	then
	640	printf "\n +++ I/O-attribute in configuration file $config_file has the invalid"
	641	printf "\n value \"$s2\". Only \"in\" and \"out\" are allowed!"
	642	locat=connect; exit
	643	fi
	644	IFS="$IFSALT"
	645	fi
	646
	647	done < $fileconnection_file
	648
	649
	650
[2501]	651	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	652	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	653	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	654	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	655	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	656	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	657
	658
	659
[2380]	660	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	661	if [[ $run_coupled_model = true ]]
	662	then
	663
	664	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	665	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	666
	667	if (( $cores_ocean + $cores_atmos != $cores ))
	668	then
	669
	670	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	671	printf "\n PEs (total) : $cores"
	672	printf "\n PEs (atmosphere): $cores_atmos"
	673	printf "\n PEs (ocean) : $cores_ocean"
	674	locat=coupling; exit
	675
	676	fi
	677
	678	fi
	679
	680
	681	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	682	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	683	# FOLDER
	684	if [[ $running_in_batch_mode = true ]]
	685	then
	686
[2506]	687	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	688	then
[2506]	689	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	690	printf "\n Please check the output of the palmrun-call"
	691	printf "\n that you did on your local host."
	692	locat=SOURCES_FOR_RUN; exit
	693	fi
	694
	695	else
	696
	697	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	698	# AUTOMATIC RESTART RUN
	699	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	700	if [[ $restart_run = false ]]
	701	then
	702
	703	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	704	# THE LOCAL HOST
	705	if [[ ! -d $source_path ]]
	706	then
	707	printf "\n\n +++ source path \"$source_path\" on local host"
	708	printf "\n \"$(hostname)\" does not exist"
	709	locat=source_path; exit
	710	fi
	711
[2506]	712	rm -rf $sources_for_run_catalog
	713	mkdir -p $sources_for_run_catalog
[2380]	714
	715	if [[ "$source_list" = LM ]]
	716	then
	717
	718	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	719	source_list=""
	720	cd $source_path
	721
	722
[2512]	723	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	724	if [[ ! -d ../.svn ]]
[2380]	725	then
	726	printf "\n\n +++ source directory"
	727	printf "\n \"$source_path\" "
	728	printf "\n is not under control of \"subversion\"."
[2512]	729	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	730	fi
	731
	732
	733	# LIST ALL MODIFIED SOURCE CODE FILES
	734	Filenames=""
[2404]	735	svn status > tmp_svnstatus
[2380]	736	while read line
	737	do
	738	firstc=`echo $line \| cut -c1`
	739	if [[ $firstc = M \|\| $firstc = "?" ]]
	740	then
	741	Name=`echo "$line" \| cut -c8-`
	742	extension=`echo $Name \| cut -d. -f2`
	743	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	744	then
	745	Filenames="$Filenames "$Name
	746	fi
	747	fi
[2404]	748	done < tmp_svnstatus
	749	rm -rf tmp_svnstatus
[2380]	750
	751
	752	# COPY FILES TO SOURCES_FOR_RUN_...
	753	for filename in $Filenames
	754	do
[2506]	755	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	756	source_list=$source_list"$filename "
	757	done
	758
	759	cd - > /dev/null
	760
	761
	762	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	763	elif [[ "$source_list" != "" ]]
	764	then
	765
	766	cd $source_path
	767
	768	for filename in $source_list
	769	do
	770
	771	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	772	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	773	then
	774	printf "\n +++ source code file: $filename"
	775	printf "\n must not contain (\"/\") "
	776	locat=source; exit
	777	fi
	778
	779	if [[ ! -f $filename ]]
	780	then
	781	printf "\n +++ source code file: $filename"
	782	printf "\n does not exist"
	783	locat=source; exit
	784	else
[2506]	785	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	786	fi
	787
	788	done
	789
	790	cd - > /dev/null
	791
	792	fi
	793
	794	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	795	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	796	if [[ ! -f $makefile ]]
	797	then
	798	printf "\n +++ file \"$makefile\" does not exist"
	799	locat=make; exit
	800	else
[2506]	801	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	802	fi
	803
	804
	805	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	806	if [[ "$user_source_path" != "" ]]
[2380]	807	then
	808
	809	# DOES THE DIRECTORY EXIST?
[2384]	810	if [[ ! -d $user_source_path ]]
[2380]	811	then
	812
	813	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	814	printf "\n \"$user_source_path\" "
[2380]	815	printf "\n does not exist or is not a directory."
	816	printf "\n No source code will be used from this directory!\n"
[2384]	817	user_source_path=""
[2380]	818	if [[ $silent == false ]]
	819	then
	820	sleep 2
	821	fi
	822
	823	else
	824
[2384]	825	cd $user_source_path
[2380]	826	found=false
	827
	828	Names=$(ls -1 *.f90 2>&1)
	829	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	830	Names=$(ls -1 *.F90 2>&1)
	831	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	832	Names=$(ls -1 *.F 2>&1)
	833	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	834	Names=$(ls -1 *.f 2>&1)
	835	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	836	Names=$(ls -1 *.c 2>&1)
	837	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	838
	839	cd - > /dev/null
[2506]	840	cd $sources_for_run_catalog
[2380]	841
	842	# COPY MAKEFILE IF EXISTING
[2384]	843	if [[ -f $user_source_path/Makefile ]]
[2380]	844	then
	845	printf "\n\n *** user Makefile from directory"
[2384]	846	printf "\n \"$user_source_path\" is used \n"
[2380]	847	if [[ $silent == false ]]
	848	then
	849	sleep 1
	850	fi
[2384]	851	cp $user_source_path/Makefile .
[2380]	852	fi
	853
	854	for filename in $AddFilenames
	855	do
	856	if [[ -f $filename ]]
	857	then
	858	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	859	printf "\n source code directory \"$user_source_path\" "
[2380]	860	printf "\n but was also given with option \"-s\" which means that it should be taken"
	861	printf "\n from directory \"$source_path\"."
	862	locat=source; exit
	863	fi
	864
[2384]	865	cp $user_source_path/$filename .
[2380]	866	source_list="$source_list $filename"
	867
	868	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	869	if [[ $(grep -c $filename Makefile) = 0 ]]
	870	then
	871	printf "\n\n +++ user file \"$filename\" "
	872	printf "\n is not listed in Makefile \n"
	873	locat=source; exit
	874	else
	875
	876	if [[ $found = false ]]
	877	then
	878	found=true
	879	printf "\n\n *** following user file(s) added to the"
	880	printf " files to be translated:\n "
	881	fi
	882	printf "$filename "
	883	if [[ $silent == false ]]
	884	then
	885	sleep 0.5
	886	fi
	887
	888	fi
	889	done
	890	[[ $found = true ]] && printf "\n"
	891	cd - > /dev/null
	892	fi
	893	fi
	894
	895	# COPY CONFIGURATION FILES
[2506]	896	cp $config_file $sources_for_run_catalog
	897	cp $fileconnection_file $sources_for_run_catalog
[2380]	898
	899	# COPY SHELLSCRIPTS
[2506]	900	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	901	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	902
	903	fi
	904
	905	fi
	906
[2605]	907
[2380]	908	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	909	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	910	if [[ "$global_revision" = "" ]]
	911	then
	912	global_revision=`svnversion $source_path 2>/dev/null`
	913	global_revision="Rev: $global_revision"
	914	fi
	915
	916
	917	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	918	if [[ -n $cores ]]
	919	then
	920
	921	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	922	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	923	if [[ $tasks_per_node = 0 ]]
[2380]	924	then
	925	printf "\n"
	926	printf "\n +++ option \"-T\" (tasks per node) is missing"
	927	printf "\n set -T option or define tasks_per_node in the config file"
	928	locat=tasks_per_node; (( iec = 0 )); exit
	929	fi
	930
	931	if (( cores < tasks_per_node ))
	932	then
	933	printf "\n"
	934	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	935	printf "\n given values: -T $tasks_per_node -X $cores"
	936	locat=tasks_per_node; (( iec = 0 )); exit
	937	fi
	938
	939	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	940	(( mpi_tasks = cores / threads_per_task ))
	941	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	942	(( ii = cores / tasks_per_node ))
	943	(( remaining_cores = cores - ii * tasks_per_node ))
	944	if (( remaining_cores > 0 ))
	945	then
	946	printf "\n"
	947	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	948	printf "\n divisor of the total number of cores (option \"-X\")"
	949	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	950	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	951	(( nodes = nodes + 1 ))
	952	fi
	953
	954	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	955	if [[ "$tasks_per_node" != "" ]]
	956	then
	957	TOPT="-T $tasks_per_node"
	958	fi
	959
	960	fi
	961
	962
	963	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	964	if [[ "$maximum_parallel_io_streams" = "" ]]
	965	then
	966	maximum_parallel_io_streams=$cores
	967	fi
	968
	969
	970	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	971	if [[ "$scp_port" != "" ]]
	972	then
	973	PORTOPT="-P $scp_port"
	974	SSH_PORTOPT="-p $scp_port"
	975	fi
	976
	977
	978	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	979	# CONFIG-FILE
	980	if [[ "$ssh_key" != "" ]]
	981	then
	982	ssh_key="-i $HOME/.ssh/$ssh_key"
	983	fi
	984
	985
	986	# SET QUEUE, IF NOT GIVEN
	987	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	988	then
	989
	990	if [[ $queue = none && "$defaultqueue" = "" ]]
	991	then
	992	printf "\n"
	993	printf "\n +++ no default queue given in configuration file and no queue"
	994	printf "\n given with option -q"
	995	fi
	996	if [[ $queue = none ]]
	997	then
	998	queue=$defaultqueue
	999	fi
	1000
	1001	fi
	1002
	1003
	1004	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1005	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1006	(( i = 0 ))
[2610]	1007	(( nr_of_input_files = 0 ))
[2380]	1008	while (( i < iin ))
	1009	do
	1010	(( i = i + 1 ))
	1011
	1012	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1013	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1014	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1015	then
[2610]	1016	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1017	else
[2610]	1018	eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]}
[2380]	1019	fi
	1020
[2610]	1021
[2380]	1022	# CHECK IF FILE EXISTS
	1023	if ! ls $filename* 1>/dev/null 2>&1
	1024	then
	1025
	1026	# FILES WITH ATTRIBUTE locopt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
[2610]	1027	if [[ "${transin_pre[$i]}" != "locopt" && "${transin_pre[$i]}" != "jobopt" ]]
[2380]	1028	then
	1029	printf "\n\n +++ INPUT-file: "
[2610]	1030	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1031	then
	1032	printf "\n $filename"
	1033	else
[2610]	1034	printf "\n $filename.${extin_pre[$i]}"
[2380]	1035	fi
	1036	printf "\n does not exist\n"
	1037	locat=input; exit
	1038	else
[2610]	1039	(( nr_of_input_files = nr_of_input_files + 1 ))
	1040	localin[$nr_of_input_files]="${localin_pre[$i]}"
	1041	transin[$nr_of_input_files]="unavailable"
	1042	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1043	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1044	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1045	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1046	fi
[2605]	1047
[2380]	1048	else
	1049
[2610]	1050	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND
	1051	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
	1052	if [[ "${multin[$i]}" = true ]]
	1053	then
	1054	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1055	ls -1 -d ${filename} > filelist 2>/dev/null
	1056	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1057	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1058
[2610]	1059	endings=""
	1060	while read line
	1061	do
	1062	# filename without path (i.e. after the last "/")
	1063	basefilename=$(basename ${line})
[2380]	1064
[2610]	1065	# check if there is an extension and remove it
	1066	ext=${basefilename##*.}
	1067	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1068	then
	1069	basefilename=${basefilename%.*}
	1070	fi
[2380]	1071
[2610]	1072	# check for an existing cycle number and remove it
	1073	cycle=${basefilename##*.}
	1074	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1075	then
	1076	basefilename=${basefilename%.*}
	1077	fi
[2600]	1078
[2610]	1079	# remove the fname from the beginning
	1080	length_fname=${#fname}
	1081	ending=${basefilename:${length_fname}}
	1082
	1083	# remove the ending given in the .iofiles from the beginning
	1084	endingstring="${endin_pre[$i]}"
	1085	length_ending=${#endingstring}
	1086	ending=${ending:${length_ending}}
	1087
	1088	if [[ "$ending" = "" ]]
[2600]	1089	then
[2610]	1090	# standard ending as given in the .iofiles
	1091	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1092	then
	1093	endings="$endings DEFAULT"
	1094	fi
[2600]	1095	else
[2610]	1096	# ending must start with "_", otherwise its a different file
	1097	if [[ "${ending:0:1}" = "_" ]]
	1098	then
	1099	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1100	then
	1101	endings="$endings $ending"
	1102	fi
	1103	fi
[2600]	1104	fi
[2610]	1105
	1106	done <filelist
[2380]	1107
[2610]	1108	rm filelist
[2380]	1109
[2600]	1110	else
[2610]	1111
	1112	# SINGLE NAME
	1113	endings=DEFAULT
	1114
[2600]	1115	fi
	1116
[2610]	1117	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1118	for ending in $endings
	1119	do
	1120
	1121	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1122	if [[ $ending = DEFAULT ]]
[2380]	1123	then
[2610]	1124	ending=""
	1125	fi
	1126
	1127	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1128	(( nr_of_input_files = nr_of_input_files + 1 ))
	1129	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
	1130	transin[$nr_of_input_files]="${transin_pre[$i]}"
	1131	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1132	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1133	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1134	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1135
	1136
	1137	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1138	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1139	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1140	then
	1141	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1142	else
[2610]	1143	eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]}
[2380]	1144	fi
[2610]	1145
	1146	# DETERMINE THE FILE'S CYCLE NUMBER
	1147	(( maxcycle = 0 ))
	1148	ls -1 -d $filename > filelist 2>/dev/null
	1149	ls -1 -d $filename.* >> filelist 2>/dev/null
	1150	while read line
	1151	do
	1152	# filename without path (i.e. after the last "/")
	1153	basefilename=$(basename ${line})
	1154
	1155	# check if there is an extension
	1156	extension=${basefilename##*.}
	1157	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1158	then
	1159	basefilename=${basefilename%.*}
	1160	fi
	1161
	1162	# check for an existing cycle number
	1163	cycle=${basefilename##*.}
	1164	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1165	then
	1166	(( icycle = $cycle ))
	1167	else
	1168	(( icycle = 0 ))
	1169	fi
	1170
	1171	if (( icycle > maxcycle ))
	1172	then
	1173	(( maxcycle = icycle ))
	1174
	1175	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1176	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1177	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1178	then
	1179	leading_zero=true
	1180	else
	1181	leading_zero=false
	1182	fi
	1183	fi
	1184
	1185	done <filelist
	1186	rm filelist
	1187
	1188	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1189	if [[ $leading_zero = true ]]
[2380]	1190	then
[2610]	1191	cyclestring=`printf "%03d" $maxcycle`
	1192	else
	1193	cyclestring=$maxcycle
[2380]	1194	fi
[2610]	1195
	1196	# APPEND CYCLE NUMBER TO FILENAME
	1197	if (( maxcycle > 0 ))
[2380]	1198	then
[2610]	1199	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1200	then
	1201	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1202	else
	1203	filename=${filename}.$cyclestring
	1204	fi
[2380]	1205	else
[2610]	1206	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1207	then
	1208	filename=${filename}.${extin[$nr_of_input_files]}
	1209	fi
[2380]	1210	fi
[2610]	1211
	1212	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1213	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1214	absnamein[$nr_of_input_files]=$filename
	1215	if (( maxcycle > 0 ))
[2380]	1216	then
[2610]	1217	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1218	then
	1219	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1220	else
	1221	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring
	1222	fi
[2380]	1223	else
[2610]	1224	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1225	then
	1226	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1227	else
	1228	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}
	1229	fi
[2380]	1230	fi
	1231
[2610]	1232	done
	1233
[2380]	1234	fi
[2610]	1235
[2380]	1236	done
	1237
[2610]	1238
[2380]	1239	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1240	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1241	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1242	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1243	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1244	# REMOTE HOST)
	1245	(( i = 0 ))
	1246	while (( i < iout ))
	1247	do
	1248	(( i = i + 1 ))
[2610]	1249	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1250	then
[2610]	1251	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1252	then
[2610]	1253	actionout_pre[$i]=""
	1254	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1255	then
[2610]	1256	actionout_pre[$i]=pe
	1257	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1258	then
[2610]	1259	actionout_pre[$i]=a
[2380]	1260	fi
	1261	(( maxcycle = 0 ))
[2610]	1262	eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]}
	1263	eval catalogname=${pathout_pre[$i]}
[2380]	1264	if ! ls $filename* 1>/dev/null 2>&1
	1265	then
	1266
	1267	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1268	if cat /dev/null > $filename
	1269	then
	1270	rm $filename
	1271	else
	1272
	1273	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1274	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1275	if [[ ! -d $catalogname ]]
	1276	then
	1277	if mkdir -p $catalogname
	1278	then
	1279	printf "\n\n *** directory:"
	1280	printf "\n $catalogname"
	1281	printf "\n was created\n"
	1282	else
	1283	printf "\n\n +++ OUTPUT-file:"
	1284	printf "\n $filename"
	1285	printf "\n cannot be created, because directory does not exist"
	1286	printf "\n and cannot be created either"
	1287	printf "\n"
	1288	locat=output ; exit
	1289	fi 2>/dev/null
	1290	else
	1291	printf "\n\n +++ OUTPUT-file:"
	1292	printf "\n $filename"
	1293	printf "\n cannot be created, although directory exists"
	1294	printf "\n"
	1295	locat=output ; exit
	1296	fi
	1297	fi 2>/dev/null
	1298
	1299	fi
	1300
	1301	fi
	1302	done
	1303
	1304
	1305	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1306	if [[ $running_in_batch_mode = false ]]
	1307	then
	1308	run_id=$RANDOM
	1309	job_id=${fname}.$run_id
	1310
[2566]	1311	tempdir=$fast_io_catalog/$job_id
[2380]	1312	fi
	1313
	1314
	1315	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1316	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1317	then
	1318
	1319	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1320	if [[ $ibd = 0 ]]
	1321	then
	1322	printf "\n"
	1323	printf "\n +++ no batch directives found in configuration file"
	1324	locat=config_file_batch_directives; (( iec = 0 )); exit
	1325	fi
	1326
	1327	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1328	done=false
[2384]	1329	cputime=$cpumax
[2380]	1330	while [[ $done = false ]]
	1331	do
[2384]	1332	if (( cputime == 0 ))
[2380]	1333	then
	1334	printf "\n +++ cpu-time is undefined"
	1335	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1336	printf "\n >>> "
[2384]	1337	read cputime 1>/dev/null 2>&1
[2380]	1338	else
	1339	done=true
	1340	fi
	1341	done
[2420]	1342	cpumax=$cputime
[2380]	1343
	1344	# CHECK THE MEMORY DEMAND
	1345	done=false
	1346	while [[ $done = false ]]
	1347	do
	1348	if (( memory == 0 ))
	1349	then
	1350	printf "\n +++ memory demand is undefined"
	1351	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1352	printf "\n >>> "
	1353	read memory 1>/dev/null 2>&1
	1354	else
	1355	done=true
	1356	fi
	1357	done
	1358
	1359	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1360	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1361	then
	1362	while [[ -z $remote_username ]]
	1363	do
[2420]	1364	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1365	printf "\n >>> Please type username:"
	1366	printf "\n >>> "
	1367	read remote_username
	1368	done
	1369	fi
	1370
	1371	else
	1372
[2420]	1373	if [[ $running_in_batch_mode = false ]]
	1374	then
	1375	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1376	cpumax=$cputime
	1377	else
	1378	cputime=$cpumax
	1379	fi
[2380]	1380
	1381	fi
	1382
	1383
	1384	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1385	(( cpu_hours = cputime / 3600 ))
	1386	(( resttime = cputime - cpu_hours * 3600 ))
	1387	(( cpu_minutes = resttime / 60 ))
	1388	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1389	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1390
	1391
	1392	# OUTPUT OF THE PALMRUN-HEADER
	1393	calltime=$(date)
	1394	printf "\n"
	1395	printf "#------------------------------------------------------------------------# \n"
	1396	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1397	printf "\| \| \n"
	1398	column1="called on:"; column2=$(hostname)
	1399	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1400	if [[ $create_remote_batch_job = true ]]
	1401	then
[2506]	1402	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1403	else
	1404	if [[ $running_on_remote = true ]]
	1405	then
[2506]	1406	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1407	else
[2506]	1408	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1409	fi
	1410	fi
	1411	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1412
	1413	column1="running in:"
	1414	if [[ $running_in_batch_mode = true ]]
	1415	then
	1416	column2="batch job mode"
	1417	else
	1418	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1419	then
	1420	column2="job creation mode"
	1421	else
	1422	column2="interactive run mode"
	1423	fi
	1424	fi
	1425	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1426
[2479]	1427	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1428	then
[2480]	1429	if [[ "$project_account" != "" ]]
[2479]	1430	then
	1431	column1="project account number:"
	1432	column2="$project_account"
	1433	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1434	fi
	1435	fi
	1436
[2380]	1437	if [[ -n $cores ]]
	1438	then
	1439	if [[ $run_coupled_model = false ]]
	1440	then
	1441	column1="number of cores:"; column2=$cores
	1442	else
	1443	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1444	fi
	1445	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1446	fi
	1447	if [[ -n $tasks_per_node ]]
	1448	then
	1449	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1450	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1451	if (( remaining_cores > 0 ))
	1452	then
	1453	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1454	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1455	fi
	1456	fi
	1457	if [[ $maximum_parallel_io_streams != $cores ]]
	1458	then
	1459	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1460	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1461	fi
	1462	if [[ $use_openmp = true ]]
	1463	then
	1464	column1="threads per task:"; column2="$threads_per_task"
	1465	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1466	fi
[2384]	1467	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1468	then
[2506]	1469	column1="memory demand / PE":; column2="$memory MB"
	1470	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1471	column1="job cpu time (h:m:s):"; column2="$timestring"
	1472	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1473	fi
[2380]	1474	printf "\| \| \n"
	1475	if [[ "$source_list" != "" ]]
	1476	then
	1477	if [[ "$make_options" != "" ]]
	1478	then
	1479	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1480	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1481	line=$(echo "$make_options" \| cut -c46-)
	1482	while [[ "$line" != "" ]]
	1483	do
	1484	column1=""
	1485	column2=$(echo "$line" \| cut -c-45)
	1486	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1487	line=$(echo "$line" \| cut -c46-)
	1488	done
	1489	fi
	1490	fi
	1491
	1492	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1493	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1494	line=$(echo "$cpp_options" \| cut -c46-)
	1495	while [[ "$line" != "" ]]
	1496	do
	1497	column1=""
	1498	column2=$(echo "$line" \| cut -c-45)
	1499	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1500	line=$(echo "$line" \| cut -c46-)
	1501	done
	1502
	1503	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1504	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1505	line=$(echo "$compiler_options" \| cut -c46-)
	1506	while [[ "$line" != "" ]]
	1507	do
	1508	column1=""
	1509	column2=$(echo "$line" \| cut -c-45)
	1510	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1511	line=$(echo "$line" \| cut -c46-)
	1512	done
	1513
[2388]	1514	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1515	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1516	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1517	while [[ "$line" != "" ]]
	1518	do
	1519	column1=""
	1520	column2=$(echo "$line" \| cut -c-45)
	1521	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1522	line=$(echo "$line" \| cut -c46-)
	1523	done
	1524
	1525	if [[ "$login_init_cmd" != "" ]]
	1526	then
	1527	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1528	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1529	line=$(echo "$login_init_cmd" \| cut -c46-)
	1530	while [[ "$line" != "" ]]
	1531	do
	1532	column1=""
	1533	column2=$(echo "$line" \| cut -c-45)
	1534	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1535	line=$(echo "$line" \| cut -c46-)
	1536	done
	1537	fi
	1538
	1539	if [[ "$module_commands" != "" ]]
	1540	then
	1541	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1542	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1543	line=$(echo "$module_commands" \| cut -c46-)
	1544	while [[ "$line" != "" ]]
	1545	do
	1546	column1=""
	1547	column2=$(echo "$line" \| cut -c-45)
	1548	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1549	line=$(echo "$line" \| cut -c46-)
	1550	done
	1551	fi
	1552	printf "\| \| \n"
	1553	column1="base name of files:"; column2=$fname
	1554	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1555	column1="activation string list:"; column2=$(echo $activation_string_list)
	1556	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1557
	1558	if [[ "$ocean_file_appendix" = true ]]
	1559	then
	1560	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1561	fi
	1562
	1563	if [[ "$source_list" != "" ]]
	1564	then
	1565	printf "\| \| \n"
	1566	printf "\| Files to be compiled: \| \n"
	1567	line=$source_list
	1568	while [[ "$line" != "" ]]
	1569	do
	1570	linestart=$(echo $line \| cut -c-70)
	1571	printf "\| %-70s \| \n" "$linestart"
	1572	line=$(echo "$line" \| cut -c71-)
	1573	done
	1574	fi
	1575	printf "#------------------------------------------------------------------------#"
	1576
	1577
	1578
	1579	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1580	if [[ $do_trace = true ]]
	1581	then
	1582	(( i = 0 ))
[2610]	1583	while (( i < nr_of_input_files ))
[2380]	1584	do
	1585	(( i = i + 1 ))
	1586	if (( i == 1 ))
	1587	then
	1588	printf "\n\n >>> INPUT-file assignments:\n"
	1589	fi
	1590	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1591	done
	1592	(( i = 0 ))
	1593	while (( i < iout ))
	1594	do
	1595	(( i = i + 1 ))
	1596	if (( i == 1 ))
	1597	then
	1598	printf "\n\n >>> OUTPUT-file assignments:\n"
	1599	fi
	1600	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1601	done
	1602	(( i = 0 ))
	1603	while (( i < iic ))
	1604	do
	1605	(( i = i + 1 ))
	1606	if (( i == 1 ))
	1607	then
	1608	printf "\n\n >>> INPUT-commands:\n"
	1609	fi
	1610	printf "\n ${in_command[$i]}"
	1611	done
	1612	(( i = 0 ))
	1613	while (( i < ioc ))
	1614	do
	1615	(( i = i + 1 ))
	1616	if (( i == 1 ))
	1617	then
	1618	printf "\n\n >>> OUTPUT-commands:\n"
	1619	fi
	1620	printf "\n ${out_command[$i]}"
	1621	done
	1622	fi
	1623
	1624	# QUERY FOR CONTINUE
	1625	if [[ $silent = false && $running_in_batch_mode = false ]]
	1626	then
	1627	antwort=dummy
	1628	printf "\n\n"
	1629	printf " >>> everything o.k. (y/n) ? "
	1630	while read antwort
	1631	do
	1632	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1633	then
	1634	printf " >>> everything o.k. (y/n) ? "
	1635	else
	1636	break
	1637	fi
	1638	done
	1639	if [[ $antwort = n \|\| $antwort = N ]]
	1640	then
	1641	locat=user_abort; (( iec = 0 )); exit
	1642	fi
	1643	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1644	then
[2566]	1645	printf "\n *** batch-job will be created and submitted"
[2380]	1646	else
[2566]	1647	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1648	fi
	1649	fi
	1650
	1651
	1652
	1653	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1654	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1655	then
	1656
	1657	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1658	then
[2566]	1659	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1660	else
[2566]	1661	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1662	fi
	1663
[2422]	1664	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1665	# IT SHALL BE CREATED
	1666	ask_for_make_depository=false
	1667	if [[ $create_remote_batch_job = true ]]
	1668	then
	1669
	1670	line=`grep %base_directory $config_file`
[2506]	1671	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1672	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]	1673
[2506]	1674	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1675	then
	1676	printf "\n\n +++ make depository \"${make_depository}\""
	1677	printf "\n on remote host not found!"
	1678	ask_for_make_depository=true
	1679	fi
[2506]	1680	rm ${host_configuration}_last_make_protokoll
[2422]	1681
	1682	else
	1683
	1684	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1685	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1686	if [[ ! -d ${make_depository} ]]
	1687	then
	1688	printf "\n\n +++ make depository \"${make_depository}\""
	1689	printf "\n on local host not found!"
	1690	ask_for_make_depository=true
	1691	fi
	1692
	1693	fi
	1694
	1695	if [[ $ask_for_make_depository = true ]]
	1696	then
	1697
	1698	antwort=dummy
	1699	printf "\n\n"
	1700	printf " >>> Create a new one (y/n) ? "
	1701	while read antwort
	1702	do
	1703	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1704	then
	1705	printf " >>> Create a new one (y/n) ? "
	1706	else
	1707	break
	1708	fi
	1709	done
	1710	if [[ $antwort = n \|\| $antwort = N ]]
	1711	then
	1712	locat=user_abort; (( iec = 0 )); exit
	1713	fi
	1714
[2566]	1715	if [[ $do_trace = true ]]
	1716	then
	1717	palmbuild -h $host_configuration
	1718	else
	1719	palmbuild -v -h $host_configuration
	1720	fi
[2422]	1721
	1722	if [[ $? != 0 ]]
	1723	then
	1724
	1725	# ABORT IN CASE OF COMPILATION PROBLEMS
	1726	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1727	locat=make_depository
	1728	exit
	1729	else
	1730	echo " *** now continue with creating executable and other sources"
	1731	fi
	1732
	1733	fi
	1734
[2566]	1735	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2506]	1736	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
[2380]	1737
	1738	if [[ $? != 0 ]]
	1739	then
	1740
	1741	# ABORT IN CASE OF COMPILATION PROBLEMS
	1742	printf "\n +++ error while creating executable and/or other sources"
	1743	locat=execution
[2506]	1744	rm -rf $sources_for_run_catalog
[2380]	1745	exit
	1746
	1747	else
	1748
[2566]	1749	printf " *** executable and other sources created\n"
[2506]	1750	rm -rf $sources_for_run_catalog
[2380]	1751
	1752	fi
	1753
	1754	fi
	1755
	1756
[2605]	1757	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH JOB-ATTRIBUT WILL
	1758	# BE COPIED TO THE REMOTE HOST
	1759	if [[ $create_remote_batch_job = true ]]
	1760	then
	1761	(( i = 0 ))
[2610]	1762	while (( i < nr_of_input_files ))
[2605]	1763	do
	1764	(( i = i + 1 ))
	1765	if [[ "${transin[$i]}" = job \|\| "${transin[$i]}" = jobopt ]]
	1766	then
	1767	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1768	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1769	fi
	1770	done
	1771	if (( i > 0 ))
	1772	then
	1773	printf " *** input files have been copied to the remote host\n"
	1774	fi
	1775	fi
	1776
	1777
[2380]	1778	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1779	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1780	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1781	then
	1782
	1783	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1784	if [[ $running_in_batch_mode = false ]]
	1785	then
	1786	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1787	# FOLDER
[2566]	1788	mkdir -p $tempdir
	1789	chmod go+rx $tempdir
	1790	cd $tempdir
	1791	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1792	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1793
	1794	else
	1795
	1796	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1797	printf "\n *** running in temporary directory: $tempdir"
[2380]	1798
	1799	fi
	1800
	1801
	1802	# PROVIDE THE INPUT FILES
	1803	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
	1804	(( i = 0 ))
[2610]	1805	while (( i < nr_of_input_files ))
[2380]	1806	do
	1807	(( i = i + 1 ))
	1808	if (( i == 1 ))
	1809	then
	1810	printf "\n\n *** providing INPUT-files:\n$dashes"
	1811	fi
	1812
	1813
	1814	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
	1815	if [[ "${transin[$i]}" = unavailable ]]
	1816	then
	1817	if [[ "${extin[$i]}" = "" \|\| "${extin[$i]}" = " " ]]
	1818	then
	1819	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}\" "
	1820	printf "\n is not available!"
	1821	else
	1822	printf "\n *** INFORMATIVE: input file \"${pathin[$i]}/${fname}${endin[$i]}.${extin[$i]}\" "
	1823	printf "\n is not available!"
	1824	fi
	1825	continue
	1826	fi
	1827
	1828	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1829	files_for_cores=false; filetype=file
	1830	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1831	then
	1832	files_for_cores=true; filetype=files
	1833	actionin[$i]=""
	1834	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1835	then
	1836	actionin[$i]=""
	1837	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1838	then
	1839	files_for_cores=true; filetype=files
	1840	actionin[$i]="ln"
	1841	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1842	then
	1843	actionin[$i]="ln"
	1844	fi
	1845
	1846	if [[ $files_for_cores = true ]]
	1847	then
	1848	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1849	else
	1850	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1851	fi
	1852
	1853	# INPUT-FILES TO BE LINKED
	1854	if [[ "${actionin[$i]}" = ln ]]
	1855	then
	1856
	1857	printf "\n $filetype will be linked"
	1858	if [[ $files_for_cores = false ]]
	1859	then
	1860	if [[ -f "${absnamein[$i]}" ]]
	1861	then
	1862	ln ${absnamein[$i]} ${localin[$i]}
	1863	got_tmp[$i]=true
	1864	fi
	1865	else
	1866	if [[ -d "${absnamein[$i]}" ]]
	1867	then
[2396]	1868	mkdir -p ${localin[$i]}
[2380]	1869	cd ${absnamein[$i]}
	1870	for file in $(ls *)
	1871	do
[2566]	1872	ln $file $tempdir/${localin[$i]}
[2380]	1873	done >\|/dev/null 2>&1
[2566]	1874	cd $tempdir
[2380]	1875	fi
	1876
	1877	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1878	if [[ ! -f "${localin[$i]}/_000000" ]]
	1879	then
	1880	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1881	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1882	fi
	1883
	1884	got_tmp[$i]=true
	1885	fi
	1886	fi
	1887
	1888	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
	1889	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "npe" ]]
	1890	then
	1891
	1892	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1893	then
	1894
	1895	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1896	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1897	printf "\n file will be provided for $cores processors"
[2396]	1898	mkdir -p ${localin[$i]}
[2380]	1899	ival=$cores
	1900	(( ii = 0 ))
	1901	while (( ii <= ival-1 ))
	1902	do
	1903	if (( ii < 10 ))
	1904	then
	1905	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1906	elif (( ii < 100 ))
	1907	then
	1908	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1909	elif (( ii < 1000 ))
	1910	then
	1911	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1912	else
	1913	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1914	fi
	1915	(( ii = ii + 1 ))
	1916	done
	1917
	1918	else
	1919
	1920	if [[ $files_for_cores = true ]]
	1921	then
	1922
	1923	# PROVIDE FILES FOR EACH CORE
	1924	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1925	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1926	printf "\n providing $cores files for the respective cores"
[2396]	1927	mkdir -p ${localin[$i]}
[2380]	1928	if [[ $link_local_input = true ]]
	1929	then
	1930	printf " files will be linked\n"
	1931	cd ${absnamein[$i]}
	1932	for file in $(ls *)
	1933	do
	1934	ln -f $file ${localin[$i]}
	1935	done
[2566]	1936	cd $tempdir
[2380]	1937	fi
	1938
	1939	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1940	if [[ ! -f "${localin[$i]}/_000000" ]]
	1941	then
	1942	if [[ $link_local_input = true ]]
	1943	then
	1944	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1945	fi
	1946	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1947	fi
	1948
	1949	else
	1950
	1951	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1952	if [[ $link_local_input = true ]]
	1953	then
	1954	printf " file will be linked\n"
	1955	ln -f ${absnamein[$i]} ${localin[$i]}
	1956	fi
[2605]	1957	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	1958	if [[ ! -f "${localin[$i]}" ]]
	1959	then
	1960	if [[ $link_local_input = true ]]
	1961	then
	1962	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1963	fi
[2605]	1964	if [[ $running_on_remote = true && ( "${transin[$i]}" = job \|\| "${transin[$i]}" = jobopt ) ]]
	1965	then
	1966	mv ${absnamein[$i]} ${localin[$i]}
	1967	else
	1968	cp ${absnamein[$i]} ${localin[$i]}
	1969	fi
[2380]	1970	fi
	1971	fi
	1972	fi
	1973	fi
	1974
	1975	done
	1976	if (( i != 0 ))
	1977	then
	1978	printf "\n$dashes\n *** all INPUT-files provided \n"
	1979	fi
	1980
	1981
	1982	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	1983	(( i = 0 ))
	1984	while (( i < iic ))
	1985	do
	1986	(( i = i + 1 ))
	1987	if (( i == 1 ))
	1988	then
	1989	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	1990	fi
	1991	printf "\n >>> ${in_command[$i]}"
	1992	eval ${in_command[$i]}
	1993	if (( i == iic ))
	1994	then
	1995	printf "\n$dashes\n"
	1996	fi
	1997	done
	1998
	1999
	2000	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2001	# (FILE ENVPAR WILL BE READ BY PALM)
	2002	cat > ENVPAR << EOF
[2506]	2003	&envpar run_identifier = '$fname', host = '$host_configuration',
[2380]	2004	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	2005	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2006	maximum_cpu_time_allowed = ${cpumax}.,
	2007	revision = '$global_revision',
	2008	batch_job = .${running_in_batch_mode}. /
	2009
	2010	EOF
	2011
	2012
	2013	# STARTING THE EXECUTABLE
	2014	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2015	PATH=$PATH:$tempdir
[2380]	2016
	2017
	2018	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2393]	2019	line=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/$mpi_tasks/g' \| sed 's/{{TASKS_PER_NODE}}/$tasks_per_node/g'`
	2020	line2=`echo "${execute_command}" \| sed 's/{{MPI_TASKS}}/1/g' \| sed 's/{{TASKS_PER_NODE}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2021	eval line=\"$line\"
	2022	execute_command="$line"
	2023
	2024
	2025	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2026	if [[ "$execute_command_for_combine" = "" ]]
	2027	then
	2028	eval line2=\"$line2\"
	2029	execute_command_for_combine="$line2"
	2030	fi
	2031
[2380]	2032
	2033
	2034	# PROVIDE A HOSTFILE, IF REQUIRED
	2035	if [[ "$hostfile" != "" ]]
	2036	then
	2037
	2038	if [[ $hostfile = auto ]]
	2039	then
	2040	# CREATE A NEW HOSTFILE
	2041	(( ii = 1 ))
	2042	while (( ii <= cores / threads_per_task ))
	2043	do
	2044	echo $(hostname) >> hostfile
	2045	(( ii = ii + 1 ))
	2046	done
	2047	if (( cores / threads_per_task == 0 ))
	2048	then
	2049	echo $(hostname) >> hostfile
	2050	fi
	2051
	2052	else
	2053	cp $hostfile hostfile
	2054	fi
	2055	eval line=\"`head -n $ii hostfile`\"
	2056	printf "\n *** running on: $line"
	2057	fi
	2058
	2059
	2060
	2061	# SET THE NUMBER OF OPENMP-THREADS
	2062	if [[ $use_openmp = true ]]
	2063	then
	2064	export OMP_NUM_THREADS=$threads_per_task
	2065	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2066	else
	2067	export OMP_NUM_THREADS=1
	2068	fi
	2069
	2070
[2610]	2071	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2072	if [[ $run_coupled_model = false ]]
	2073	then
	2074	if [[ "$ocean_file_appendix" = true ]]
	2075	then
	2076	echo "precursor_ocean" > coupling_steering
	2077	else
	2078	echo "precursor_atmos" > coupling_steering
	2079	fi
	2080	else
	2081	(( iia = $cores_atmos / $threads_per_task ))
	2082	(( iio = $cores_ocean / $threads_per_task ))
	2083	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2084	printf "\n\n"
	2085	echo "coupled_run $iia $iio" > coupling_steering
	2086	fi
	2087
	2088	printf "\n *** execute command:"
	2089	printf "\n \"$execute_command\" \n\n"
	2090
	2091	$execute_command < coupling_steering
	2092
	2093	if [[ $? != 0 ]]
	2094	then
	2095
	2096	# ABORT IN CASE OF RUNTIME ERRORS
	2097	printf "\n +++ runtime error occured"
	2098	locat=execution
	2099	exit
	2100
	2101	else
	2102
	2103	printf "\n$dashes\n *** execution finished \n"
	2104
	2105	fi
	2106
	2107
	2108	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2109	# BY EACH CORE INTO ONE FILE
	2110	if [[ ! -f combine_plot_fields.x ]]
	2111	then
	2112
	2113	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2114	printf "\n 2d- and/or 3d-data may be incomplete!"
	2115	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2116
	2117	elif [[ "$combine_plot_fields" == true ]]
	2118	then
	2119
	2120	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2121	$execute_command_for_combine
	2122
	2123	else
	2124
	2125	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2126	# DATA OUTPUT
[2380]	2127	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2128	fi
	2129
	2130
	2131
	2132	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2133	(( i = 0 ))
	2134	while (( i < ioc ))
	2135	do
	2136	(( i = i + 1 ))
	2137	if (( i == 1 ))
	2138	then
	2139	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2140	fi
	2141	printf "\n >>> ${out_command[$i]}"
	2142	eval ${out_command[$i]}
	2143	if (( i == ioc ))
	2144	then
	2145	printf "\n$dashes\n"
	2146	fi
	2147	done
	2148
	2149
[2610]	2150	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2151	# WILDCARDS
[2380]	2152	(( i = 0 ))
[2610]	2153	(( nr_of_output_files = 0 ))
	2154
[2380]	2155	while (( i < iout ))
	2156	do
[2610]	2157
[2380]	2158	(( i = i + 1 ))
[2610]	2159
	2160	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2161	# CREATE A LIST FOR THE DETECTED ENDINGS
	2162	if [[ "${multout[$i]}" = true ]]
	2163	then
	2164	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2165	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2166	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2167
	2168	endings="DEFAULT"
	2169	while read line
	2170	do
	2171	# remove the local name from the beginning
	2172	localnamestring="${localout_pre[$i]}"
	2173	length_localname=${#localnamestring}
	2174	ending=${line:${length_localname}}
	2175
	2176	if [[ "$ending" != "" ]]
	2177	then
	2178	endings="$endings $ending"
	2179	fi
	2180
	2181	done <filelist
	2182
	2183	rm filelist
	2184
	2185	else
	2186
	2187	# SINGLE NAME
	2188	endings=DEFAULT
	2189
	2190	fi
	2191
	2192	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2193	for ending in $endings
	2194	do
	2195
	2196	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2197	if [[ $ending = DEFAULT ]]
	2198	then
	2199	ending=""
	2200	fi
	2201
	2202	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2203	(( nr_of_output_files = nr_of_output_files + 1 ))
	2204	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2205	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2206	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2207	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2208	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2209	extout[$nr_of_output_files]="${extout_pre[$i]}"
	2210
	2211	done
	2212
	2213	done
	2214
	2215
	2216
	2217
	2218	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2219	(( i = 0 ))
	2220	while (( i < nr_of_output_files ))
	2221	do
	2222	(( i = i + 1 ))
[2380]	2223	if (( i == 1 ))
	2224	then
	2225	printf "\n\n *** saving OUTPUT-files:"
	2226
	2227	# GET RUN NUMBER ASSIGNED BY PALM
	2228	if [[ -f RUN_NUMBER ]]
	2229	then
	2230	read run_number < RUN_NUMBER
	2231	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2232	usecycle_option="-U $run_number"
	2233	else
	2234	run_number=0
	2235	usecycle_option=""
	2236	fi
	2237	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2238	then
[2404]	2239	printf "\n *** in case of SCP transfers to local host"
	2240	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2241	fi
	2242	printf "\n$dashes"
	2243	fi
	2244
	2245	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2246	then
	2247
[2610]	2248	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	2249
	2250	# DETERMINE THE CYCLE NUMBER
	2251	ls -1 -d $filename > filelist 2>/dev/null
	2252	ls -1 -d $filename.* >> filelist 2>/dev/null
	2253	while read line
	2254	do
	2255
	2256	# filename without path (i.e. after the last "/")
	2257	basefilename=$(basename ${line})
	2258
	2259	# check if there is an extension
	2260	extension=${basefilename##*.}
	2261	if [[ "$extension" = "${extout[$i]}" ]]
	2262	then
	2263	basefilename=${basefilename%.*}
	2264	fi
	2265
	2266	# check for an existing cycle number
	2267	cycle=${basefilename##*.}
	2268	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2269	then
	2270	(( icycle = $cycle + 1 ))
	2271	else
	2272	(( icycle = 1 ))
	2273	fi
	2274
	2275	if (( icycle > maxcycle ))
	2276	then
	2277	(( maxcycle = icycle ))
	2278	fi
	2279
	2280	done <filelist
	2281	rm filelist
	2282
	2283
	2284	# SET THE CYCLE NUMBER
	2285	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2286	if [[ "${actionout[$i]}" = a ]]
	2287	then
	2288	(( maxcycle = maxcycle - 1 ))
	2289	fi
	2290
	2291	(( cycnum[$i] = maxcycle ))
	2292	pathout[$i]=$filename
	2293
	2294
	2295	# ADD CYCLE NUMBER TO FILENAME
	2296	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2297	if [[ "${actionout[$i]}" != "a" ]]
	2298	then
	2299	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2300	# WITH AN EXISTING CYCLE NUMBER
	2301	if (( run_number >= cycnum[$i] ))
	2302	then
	2303	(( cycnum[$i] = run_number ))
	2304	else
	2305	if (( run_number > 0 ))
	2306	then
	2307	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2308	fi
	2309	fi
	2310	fi
	2311	if (( cycnum[$i] > 0 ))
	2312	then
[2600]	2313	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2314	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2315	fi
	2316	fi
	2317
	2318	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2319	files_for_cores=false; filetype=file
	2320	link_local_output=false
	2321	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2322	then
	2323	files_for_cores=true; filetype=directory
	2324	actionout[$i]=""
	2325	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2326	then
	2327	actionout[$i]=""
	2328	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2329	then
	2330	files_for_cores=true; filetype=directory
	2331	link_local_output=true
	2332	actionout[$i]=""
	2333	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2334	then
	2335	link_local_output
	2336	actionout[$i]=""
	2337	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2338	then
	2339	files_for_cores=true; filetype=directory
	2340	actionout[$i]="tr"
	2341	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2342	then
	2343	actionout[$i]="tr"
	2344	fi
	2345
	2346	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2347	then
	2348	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2349	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2350	then
	2351	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2352	else
	2353
	2354
	2355	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2356	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2357	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2358	then
	2359	if [[ $running_on_remote = true ]]
	2360	then
	2361
	2362	# SET OPTIONS FOR TRANSFER
	2363	if [[ "${actionout[$i]}" = tr ]]
	2364	then
	2365	if [[ $files_for_cores = false ]]
	2366	then
	2367	catalog_option=""
	2368	catalog_string=""
	2369	else
	2370	catalog_option="-c"
	2371	catalog_string="/"
	2372	fi
	2373	append_option=""
	2374	append_string=""
	2375	else
	2376	append_option="-A"
	2377	append_string="append"
	2378	fi
	2379
	2380	transfer_failed=false
	2381	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2506]	2382	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2383
	2384	# TRANSFER VIA SCP
	2385	if [[ "$remote_loginnode" != "" ]]
	2386	then
[2566]	2387	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]	2388	else
[2506]	2389	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]	2390	fi
	2391	[[ $? != 0 ]] && transfer_failed=true
	2392
	2393
	2394	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2395	if [[ $transfer_failed = true ]]
	2396	then
	2397	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2506]	2398	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
[2380]	2399
	2400	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2401	eval local_catalog=${pathout[$i]}
	2402	if [[ ! -d $local_catalog ]]
	2403	then
	2404	printf " *** local directory does not exist. Trying to create:\n"
	2405	printf " $local_catalog \n"
	2406	mkdir -p $local_catalog
	2407	fi
[2506]	2408	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
[2380]	2409	transfer_problems=true
	2410	fi
	2411
	2412	else
	2413
	2414	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2415	# BE COPIED OR APPENDED ON THIS MACHINE
	2416	if [[ "${actionout[$i]}" = tr ]]
	2417	then
	2418	actionout[$i]=""
	2419	else
	2420	actionout[$i]="a"
	2421	fi
	2422	fi
	2423	fi
	2424
	2425
	2426	# APPEND ON THIS MACHINE
	2427	if [[ "${actionout[$i]}" = "a" ]]
	2428	then
	2429	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2430	then
	2431	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2432	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2433	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2434	else
	2435	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2436	printf "\n ${pathout[$i]}\n"
	2437	cat ${localout[$i]} >> ${pathout[$i]}
	2438	fi
	2439	fi
	2440
	2441	# COPY ON THIS MACHINE
	2442	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2443	# ON DIFFERENT FILE-SYSTEMS
	2444	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2445	then
	2446
	2447	# COPY IN CASE OF RUNS ON SINGLE CORES
	2448	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2449	then
	2450	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2451	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2452	if [[ $link_local_output = true ]]
	2453	then
	2454	printf " file will be linked\n"
	2455	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2456	fi
	2457	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2458	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2459	then
	2460	if [[ $link_local_output = true ]]
	2461	then
	2462	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2463	fi
	2464	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2465	else
	2466	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2467	fi
	2468	else
	2469	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2470	printf "\n ${pathout[$i]}\n"
	2471	if [[ $link_local_output = true ]]
	2472	then
	2473	printf " file will be linked\n"
	2474	ln -f ${localout[$i]} ${pathout[$i]}
	2475	fi
	2476	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2477	if [[ ! -f "${pathout[$i]}" ]]
	2478	then
	2479	if [[ $link_local_output = true ]]
	2480	then
	2481	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2482	fi
	2483	cp ${localout[$i]} ${pathout[$i]}
	2484	else
	2485	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2486	fi
	2487	fi
	2488
	2489	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2490	then
	2491
	2492	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2493	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2494	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2495	printf "\n ${pathout[$i]}\n"
	2496	if [[ $link_local_output = true ]]
	2497	then
	2498	printf " files will be linked\n"
[2396]	2499	mkdir -p ${pathout[$i]}
[2380]	2500	cd ${localout[$i]}
	2501	for file in $(ls *)
	2502	do
	2503	ln -f $file ${pathout[$i]}
	2504	done >\|/dev/null 2>&1
[2566]	2505	cd $tempdir
[2380]	2506	fi
	2507
	2508	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2509	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2510	then
	2511	if [[ $link_local_output = true ]]
	2512	then
	2513	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2514	fi
	2515	cp -r ${localout[$i]}/* ${pathout[$i]}
	2516	fi
	2517
	2518	fi
	2519	fi
	2520	done
	2521
	2522	if (( i != 0 ))
	2523	then
	2524	if [[ $transfer_problems = true ]]
	2525	then
	2526	printf "\n$dashes\n *** OUTPUT-files saved"
	2527	printf "\n +++ WARNING: some data transfers failed! \n"
	2528	else
	2529	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2530	fi
	2531	fi
	2532
	2533
	2534	# IF REQUIRED, START A RESTART-JOB
	2535	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2536	if [[ -f CONTINUE_RUN ]]
	2537	then
	2538
	2539	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2540	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2541	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2542	# -b START A BATCH JOB
	2543	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2544	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2545	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2546
	2547
	2548	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2549	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2550	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2551	then
[2381]	2552	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2553	fi
	2554
	2555
	2556	# START THE RESTART-JOB
	2557	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2558	echo " $prc"
	2559	printf "\n$dashes\n"
	2560	if [[ $running_on_remote = true ]]
	2561	then
	2562
	2563	echo "*** ssh will be used to initiate restart-runs!"
	2564	echo " return_address=\"$return_address\" "
	2565	echo " return_username=\"$local_username\" "
	2566
	2567	if [[ "$remote_loginnode" != "" ]]
	2568	then
[2420]	2569	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]	2570	else
[2420]	2571	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2572	fi
	2573
	2574	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2575	sleep 30
	2576
	2577	else
	2578
	2579	# START THE RESTART JOB ON THE LOCAL HOST
	2580	eval $prc # THE ' MUST BE EVALUATED
	2581	cd - > /dev/null
	2582
	2583	fi
	2584	printf "\n$dashes\n *** restart-run initiated \n"
	2585
	2586
	2587	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2588	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2589	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2590	# MAY BE VERY HUGE)
	2591	(( i = 0 ))
[2610]	2592	while (( i < nr_of_input_files ))
[2380]	2593	do
	2594	(( i = i + 1 ))
	2595	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2596	then
	2597	rm -r ${absnamein[$i]}
	2598	fi
	2599	done
	2600
	2601	fi
	2602
	2603
	2604	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2605	cd $HOME
[2566]	2606	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2607
	2608
	2609	else
	2610
	2611
	2612	# PREPARING ACTIONS,
	2613	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2614
	2615	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2506]	2616	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2617	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2618	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2619	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2620	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2621	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2622	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2623	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2624	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2625	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2626	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2627	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2628	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2629	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2630	if [[ $create_remote_batch_job = true ]]
	2631	then
	2632	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2633	if [[ $do_trace = true ]]
	2634	then
	2635	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2636	fi
[2380]	2637	elif [[ $create_batch_job = true ]]
	2638	then
	2639	palmrun_com=${palmrun_com}" -j"
[2420]	2640	if [[ $do_trace = true ]]
	2641	then
	2642	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2643	fi
[2380]	2644	fi
	2645
	2646
	2647	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2648	# REMOTE HOST
[2506]	2649	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2650	job_protocol_file=$job_protocol_file_local
	2651	if [[ $create_remote_batch_job = true ]]
	2652	then
[2506]	2653	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2654	job_protocol_file=$job_protocol_file_remote
	2655	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2656	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2657	fi
	2658
	2659
	2660	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2661	jobfile=jobfile.$run_id
	2662
	2663
	2664	# FIRST CREATE THE BATCH DIRECTIVES
	2665	(( i = 0 ))
	2666	while (( i < ibd ))
	2667	do
	2668	(( i = i + 1 ))
[2566]	2669	line=`echo "${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]	2670	eval line=\"$line\"
	2671	echo "$line" >> $jobfile
	2672	done
	2673	echo " " >> $jobfile
	2674
	2675
	2676	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2677	# PROTOCOL
	2678	if [[ $create_remote_batch_job = true ]]
	2679	then
	2680	echo "set +vx" >> $jobfile
	2681	echo "trap '" >> $jobfile
	2682	echo "set +vx" >> $jobfile
	2683	echo "cd ${remote_jobcatalog}" >> $jobfile
	2684	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2685
	2686	# ADD THE BATCH DIRECTIVES
	2687	(( i = 0 ))
	2688	while (( i < ibdt ))
	2689	do
	2690	(( i = i + 1 ))
[2506]	2691	line=`echo "${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]	2692	eval line=\"$line\"
	2693	echo "$line" >> $jobfile
	2694	done
	2695	echo " " >> $jobfile
	2696
	2697	echo "set -x" >> $jobfile
[2506]	2698	echo "${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]	2699	echo "%%END%%" >> $jobfile
	2700	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2701	echo "$submit_command $scpjob_file" >> $jobfile
	2702	echo "rm $scpjob_file" >> $jobfile
[2404]	2703	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2704	echo "set -x" >> $jobfile
	2705	echo " ' exit" >> $jobfile
	2706	fi
	2707
	2708
	2709	# ACTIVATE ERROR-TRACEBACK
	2710	if [[ $do_trace = true ]]
	2711	then
	2712	echo "set -x" >> $jobfile
	2713	else
	2714	echo "set +vx" >> $jobfile
	2715	fi
	2716
	2717
	2718	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2719	if [[ "$login_init_cmd" != "" ]]
	2720	then
	2721	echo "$login_init_cmd" >> $jobfile
	2722	fi
	2723	if [[ "$module_commands" != "" ]]
	2724	then
	2725	echo "$module_commands" >> $jobfile
	2726	fi
	2727
	2728
	2729	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2730	if [[ $create_remote_batch_job = true ]]
	2731	then
	2732	echo "mkdir $tempdir" >> $jobfile
	2733	echo "chmod go+rx $tempdir" >> $jobfile
	2734	else
	2735	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2736	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2737	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2738	mkdir $tempdir
	2739	chmod go+rx $tempdir
	2740	fi
	2741	echo "cd $tempdir" >> $jobfile
	2742	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2743	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2744	echo "export PATH=.:\$PATH" >> $jobfile
	2745	echo "export execute_palmrun=true" >> $jobfile
	2746
	2747
	2748	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2749	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2750	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2751	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2752	echo "export LOCAL_PWD" >> $jobfile
	2753
	2754
	2755	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2756	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2757	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2758
	2759
	2760	# CALL PALMRUN WITHIN THE JOB
	2761	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2762	echo "set -x" >> $jobfile
	2763	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2764
	2765
	2766	# TRANSFER JOBFILE TO THE TARGET HOST
	2767	if [[ $create_jobfile_only = false ]]
	2768	then
	2769
	2770	if [[ $create_remote_batch_job = true ]]
	2771	then
	2772
[2420]	2773	echo " "
[2566]	2774	echo " *** transfer of job to remote host via scp"
[2420]	2775	if [[ $do_trace = true ]]
	2776	then
[2506]	2777	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2778	fi
[2566]	2779	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2780
[2566]	2781	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2782	if [[ $do_trace = true ]]
	2783	then
[2506]	2784	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]	2785	fi
[2506]	2786	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]	2787
	2788	elif [[ $create_batch_job = true ]]
	2789	then
	2790
[2385]	2791	eval local_jobcatalog=$local_jobcatalog
[2506]	2792	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2793	cd $local_jobcatalog
[2380]	2794	echo " "
[2420]	2795	echo " *** submit the job"
	2796	if [[ $do_trace = true ]]
	2797	then
[2506]	2798	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2799	fi
[2506]	2800	$submit_command ${host_configuration}_${job_id}
	2801	rm ${host_configuration}_${job_id}
[2380]	2802	cd - > /dev/null
	2803
	2804	fi
	2805
	2806	rm -rf $jobfile
	2807
	2808	else
	2809
	2810	printf "\n *** jobfile created under name \"$jobfile\" "
	2811	printf "\n no batch-job has been sent!"
	2812
	2813	fi
	2814
	2815	fi # END OF REMOTE-PART

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