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source: palm/trunk/SCRIPTS/palmrun @ 2821

Last change on this file since 2821 was 2799, checked in by raasch, 7 years ago
parameters are allowed in output commands (OC:)
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 95.5 KB

Rev	Line
[2380]	1	#!/bin/bash
	2
	3	# palmrun - script for running PALM jobs
	4
	5	#--------------------------------------------------------------------------------#
[2696]	6	# This file is part of the PALM model system.
[2380]	7	#
	8	# PALM is free software: you can redistribute it and/or modify it under the terms
	9	# of the GNU General Public License as published by the Free Software Foundation,
	10	# either version 3 of the License, or (at your option) any later version.
	11	#
	12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
	13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	15	#
	16	# You should have received a copy of the GNU General Public License along with
	17	# PALM. If not, see <http://www.gnu.org/licenses/>.
	18	#
[2718]	19	# Copyright 2017-2018 Leibniz Universitaet Hannover
[2380]	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
	23	# ------------------
	24	#
[2410]	25	#
[2380]	26	# Former revisions:
	27	# -----------------
[2732]	28	# $Id: palmrun 2718 2018-01-02 08:49:38Z maronga $
[2799]	29	# parameters are allowed in output commands (OC:)
	30	#
	31	# 2718 2018-01-02 08:49:38Z maronga
[2789]	32	# bugfix: exit if no queue has been given neither with option -q nor in the
	33	# configuration file
	34	#
	35	# 2718 2018-01-02 08:49:38Z maronga
[2762]	36	# file connection file from trunk/SCRIPTS is taken by default
	37	#
	38	# 2718 2018-01-02 08:49:38Z maronga
[2716]	39	# Corrected "Former revisions" section
	40	#
	41	# 2696 2017-12-14 17:12:51Z kanani
	42	# Change in file header (GPL part)
	43	#
	44	# 2693 2017-12-13 12:33:49Z raasch
[2693]	45	# replacement of variables given by {{<variable>}} in configuration file is now
	46	# done in a more general way, variable names are written in small letters
	47	#
	48	# 2670 2017-12-06 16:32:19Z raasch
[2670]	49	# test printouts removed
	50	#
	51	# 2669 2017-12-06 16:03:27Z raasch
[2669]	52	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	53	# removed,
	54	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	55	# files,
	56	# informative messages in case of missing optional input files shortened
	57	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	58	#
	59	# 2638 2017-11-23 12:44:23Z raasch
[2610]	60	# use of wildcards in file connection statements enabled
	61	#
	62	# 2605 2017-11-09 15:31:46Z raasch
[2605]	63	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	64	# will not be sent with the job file any more, but copied into the
[2610]	65	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	66	#
	67	# 2600 2017-11-01 14:11:20Z raasch
[2600]	68	# cycle numbers are made three digits wide
	69	#
	70	# 2566 2017-10-20 08:50:47Z raasch
[2566]	71	# execute command for combine_plot_fields added
	72	# "TEMPDIR" renamed "tempdir"
	73	# temporary working directory for local batch jobs is created immediately within
	74	# the user's palmrun call, due to a requirement of the "grid engine" batch
	75	# system, where the working directory is given with batch directive -wd and must
	76	# already exist when the job is submitted,
	77	# informative messages in non-trace mode reduced and partly reformatted
	78	#
	79	# 2551 2017-10-18 07:25:11Z raasch
[2551]	80	# TEMPDIR added as replacement string to be used in batch directives
	81	#
	82	# 2512 2017-10-04 08:26:59Z raasch
[2507]	83	# bugfix for determining cycle numbers of NetCDF input files
	84	#
	85	# 2506 2017-09-29 08:30:37Z raasch
[2506]	86	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	87	# host configuration added to SOURCES_FOR_RUN_... folder name
	88	# host_identifier renamed host_configuration
	89	# option -W added to allow for job dependencies
	90	#
	91	# 2501 2017-09-26 11:41:55Z raasch
[2501]	92	# default value for number of cores (option -X) set to 1
	93	# bugfix for mechanism which overwrites configuration file settings with values
	94	# provided by palmrun options
	95	#
	96	# 2499 2017-09-22 16:47:58Z kanani
[2499]	97	# option -h named configuration identifier
	98	#
	99	# 2480 2017-09-19 06:24:14Z maronga
[2480]	100	# bugfix for last revision
	101	#
	102	# 2479 2017-09-19 06:12:16Z raasch
[2479]	103	# option -A (project account number) added
	104	#
	105	# 2422 2017-09-08 08:25:41Z raasch
[2410]	106	# initial revision
[2380]	107	#
	108	#--------------------------------------------------------------------------------#
	109	# palmrun - script for running PALM jobs on local and remote hosts
	110	#--------------------------------------------------------------------------------#
	111
	112
	113
	114	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	115
	116	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	117	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	118	# (TOO MANY ARGUMENTS - PROBLEM)
	119	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	120
[2610]	121	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	122	typeset -i nr_of_output_files=0
[2380]	123	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	124	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	125	# SCRIPT-OPTION ARGUMENTS
	126	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	127	typeset -i icycle inode ival maxcycle mpi_tasks
	128	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	129
	130	activation_string_list=""
	131	AddFilenames=""
	132	combine_plot_fields=true
	133	compiler_name=""
	134	compiler_name_ser=""
	135	compiler_options=""
[2501]	136	cores=1
[2380]	137	cores_atmos=0
	138	cores_ocean=0
	139	coupled_dist=""
	140	cpp_options=""
	141	cpumax=0
[2506]	142	create_batch_job=false
[2380]	143	create_jobfile_only=false
	144	create_remote_batch_job=false
	145	dashes=" ----------------------------------------------------------------------------"
	146	defaultqueue=""
[2506]	147	delete_temporary_catalog=true
[2380]	148	do_compile=true
	149	do_trace=false
	150	executable=""
	151	execute_command=""
	152	execution_error=false
[2762]	153	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	154	fname=test
	155	global_revision=""
[2506]	156	host_configuration="default"
[2380]	157	hostfile=""
	158	hp=""
	159	keep_data_from_previous_run=false
	160	link_local_input=false
	161	link_local_output=false
[2388]	162	linker_options=""
[2385]	163	local_jobcatalog=""
[2380]	164	locat=normal
	165	makefile=""
	166	max_par_io_str=""
	167	prc=$0
	168	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	169	do
	170	prc=`echo $prc \| cut -f2- -d"/"`
	171	done
	172	module_calls=""
[2506]	173	palmrun_memory=""
[2380]	174	palmrun_script_name=$prc
	175	openmp=false
[2506]	176	previous_job=""
[2479]	177	project_account=""
[2380]	178	queue=none
	179	restart_run=false
	180	return_address=""
[2385]	181	remote_jobcatalog=""
[2380]	182	remote_username=""
	183	running_in_batch_mode=false
	184	run_coupled_model=false
	185	run_id=""
	186	silent=false
	187	source_list=""
	188	source_path=""
[2501]	189	tasks_per_node=0
[2380]	190	threads_per_task=1
	191	transfer_problems=false
[2384]	192	user_source_path=""
[2506]	193	use_existing_sources_folder=""
[2380]	194	use_openmp=false
[2732]	195	version="palmrun 1.0 Rev$Rev: 2799 $"
[2380]	196	working_directory=`pwd`
	197	write_binary=""
	198	TOPT=""
	199
	200
	201	# ERROR HANDLING IN CASE OF EXIT
[2404]	202	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	203	then
	204
	205	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	206	(( i = 0 ))
	207	while (( i < iec ))
	208	do
	209	(( i = i + 1 ))
	210	printf "\n *** Execution of ERROR-command:\n"
	211	printf " >>> ${err_command[$i]}\n"
	212	eval ${err_command[$i]}
	213	done
[2566]	214	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	215	printf "\n\n+++ palmrun killed \n\n"
	216	elif [[ $locat != control_c ]]
	217	then
[2566]	218	printf "\n --> palmrun finished\n\n"
[2380]	219	fi' exit
	220
	221
	222	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	223	trap 'cd; rm -rf $tempdir
[2380]	224	printf "\n+++ palmrun killed by \"^C\" \n\n"
	225	locat=control_c
	226	exit
	227	' 2
	228
	229
	230	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	231	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	232	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]	233	do
	234	case $option in
	235	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	236	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	237	(b) create_batch_job=true; prc="$prc -b";;
	238	(B) delete_temporary_catalog=false; prc="$prc -B";;
	239	(C) restart_run=true; prc="$prc -C";;
	240	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	241	(F) create_jobfile_only=true;;
	242	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	243	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	244	(j) running_in_batch_mode=true;;
	245	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	246	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	247	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	248	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	249	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	250	(r) run_id=$OPTARG;;
	251	(R) return_address=$OPTARG;;
	252	(s) source_list=$OPTARG;;
[2501]	253	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	254	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	255	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	256	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	257	(v) silent=true; prc="$prc -v";;
[2506]	258	(V) use_existing_sources_folder="-V";;
[2380]	259	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	260	(W) previous_job=$OPTARG;;
[2380]	261	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	262	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	263	(y) ocean_file_appendix=true; prc="$prc -y";;
	264	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	265	(Z) combine_plot_fields=false; prc="$prc -Z";;
	266	(\?) printf "\n +++ unknown option $OPTARG \n"
	267	printf "\n --> type \"$0 ?\" for available options \n"
	268	locat=parameter;exit;;
	269	esac
	270	done
	271
	272
	273	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	274	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	275	(( to_shift = $OPTIND - 1 ))
	276	shift $to_shift
	277
	278	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	279	if [[ "$1" = "?" ]]
	280	then
	281	(printf "\n *** Description of available palmrun options:\n"
	282	printf "\n Option Description Default-Value"
	283	printf "\n -a activation string list \"\" "
[2479]	284	printf "\n -A project account number ---"
[2380]	285	printf "\n -b batch-job on local machine ---"
	286	printf "\n -B do not delete temporary directory at end ---"
	287	printf "\n -d base name of files attached to program test"
	288	printf "\n -F create batch job file only ---"
[2506]	289	printf "\n -h host configuration \"default\" "
[2380]	290	printf "\n -k keep data from previous run"
	291	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	292	printf "\n -M Makefile name Makefile"
	293	printf "\n -O threads per openMP task ---"
	294	printf "\n -q queue \"$queue\" "
	295	printf "\n -s filenames of routines to be compiled \"\" "
	296	printf "\n must end with .f, .f90, .F, or .c !"
	297	printf "\n use \"..\" for more than one file and wildcards"
	298	printf "\n -s LM compiles all locally modified files"
	299	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	300	printf "\n -T tasks per node ---"
[2380]	301	printf "\n -u username on remote machine \"\" "
	302	printf "\n -v no prompt for confirmation ---"
[2506]	303	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	304	printf "\n -w maximum parallel io streams as given by -X"
[2506]	305	printf "\n -W name of job to wait for ---"
[2380]	306	printf "\n -x tracing of palmrun for debug purposes ---"
	307	printf "\n -X # of processors (on parallel machines) 1"
	308	printf "\n -y add appendix \"_O\" to all local output"
	309	printf "\n files (ocean precursor runs followed by"
	310	printf "\n coupled atmosphere-ocean runs) ---"
	311	printf "\n -Y run coupled model, \"#1 #2\" with"
	312	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	313	printf "\n -Z skip combine_plot_fields at the end of "
	314	printf "\n the simulation ---"
	315	printf "\n "
	316	printf "\n Possible values of positional parameter <modus>:"
	317	printf "\n \"?\" - this outline \n\n") \| more
	318	exit
	319	elif [[ "$1" != "" ]]
	320	then
	321	printf "\n +++ positional parameter $1 unknown \n"
	322	locat=parameter; exit
	323	fi
	324
	325
	326
	327	# SHORT STARTING MESSAGE
	328	printf "\n*** $version "
	329	printf "\n will be executed. Please wait ..."
	330
	331
[2506]	332	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	333	config_file=.palm.config.$host_configuration
	334	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
[2380]	335
	336
	337	# CHECK, IF CONFIGURATION FILE EXISTS
	338	if [[ ! -f $config_file ]]
	339	then
	340	printf "\n\n +++ configuration file: "
	341	printf "\n $config_file"
	342	printf "\n does not exist"
	343	locat=connect; exit
	344	fi
	345
	346
[2762]	347	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	348	if [[ -f .palm.iofiles ]]
	349	then
	350	fileconnection_file=.palm.iofiles
	351	fi
	352
	353
[2380]	354	# CHECK, IF FILE CONNECTION FILE EXISTS
	355	if [[ ! -f $fileconnection_file ]]
	356	then
	357	printf "\n\n +++ file connection file: "
	358	printf "\n $fileconnection_file"
	359	printf "\n does not exist"
	360	locat=connect; exit
	361	fi
	362
	363
[2404]	364	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	365	if [[ "$activation_string_list" = "" ]]
	366	then
	367	printf "\n\n +++ no activation string list given: "
	368	printf "\n please set palmrun option \"-a\" "
	369	locat=palmrun_option; exit
	370	fi
	371
	372
	373	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	374	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	375	then
	376	write_binary=true
	377	else
	378	write_binary=false
	379	fi
	380
	381
[2380]	382	# READ AND EVALUATE THE CONFIGURATION-FILE
	383	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	384
	385	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	386	while read line
	387	do
	388
	389	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	390	eval line=\"$line\"
	391
	392
	393	# INTERPRET THE LINE
	394	if [[ "$(echo $line)" = "" ]]
	395	then
	396
	397	# EMPTY LINE, NO ACTION
	398	continue
	399
	400	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	401	then
	402
	403	# LINE IS A COMMENT LINE
	404	continue
	405
	406	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	407	then
	408
	409	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	410	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	411	value=`echo $line \| cut -d" " -s -f2-`
	412
	413
	414	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	415	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	416	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	417	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	418	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	419	# CONFIGURATION-FILE.
	420	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	421	then
	422	eval export $var="\$value"
	423
	424	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	425	if [[ $do_trace = true ]]
	426	then
	427	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	428	fi
	429	fi
	430
	431	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	432	then
	433
	434	# LINE DEFINES BATCH-DIRECTIVE
	435	(( ibd = ibd + 1 ))
	436	line=$(echo $line \| cut -c4-)
	437	batch_directive[$ibd]="$line"
	438
	439	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	440	then
	441
	442	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	443	# REMOTE TO A LOCAL HOST
	444	(( ibdt = ibdt + 1 ))
	445	line=$(echo $line \| cut -c5-)
	446	batch_directive_transfer[$ibdt]="$line"
	447
	448	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	449	then
	450
	451	# LINE DEFINES ERROR-COMMAND
	452	(( iec = iec + 1 ))
	453	line=$(echo $line \| cut -c4-)
	454	err_command[$iec]="$line"
	455
	456	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	457	then
	458
	459	# LINE DEFINES INPUT-COMMAND
	460	(( iic = iic + 1 ))
	461	line=$(echo $line \| cut -c4-)
	462	in_command[$iic]="$line"
	463
	464	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	465	then
	466
	467	# LINE DEFINES OUTPUT-COMMAND
	468	(( ioc = ioc + 1 ))
	469	line=$(echo $line \| cut -c4-)
	470	out_command[$ioc]="$line"
	471
	472	else
	473
	474	# SKIP ALL OTHER LINES
	475	continue
	476
	477	fi
	478
	479	done < $config_file
	480
	481
	482	# CHECK SETTING OF REQUIRED PARAMETERS
	483	if [[ "$compiler_name" = "" ]]
	484	then
	485	printf "\n +++ no compiler name found in $config_file"
	486	printf "\n Please add line \"compiler_name ...\" to that file."
	487	locat=config_file; exit
	488	fi
	489	if [[ "$compiler_name_ser" = "" ]]
	490	then
	491	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	492	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	493	locat=config_file; exit
	494	fi
	495	if [[ "$compiler_options" = "" ]]
	496	then
	497	printf "\n +++ no compiler options found in $config_file"
	498	printf "\n Please add line \"compiler_options ...\" to that file."
	499	locat=config_file; exit
	500	fi
[2388]	501	if [[ "$linker_options" = "" ]]
[2380]	502	then
[2388]	503	printf "\n +++ no linker options found in $config_file"
	504	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	505	locat=config_file; exit
	506	fi
	507	if [[ "$execute_command" = "" ]]
	508	then
	509	printf "\n +++ no execute command found in $config_file"
	510	printf "\n Please add line \"execute_command ...\" to that file."
	511	locat=config_file; exit
	512	fi
	513
	514	if [[ "$hostfile" != "" ]]
	515	then
	516	if [[ $hostfile != auto && ! -f $hostfile ]]
	517	then
	518	printf "\n +++ no hostfile \"$hostfile\" found"
	519	printf "\n Please check line \"hostfile ...\" in $config_file"
	520	locat=config_file; exit
	521	fi
	522	fi
	523
	524
	525	# DETERMINE THE CALL STATUS
	526	if [[ "$return_address" != "" ]]
	527	then
	528
	529	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	530	# BATCH MODE AND ...
	531	running_on_remote=true
	532
	533	else
	534
	535	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	536	if [[ "$remote_ip" != "" ]]
	537	then
	538
	539	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	540	create_remote_batch_job=true
	541
	542	fi
	543	running_on_remote=false
	544	fi
	545
	546
	547
	548	# READ AND EVALUATE THE I/O-FILE LIST
	549	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	550
	551	# READ THE FILE CONNECTION FILE LINE BY LINE
	552	while read line
	553	do
	554
[2669]	555	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	556	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	557
	558	# INTERPRET THE LINE
	559	if [[ "$(echo $line)" = "" ]]
	560	then
	561	# EMPTY LINE, NO ACTION
	562	continue
	563
	564	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	565	then
	566
	567	# LINE IS A COMMENT LINE
	568	true
	569
	570	else
	571
	572	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	573	# s2a: in/out - field
[2669]	574	# s2b: action - field (optional)
	575	s1=`echo "$line" \| cut -d" " -f1`
	576	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	577	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	578	then
[2669]	579	s2a=$s2
[2380]	580	s2b=""
	581	else
[2669]	582	s2a=`echo $s2 \| cut -d":" -f1`
	583	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	584	fi
[2669]	585	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	586	s4=`echo "$line" \| cut -d" " -s -f4`
	587	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	588	s5=`echo "$line" \| cut -d" " -s -f5`
	589	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	590
	591
	592	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	593	# INPUT- OR OUTPUT-LIST.
	594	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	595	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	596	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	597	# IS NOT CHECKED AND STORED.
[2610]	598	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	599	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	600	then
	601	found=false
	602	for actual in $activation_string_list
	603	do
	604	for formal in $s3
	605	do
	606	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	607	done
	608	done
	609	if [[ $found = true ]]
	610	then
	611	(( iin = iin + 1 ))
[2669]	612	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	613	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	614	if [[ "$s2a" = inopt ]]
	615	then
	616	optin_pre[$iin]=yes
	617	else
	618	optin_pre[$iin]=no
	619	fi
[2605]	620
	621	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	622	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	623	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	624	then
[2610]	625	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	626	fi
	627
[2610]	628	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	629	# THE WILDCARD FROM THE ENDING
	630	if [[ "${s5: -1}" = "*" ]]
	631	then
[2669]	632	if [[ "$s2b" = "di" ]]
[2610]	633	then
	634	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	635	printf "\n see file \"$fileconnection_file\", line"
	636	printf "\n$line"
	637	locat=iofiles_file; exit
	638	fi
	639	multin[$iin]=true
	640	string=${endin_pre[$iin]}
	641	endin_pre[$iin]="${string%?}"
	642	else
	643	multin[$iin]=false
	644	fi
[2380]	645	fi
[2669]	646	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	647	then
	648	found=false
	649	for actual in $activation_string_list
	650	do
	651	for formal in $s3
	652	do
[2670]	653	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	654	done
	655	done
	656	if [[ $found = true ]]
	657	then
	658	(( iout = iout + 1 ))
[2669]	659	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	660	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	661
[2669]	662	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	663	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	664	if [[ $formal = wildcard ]]
	665	then
	666	warnout_pre[$iout]=false
	667	else
	668	warnout_pre[$iout]=true
	669	fi
	670
[2610]	671	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	672	# THE WILDCARD FROM THE LOCAL FILENAME
	673	if [[ "${s1: -1}" = "*" ]]
	674	then
[2669]	675	if [[ "$s2b" = "di" ]]
[2610]	676	then
	677	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	678	printf "\n see file \"$fileconnection_file\", line"
	679	printf "\n$line"
	680	locat=iofiles_file; exit
	681	fi
	682	multout[$iout]=true
	683	string=${localout_pre[$iout]}
	684	localout_pre[$iout]="${string%?}"
	685	else
	686	multout[$iout]=false
	687	fi
[2380]	688	fi
[2669]	689	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	690	then
[2669]	691	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	692	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	693	locat=connect; exit
	694	fi
	695	IFS="$IFSALT"
	696	fi
	697
	698	done < $fileconnection_file
	699
	700
	701
[2501]	702	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	703	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	704	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	705	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	706	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	707	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	708
	709
	710
[2380]	711	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	712	if [[ $run_coupled_model = true ]]
	713	then
	714
	715	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	716	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	717
	718	if (( $cores_ocean + $cores_atmos != $cores ))
	719	then
	720
	721	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	722	printf "\n PEs (total) : $cores"
	723	printf "\n PEs (atmosphere): $cores_atmos"
	724	printf "\n PEs (ocean) : $cores_ocean"
	725	locat=coupling; exit
	726
	727	fi
	728
	729	fi
	730
	731
	732	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	733	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	734	# FOLDER
	735	if [[ $running_in_batch_mode = true ]]
	736	then
	737
[2506]	738	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	739	then
[2506]	740	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	741	printf "\n Please check the output of the palmrun-call"
	742	printf "\n that you did on your local host."
	743	locat=SOURCES_FOR_RUN; exit
	744	fi
	745
	746	else
	747
	748	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	749	# AUTOMATIC RESTART RUN
	750	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	751	if [[ $restart_run = false ]]
	752	then
	753
	754	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	755	# THE LOCAL HOST
	756	if [[ ! -d $source_path ]]
	757	then
	758	printf "\n\n +++ source path \"$source_path\" on local host"
	759	printf "\n \"$(hostname)\" does not exist"
	760	locat=source_path; exit
	761	fi
	762
[2506]	763	rm -rf $sources_for_run_catalog
	764	mkdir -p $sources_for_run_catalog
[2380]	765
	766	if [[ "$source_list" = LM ]]
	767	then
	768
	769	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	770	source_list=""
	771	cd $source_path
	772
	773
[2512]	774	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	775	if [[ ! -d ../.svn ]]
[2380]	776	then
	777	printf "\n\n +++ source directory"
	778	printf "\n \"$source_path\" "
	779	printf "\n is not under control of \"subversion\"."
[2512]	780	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	781	fi
	782
	783
	784	# LIST ALL MODIFIED SOURCE CODE FILES
	785	Filenames=""
[2404]	786	svn status > tmp_svnstatus
[2380]	787	while read line
	788	do
	789	firstc=`echo $line \| cut -c1`
	790	if [[ $firstc = M \|\| $firstc = "?" ]]
	791	then
	792	Name=`echo "$line" \| cut -c8-`
	793	extension=`echo $Name \| cut -d. -f2`
	794	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	795	then
	796	Filenames="$Filenames "$Name
	797	fi
	798	fi
[2404]	799	done < tmp_svnstatus
	800	rm -rf tmp_svnstatus
[2380]	801
	802
	803	# COPY FILES TO SOURCES_FOR_RUN_...
	804	for filename in $Filenames
	805	do
[2506]	806	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	807	source_list=$source_list"$filename "
	808	done
	809
	810	cd - > /dev/null
	811
	812
	813	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	814	elif [[ "$source_list" != "" ]]
	815	then
	816
	817	cd $source_path
	818
	819	for filename in $source_list
	820	do
	821
	822	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	823	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	824	then
	825	printf "\n +++ source code file: $filename"
	826	printf "\n must not contain (\"/\") "
	827	locat=source; exit
	828	fi
	829
	830	if [[ ! -f $filename ]]
	831	then
	832	printf "\n +++ source code file: $filename"
	833	printf "\n does not exist"
	834	locat=source; exit
	835	else
[2506]	836	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	837	fi
	838
	839	done
	840
	841	cd - > /dev/null
	842
	843	fi
	844
	845	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	846	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	847	if [[ ! -f $makefile ]]
	848	then
	849	printf "\n +++ file \"$makefile\" does not exist"
	850	locat=make; exit
	851	else
[2506]	852	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	853	fi
	854
	855
	856	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	857	if [[ "$user_source_path" != "" ]]
[2380]	858	then
	859
	860	# DOES THE DIRECTORY EXIST?
[2384]	861	if [[ ! -d $user_source_path ]]
[2380]	862	then
	863
	864	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	865	printf "\n \"$user_source_path\" "
[2380]	866	printf "\n does not exist or is not a directory."
	867	printf "\n No source code will be used from this directory!\n"
[2384]	868	user_source_path=""
[2380]	869	if [[ $silent == false ]]
	870	then
	871	sleep 2
	872	fi
	873
	874	else
	875
[2384]	876	cd $user_source_path
[2380]	877	found=false
	878
	879	Names=$(ls -1 *.f90 2>&1)
	880	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	881	Names=$(ls -1 *.F90 2>&1)
	882	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	883	Names=$(ls -1 *.F 2>&1)
	884	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	885	Names=$(ls -1 *.f 2>&1)
	886	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	887	Names=$(ls -1 *.c 2>&1)
	888	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	889
	890	cd - > /dev/null
[2506]	891	cd $sources_for_run_catalog
[2380]	892
	893	# COPY MAKEFILE IF EXISTING
[2384]	894	if [[ -f $user_source_path/Makefile ]]
[2380]	895	then
	896	printf "\n\n *** user Makefile from directory"
[2384]	897	printf "\n \"$user_source_path\" is used \n"
[2380]	898	if [[ $silent == false ]]
	899	then
	900	sleep 1
	901	fi
[2384]	902	cp $user_source_path/Makefile .
[2380]	903	fi
	904
	905	for filename in $AddFilenames
	906	do
	907	if [[ -f $filename ]]
	908	then
	909	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	910	printf "\n source code directory \"$user_source_path\" "
[2380]	911	printf "\n but was also given with option \"-s\" which means that it should be taken"
	912	printf "\n from directory \"$source_path\"."
	913	locat=source; exit
	914	fi
	915
[2384]	916	cp $user_source_path/$filename .
[2380]	917	source_list="$source_list $filename"
	918
	919	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	920	if [[ $(grep -c $filename Makefile) = 0 ]]
	921	then
	922	printf "\n\n +++ user file \"$filename\" "
	923	printf "\n is not listed in Makefile \n"
	924	locat=source; exit
	925	else
	926
	927	if [[ $found = false ]]
	928	then
	929	found=true
	930	printf "\n\n *** following user file(s) added to the"
	931	printf " files to be translated:\n "
	932	fi
	933	printf "$filename "
	934	if [[ $silent == false ]]
	935	then
	936	sleep 0.5
	937	fi
	938
	939	fi
	940	done
	941	[[ $found = true ]] && printf "\n"
	942	cd - > /dev/null
	943	fi
	944	fi
	945
	946	# COPY CONFIGURATION FILES
[2506]	947	cp $config_file $sources_for_run_catalog
	948	cp $fileconnection_file $sources_for_run_catalog
[2380]	949
	950	# COPY SHELLSCRIPTS
[2506]	951	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	952	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	953
	954	fi
	955
	956	fi
	957
[2605]	958
[2380]	959	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	960	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	961	if [[ "$global_revision" = "" ]]
	962	then
	963	global_revision=`svnversion $source_path 2>/dev/null`
	964	global_revision="Rev: $global_revision"
	965	fi
	966
	967
	968	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	969	if [[ -n $cores ]]
	970	then
	971
	972	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	973	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	974	if [[ $tasks_per_node = 0 ]]
[2380]	975	then
	976	printf "\n"
	977	printf "\n +++ option \"-T\" (tasks per node) is missing"
	978	printf "\n set -T option or define tasks_per_node in the config file"
	979	locat=tasks_per_node; (( iec = 0 )); exit
	980	fi
	981
	982	if (( cores < tasks_per_node ))
	983	then
	984	printf "\n"
	985	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	986	printf "\n given values: -T $tasks_per_node -X $cores"
	987	locat=tasks_per_node; (( iec = 0 )); exit
	988	fi
	989
	990	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	991	(( mpi_tasks = cores / threads_per_task ))
	992	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	993	(( ii = cores / tasks_per_node ))
	994	(( remaining_cores = cores - ii * tasks_per_node ))
	995	if (( remaining_cores > 0 ))
	996	then
	997	printf "\n"
	998	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	999	printf "\n divisor of the total number of cores (option \"-X\")"
	1000	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1001	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1002	(( nodes = nodes + 1 ))
	1003	fi
	1004
	1005	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	1006	if [[ "$tasks_per_node" != "" ]]
	1007	then
	1008	TOPT="-T $tasks_per_node"
	1009	fi
	1010
	1011	fi
	1012
	1013
	1014	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1015	if [[ "$maximum_parallel_io_streams" = "" ]]
	1016	then
	1017	maximum_parallel_io_streams=$cores
	1018	fi
	1019
	1020
	1021	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1022	if [[ "$scp_port" != "" ]]
	1023	then
	1024	PORTOPT="-P $scp_port"
	1025	SSH_PORTOPT="-p $scp_port"
	1026	fi
	1027
	1028
	1029	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1030	# CONFIG-FILE
	1031	if [[ "$ssh_key" != "" ]]
	1032	then
	1033	ssh_key="-i $HOME/.ssh/$ssh_key"
	1034	fi
	1035
	1036
	1037	# SET QUEUE, IF NOT GIVEN
	1038	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1039	then
	1040
	1041	if [[ $queue = none && "$defaultqueue" = "" ]]
	1042	then
	1043	printf "\n"
	1044	printf "\n +++ no default queue given in configuration file and no queue"
	1045	printf "\n given with option -q"
[2789]	1046	locat=queue; exit
[2380]	1047	fi
	1048	if [[ $queue = none ]]
	1049	then
	1050	queue=$defaultqueue
	1051	fi
	1052
	1053	fi
	1054
	1055
	1056	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1057	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1058	(( i = 0 ))
[2610]	1059	(( nr_of_input_files = 0 ))
[2380]	1060	while (( i < iin ))
	1061	do
	1062	(( i = i + 1 ))
	1063
	1064	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1065	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1066	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1067	then
[2610]	1068	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1069	else
[2610]	1070	eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]}
[2380]	1071	fi
	1072
[2610]	1073
[2380]	1074	# CHECK IF FILE EXISTS
	1075	if ! ls $filename* 1>/dev/null 2>&1
	1076	then
	1077
[2669]	1078	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1079	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1080	then
	1081	printf "\n\n +++ INPUT-file: "
[2610]	1082	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1083	then
	1084	printf "\n $filename"
	1085	else
[2610]	1086	printf "\n $filename.${extin_pre[$i]}"
[2380]	1087	fi
	1088	printf "\n does not exist\n"
	1089	locat=input; exit
	1090	else
[2610]	1091	(( nr_of_input_files = nr_of_input_files + 1 ))
	1092	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1093	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1094	actionin[$nr_of_input_files]="unavailable"
[2610]	1095	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1096	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1097	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1098	fi
[2605]	1099
[2380]	1100	else
	1101
[2610]	1102	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND
	1103	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
	1104	if [[ "${multin[$i]}" = true ]]
	1105	then
	1106	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1107	ls -1 -d ${filename} > filelist 2>/dev/null
	1108	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1109	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1110
[2610]	1111	endings=""
	1112	while read line
	1113	do
	1114	# filename without path (i.e. after the last "/")
	1115	basefilename=$(basename ${line})
[2380]	1116
[2610]	1117	# check if there is an extension and remove it
	1118	ext=${basefilename##*.}
	1119	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1120	then
	1121	basefilename=${basefilename%.*}
	1122	fi
[2380]	1123
[2610]	1124	# check for an existing cycle number and remove it
	1125	cycle=${basefilename##*.}
	1126	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1127	then
	1128	basefilename=${basefilename%.*}
	1129	fi
[2600]	1130
[2610]	1131	# remove the fname from the beginning
	1132	length_fname=${#fname}
	1133	ending=${basefilename:${length_fname}}
	1134
	1135	# remove the ending given in the .iofiles from the beginning
	1136	endingstring="${endin_pre[$i]}"
	1137	length_ending=${#endingstring}
	1138	ending=${ending:${length_ending}}
	1139
	1140	if [[ "$ending" = "" ]]
[2600]	1141	then
[2610]	1142	# standard ending as given in the .iofiles
	1143	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1144	then
	1145	endings="$endings DEFAULT"
	1146	fi
[2600]	1147	else
[2610]	1148	# ending must start with "_", otherwise its a different file
	1149	if [[ "${ending:0:1}" = "_" ]]
	1150	then
	1151	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1152	then
	1153	endings="$endings $ending"
	1154	fi
	1155	fi
[2600]	1156	fi
[2610]	1157
	1158	done <filelist
[2380]	1159
[2610]	1160	rm filelist
[2380]	1161
[2600]	1162	else
[2610]	1163
	1164	# SINGLE NAME
	1165	endings=DEFAULT
	1166
[2600]	1167	fi
	1168
[2610]	1169	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1170	for ending in $endings
	1171	do
	1172
	1173	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1174	if [[ $ending = DEFAULT ]]
[2380]	1175	then
[2610]	1176	ending=""
	1177	fi
	1178
	1179	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1180	(( nr_of_input_files = nr_of_input_files + 1 ))
	1181	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1182	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1183	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1184	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1185	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1186	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1187
	1188
	1189	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1190	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1191	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1192	then
	1193	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1194	else
[2610]	1195	eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]}
[2380]	1196	fi
[2610]	1197
	1198	# DETERMINE THE FILE'S CYCLE NUMBER
	1199	(( maxcycle = 0 ))
	1200	ls -1 -d $filename > filelist 2>/dev/null
	1201	ls -1 -d $filename.* >> filelist 2>/dev/null
	1202	while read line
	1203	do
	1204	# filename without path (i.e. after the last "/")
	1205	basefilename=$(basename ${line})
	1206
	1207	# check if there is an extension
	1208	extension=${basefilename##*.}
	1209	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1210	then
	1211	basefilename=${basefilename%.*}
	1212	fi
	1213
	1214	# check for an existing cycle number
	1215	cycle=${basefilename##*.}
	1216	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1217	then
[2669]	1218	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1219	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1220	(( icycle = $((10#$cycle)) ))
[2610]	1221	else
	1222	(( icycle = 0 ))
	1223	fi
	1224
	1225	if (( icycle > maxcycle ))
	1226	then
	1227	(( maxcycle = icycle ))
	1228
	1229	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1230	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1231	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1232	then
	1233	leading_zero=true
	1234	else
	1235	leading_zero=false
	1236	fi
	1237	fi
	1238
	1239	done <filelist
	1240	rm filelist
	1241
	1242	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1243	if [[ $leading_zero = true ]]
[2380]	1244	then
[2610]	1245	cyclestring=`printf "%03d" $maxcycle`
	1246	else
	1247	cyclestring=$maxcycle
[2380]	1248	fi
[2610]	1249
	1250	# APPEND CYCLE NUMBER TO FILENAME
	1251	if (( maxcycle > 0 ))
[2380]	1252	then
[2610]	1253	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1254	then
	1255	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1256	else
	1257	filename=${filename}.$cyclestring
	1258	fi
[2380]	1259	else
[2610]	1260	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1261	then
	1262	filename=${filename}.${extin[$nr_of_input_files]}
	1263	fi
[2380]	1264	fi
[2610]	1265
	1266	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1267	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1268	absnamein[$nr_of_input_files]=$filename
	1269	if (( maxcycle > 0 ))
[2380]	1270	then
[2610]	1271	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1272	then
	1273	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1274	else
	1275	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring
	1276	fi
[2380]	1277	else
[2610]	1278	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1279	then
	1280	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1281	else
	1282	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}
	1283	fi
[2380]	1284	fi
	1285
[2610]	1286	done
	1287
[2380]	1288	fi
[2610]	1289
[2380]	1290	done
	1291
[2610]	1292
[2380]	1293	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1294	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1295	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1296	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1297	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1298	# REMOTE HOST)
	1299	(( i = 0 ))
	1300	while (( i < iout ))
	1301	do
	1302	(( i = i + 1 ))
[2610]	1303	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1304	then
[2610]	1305	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1306	then
[2610]	1307	actionout_pre[$i]=""
	1308	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1309	then
[2610]	1310	actionout_pre[$i]=pe
	1311	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1312	then
[2610]	1313	actionout_pre[$i]=a
[2380]	1314	fi
	1315	(( maxcycle = 0 ))
[2610]	1316	eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]}
	1317	eval catalogname=${pathout_pre[$i]}
[2380]	1318	if ! ls $filename* 1>/dev/null 2>&1
	1319	then
	1320
	1321	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1322	if cat /dev/null > $filename
	1323	then
	1324	rm $filename
	1325	else
	1326
	1327	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1328	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1329	if [[ ! -d $catalogname ]]
	1330	then
	1331	if mkdir -p $catalogname
	1332	then
	1333	printf "\n\n *** directory:"
	1334	printf "\n $catalogname"
	1335	printf "\n was created\n"
	1336	else
	1337	printf "\n\n +++ OUTPUT-file:"
	1338	printf "\n $filename"
	1339	printf "\n cannot be created, because directory does not exist"
	1340	printf "\n and cannot be created either"
	1341	printf "\n"
	1342	locat=output ; exit
	1343	fi 2>/dev/null
	1344	else
	1345	printf "\n\n +++ OUTPUT-file:"
	1346	printf "\n $filename"
	1347	printf "\n cannot be created, although directory exists"
	1348	printf "\n"
	1349	locat=output ; exit
	1350	fi
	1351	fi 2>/dev/null
	1352
	1353	fi
	1354
	1355	fi
	1356	done
	1357
	1358
	1359	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1360	if [[ $running_in_batch_mode = false ]]
	1361	then
	1362	run_id=$RANDOM
	1363	job_id=${fname}.$run_id
	1364
[2566]	1365	tempdir=$fast_io_catalog/$job_id
[2380]	1366	fi
	1367
	1368
	1369	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1370	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1371	then
	1372
	1373	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1374	if [[ $ibd = 0 ]]
	1375	then
	1376	printf "\n"
	1377	printf "\n +++ no batch directives found in configuration file"
	1378	locat=config_file_batch_directives; (( iec = 0 )); exit
	1379	fi
	1380
	1381	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1382	done=false
[2384]	1383	cputime=$cpumax
[2380]	1384	while [[ $done = false ]]
	1385	do
[2384]	1386	if (( cputime == 0 ))
[2380]	1387	then
	1388	printf "\n +++ cpu-time is undefined"
	1389	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1390	printf "\n >>> "
[2384]	1391	read cputime 1>/dev/null 2>&1
[2380]	1392	else
	1393	done=true
	1394	fi
	1395	done
[2420]	1396	cpumax=$cputime
[2380]	1397
	1398	# CHECK THE MEMORY DEMAND
	1399	done=false
	1400	while [[ $done = false ]]
	1401	do
	1402	if (( memory == 0 ))
	1403	then
	1404	printf "\n +++ memory demand is undefined"
	1405	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1406	printf "\n >>> "
	1407	read memory 1>/dev/null 2>&1
	1408	else
	1409	done=true
	1410	fi
	1411	done
	1412
	1413	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1414	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1415	then
	1416	while [[ -z $remote_username ]]
	1417	do
[2420]	1418	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1419	printf "\n >>> Please type username:"
	1420	printf "\n >>> "
	1421	read remote_username
	1422	done
	1423	fi
	1424
	1425	else
	1426
[2420]	1427	if [[ $running_in_batch_mode = false ]]
	1428	then
	1429	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1430	cpumax=$cputime
	1431	else
	1432	cputime=$cpumax
	1433	fi
[2380]	1434
	1435	fi
	1436
	1437
	1438	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1439	(( cpu_hours = cputime / 3600 ))
	1440	(( resttime = cputime - cpu_hours * 3600 ))
	1441	(( cpu_minutes = resttime / 60 ))
	1442	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1443	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1444
	1445
	1446	# OUTPUT OF THE PALMRUN-HEADER
	1447	calltime=$(date)
	1448	printf "\n"
	1449	printf "#------------------------------------------------------------------------# \n"
	1450	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1451	printf "\| \| \n"
	1452	column1="called on:"; column2=$(hostname)
	1453	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1454	if [[ $create_remote_batch_job = true ]]
	1455	then
[2506]	1456	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1457	else
	1458	if [[ $running_on_remote = true ]]
	1459	then
[2506]	1460	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1461	else
[2506]	1462	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1463	fi
	1464	fi
	1465	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1466
	1467	column1="running in:"
	1468	if [[ $running_in_batch_mode = true ]]
	1469	then
	1470	column2="batch job mode"
	1471	else
	1472	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1473	then
	1474	column2="job creation mode"
	1475	else
	1476	column2="interactive run mode"
	1477	fi
	1478	fi
	1479	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1480
[2479]	1481	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1482	then
[2480]	1483	if [[ "$project_account" != "" ]]
[2479]	1484	then
	1485	column1="project account number:"
	1486	column2="$project_account"
	1487	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1488	fi
	1489	fi
	1490
[2380]	1491	if [[ -n $cores ]]
	1492	then
	1493	if [[ $run_coupled_model = false ]]
	1494	then
	1495	column1="number of cores:"; column2=$cores
	1496	else
	1497	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1498	fi
	1499	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1500	fi
	1501	if [[ -n $tasks_per_node ]]
	1502	then
	1503	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1504	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1505	if (( remaining_cores > 0 ))
	1506	then
	1507	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1508	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1509	fi
	1510	fi
	1511	if [[ $maximum_parallel_io_streams != $cores ]]
	1512	then
	1513	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1514	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1515	fi
	1516	if [[ $use_openmp = true ]]
	1517	then
	1518	column1="threads per task:"; column2="$threads_per_task"
	1519	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1520	fi
[2384]	1521	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1522	then
[2506]	1523	column1="memory demand / PE":; column2="$memory MB"
	1524	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1525	column1="job cpu time (h:m:s):"; column2="$timestring"
	1526	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1527	fi
[2380]	1528	printf "\| \| \n"
	1529	if [[ "$source_list" != "" ]]
	1530	then
	1531	if [[ "$make_options" != "" ]]
	1532	then
	1533	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1534	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1535	line=$(echo "$make_options" \| cut -c46-)
	1536	while [[ "$line" != "" ]]
	1537	do
	1538	column1=""
	1539	column2=$(echo "$line" \| cut -c-45)
	1540	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1541	line=$(echo "$line" \| cut -c46-)
	1542	done
	1543	fi
	1544	fi
	1545
	1546	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1547	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1548	line=$(echo "$cpp_options" \| cut -c46-)
	1549	while [[ "$line" != "" ]]
	1550	do
	1551	column1=""
	1552	column2=$(echo "$line" \| cut -c-45)
	1553	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1554	line=$(echo "$line" \| cut -c46-)
	1555	done
	1556
	1557	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1558	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1559	line=$(echo "$compiler_options" \| cut -c46-)
	1560	while [[ "$line" != "" ]]
	1561	do
	1562	column1=""
	1563	column2=$(echo "$line" \| cut -c-45)
	1564	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1565	line=$(echo "$line" \| cut -c46-)
	1566	done
	1567
[2388]	1568	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1569	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1570	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1571	while [[ "$line" != "" ]]
	1572	do
	1573	column1=""
	1574	column2=$(echo "$line" \| cut -c-45)
	1575	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1576	line=$(echo "$line" \| cut -c46-)
	1577	done
	1578
	1579	if [[ "$login_init_cmd" != "" ]]
	1580	then
	1581	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1582	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1583	line=$(echo "$login_init_cmd" \| cut -c46-)
	1584	while [[ "$line" != "" ]]
	1585	do
	1586	column1=""
	1587	column2=$(echo "$line" \| cut -c-45)
	1588	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1589	line=$(echo "$line" \| cut -c46-)
	1590	done
	1591	fi
	1592
	1593	if [[ "$module_commands" != "" ]]
	1594	then
	1595	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1596	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1597	line=$(echo "$module_commands" \| cut -c46-)
	1598	while [[ "$line" != "" ]]
	1599	do
	1600	column1=""
	1601	column2=$(echo "$line" \| cut -c-45)
	1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1603	line=$(echo "$line" \| cut -c46-)
	1604	done
	1605	fi
	1606	printf "\| \| \n"
	1607	column1="base name of files:"; column2=$fname
	1608	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1609	column1="activation string list:"; column2=$(echo $activation_string_list)
	1610	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1611
	1612	if [[ "$ocean_file_appendix" = true ]]
	1613	then
	1614	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1615	fi
	1616
	1617	if [[ "$source_list" != "" ]]
	1618	then
	1619	printf "\| \| \n"
	1620	printf "\| Files to be compiled: \| \n"
	1621	line=$source_list
	1622	while [[ "$line" != "" ]]
	1623	do
	1624	linestart=$(echo $line \| cut -c-70)
	1625	printf "\| %-70s \| \n" "$linestart"
	1626	line=$(echo "$line" \| cut -c71-)
	1627	done
	1628	fi
	1629	printf "#------------------------------------------------------------------------#"
	1630
	1631
	1632
	1633	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1634	if [[ $do_trace = true ]]
	1635	then
	1636	(( i = 0 ))
[2610]	1637	while (( i < nr_of_input_files ))
[2380]	1638	do
	1639	(( i = i + 1 ))
	1640	if (( i == 1 ))
	1641	then
	1642	printf "\n\n >>> INPUT-file assignments:\n"
	1643	fi
	1644	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1645	done
	1646	(( i = 0 ))
	1647	while (( i < iout ))
	1648	do
	1649	(( i = i + 1 ))
	1650	if (( i == 1 ))
	1651	then
	1652	printf "\n\n >>> OUTPUT-file assignments:\n"
	1653	fi
	1654	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1655	done
	1656	(( i = 0 ))
	1657	while (( i < iic ))
	1658	do
	1659	(( i = i + 1 ))
	1660	if (( i == 1 ))
	1661	then
	1662	printf "\n\n >>> INPUT-commands:\n"
	1663	fi
	1664	printf "\n ${in_command[$i]}"
	1665	done
	1666	(( i = 0 ))
	1667	while (( i < ioc ))
	1668	do
	1669	(( i = i + 1 ))
	1670	if (( i == 1 ))
	1671	then
	1672	printf "\n\n >>> OUTPUT-commands:\n"
	1673	fi
	1674	printf "\n ${out_command[$i]}"
	1675	done
	1676	fi
	1677
	1678	# QUERY FOR CONTINUE
	1679	if [[ $silent = false && $running_in_batch_mode = false ]]
	1680	then
	1681	antwort=dummy
	1682	printf "\n\n"
	1683	printf " >>> everything o.k. (y/n) ? "
	1684	while read antwort
	1685	do
	1686	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1687	then
	1688	printf " >>> everything o.k. (y/n) ? "
	1689	else
	1690	break
	1691	fi
	1692	done
	1693	if [[ $antwort = n \|\| $antwort = N ]]
	1694	then
	1695	locat=user_abort; (( iec = 0 )); exit
	1696	fi
	1697	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1698	then
[2566]	1699	printf "\n *** batch-job will be created and submitted"
[2380]	1700	else
[2566]	1701	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1702	fi
	1703	fi
	1704
	1705
	1706
	1707	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1708	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1709	then
	1710
	1711	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1712	then
[2566]	1713	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1714	else
[2566]	1715	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1716	fi
	1717
[2422]	1718	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1719	# IT SHALL BE CREATED
	1720	ask_for_make_depository=false
	1721	if [[ $create_remote_batch_job = true ]]
	1722	then
	1723
	1724	line=`grep %base_directory $config_file`
[2506]	1725	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1726	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]	1727
[2506]	1728	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1729	then
	1730	printf "\n\n +++ make depository \"${make_depository}\""
	1731	printf "\n on remote host not found!"
	1732	ask_for_make_depository=true
	1733	fi
[2506]	1734	rm ${host_configuration}_last_make_protokoll
[2422]	1735
	1736	else
	1737
	1738	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1739	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1740	if [[ ! -d ${make_depository} ]]
	1741	then
	1742	printf "\n\n +++ make depository \"${make_depository}\""
	1743	printf "\n on local host not found!"
	1744	ask_for_make_depository=true
	1745	fi
	1746
	1747	fi
	1748
	1749	if [[ $ask_for_make_depository = true ]]
	1750	then
	1751
	1752	antwort=dummy
	1753	printf "\n\n"
	1754	printf " >>> Create a new one (y/n) ? "
	1755	while read antwort
	1756	do
	1757	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1758	then
	1759	printf " >>> Create a new one (y/n) ? "
	1760	else
	1761	break
	1762	fi
	1763	done
	1764	if [[ $antwort = n \|\| $antwort = N ]]
	1765	then
	1766	locat=user_abort; (( iec = 0 )); exit
	1767	fi
	1768
[2566]	1769	if [[ $do_trace = true ]]
	1770	then
	1771	palmbuild -h $host_configuration
	1772	else
	1773	palmbuild -v -h $host_configuration
	1774	fi
[2422]	1775
	1776	if [[ $? != 0 ]]
	1777	then
	1778
	1779	# ABORT IN CASE OF COMPILATION PROBLEMS
	1780	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1781	locat=make_depository
	1782	exit
	1783	else
	1784	echo " *** now continue with creating executable and other sources"
	1785	fi
	1786
	1787	fi
	1788
[2566]	1789	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2506]	1790	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
[2380]	1791
	1792	if [[ $? != 0 ]]
	1793	then
	1794
	1795	# ABORT IN CASE OF COMPILATION PROBLEMS
	1796	printf "\n +++ error while creating executable and/or other sources"
	1797	locat=execution
[2506]	1798	rm -rf $sources_for_run_catalog
[2380]	1799	exit
	1800
	1801	else
	1802
[2566]	1803	printf " *** executable and other sources created\n"
[2506]	1804	rm -rf $sources_for_run_catalog
[2380]	1805
	1806	fi
	1807
	1808	fi
	1809
	1810
[2669]	1811	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1812	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1813	if [[ $create_remote_batch_job = true ]]
	1814	then
	1815	(( i = 0 ))
[2610]	1816	while (( i < nr_of_input_files ))
[2605]	1817	do
	1818	(( i = i + 1 ))
[2669]	1819	if [[ "${actionin[$i]}" = tr ]]
[2605]	1820	then
	1821	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1822	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1823	fi
	1824	done
	1825	if (( i > 0 ))
	1826	then
	1827	printf " *** input files have been copied to the remote host\n"
	1828	fi
	1829	fi
	1830
	1831
[2380]	1832	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1833	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1834	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1835	then
	1836
	1837	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1838	if [[ $running_in_batch_mode = false ]]
	1839	then
	1840	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1841	# FOLDER
[2566]	1842	mkdir -p $tempdir
	1843	chmod go+rx $tempdir
	1844	cd $tempdir
	1845	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1846	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1847
	1848	else
	1849
	1850	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1851	printf "\n *** running in temporary directory: $tempdir"
[2380]	1852
	1853	fi
	1854
	1855
	1856	# PROVIDE THE INPUT FILES
	1857	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1858	optional_files_missing=false
[2380]	1859	(( i = 0 ))
[2610]	1860	while (( i < nr_of_input_files ))
[2380]	1861	do
	1862	(( i = i + 1 ))
	1863	if (( i == 1 ))
	1864	then
	1865	printf "\n\n *** providing INPUT-files:\n$dashes"
	1866	fi
	1867
	1868
	1869	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1870	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1871	then
[2669]	1872	optional_files_missing=true
[2380]	1873	continue
	1874	fi
	1875
	1876	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1877	files_for_cores=false; filetype=file
	1878	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1879	then
	1880	files_for_cores=true; filetype=files
	1881	actionin[$i]=""
	1882	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1883	then
	1884	actionin[$i]=""
	1885	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1886	then
	1887	files_for_cores=true; filetype=files
	1888	actionin[$i]="ln"
	1889	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1890	then
	1891	actionin[$i]="ln"
	1892	fi
	1893
	1894	if [[ $files_for_cores = true ]]
	1895	then
	1896	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1897	else
	1898	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1899	fi
	1900
	1901	# INPUT-FILES TO BE LINKED
	1902	if [[ "${actionin[$i]}" = ln ]]
	1903	then
	1904
	1905	printf "\n $filetype will be linked"
	1906	if [[ $files_for_cores = false ]]
	1907	then
	1908	if [[ -f "${absnamein[$i]}" ]]
	1909	then
	1910	ln ${absnamein[$i]} ${localin[$i]}
	1911	got_tmp[$i]=true
	1912	fi
	1913	else
	1914	if [[ -d "${absnamein[$i]}" ]]
	1915	then
[2396]	1916	mkdir -p ${localin[$i]}
[2380]	1917	cd ${absnamein[$i]}
	1918	for file in $(ls *)
	1919	do
[2566]	1920	ln $file $tempdir/${localin[$i]}
[2380]	1921	done >\|/dev/null 2>&1
[2566]	1922	cd $tempdir
[2380]	1923	fi
	1924
	1925	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1926	if [[ ! -f "${localin[$i]}/_000000" ]]
	1927	then
	1928	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1929	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1930	fi
	1931
	1932	got_tmp[$i]=true
	1933	fi
	1934	fi
	1935
	1936	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	1937	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	1938	then
	1939
	1940	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1941	then
	1942
	1943	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1944	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1945	printf "\n file will be provided for $cores processors"
[2396]	1946	mkdir -p ${localin[$i]}
[2380]	1947	ival=$cores
	1948	(( ii = 0 ))
	1949	while (( ii <= ival-1 ))
	1950	do
	1951	if (( ii < 10 ))
	1952	then
	1953	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1954	elif (( ii < 100 ))
	1955	then
	1956	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1957	elif (( ii < 1000 ))
	1958	then
	1959	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1960	else
	1961	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1962	fi
	1963	(( ii = ii + 1 ))
	1964	done
	1965
	1966	else
	1967
	1968	if [[ $files_for_cores = true ]]
	1969	then
	1970
	1971	# PROVIDE FILES FOR EACH CORE
	1972	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1973	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1974	printf "\n providing $cores files for the respective cores"
[2396]	1975	mkdir -p ${localin[$i]}
[2380]	1976	if [[ $link_local_input = true ]]
	1977	then
	1978	printf " files will be linked\n"
	1979	cd ${absnamein[$i]}
	1980	for file in $(ls *)
	1981	do
	1982	ln -f $file ${localin[$i]}
	1983	done
[2566]	1984	cd $tempdir
[2380]	1985	fi
	1986
	1987	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1988	if [[ ! -f "${localin[$i]}/_000000" ]]
	1989	then
	1990	if [[ $link_local_input = true ]]
	1991	then
	1992	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1993	fi
	1994	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1995	fi
	1996
	1997	else
	1998
	1999	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2000	if [[ $link_local_input = true ]]
	2001	then
	2002	printf " file will be linked\n"
	2003	ln -f ${absnamein[$i]} ${localin[$i]}
	2004	fi
[2605]	2005	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2006	if [[ ! -f "${localin[$i]}" ]]
	2007	then
	2008	if [[ $link_local_input = true ]]
	2009	then
	2010	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2011	fi
[2669]	2012	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2013	then
	2014	mv ${absnamein[$i]} ${localin[$i]}
	2015	else
	2016	cp ${absnamein[$i]} ${localin[$i]}
	2017	fi
[2380]	2018	fi
	2019	fi
	2020	fi
	2021	fi
	2022
	2023	done
	2024	if (( i != 0 ))
	2025	then
[2669]	2026	if [[ $optional_files_missing = true ]]
	2027	then
	2028	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2029	fi
[2380]	2030	printf "\n$dashes\n *** all INPUT-files provided \n"
	2031	fi
	2032
	2033
	2034	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2035	(( i = 0 ))
	2036	while (( i < iic ))
	2037	do
	2038	(( i = i + 1 ))
	2039	if (( i == 1 ))
	2040	then
	2041	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2042	fi
	2043	printf "\n >>> ${in_command[$i]}"
	2044	eval ${in_command[$i]}
	2045	if (( i == iic ))
	2046	then
	2047	printf "\n$dashes\n"
	2048	fi
	2049	done
	2050
	2051
	2052	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2053	# (FILE ENVPAR WILL BE READ BY PALM)
	2054	cat > ENVPAR << EOF
[2506]	2055	&envpar run_identifier = '$fname', host = '$host_configuration',
[2380]	2056	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	2057	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2058	maximum_cpu_time_allowed = ${cpumax}.,
	2059	revision = '$global_revision',
	2060	batch_job = .${running_in_batch_mode}. /
	2061
	2062	EOF
	2063
	2064
	2065	# STARTING THE EXECUTABLE
	2066	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2067	PATH=$PATH:$tempdir
[2380]	2068
	2069
	2070	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2071	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2072	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2073	eval line=\"$line\"
	2074	execute_command="$line"
	2075
	2076
	2077	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2078	if [[ "$execute_command_for_combine" = "" ]]
	2079	then
	2080	eval line2=\"$line2\"
	2081	execute_command_for_combine="$line2"
	2082	fi
	2083
[2380]	2084
	2085
	2086	# PROVIDE A HOSTFILE, IF REQUIRED
	2087	if [[ "$hostfile" != "" ]]
	2088	then
	2089
	2090	if [[ $hostfile = auto ]]
	2091	then
	2092	# CREATE A NEW HOSTFILE
	2093	(( ii = 1 ))
	2094	while (( ii <= cores / threads_per_task ))
	2095	do
	2096	echo $(hostname) >> hostfile
	2097	(( ii = ii + 1 ))
	2098	done
	2099	if (( cores / threads_per_task == 0 ))
	2100	then
	2101	echo $(hostname) >> hostfile
	2102	fi
	2103
	2104	else
	2105	cp $hostfile hostfile
	2106	fi
	2107	eval line=\"`head -n $ii hostfile`\"
	2108	printf "\n *** running on: $line"
	2109	fi
	2110
	2111
	2112
	2113	# SET THE NUMBER OF OPENMP-THREADS
	2114	if [[ $use_openmp = true ]]
	2115	then
	2116	export OMP_NUM_THREADS=$threads_per_task
	2117	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2118	else
	2119	export OMP_NUM_THREADS=1
	2120	fi
	2121
	2122
[2610]	2123	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2124	if [[ $run_coupled_model = false ]]
	2125	then
	2126	if [[ "$ocean_file_appendix" = true ]]
	2127	then
	2128	echo "precursor_ocean" > coupling_steering
	2129	else
	2130	echo "precursor_atmos" > coupling_steering
	2131	fi
	2132	else
	2133	(( iia = $cores_atmos / $threads_per_task ))
	2134	(( iio = $cores_ocean / $threads_per_task ))
	2135	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2136	printf "\n\n"
	2137	echo "coupled_run $iia $iio" > coupling_steering
	2138	fi
	2139
	2140	printf "\n *** execute command:"
	2141	printf "\n \"$execute_command\" \n\n"
	2142
	2143	$execute_command < coupling_steering
	2144
	2145	if [[ $? != 0 ]]
	2146	then
	2147
	2148	# ABORT IN CASE OF RUNTIME ERRORS
	2149	printf "\n +++ runtime error occured"
	2150	locat=execution
	2151	exit
	2152
	2153	else
	2154
	2155	printf "\n$dashes\n *** execution finished \n"
	2156
	2157	fi
	2158
	2159
	2160	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2161	# BY EACH CORE INTO ONE FILE
	2162	if [[ ! -f combine_plot_fields.x ]]
	2163	then
	2164
	2165	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2166	printf "\n 2d- and/or 3d-data may be incomplete!"
	2167	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2168
	2169	elif [[ "$combine_plot_fields" == true ]]
	2170	then
	2171
	2172	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2173	$execute_command_for_combine
	2174
	2175	else
	2176
	2177	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2178	# DATA OUTPUT
[2380]	2179	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2180	fi
	2181
	2182
	2183
	2184	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2185	(( i = 0 ))
	2186	while (( i < ioc ))
	2187	do
	2188	(( i = i + 1 ))
	2189	if (( i == 1 ))
	2190	then
	2191	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2192	fi
[2799]	2193
	2194	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2195	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2196
[2380]	2197	printf "\n >>> ${out_command[$i]}"
	2198	eval ${out_command[$i]}
	2199	if (( i == ioc ))
	2200	then
	2201	printf "\n$dashes\n"
	2202	fi
	2203	done
	2204
	2205
[2610]	2206	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2207	# WILDCARDS
[2380]	2208	(( i = 0 ))
[2610]	2209	(( nr_of_output_files = 0 ))
	2210
[2380]	2211	while (( i < iout ))
	2212	do
[2610]	2213
[2380]	2214	(( i = i + 1 ))
[2610]	2215
	2216	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2217	# CREATE A LIST FOR THE DETECTED ENDINGS
	2218	if [[ "${multout[$i]}" = true ]]
	2219	then
	2220	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2221	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2222	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2223
	2224	endings="DEFAULT"
	2225	while read line
	2226	do
	2227	# remove the local name from the beginning
	2228	localnamestring="${localout_pre[$i]}"
	2229	length_localname=${#localnamestring}
	2230	ending=${line:${length_localname}}
	2231
	2232	if [[ "$ending" != "" ]]
	2233	then
	2234	endings="$endings $ending"
	2235	fi
	2236
	2237	done <filelist
	2238
	2239	rm filelist
	2240
	2241	else
	2242
	2243	# SINGLE NAME
	2244	endings=DEFAULT
	2245
	2246	fi
	2247
	2248	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2249	for ending in $endings
	2250	do
	2251
	2252	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2253	if [[ $ending = DEFAULT ]]
	2254	then
	2255	ending=""
	2256	fi
	2257
	2258	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2259	(( nr_of_output_files = nr_of_output_files + 1 ))
	2260	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2261	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2262	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2263	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2264	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2265	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2266	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2267
	2268	done
	2269
	2270	done
	2271
	2272
	2273
	2274
	2275	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2276	(( i = 0 ))
	2277	while (( i < nr_of_output_files ))
	2278	do
	2279	(( i = i + 1 ))
[2380]	2280	if (( i == 1 ))
	2281	then
	2282	printf "\n\n *** saving OUTPUT-files:"
	2283
	2284	# GET RUN NUMBER ASSIGNED BY PALM
	2285	if [[ -f RUN_NUMBER ]]
	2286	then
	2287	read run_number < RUN_NUMBER
	2288	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2289	usecycle_option="-U $run_number"
	2290	else
	2291	run_number=0
	2292	usecycle_option=""
	2293	fi
	2294	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2295	then
[2404]	2296	printf "\n *** in case of SCP transfers to local host"
	2297	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2298	fi
	2299	printf "\n$dashes"
	2300	fi
	2301
	2302	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2303	then
	2304
[2610]	2305	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	2306
	2307	# DETERMINE THE CYCLE NUMBER
	2308	ls -1 -d $filename > filelist 2>/dev/null
	2309	ls -1 -d $filename.* >> filelist 2>/dev/null
	2310	while read line
	2311	do
	2312
	2313	# filename without path (i.e. after the last "/")
	2314	basefilename=$(basename ${line})
	2315
	2316	# check if there is an extension
	2317	extension=${basefilename##*.}
	2318	if [[ "$extension" = "${extout[$i]}" ]]
	2319	then
	2320	basefilename=${basefilename%.*}
	2321	fi
	2322
	2323	# check for an existing cycle number
	2324	cycle=${basefilename##*.}
	2325	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2326	then
[2669]	2327	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2328	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2329	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2330	else
	2331	(( icycle = 1 ))
	2332	fi
	2333
	2334	if (( icycle > maxcycle ))
	2335	then
	2336	(( maxcycle = icycle ))
	2337	fi
	2338
	2339	done <filelist
	2340	rm filelist
	2341
	2342
	2343	# SET THE CYCLE NUMBER
	2344	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2345	if [[ "${actionout[$i]}" = a ]]
	2346	then
	2347	(( maxcycle = maxcycle - 1 ))
	2348	fi
	2349
	2350	(( cycnum[$i] = maxcycle ))
	2351	pathout[$i]=$filename
	2352
	2353
	2354	# ADD CYCLE NUMBER TO FILENAME
	2355	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2356	if [[ "${actionout[$i]}" != "a" ]]
	2357	then
	2358	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2359	# WITH AN EXISTING CYCLE NUMBER
	2360	if (( run_number >= cycnum[$i] ))
	2361	then
	2362	(( cycnum[$i] = run_number ))
	2363	else
	2364	if (( run_number > 0 ))
	2365	then
	2366	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2367	fi
	2368	fi
	2369	fi
	2370	if (( cycnum[$i] > 0 ))
	2371	then
[2600]	2372	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2373	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2374	fi
	2375	fi
	2376
	2377	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2378	files_for_cores=false; filetype=file
	2379	link_local_output=false
	2380	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2381	then
	2382	files_for_cores=true; filetype=directory
	2383	actionout[$i]=""
	2384	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2385	then
	2386	actionout[$i]=""
	2387	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2388	then
	2389	files_for_cores=true; filetype=directory
	2390	link_local_output=true
	2391	actionout[$i]=""
	2392	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2393	then
	2394	link_local_output
	2395	actionout[$i]=""
	2396	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2397	then
	2398	files_for_cores=true; filetype=directory
	2399	actionout[$i]="tr"
	2400	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2401	then
	2402	actionout[$i]="tr"
	2403	fi
	2404
	2405	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2406	then
[2669]	2407	if [[ ${warnout[$i]} = true ]]
	2408	then
	2409	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2410	fi
[2380]	2411	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2412	then
[2669]	2413	if [[ ${warnout[$i]} = true ]]
	2414	then
	2415	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2416	fi
[2380]	2417	else
	2418
	2419
	2420	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2421	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2422	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2423	then
	2424	if [[ $running_on_remote = true ]]
	2425	then
	2426
	2427	# SET OPTIONS FOR TRANSFER
	2428	if [[ "${actionout[$i]}" = tr ]]
	2429	then
	2430	if [[ $files_for_cores = false ]]
	2431	then
	2432	catalog_option=""
	2433	catalog_string=""
	2434	else
	2435	catalog_option="-c"
	2436	catalog_string="/"
	2437	fi
	2438	append_option=""
	2439	append_string=""
	2440	else
	2441	append_option="-A"
	2442	append_string="append"
	2443	fi
	2444
	2445	transfer_failed=false
	2446	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2506]	2447	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2448
	2449	# TRANSFER VIA SCP
	2450	if [[ "$remote_loginnode" != "" ]]
	2451	then
[2566]	2452	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]	2453	else
[2506]	2454	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]	2455	fi
	2456	[[ $? != 0 ]] && transfer_failed=true
	2457
	2458
	2459	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2460	if [[ $transfer_failed = true ]]
	2461	then
	2462	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2506]	2463	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
[2380]	2464
	2465	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2466	eval local_catalog=${pathout[$i]}
	2467	if [[ ! -d $local_catalog ]]
	2468	then
	2469	printf " *** local directory does not exist. Trying to create:\n"
	2470	printf " $local_catalog \n"
	2471	mkdir -p $local_catalog
	2472	fi
[2506]	2473	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
[2380]	2474	transfer_problems=true
	2475	fi
	2476
	2477	else
	2478
	2479	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2480	# BE COPIED OR APPENDED ON THIS MACHINE
	2481	if [[ "${actionout[$i]}" = tr ]]
	2482	then
	2483	actionout[$i]=""
	2484	else
	2485	actionout[$i]="a"
	2486	fi
	2487	fi
	2488	fi
	2489
	2490
	2491	# APPEND ON THIS MACHINE
	2492	if [[ "${actionout[$i]}" = "a" ]]
	2493	then
	2494	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2495	then
	2496	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2497	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2498	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2499	else
	2500	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2501	printf "\n ${pathout[$i]}\n"
	2502	cat ${localout[$i]} >> ${pathout[$i]}
	2503	fi
	2504	fi
	2505
	2506	# COPY ON THIS MACHINE
	2507	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2508	# ON DIFFERENT FILE-SYSTEMS
	2509	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2510	then
	2511
	2512	# COPY IN CASE OF RUNS ON SINGLE CORES
	2513	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2514	then
	2515	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2516	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2517	if [[ $link_local_output = true ]]
	2518	then
	2519	printf " file will be linked\n"
	2520	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2521	fi
	2522	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2523	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2524	then
	2525	if [[ $link_local_output = true ]]
	2526	then
	2527	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2528	fi
	2529	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2530	else
	2531	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2532	fi
	2533	else
	2534	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2535	printf "\n ${pathout[$i]}\n"
	2536	if [[ $link_local_output = true ]]
	2537	then
	2538	printf " file will be linked\n"
	2539	ln -f ${localout[$i]} ${pathout[$i]}
	2540	fi
	2541	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2542	if [[ ! -f "${pathout[$i]}" ]]
	2543	then
	2544	if [[ $link_local_output = true ]]
	2545	then
	2546	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2547	fi
	2548	cp ${localout[$i]} ${pathout[$i]}
	2549	else
	2550	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2551	fi
	2552	fi
	2553
	2554	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2555	then
	2556
	2557	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2558	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2559	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2560	printf "\n ${pathout[$i]}\n"
	2561	if [[ $link_local_output = true ]]
	2562	then
	2563	printf " files will be linked\n"
[2396]	2564	mkdir -p ${pathout[$i]}
[2380]	2565	cd ${localout[$i]}
	2566	for file in $(ls *)
	2567	do
	2568	ln -f $file ${pathout[$i]}
	2569	done >\|/dev/null 2>&1
[2566]	2570	cd $tempdir
[2380]	2571	fi
	2572
	2573	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2574	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2575	then
	2576	if [[ $link_local_output = true ]]
	2577	then
	2578	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2579	fi
	2580	cp -r ${localout[$i]}/* ${pathout[$i]}
	2581	fi
	2582
	2583	fi
	2584	fi
	2585	done
	2586
	2587	if (( i != 0 ))
	2588	then
	2589	if [[ $transfer_problems = true ]]
	2590	then
	2591	printf "\n$dashes\n *** OUTPUT-files saved"
	2592	printf "\n +++ WARNING: some data transfers failed! \n"
	2593	else
	2594	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2595	fi
	2596	fi
	2597
	2598
	2599	# IF REQUIRED, START A RESTART-JOB
	2600	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2601	if [[ -f CONTINUE_RUN ]]
	2602	then
	2603
	2604	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2605	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2606	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2607	# -b START A BATCH JOB
	2608	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2609	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2610	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2611
	2612
	2613	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2614	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2615	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2616	then
[2381]	2617	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2618	fi
	2619
	2620
	2621	# START THE RESTART-JOB
	2622	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2623	echo " $prc"
	2624	printf "\n$dashes\n"
	2625	if [[ $running_on_remote = true ]]
	2626	then
	2627
	2628	echo "*** ssh will be used to initiate restart-runs!"
	2629	echo " return_address=\"$return_address\" "
	2630	echo " return_username=\"$local_username\" "
	2631
	2632	if [[ "$remote_loginnode" != "" ]]
	2633	then
[2420]	2634	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]	2635	else
[2420]	2636	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2637	fi
	2638
	2639	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2640	sleep 30
	2641
	2642	else
	2643
	2644	# START THE RESTART JOB ON THE LOCAL HOST
	2645	eval $prc # THE ' MUST BE EVALUATED
	2646	cd - > /dev/null
	2647
	2648	fi
	2649	printf "\n$dashes\n *** restart-run initiated \n"
	2650
	2651
	2652	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2653	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2654	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2655	# MAY BE VERY HUGE)
	2656	(( i = 0 ))
[2610]	2657	while (( i < nr_of_input_files ))
[2380]	2658	do
	2659	(( i = i + 1 ))
	2660	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2661	then
	2662	rm -r ${absnamein[$i]}
	2663	fi
	2664	done
	2665
	2666	fi
	2667
	2668
	2669	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2670	cd $HOME
[2566]	2671	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2672
	2673
	2674	else
	2675
	2676
	2677	# PREPARING ACTIONS,
	2678	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2679
	2680	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2506]	2681	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2682	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2683	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2684	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2685	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2686	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2687	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2688	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2689	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2690	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2691	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2692	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2693	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2694	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2695	if [[ $create_remote_batch_job = true ]]
	2696	then
	2697	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2698	if [[ $do_trace = true ]]
	2699	then
	2700	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2701	fi
[2380]	2702	elif [[ $create_batch_job = true ]]
	2703	then
	2704	palmrun_com=${palmrun_com}" -j"
[2420]	2705	if [[ $do_trace = true ]]
	2706	then
	2707	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2708	fi
[2380]	2709	fi
	2710
	2711
	2712	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2713	# REMOTE HOST
[2506]	2714	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2715	job_protocol_file=$job_protocol_file_local
	2716	if [[ $create_remote_batch_job = true ]]
	2717	then
[2506]	2718	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2719	job_protocol_file=$job_protocol_file_remote
	2720	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2721	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2722	fi
	2723
	2724
	2725	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2726	jobfile=jobfile.$run_id
	2727
	2728
	2729	# FIRST CREATE THE BATCH DIRECTIVES
	2730	(( i = 0 ))
	2731	while (( i < ibd ))
	2732	do
	2733	(( i = i + 1 ))
[2693]	2734	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2735	eval line=\"$line\"
	2736	echo "$line" >> $jobfile
	2737	done
	2738	echo " " >> $jobfile
	2739
	2740
	2741	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2742	# PROTOCOL
	2743	if [[ $create_remote_batch_job = true ]]
	2744	then
	2745	echo "set +vx" >> $jobfile
	2746	echo "trap '" >> $jobfile
	2747	echo "set +vx" >> $jobfile
	2748	echo "cd ${remote_jobcatalog}" >> $jobfile
	2749	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2750
	2751	# ADD THE BATCH DIRECTIVES
	2752	(( i = 0 ))
	2753	while (( i < ibdt ))
	2754	do
	2755	(( i = i + 1 ))
[2693]	2756	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2757	eval line=\"$line\"
	2758	echo "$line" >> $jobfile
	2759	done
	2760	echo " " >> $jobfile
	2761
	2762	echo "set -x" >> $jobfile
[2506]	2763	echo "${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]	2764	echo "%%END%%" >> $jobfile
	2765	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2766	echo "$submit_command $scpjob_file" >> $jobfile
	2767	echo "rm $scpjob_file" >> $jobfile
[2404]	2768	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2769	echo "set -x" >> $jobfile
	2770	echo " ' exit" >> $jobfile
	2771	fi
	2772
	2773
	2774	# ACTIVATE ERROR-TRACEBACK
	2775	if [[ $do_trace = true ]]
	2776	then
	2777	echo "set -x" >> $jobfile
	2778	else
	2779	echo "set +vx" >> $jobfile
	2780	fi
	2781
	2782
	2783	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2784	if [[ "$login_init_cmd" != "" ]]
	2785	then
	2786	echo "$login_init_cmd" >> $jobfile
	2787	fi
	2788	if [[ "$module_commands" != "" ]]
	2789	then
	2790	echo "$module_commands" >> $jobfile
	2791	fi
	2792
	2793
	2794	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2795	if [[ $create_remote_batch_job = true ]]
	2796	then
	2797	echo "mkdir $tempdir" >> $jobfile
	2798	echo "chmod go+rx $tempdir" >> $jobfile
	2799	else
	2800	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2801	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2802	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2803	mkdir $tempdir
	2804	chmod go+rx $tempdir
	2805	fi
	2806	echo "cd $tempdir" >> $jobfile
	2807	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2808	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2809	echo "export PATH=.:\$PATH" >> $jobfile
	2810	echo "export execute_palmrun=true" >> $jobfile
	2811
	2812
	2813	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2814	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2815	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2816	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2817	echo "export LOCAL_PWD" >> $jobfile
	2818
	2819
	2820	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2821	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2822	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2823
	2824
	2825	# CALL PALMRUN WITHIN THE JOB
	2826	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2827	echo "set -x" >> $jobfile
	2828	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2829
	2830
	2831	# TRANSFER JOBFILE TO THE TARGET HOST
	2832	if [[ $create_jobfile_only = false ]]
	2833	then
	2834
	2835	if [[ $create_remote_batch_job = true ]]
	2836	then
	2837
[2420]	2838	echo " "
[2566]	2839	echo " *** transfer of job to remote host via scp"
[2420]	2840	if [[ $do_trace = true ]]
	2841	then
[2506]	2842	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2843	fi
[2566]	2844	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2845
[2566]	2846	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2847	if [[ $do_trace = true ]]
	2848	then
[2506]	2849	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]	2850	fi
[2506]	2851	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]	2852
	2853	elif [[ $create_batch_job = true ]]
	2854	then
	2855
[2385]	2856	eval local_jobcatalog=$local_jobcatalog
[2506]	2857	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2858	cd $local_jobcatalog
[2380]	2859	echo " "
[2420]	2860	echo " *** submit the job"
	2861	if [[ $do_trace = true ]]
	2862	then
[2506]	2863	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2864	fi
[2506]	2865	$submit_command ${host_configuration}_${job_id}
	2866	rm ${host_configuration}_${job_id}
[2380]	2867	cd - > /dev/null
	2868
	2869	fi
	2870
	2871	rm -rf $jobfile
	2872
	2873	else
	2874
	2875	printf "\n *** jobfile created under name \"$jobfile\" "
	2876	printf "\n no batch-job has been sent!"
	2877
	2878	fi
	2879
	2880	fi # END OF REMOTE-PART

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