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source: palm/trunk/SCRIPTS/palmrun @ 3458

Last change on this file since 3458 was 3455, checked in by raasch, 6 years ago
options -h and -d renamed -c and -r, respectively, job_queue renamed job_logfiles in sveral configuration files
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 100.8 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	# -----------------
[3032]	28	# $Id: palmrun 3455 2018-10-30 14:12:31Z kanani $
[3455]	29	# options -h and -d renamed -c and -r, respectively
	30	#
	31	# 3402 2018-10-23 11:49:24Z knoop
[3346]	32	# job_id is set for compatibility reasons with older versions of config files
	33	#
	34	# 3313 2018-10-06 15:22:48Z knoop
[3294]	35	# more detailed error message for outdated fileconnection file
	36	#
	37	# 3236 2018-09-10 09:07:06Z raasch
[3236]	38	# warning issued in case of file connection file version mismatch,
	39	# host_configuration renamed configuration_identifier,
	40	# "host identifier" in header output renamed "config. identifier",
	41	# jobname renamed run_identifier,
	42	# run_id renamed run_id_number
	43	# job_id renamed run_id
	44	# option -r renamed -i
	45	#
	46	# 3151 2018-07-19 08:45:38Z raasch
[3151]	47	# removed additional listing of files to be compiled, print PALM code revision
	48	# in header
	49	#
	50	# 3132 2018-07-16 11:44:58Z raasch
[3132]	51	# create consistent error messages in case of failed restarts,
	52	# check existence of remote job catalog
	53	#
	54	# 3043 2018-05-25 10:47:54Z raasch
[3043]	55	# check for setting of fast_io_catalog
	56	#
	57	# 3033 2018-05-23 15:26:19Z raasch
[3025]	58	# -T option not required for interactive runs (tasks per node =
	59	# total number of cores is assumed as default, if option is not given),
	60	# reformatting of a few messages,
	61	# bugfix: destination output directory is created if attribute "pe" is set in
	62	# .palm.iofiles
	63	#
	64	# 2718 2018-01-02 08:49:38Z maronga
[2993]	65	# bugfix of r2990
	66	#
	67	# 2718 2018-01-02 08:49:38Z maronga
[2990]	68	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	69	# not in the working directory from where palmrun is called
	70	#
	71	# 2718 2018-01-02 08:49:38Z maronga
[2957]	72	# svfout in the activation string will be replaced now by svfin in case of
	73	# automatic restarts
	74	#
	75	# 2718 2018-01-02 08:49:38Z maronga
[2906]	76	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	77	# the possible output or input of sky view factors
	78	#
	79	# 2718 2018-01-02 08:49:38Z maronga
[2834]	80	# "fname" renamed to "jobname"
	81	#
	82	# 2718 2018-01-02 08:49:38Z maronga
[2799]	83	# parameters are allowed in output commands (OC:)
	84	#
	85	# 2718 2018-01-02 08:49:38Z maronga
[2789]	86	# bugfix: exit if no queue has been given neither with option -q nor in the
	87	# configuration file
	88	#
	89	# 2718 2018-01-02 08:49:38Z maronga
[2762]	90	# file connection file from trunk/SCRIPTS is taken by default
	91	#
	92	# 2718 2018-01-02 08:49:38Z maronga
[2716]	93	# Corrected "Former revisions" section
	94	#
	95	# 2696 2017-12-14 17:12:51Z kanani
	96	# Change in file header (GPL part)
	97	#
	98	# 2693 2017-12-13 12:33:49Z raasch
[2693]	99	# replacement of variables given by {{<variable>}} in configuration file is now
	100	# done in a more general way, variable names are written in small letters
	101	#
	102	# 2670 2017-12-06 16:32:19Z raasch
[2670]	103	# test printouts removed
	104	#
	105	# 2669 2017-12-06 16:03:27Z raasch
[2669]	106	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	107	# removed,
	108	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	109	# files,
	110	# informative messages in case of missing optional input files shortened
	111	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	112	#
	113	# 2638 2017-11-23 12:44:23Z raasch
[2610]	114	# use of wildcards in file connection statements enabled
	115	#
	116	# 2605 2017-11-09 15:31:46Z raasch
[2605]	117	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	118	# will not be sent with the job file any more, but copied into the
[2610]	119	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	120	#
	121	# 2600 2017-11-01 14:11:20Z raasch
[2600]	122	# cycle numbers are made three digits wide
	123	#
	124	# 2566 2017-10-20 08:50:47Z raasch
[2566]	125	# execute command for combine_plot_fields added
	126	# "TEMPDIR" renamed "tempdir"
	127	# temporary working directory for local batch jobs is created immediately within
	128	# the user's palmrun call, due to a requirement of the "grid engine" batch
	129	# system, where the working directory is given with batch directive -wd and must
	130	# already exist when the job is submitted,
	131	# informative messages in non-trace mode reduced and partly reformatted
	132	#
	133	# 2551 2017-10-18 07:25:11Z raasch
[2551]	134	# TEMPDIR added as replacement string to be used in batch directives
	135	#
	136	# 2512 2017-10-04 08:26:59Z raasch
[2507]	137	# bugfix for determining cycle numbers of NetCDF input files
	138	#
	139	# 2506 2017-09-29 08:30:37Z raasch
[2506]	140	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	141	# host configuration added to SOURCES_FOR_RUN_... folder name
	142	# host_identifier renamed host_configuration
	143	# option -W added to allow for job dependencies
	144	#
	145	# 2501 2017-09-26 11:41:55Z raasch
[2501]	146	# default value for number of cores (option -X) set to 1
	147	# bugfix for mechanism which overwrites configuration file settings with values
	148	# provided by palmrun options
	149	#
	150	# 2499 2017-09-22 16:47:58Z kanani
[2499]	151	# option -h named configuration identifier
	152	#
	153	# 2480 2017-09-19 06:24:14Z maronga
[2480]	154	# bugfix for last revision
	155	#
	156	# 2479 2017-09-19 06:12:16Z raasch
[2479]	157	# option -A (project account number) added
	158	#
	159	# 2422 2017-09-08 08:25:41Z raasch
[2410]	160	# initial revision
[2380]	161	#
	162	#--------------------------------------------------------------------------------#
	163	# palmrun - script for running PALM jobs on local and remote hosts
	164	#--------------------------------------------------------------------------------#
	165
	166
	167
	168	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	169
	170	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	171	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	172	# (TOO MANY ARGUMENTS - PROBLEM)
	173	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	174
[2610]	175	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	176	typeset -i nr_of_output_files=0
[2380]	177	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	178	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	179	# SCRIPT-OPTION ARGUMENTS
	180	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	181	typeset -i icycle inode ival maxcycle mpi_tasks
	182	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	183
	184	activation_string_list=""
	185	AddFilenames=""
	186	combine_plot_fields=true
	187	compiler_name=""
	188	compiler_name_ser=""
	189	compiler_options=""
[3236]	190	configuration_identifier="default"
[2501]	191	cores=1
[2380]	192	cores_atmos=0
	193	cores_ocean=0
	194	coupled_dist=""
	195	cpp_options=""
	196	cpumax=0
[2506]	197	create_batch_job=false
[2380]	198	create_jobfile_only=false
	199	create_remote_batch_job=false
	200	dashes=" ----------------------------------------------------------------------------"
	201	defaultqueue=""
[2506]	202	delete_temporary_catalog=true
[2380]	203	do_compile=true
	204	do_trace=false
	205	executable=""
	206	execute_command=""
	207	execution_error=false
[2762]	208	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	209	global_revision=""
	210	hostfile=""
	211	hp=""
	212	keep_data_from_previous_run=false
	213	link_local_input=false
	214	link_local_output=false
[2388]	215	linker_options=""
[2385]	216	local_jobcatalog=""
[2380]	217	locat=normal
	218	makefile=""
	219	max_par_io_str=""
	220	prc=$0
	221	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	222	do
	223	prc=`echo $prc \| cut -f2- -d"/"`
	224	done
	225	module_calls=""
[2506]	226	palmrun_memory=""
[2380]	227	palmrun_script_name=$prc
	228	openmp=false
[2506]	229	previous_job=""
[2479]	230	project_account=""
[2380]	231	queue=none
[2906]	232	read_svf=""
[2380]	233	restart_run=false
	234	return_address=""
[2385]	235	remote_jobcatalog=""
[2380]	236	remote_username=""
	237	running_in_batch_mode=false
[3313]	238	running_in_test_mode=false
[2380]	239	run_coupled_model=false
	240	run_id=""
[3236]	241	run_id_number=""
	242	run_identifier=test
[2380]	243	silent=false
	244	source_list=""
	245	source_path=""
[2501]	246	tasks_per_node=0
[2380]	247	threads_per_task=1
	248	transfer_problems=false
[2384]	249	user_source_path=""
[2506]	250	use_existing_sources_folder=""
[2380]	251	use_openmp=false
[3033]	252	version="palmrun 1.0 Rev$Rev: 3455 $"
[2380]	253	working_directory=`pwd`
	254	write_binary=""
[2906]	255	write_svf=""
[2380]	256
	257
	258	# ERROR HANDLING IN CASE OF EXIT
[2404]	259	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	260	then
	261
	262	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	263	(( i = 0 ))
	264	while (( i < iec ))
	265	do
	266	(( i = i + 1 ))
	267	printf "\n *** Execution of ERROR-command:\n"
	268	printf " >>> ${err_command[$i]}\n"
	269	eval ${err_command[$i]}
	270	done
[2566]	271	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	272	printf "\n\n+++ palmrun crashed \n\n"
	273	exit 1
	274	elif [[ $locat != normal ]]
[2380]	275	then
[3312]	276	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	277	printf "\n+++ palmrun killed by \"^C\" \n\n"
	278	exit 2
	279	else
[2566]	280	printf "\n --> palmrun finished\n\n"
[3312]	281	exit 0
[2380]	282	fi' exit
	283
	284
	285	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	286	trap 'locat=control_c
	287	exit 1
[2380]	288	' 2
	289
	290
	291	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	292	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	293	while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
[2380]	294	do
	295	case $option in
	296	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	297	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	298	(b) create_batch_job=true; prc="$prc -b";;
	299	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	300	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	301	(C) restart_run=true; prc="$prc -C";;
	302	(F) create_jobfile_only=true;;
	303	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	304	(i) run_id_number=$OPTARG;;
[2380]	305	(j) running_in_batch_mode=true;;
	306	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	307	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	308	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	309	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	310	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	311	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	312	(R) return_address=$OPTARG;;
	313	(s) source_list=$OPTARG;;
[2501]	314	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	315	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	316	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	317	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	318	(v) silent=true; prc="$prc -v";;
[2506]	319	(V) use_existing_sources_folder="-V";;
[2380]	320	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	321	(W) previous_job=$OPTARG;;
[2380]	322	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	323	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	324	(y) ocean_file_appendix=true; prc="$prc -y";;
	325	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	326	(z) running_in_test_mode=true;;
[2380]	327	(Z) combine_plot_fields=false; prc="$prc -Z";;
	328	(\?) printf "\n +++ unknown option $OPTARG \n"
	329	printf "\n --> type \"$0 ?\" for available options \n"
	330	locat=parameter;exit;;
	331	esac
	332	done
	333
	334
	335	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	336	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	337	(( to_shift = $OPTIND - 1 ))
	338	shift $to_shift
	339
	340	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	341	if [[ "$1" = "?" ]]
	342	then
	343	(printf "\n *** Description of available palmrun options:\n"
	344	printf "\n Option Description Default-Value"
	345	printf "\n -a activation string list \"\" "
[2479]	346	printf "\n -A project account number ---"
[2380]	347	printf "\n -b batch-job on local machine ---"
	348	printf "\n -B do not delete temporary directory at end ---"
[3455]	349	printf "\n -c configuration identifier \"default\" "
[2380]	350	printf "\n -F create batch job file only ---"
	351	printf "\n -k keep data from previous run"
	352	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	353	printf "\n -M Makefile name Makefile"
	354	printf "\n -O threads per openMP task ---"
	355	printf "\n -q queue \"$queue\" "
[3455]	356	printf "\n -r run identifier test"
[2380]	357	printf "\n -s filenames of routines to be compiled \"\" "
	358	printf "\n must end with .f, .f90, .F, or .c !"
	359	printf "\n use \"..\" for more than one file and wildcards"
	360	printf "\n -s LM compiles all locally modified files"
	361	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	362	printf "\n -T tasks per node ---"
[2380]	363	printf "\n -u username on remote machine \"\" "
	364	printf "\n -v no prompt for confirmation ---"
[2506]	365	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	366	printf "\n -w maximum parallel io streams as given by -X"
[2506]	367	printf "\n -W name of job to wait for ---"
[2380]	368	printf "\n -x tracing of palmrun for debug purposes ---"
	369	printf "\n -X # of processors (on parallel machines) 1"
	370	printf "\n -y add appendix \"_O\" to all local output"
	371	printf "\n files (ocean precursor runs followed by"
	372	printf "\n coupled atmosphere-ocean runs) ---"
	373	printf "\n -Y run coupled model, \"#1 #2\" with"
	374	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	375	printf "\n -Z skip combine_plot_fields at the end of "
	376	printf "\n the simulation ---"
	377	printf "\n "
	378	printf "\n Possible values of positional parameter <modus>:"
	379	printf "\n \"?\" - this outline \n\n") \| more
	380	exit
	381	elif [[ "$1" != "" ]]
	382	then
	383	printf "\n +++ positional parameter $1 unknown \n"
	384	locat=parameter; exit
	385	fi
	386
	387
	388
	389	# SHORT STARTING MESSAGE
	390	printf "\n*** $version "
	391	printf "\n will be executed. Please wait ..."
	392
	393
[2506]	394	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	395	config_file=.palm.config.$configuration_identifier
	396	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	397
	398
	399	# CHECK, IF CONFIGURATION FILE EXISTS
	400	if [[ ! -f $config_file ]]
	401	then
	402	printf "\n\n +++ configuration file: "
	403	printf "\n $config_file"
	404	printf "\n does not exist"
	405	locat=connect; exit
	406	fi
	407
	408
[2762]	409	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	410	if [[ -f .palm.iofiles ]]
	411	then
[3236]	412
	413	# CHECK VERSION MISMATCH
	414	if [[ $running_in_batch_mode != true ]]
	415	then
	416	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	417	then
	418	printf "\n\n +++ WARNING: A file connection file has been found in your"
	419	printf "\n working directory, but its revision does not match"
	420	printf "\n the revision of the default (trunk) version."
[3294]	421	printf "\n You may need to update your connection file"
	422	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	423	fi
	424	fi
	425
[2762]	426	fileconnection_file=.palm.iofiles
[3236]	427
[2762]	428	fi
	429
	430
[2380]	431	# CHECK, IF FILE CONNECTION FILE EXISTS
	432	if [[ ! -f $fileconnection_file ]]
	433	then
	434	printf "\n\n +++ file connection file: "
	435	printf "\n $fileconnection_file"
	436	printf "\n does not exist"
	437	locat=connect; exit
	438	fi
	439
	440
[2404]	441	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	442	if [[ "$activation_string_list" = "" ]]
	443	then
	444	printf "\n\n +++ no activation string list given: "
	445	printf "\n please set palmrun option \"-a\" "
	446	locat=palmrun_option; exit
	447	fi
	448
	449
	450	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	451	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	452	then
	453	write_binary=true
	454	else
	455	write_binary=false
	456	fi
	457
[2906]	458	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	459	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	460	then
	461	write_svf=true
	462	else
	463	write_svf=false
	464	fi
[2404]	465
[2906]	466	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	467	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	468	then
	469	read_svf=true
	470	else
	471	read_svf=false
	472	fi
	473
	474
[2380]	475	# READ AND EVALUATE THE CONFIGURATION-FILE
	476	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	477
	478	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	479	while read line
	480	do
	481
	482	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	483	eval line=\"$line\"
	484
	485
	486	# INTERPRET THE LINE
	487	if [[ "$(echo $line)" = "" ]]
	488	then
	489
	490	# EMPTY LINE, NO ACTION
	491	continue
	492
	493	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	494	then
	495
	496	# LINE IS A COMMENT LINE
	497	continue
	498
	499	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	500	then
	501
	502	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	503	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	504	value=`echo $line \| cut -d" " -s -f2-`
	505
	506
	507	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	508	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	509	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	510	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	511	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	512	# CONFIGURATION-FILE.
	513	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	514	then
	515	eval export $var="\$value"
	516
	517	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	518	if [[ $do_trace = true ]]
	519	then
	520	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	521	fi
	522	fi
	523
	524	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	525	then
	526
	527	# LINE DEFINES BATCH-DIRECTIVE
	528	(( ibd = ibd + 1 ))
	529	line=$(echo $line \| cut -c4-)
	530	batch_directive[$ibd]="$line"
	531
	532	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	533	then
	534
	535	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	536	# REMOTE TO A LOCAL HOST
	537	(( ibdt = ibdt + 1 ))
	538	line=$(echo $line \| cut -c5-)
	539	batch_directive_transfer[$ibdt]="$line"
	540
	541	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	542	then
	543
	544	# LINE DEFINES ERROR-COMMAND
	545	(( iec = iec + 1 ))
	546	line=$(echo $line \| cut -c4-)
	547	err_command[$iec]="$line"
	548
	549	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	550	then
	551
	552	# LINE DEFINES INPUT-COMMAND
	553	(( iic = iic + 1 ))
	554	line=$(echo $line \| cut -c4-)
	555	in_command[$iic]="$line"
	556
	557	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	558	then
	559
	560	# LINE DEFINES OUTPUT-COMMAND
	561	(( ioc = ioc + 1 ))
	562	line=$(echo $line \| cut -c4-)
	563	out_command[$ioc]="$line"
	564
	565	else
	566
	567	# SKIP ALL OTHER LINES
	568	continue
	569
	570	fi
	571
	572	done < $config_file
	573
	574
	575	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	576	if [[ "$fast_io_catalog" = "" ]]
	577	then
	578	printf "\n +++ no fast_io_catalog found in $config_file"
	579	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	580	locat=config_file; exit
	581	fi
[2380]	582	if [[ "$compiler_name" = "" ]]
	583	then
	584	printf "\n +++ no compiler name found in $config_file"
	585	printf "\n Please add line \"compiler_name ...\" to that file."
	586	locat=config_file; exit
	587	fi
	588	if [[ "$compiler_name_ser" = "" ]]
	589	then
	590	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	591	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	592	locat=config_file; exit
	593	fi
	594	if [[ "$compiler_options" = "" ]]
	595	then
	596	printf "\n +++ no compiler options found in $config_file"
	597	printf "\n Please add line \"compiler_options ...\" to that file."
	598	locat=config_file; exit
	599	fi
[2388]	600	if [[ "$linker_options" = "" ]]
[2380]	601	then
[2388]	602	printf "\n +++ no linker options found in $config_file"
	603	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	604	locat=config_file; exit
	605	fi
	606	if [[ "$execute_command" = "" ]]
	607	then
	608	printf "\n +++ no execute command found in $config_file"
	609	printf "\n Please add line \"execute_command ...\" to that file."
	610	locat=config_file; exit
	611	fi
	612
	613	if [[ "$hostfile" != "" ]]
	614	then
	615	if [[ $hostfile != auto && ! -f $hostfile ]]
	616	then
	617	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	618	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	619	locat=config_file; exit
	620	fi
	621	fi
	622
	623
	624	# DETERMINE THE CALL STATUS
	625	if [[ "$return_address" != "" ]]
	626	then
	627
	628	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	629	# BATCH MODE AND ...
	630	running_on_remote=true
	631
	632	else
	633
	634	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	635	if [[ "$remote_ip" != "" ]]
	636	then
	637
	638	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	639	create_remote_batch_job=true
	640
[3132]	641	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	642	if [[ "$remote_jobcatalog" = "" ]]
	643	then
	644	printf "\n +++ no remote jobcatalog found in $config_file"
	645	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	646	locat=config_file; exit
	647	fi
	648
	649
[2380]	650	fi
	651	running_on_remote=false
	652	fi
	653
	654
	655
	656	# READ AND EVALUATE THE I/O-FILE LIST
	657	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	658
	659	# READ THE FILE CONNECTION FILE LINE BY LINE
	660	while read line
	661	do
	662
[2669]	663	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	664	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	665
	666	# INTERPRET THE LINE
	667	if [[ "$(echo $line)" = "" ]]
	668	then
	669	# EMPTY LINE, NO ACTION
	670	continue
	671
	672	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	673	then
	674
	675	# LINE IS A COMMENT LINE
	676	true
	677
	678	else
	679
	680	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	681	# s2a: in/out - field
[2669]	682	# s2b: action - field (optional)
	683	s1=`echo "$line" \| cut -d" " -f1`
	684	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	685	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	686	then
[2669]	687	s2a=$s2
[2380]	688	s2b=""
	689	else
[2669]	690	s2a=`echo $s2 \| cut -d":" -f1`
	691	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	692	fi
[2669]	693	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	694	s4=`echo "$line" \| cut -d" " -s -f4`
	695	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	696	s5=`echo "$line" \| cut -d" " -s -f5`
	697	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	698
	699
	700	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	701	# INPUT- OR OUTPUT-LIST.
	702	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	703	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	704	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	705	# IS NOT CHECKED AND STORED.
[2610]	706	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	707	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	708	then
	709	found=false
	710	for actual in $activation_string_list
	711	do
	712	for formal in $s3
	713	do
	714	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	715	done
	716	done
	717	if [[ $found = true ]]
	718	then
	719	(( iin = iin + 1 ))
[2669]	720	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	721	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	722	if [[ "$s2a" = inopt ]]
	723	then
	724	optin_pre[$iin]=yes
	725	else
	726	optin_pre[$iin]=no
	727	fi
[2605]	728
	729	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	730	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	731	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	732	then
[2610]	733	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	734	fi
	735
[2610]	736	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	737	# THE WILDCARD FROM THE ENDING
	738	if [[ "${s5: -1}" = "*" ]]
	739	then
[2669]	740	if [[ "$s2b" = "di" ]]
[2610]	741	then
	742	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	743	printf "\n see file \"$fileconnection_file\", line"
	744	printf "\n$line"
	745	locat=iofiles_file; exit
	746	fi
	747	multin[$iin]=true
	748	string=${endin_pre[$iin]}
	749	endin_pre[$iin]="${string%?}"
	750	else
	751	multin[$iin]=false
	752	fi
[2380]	753	fi
[2669]	754	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	755	then
	756	found=false
	757	for actual in $activation_string_list
	758	do
	759	for formal in $s3
	760	do
[2670]	761	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	762	done
	763	done
	764	if [[ $found = true ]]
	765	then
	766	(( iout = iout + 1 ))
[2669]	767	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	768	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	769
[2669]	770	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	771	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	772	if [[ $formal = wildcard ]]
	773	then
	774	warnout_pre[$iout]=false
	775	else
	776	warnout_pre[$iout]=true
	777	fi
	778
[2610]	779	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	780	# THE WILDCARD FROM THE LOCAL FILENAME
	781	if [[ "${s1: -1}" = "*" ]]
	782	then
[2669]	783	if [[ "$s2b" = "di" ]]
[2610]	784	then
	785	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	786	printf "\n see file \"$fileconnection_file\", line"
	787	printf "\n$line"
	788	locat=iofiles_file; exit
	789	fi
	790	multout[$iout]=true
	791	string=${localout_pre[$iout]}
	792	localout_pre[$iout]="${string%?}"
	793	else
	794	multout[$iout]=false
	795	fi
[2380]	796	fi
[2669]	797	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	798	then
[2669]	799	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	800	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	801	locat=connect; exit
	802	fi
	803	IFS="$IFSALT"
	804	fi
	805
	806	done < $fileconnection_file
	807
	808
	809
[2501]	810	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	811	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	812	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	813	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	814	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	815	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	816
	817
	818
[2380]	819	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	820	if [[ $run_coupled_model = true ]]
	821	then
	822
	823	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	824	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	825
	826	if (( $cores_ocean + $cores_atmos != $cores ))
	827	then
	828
	829	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	830	printf "\n PEs (total) : $cores"
	831	printf "\n PEs (atmosphere): $cores_atmos"
	832	printf "\n PEs (ocean) : $cores_ocean"
	833	locat=coupling; exit
	834
	835	fi
	836
	837	fi
	838
	839
	840	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	841	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	842	# FOLDER
	843	if [[ $running_in_batch_mode = true ]]
	844	then
	845
[2506]	846	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	847	then
[2506]	848	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	849	printf "\n Please check the output of the palmrun-call"
	850	printf "\n that you did on your local host."
	851	locat=SOURCES_FOR_RUN; exit
	852	fi
	853
	854	else
	855
	856	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	857	# AUTOMATIC RESTART RUN
	858	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	859	if [[ $restart_run = false ]]
	860	then
	861
	862	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	863	# THE LOCAL HOST
	864	if [[ ! -d $source_path ]]
	865	then
	866	printf "\n\n +++ source path \"$source_path\" on local host"
	867	printf "\n \"$(hostname)\" does not exist"
	868	locat=source_path; exit
	869	fi
	870
[2990]	871	rm -rf ${base_directory}/${sources_for_run_catalog}
	872	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	873
	874	if [[ "$source_list" = LM ]]
	875	then
	876
	877	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	878	source_list=""
	879	cd $source_path
	880
	881
[2512]	882	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	883	if [[ ! -d ../.svn ]]
[2380]	884	then
	885	printf "\n\n +++ source directory"
	886	printf "\n \"$source_path\" "
	887	printf "\n is not under control of \"subversion\"."
[2512]	888	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	889	fi
	890
	891
	892	# LIST ALL MODIFIED SOURCE CODE FILES
	893	Filenames=""
[2404]	894	svn status > tmp_svnstatus
[2380]	895	while read line
	896	do
	897	firstc=`echo $line \| cut -c1`
	898	if [[ $firstc = M \|\| $firstc = "?" ]]
	899	then
	900	Name=`echo "$line" \| cut -c8-`
	901	extension=`echo $Name \| cut -d. -f2`
	902	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	903	then
	904	Filenames="$Filenames "$Name
	905	fi
	906	fi
[2404]	907	done < tmp_svnstatus
	908	rm -rf tmp_svnstatus
[2380]	909
	910
	911	# COPY FILES TO SOURCES_FOR_RUN_...
	912	for filename in $Filenames
	913	do
[2990]	914	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	915	source_list=$source_list"$filename "
	916	done
	917
	918	cd - > /dev/null
	919
	920
	921	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	922	elif [[ "$source_list" != "" ]]
	923	then
	924
	925	cd $source_path
	926
	927	for filename in $source_list
	928	do
	929
	930	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	931	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	932	then
	933	printf "\n +++ source code file: $filename"
	934	printf "\n must not contain (\"/\") "
	935	locat=source; exit
	936	fi
	937
	938	if [[ ! -f $filename ]]
	939	then
	940	printf "\n +++ source code file: $filename"
	941	printf "\n does not exist"
	942	locat=source; exit
	943	else
[2990]	944	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	945	fi
	946
	947	done
	948
	949	cd - > /dev/null
	950
	951	fi
	952
	953	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	954	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	955	if [[ ! -f $makefile ]]
	956	then
	957	printf "\n +++ file \"$makefile\" does not exist"
	958	locat=make; exit
	959	else
[2990]	960	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	961	fi
	962
	963
	964	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	965	if [[ "$user_source_path" != "" ]]
[2380]	966	then
	967
	968	# DOES THE DIRECTORY EXIST?
[2384]	969	if [[ ! -d $user_source_path ]]
[2380]	970	then
	971
	972	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	973	printf "\n \"$user_source_path\" "
[2380]	974	printf "\n does not exist or is not a directory."
	975	printf "\n No source code will be used from this directory!\n"
[2384]	976	user_source_path=""
[2380]	977	if [[ $silent == false ]]
	978	then
	979	sleep 2
	980	fi
	981
	982	else
	983
[2384]	984	cd $user_source_path
[2380]	985
	986	Names=$(ls -1 *.f90 2>&1)
	987	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	988	Names=$(ls -1 *.F90 2>&1)
	989	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	990	Names=$(ls -1 *.F 2>&1)
	991	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	992	Names=$(ls -1 *.f 2>&1)
	993	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	994	Names=$(ls -1 *.c 2>&1)
	995	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	996
	997	cd - > /dev/null
[2990]	998	cd ${base_directory}/${sources_for_run_catalog}
[2380]	999
	1000	# COPY MAKEFILE IF EXISTING
[2384]	1001	if [[ -f $user_source_path/Makefile ]]
[2380]	1002	then
	1003	printf "\n\n *** user Makefile from directory"
[2384]	1004	printf "\n \"$user_source_path\" is used \n"
[2380]	1005	if [[ $silent == false ]]
	1006	then
	1007	sleep 1
	1008	fi
[2384]	1009	cp $user_source_path/Makefile .
[2380]	1010	fi
	1011
	1012	for filename in $AddFilenames
	1013	do
	1014	if [[ -f $filename ]]
	1015	then
	1016	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1017	printf "\n source code directory \"$user_source_path\" "
[2380]	1018	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1019	printf "\n from directory \"$source_path\"."
	1020	locat=source; exit
	1021	fi
	1022
[2384]	1023	cp $user_source_path/$filename .
[2380]	1024	source_list="$source_list $filename"
	1025
	1026	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1027	if [[ $(grep -c $filename Makefile) = 0 ]]
	1028	then
	1029	printf "\n\n +++ user file \"$filename\" "
	1030	printf "\n is not listed in Makefile \n"
	1031	locat=source; exit
	1032	fi
	1033	done
	1034	cd - > /dev/null
	1035	fi
	1036	fi
	1037
	1038	# COPY CONFIGURATION FILES
[2990]	1039	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1040	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1041
	1042	# COPY SHELLSCRIPTS
[2990]	1043	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1044	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1045
	1046	fi
	1047
	1048	fi
	1049
[2605]	1050
[2380]	1051	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1052	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1053	if [[ "$global_revision" = "" ]]
	1054	then
	1055	global_revision=`svnversion $source_path 2>/dev/null`
	1056	global_revision="Rev: $global_revision"
	1057	fi
	1058
	1059
	1060	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1061	if [[ -n $cores ]]
	1062	then
	1063
	1064	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1065	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1066	if [[ $tasks_per_node = 0 ]]
[2380]	1067	then
[3025]	1068	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1069	then
	1070	printf "\n"
	1071	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1072	printf "\n set -T option or define tasks_per_node in the config file"
	1073	locat=tasks_per_node; (( iec = 0 )); exit
	1074	else
	1075	# DEFAULT FOR INTERACTIVE RUN
	1076	tasks_per_node=$cores
	1077	fi
[2380]	1078	fi
	1079
	1080	if (( cores < tasks_per_node ))
	1081	then
	1082	printf "\n"
	1083	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1084	printf "\n given values: -T $tasks_per_node -X $cores"
	1085	locat=tasks_per_node; (( iec = 0 )); exit
	1086	fi
	1087
	1088	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1089	(( mpi_tasks = cores / threads_per_task ))
	1090	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1091	(( ii = cores / tasks_per_node ))
	1092	(( remaining_cores = cores - ii * tasks_per_node ))
	1093	if (( remaining_cores > 0 ))
	1094	then
	1095	printf "\n"
	1096	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1097	printf "\n divisor of the total number of cores (option \"-X\")"
	1098	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1099	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1100	(( nodes = nodes + 1 ))
	1101	fi
	1102
	1103	fi
	1104
	1105
	1106	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1107	if [[ "$maximum_parallel_io_streams" = "" ]]
	1108	then
	1109	maximum_parallel_io_streams=$cores
	1110	fi
	1111
	1112
	1113	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1114	if [[ "$scp_port" != "" ]]
	1115	then
	1116	PORTOPT="-P $scp_port"
	1117	SSH_PORTOPT="-p $scp_port"
	1118	fi
	1119
	1120
	1121	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1122	# CONFIG-FILE
	1123	if [[ "$ssh_key" != "" ]]
	1124	then
	1125	ssh_key="-i $HOME/.ssh/$ssh_key"
	1126	fi
	1127
	1128
	1129	# SET QUEUE, IF NOT GIVEN
	1130	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1131	then
	1132
	1133	if [[ $queue = none && "$defaultqueue" = "" ]]
	1134	then
	1135	printf "\n"
	1136	printf "\n +++ no default queue given in configuration file and no queue"
	1137	printf "\n given with option -q"
[2789]	1138	locat=queue; exit
[2380]	1139	fi
	1140	if [[ $queue = none ]]
	1141	then
	1142	queue=$defaultqueue
	1143	fi
	1144
	1145	fi
	1146
	1147
	1148	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1149	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1150	(( i = 0 ))
[2610]	1151	(( nr_of_input_files = 0 ))
[2380]	1152	while (( i < iin ))
	1153	do
	1154	(( i = i + 1 ))
	1155
	1156	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1157	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1158	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1159	then
[2610]	1160	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1161	else
[3236]	1162	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1163	fi
	1164
[2610]	1165
[2380]	1166	# CHECK IF FILE EXISTS
	1167	if ! ls $filename* 1>/dev/null 2>&1
	1168	then
	1169
[2669]	1170	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1171	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1172	then
	1173	printf "\n\n +++ INPUT-file: "
[2610]	1174	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1175	then
	1176	printf "\n $filename"
	1177	else
[2610]	1178	printf "\n $filename.${extin_pre[$i]}"
[2380]	1179	fi
	1180	printf "\n does not exist\n"
	1181	locat=input; exit
	1182	else
[2610]	1183	(( nr_of_input_files = nr_of_input_files + 1 ))
	1184	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1185	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1186	actionin[$nr_of_input_files]="unavailable"
[2610]	1187	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1188	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1189	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1190	fi
[2605]	1191
[2380]	1192	else
	1193
[3236]	1194	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1195	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1196	# ENDINGS
[2610]	1197	if [[ "${multin[$i]}" = true ]]
	1198	then
	1199	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1200	ls -1 -d ${filename} > filelist 2>/dev/null
	1201	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1202	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1203
[2610]	1204	endings=""
	1205	while read line
	1206	do
	1207	# filename without path (i.e. after the last "/")
	1208	basefilename=$(basename ${line})
[2380]	1209
[2610]	1210	# check if there is an extension and remove it
	1211	ext=${basefilename##*.}
	1212	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1213	then
	1214	basefilename=${basefilename%.*}
	1215	fi
[2380]	1216
[2610]	1217	# check for an existing cycle number and remove it
	1218	cycle=${basefilename##*.}
	1219	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1220	then
	1221	basefilename=${basefilename%.*}
	1222	fi
[2600]	1223
[3236]	1224	# remove the run_identifier from the beginning
	1225	length_run_identifier=${#run_identifier}
	1226	ending=${basefilename:${length_run_identifier}}
[2610]	1227
	1228	# remove the ending given in the .iofiles from the beginning
	1229	endingstring="${endin_pre[$i]}"
	1230	length_ending=${#endingstring}
	1231	ending=${ending:${length_ending}}
	1232
	1233	if [[ "$ending" = "" ]]
[2600]	1234	then
[2610]	1235	# standard ending as given in the .iofiles
	1236	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1237	then
	1238	endings="$endings DEFAULT"
	1239	fi
[2600]	1240	else
[2610]	1241	# ending must start with "_", otherwise its a different file
	1242	if [[ "${ending:0:1}" = "_" ]]
	1243	then
	1244	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1245	then
	1246	endings="$endings $ending"
	1247	fi
	1248	fi
[2600]	1249	fi
[2610]	1250
	1251	done <filelist
[2380]	1252
[2610]	1253	rm filelist
[2380]	1254
[2600]	1255	else
[2610]	1256
	1257	# SINGLE NAME
	1258	endings=DEFAULT
	1259
[2600]	1260	fi
	1261
[2610]	1262	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1263	for ending in $endings
	1264	do
	1265
	1266	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1267	if [[ $ending = DEFAULT ]]
[2380]	1268	then
[2610]	1269	ending=""
	1270	fi
	1271
	1272	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1273	(( nr_of_input_files = nr_of_input_files + 1 ))
	1274	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1275	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1276	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1277	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1278	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1279	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1280
	1281
	1282	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1283	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1284	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1285	then
	1286	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1287	else
[3236]	1288	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1289	fi
[2610]	1290
	1291	# DETERMINE THE FILE'S CYCLE NUMBER
	1292	(( maxcycle = 0 ))
	1293	ls -1 -d $filename > filelist 2>/dev/null
	1294	ls -1 -d $filename.* >> filelist 2>/dev/null
	1295	while read line
	1296	do
	1297	# filename without path (i.e. after the last "/")
	1298	basefilename=$(basename ${line})
	1299
	1300	# check if there is an extension
	1301	extension=${basefilename##*.}
	1302	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1303	then
	1304	basefilename=${basefilename%.*}
	1305	fi
	1306
	1307	# check for an existing cycle number
	1308	cycle=${basefilename##*.}
	1309	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1310	then
[2669]	1311	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1312	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1313	(( icycle = $((10#$cycle)) ))
[2610]	1314	else
	1315	(( icycle = 0 ))
	1316	fi
	1317
	1318	if (( icycle > maxcycle ))
	1319	then
	1320	(( maxcycle = icycle ))
	1321
	1322	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1323	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1324	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1325	then
	1326	leading_zero=true
	1327	else
	1328	leading_zero=false
	1329	fi
	1330	fi
	1331
	1332	done <filelist
	1333	rm filelist
	1334
	1335	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1336	if [[ $leading_zero = true ]]
[2380]	1337	then
[2610]	1338	cyclestring=`printf "%03d" $maxcycle`
	1339	else
	1340	cyclestring=$maxcycle
[2380]	1341	fi
[2610]	1342
	1343	# APPEND CYCLE NUMBER TO FILENAME
	1344	if (( maxcycle > 0 ))
[2380]	1345	then
[2610]	1346	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1347	then
	1348	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1349	else
	1350	filename=${filename}.$cyclestring
	1351	fi
[2380]	1352	else
[2610]	1353	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1354	then
	1355	filename=${filename}.${extin[$nr_of_input_files]}
	1356	fi
[2380]	1357	fi
[2610]	1358
	1359	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1360	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1361	absnamein[$nr_of_input_files]=$filename
	1362	if (( maxcycle > 0 ))
[2380]	1363	then
[2610]	1364	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1365	then
	1366	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1367	else
[3236]	1368	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1369	fi
[2380]	1370	else
[2610]	1371	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1372	then
	1373	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1374	else
[3236]	1375	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1376	fi
[2380]	1377	fi
	1378
[2610]	1379	done
	1380
[2380]	1381	fi
[2610]	1382
[2380]	1383	done
	1384
[2610]	1385
[2380]	1386	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1387	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1388	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1389	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1390	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1391	# REMOTE HOST)
	1392	(( i = 0 ))
	1393	while (( i < iout ))
	1394	do
	1395	(( i = i + 1 ))
[2610]	1396	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1397	then
[2610]	1398	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1399	then
[2610]	1400	actionout_pre[$i]=""
	1401	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1402	then
[2610]	1403	actionout_pre[$i]=pe
	1404	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1405	then
[2610]	1406	actionout_pre[$i]=a
[2380]	1407	fi
	1408	(( maxcycle = 0 ))
[3236]	1409	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1410	eval catalogname=${pathout_pre[$i]}
[2380]	1411	if ! ls $filename* 1>/dev/null 2>&1
	1412	then
	1413
	1414	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1415	if cat /dev/null > $filename
	1416	then
	1417	rm $filename
	1418	else
	1419
	1420	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1421	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1422	if [[ ! -d $catalogname ]]
	1423	then
	1424	if mkdir -p $catalogname
	1425	then
	1426	printf "\n\n *** directory:"
	1427	printf "\n $catalogname"
	1428	printf "\n was created\n"
	1429	else
	1430	printf "\n\n +++ OUTPUT-file:"
	1431	printf "\n $filename"
	1432	printf "\n cannot be created, because directory does not exist"
	1433	printf "\n and cannot be created either"
	1434	printf "\n"
	1435	locat=output ; exit
	1436	fi 2>/dev/null
	1437	else
	1438	printf "\n\n +++ OUTPUT-file:"
	1439	printf "\n $filename"
	1440	printf "\n cannot be created, although directory exists"
	1441	printf "\n"
	1442	locat=output ; exit
	1443	fi
	1444	fi 2>/dev/null
	1445
	1446	fi
	1447
	1448	fi
	1449	done
	1450
	1451
	1452	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1453	if [[ $running_in_batch_mode = false ]]
	1454	then
[3236]	1455	run_id_number=$RANDOM
	1456	run_id=${run_identifier}.$run_id_number
[2380]	1457
[3236]	1458	tempdir=$fast_io_catalog/$run_id
[3346]	1459
	1460	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1461	export job_id=$run_id
	1462
[2380]	1463	fi
	1464
	1465
	1466	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1467	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1468	then
	1469
	1470	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1471	if [[ $ibd = 0 ]]
	1472	then
	1473	printf "\n"
	1474	printf "\n +++ no batch directives found in configuration file"
	1475	locat=config_file_batch_directives; (( iec = 0 )); exit
	1476	fi
	1477
	1478	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1479	done=false
[2384]	1480	cputime=$cpumax
[2380]	1481	while [[ $done = false ]]
	1482	do
[2384]	1483	if (( cputime == 0 ))
[2380]	1484	then
	1485	printf "\n +++ cpu-time is undefined"
	1486	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1487	printf "\n >>> "
[2384]	1488	read cputime 1>/dev/null 2>&1
[2380]	1489	else
	1490	done=true
	1491	fi
	1492	done
[2420]	1493	cpumax=$cputime
[2380]	1494
	1495	# CHECK THE MEMORY DEMAND
	1496	done=false
	1497	while [[ $done = false ]]
	1498	do
	1499	if (( memory == 0 ))
	1500	then
	1501	printf "\n +++ memory demand is undefined"
	1502	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1503	printf "\n >>> "
	1504	read memory 1>/dev/null 2>&1
	1505	else
	1506	done=true
	1507	fi
	1508	done
	1509
	1510	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1511	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1512	then
	1513	while [[ -z $remote_username ]]
	1514	do
[2420]	1515	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1516	printf "\n >>> Please type username:"
	1517	printf "\n >>> "
	1518	read remote_username
	1519	done
	1520	fi
	1521
	1522	else
	1523
[2420]	1524	if [[ $running_in_batch_mode = false ]]
	1525	then
	1526	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1527	cpumax=$cputime
	1528	else
	1529	cputime=$cpumax
	1530	fi
[2380]	1531
	1532	fi
	1533
	1534
	1535	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1536	(( cpu_hours = cputime / 3600 ))
	1537	(( resttime = cputime - cpu_hours * 3600 ))
	1538	(( cpu_minutes = resttime / 60 ))
	1539	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1540	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1541
	1542
	1543	# OUTPUT OF THE PALMRUN-HEADER
	1544	calltime=$(date)
	1545	printf "\n"
	1546	printf "#------------------------------------------------------------------------# \n"
	1547	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1548	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1549	printf "\| \| \n"
	1550	column1="called on:"; column2=$(hostname)
	1551	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1552	if [[ $create_remote_batch_job = true ]]
	1553	then
[3236]	1554	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1555	else
	1556	if [[ $running_on_remote = true ]]
	1557	then
[3236]	1558	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1559	else
[3236]	1560	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1561	fi
	1562	fi
	1563	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1564
	1565	column1="running in:"
	1566	if [[ $running_in_batch_mode = true ]]
	1567	then
	1568	column2="batch job mode"
	1569	else
	1570	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1571	then
	1572	column2="job creation mode"
	1573	else
	1574	column2="interactive run mode"
	1575	fi
	1576	fi
	1577	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1578
[2479]	1579	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1580	then
[2480]	1581	if [[ "$project_account" != "" ]]
[2479]	1582	then
	1583	column1="project account number:"
	1584	column2="$project_account"
	1585	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1586	fi
	1587	fi
	1588
[2380]	1589	if [[ -n $cores ]]
	1590	then
	1591	if [[ $run_coupled_model = false ]]
	1592	then
	1593	column1="number of cores:"; column2=$cores
	1594	else
	1595	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1596	fi
	1597	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1598	fi
	1599	if [[ -n $tasks_per_node ]]
	1600	then
	1601	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1603	if (( remaining_cores > 0 ))
	1604	then
	1605	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1606	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1607	fi
	1608	fi
	1609	if [[ $maximum_parallel_io_streams != $cores ]]
	1610	then
	1611	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1612	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1613	fi
	1614	if [[ $use_openmp = true ]]
	1615	then
	1616	column1="threads per task:"; column2="$threads_per_task"
	1617	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1618	fi
[2384]	1619	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1620	then
[2506]	1621	column1="memory demand / PE":; column2="$memory MB"
	1622	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1623	column1="job cpu time (h:m:s):"; column2="$timestring"
	1624	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1625	fi
[2380]	1626	printf "\| \| \n"
	1627	if [[ "$source_list" != "" ]]
	1628	then
	1629	if [[ "$make_options" != "" ]]
	1630	then
	1631	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1632	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1633	line=$(echo "$make_options" \| cut -c46-)
	1634	while [[ "$line" != "" ]]
	1635	do
	1636	column1=""
	1637	column2=$(echo "$line" \| cut -c-45)
	1638	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1639	line=$(echo "$line" \| cut -c46-)
	1640	done
	1641	fi
	1642	fi
	1643
	1644	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1645	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1646	line=$(echo "$cpp_options" \| cut -c46-)
	1647	while [[ "$line" != "" ]]
	1648	do
	1649	column1=""
	1650	column2=$(echo "$line" \| cut -c-45)
	1651	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1652	line=$(echo "$line" \| cut -c46-)
	1653	done
	1654
	1655	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1656	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1657	line=$(echo "$compiler_options" \| cut -c46-)
	1658	while [[ "$line" != "" ]]
	1659	do
	1660	column1=""
	1661	column2=$(echo "$line" \| cut -c-45)
	1662	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1663	line=$(echo "$line" \| cut -c46-)
	1664	done
	1665
[2388]	1666	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1667	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1668	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1669	while [[ "$line" != "" ]]
	1670	do
	1671	column1=""
	1672	column2=$(echo "$line" \| cut -c-45)
	1673	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1674	line=$(echo "$line" \| cut -c46-)
	1675	done
	1676
	1677	if [[ "$login_init_cmd" != "" ]]
	1678	then
	1679	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1680	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1681	line=$(echo "$login_init_cmd" \| cut -c46-)
	1682	while [[ "$line" != "" ]]
	1683	do
	1684	column1=""
	1685	column2=$(echo "$line" \| cut -c-45)
	1686	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1687	line=$(echo "$line" \| cut -c46-)
	1688	done
	1689	fi
	1690
	1691	if [[ "$module_commands" != "" ]]
	1692	then
	1693	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1694	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1695	line=$(echo "$module_commands" \| cut -c46-)
	1696	while [[ "$line" != "" ]]
	1697	do
	1698	column1=""
	1699	column2=$(echo "$line" \| cut -c-45)
	1700	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1701	line=$(echo "$line" \| cut -c46-)
	1702	done
	1703	fi
	1704	printf "\| \| \n"
[3236]	1705	column1="run identifier:"; column2=$run_identifier
[2380]	1706	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1707	column1="activation string list:"; column2=$(echo $activation_string_list)
	1708	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1709
	1710	if [[ "$ocean_file_appendix" = true ]]
	1711	then
	1712	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1713	fi
	1714
	1715	if [[ "$source_list" != "" ]]
	1716	then
	1717	printf "\| \| \n"
	1718	printf "\| Files to be compiled: \| \n"
	1719	line=$source_list
	1720	while [[ "$line" != "" ]]
	1721	do
	1722	linestart=$(echo $line \| cut -c-70)
	1723	printf "\| %-70s \| \n" "$linestart"
	1724	line=$(echo "$line" \| cut -c71-)
	1725	done
	1726	fi
	1727	printf "#------------------------------------------------------------------------#"
	1728
	1729
	1730
	1731	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1732	if [[ $do_trace = true ]]
	1733	then
	1734	(( i = 0 ))
[2610]	1735	while (( i < nr_of_input_files ))
[2380]	1736	do
	1737	(( i = i + 1 ))
	1738	if (( i == 1 ))
	1739	then
	1740	printf "\n\n >>> INPUT-file assignments:\n"
	1741	fi
	1742	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1743	done
	1744	(( i = 0 ))
	1745	while (( i < iout ))
	1746	do
	1747	(( i = i + 1 ))
	1748	if (( i == 1 ))
	1749	then
	1750	printf "\n\n >>> OUTPUT-file assignments:\n"
	1751	fi
	1752	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1753	done
	1754	(( i = 0 ))
	1755	while (( i < iic ))
	1756	do
	1757	(( i = i + 1 ))
	1758	if (( i == 1 ))
	1759	then
	1760	printf "\n\n >>> INPUT-commands:\n"
	1761	fi
	1762	printf "\n ${in_command[$i]}"
	1763	done
	1764	(( i = 0 ))
	1765	while (( i < ioc ))
	1766	do
	1767	(( i = i + 1 ))
	1768	if (( i == 1 ))
	1769	then
	1770	printf "\n\n >>> OUTPUT-commands:\n"
	1771	fi
	1772	printf "\n ${out_command[$i]}"
	1773	done
	1774	fi
	1775
	1776	# QUERY FOR CONTINUE
	1777	if [[ $silent = false && $running_in_batch_mode = false ]]
	1778	then
	1779	antwort=dummy
	1780	printf "\n\n"
	1781	printf " >>> everything o.k. (y/n) ? "
	1782	while read antwort
	1783	do
	1784	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1785	then
	1786	printf " >>> everything o.k. (y/n) ? "
	1787	else
	1788	break
	1789	fi
	1790	done
	1791	if [[ $antwort = n \|\| $antwort = N ]]
	1792	then
	1793	locat=user_abort; (( iec = 0 )); exit
	1794	fi
	1795	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1796	then
[2566]	1797	printf "\n *** batch-job will be created and submitted"
[2380]	1798	else
[2566]	1799	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1800	fi
	1801	fi
	1802
	1803
	1804
	1805	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1806	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1807	then
	1808
	1809	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1810	then
[2566]	1811	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1812	else
[2566]	1813	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1814	fi
	1815
[2422]	1816	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1817	# IT SHALL BE CREATED
	1818	ask_for_make_depository=false
	1819	if [[ $create_remote_batch_job = true ]]
	1820	then
	1821
	1822	line=`grep %base_directory $config_file`
[3236]	1823	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
	1824	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1825
[3236]	1826	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1827	then
	1828	printf "\n\n +++ make depository \"${make_depository}\""
	1829	printf "\n on remote host not found!"
	1830	ask_for_make_depository=true
	1831	fi
[3236]	1832	rm ${configuration_identifier}_last_make_protokoll
[2422]	1833
	1834	else
	1835
	1836	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1837	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1838	if [[ ! -d ${make_depository} ]]
	1839	then
	1840	printf "\n\n +++ make depository \"${make_depository}\""
	1841	printf "\n on local host not found!"
	1842	ask_for_make_depository=true
	1843	fi
	1844
	1845	fi
	1846
	1847	if [[ $ask_for_make_depository = true ]]
	1848	then
	1849
	1850	antwort=dummy
	1851	printf "\n\n"
	1852	printf " >>> Create a new one (y/n) ? "
	1853	while read antwort
	1854	do
	1855	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1856	then
	1857	printf " >>> Create a new one (y/n) ? "
	1858	else
	1859	break
	1860	fi
	1861	done
	1862	if [[ $antwort = n \|\| $antwort = N ]]
	1863	then
	1864	locat=user_abort; (( iec = 0 )); exit
	1865	fi
	1866
[2566]	1867	if [[ $do_trace = true ]]
	1868	then
[3455]	1869	palmbuild -c $configuration_identifier
[2566]	1870	else
[3455]	1871	palmbuild -v -c $configuration_identifier
[2566]	1872	fi
[2422]	1873
[3312]	1874	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1875	then
	1876
	1877	# ABORT IN CASE OF COMPILATION PROBLEMS
	1878	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1879	locat=make_depository
	1880	exit
	1881	else
	1882	echo " *** now continue with creating executable and other sources"
	1883	fi
	1884
	1885	fi
	1886
[2566]	1887	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1888	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1889
[3312]	1890	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1891	then
	1892
	1893	# ABORT IN CASE OF COMPILATION PROBLEMS
	1894	printf "\n +++ error while creating executable and/or other sources"
	1895	locat=execution
[2990]	1896	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1897	exit
	1898
	1899	else
	1900
[2566]	1901	printf " *** executable and other sources created\n"
[2990]	1902	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1903
	1904	fi
	1905
	1906	fi
	1907
	1908
[2669]	1909	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1910	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1911	if [[ $create_remote_batch_job = true ]]
	1912	then
	1913	(( i = 0 ))
[2610]	1914	while (( i < nr_of_input_files ))
[2605]	1915	do
	1916	(( i = i + 1 ))
[2669]	1917	if [[ "${actionin[$i]}" = tr ]]
[2605]	1918	then
	1919	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1920	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1921	fi
	1922	done
	1923	if (( i > 0 ))
	1924	then
[3025]	1925	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1926	fi
	1927	fi
	1928
	1929
[2380]	1930	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1931	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1932	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1933	then
	1934
	1935	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1936	if [[ $running_in_batch_mode = false ]]
	1937	then
	1938	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1939	# FOLDER
[2566]	1940	mkdir -p $tempdir
	1941	chmod go+rx $tempdir
	1942	cd $tempdir
	1943	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1944	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1945
	1946	else
	1947
	1948	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1949	printf "\n *** running in temporary directory: $tempdir"
[2380]	1950
	1951	fi
	1952
	1953
	1954	# PROVIDE THE INPUT FILES
	1955	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1956	optional_files_missing=false
[2380]	1957	(( i = 0 ))
[2610]	1958	while (( i < nr_of_input_files ))
[2380]	1959	do
	1960	(( i = i + 1 ))
	1961	if (( i == 1 ))
	1962	then
	1963	printf "\n\n *** providing INPUT-files:\n$dashes"
	1964	fi
	1965
	1966
	1967	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1968	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1969	then
[2669]	1970	optional_files_missing=true
[2380]	1971	continue
	1972	fi
	1973
	1974	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1975	files_for_cores=false; filetype=file
	1976	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1977	then
	1978	files_for_cores=true; filetype=files
	1979	actionin[$i]=""
	1980	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1981	then
	1982	actionin[$i]=""
	1983	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1984	then
	1985	files_for_cores=true; filetype=files
	1986	actionin[$i]="ln"
	1987	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1988	then
	1989	actionin[$i]="ln"
	1990	fi
	1991
	1992	if [[ $files_for_cores = true ]]
	1993	then
	1994	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1995	else
	1996	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1997	fi
	1998
	1999	# INPUT-FILES TO BE LINKED
	2000	if [[ "${actionin[$i]}" = ln ]]
	2001	then
	2002
	2003	printf "\n $filetype will be linked"
	2004	if [[ $files_for_cores = false ]]
	2005	then
	2006	if [[ -f "${absnamein[$i]}" ]]
	2007	then
	2008	ln ${absnamein[$i]} ${localin[$i]}
	2009	got_tmp[$i]=true
	2010	fi
	2011	else
	2012	if [[ -d "${absnamein[$i]}" ]]
	2013	then
[2396]	2014	mkdir -p ${localin[$i]}
[2380]	2015	cd ${absnamein[$i]}
	2016	for file in $(ls *)
	2017	do
[2566]	2018	ln $file $tempdir/${localin[$i]}
[2380]	2019	done >\|/dev/null 2>&1
[2566]	2020	cd $tempdir
[2380]	2021	fi
	2022
	2023	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2024	if [[ ! -f "${localin[$i]}/_000000" ]]
	2025	then
	2026	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2027	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2028	fi
	2029
	2030	got_tmp[$i]=true
	2031	fi
	2032	fi
	2033
	2034	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2035	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2036	then
	2037
	2038	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2039	then
	2040
	2041	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2042	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2043	printf "\n file will be provided for $cores processors"
[2396]	2044	mkdir -p ${localin[$i]}
[2380]	2045	ival=$cores
	2046	(( ii = 0 ))
	2047	while (( ii <= ival-1 ))
	2048	do
	2049	if (( ii < 10 ))
	2050	then
	2051	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2052	elif (( ii < 100 ))
	2053	then
	2054	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2055	elif (( ii < 1000 ))
	2056	then
	2057	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2058	else
	2059	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2060	fi
	2061	(( ii = ii + 1 ))
	2062	done
	2063
	2064	else
	2065
	2066	if [[ $files_for_cores = true ]]
	2067	then
	2068
	2069	# PROVIDE FILES FOR EACH CORE
	2070	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2071	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2072	printf "\n providing $cores files for the respective cores"
[2396]	2073	mkdir -p ${localin[$i]}
[2380]	2074	if [[ $link_local_input = true ]]
	2075	then
	2076	printf " files will be linked\n"
	2077	cd ${absnamein[$i]}
	2078	for file in $(ls *)
	2079	do
	2080	ln -f $file ${localin[$i]}
	2081	done
[2566]	2082	cd $tempdir
[2380]	2083	fi
	2084
	2085	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2086	if [[ ! -f "${localin[$i]}/_000000" ]]
	2087	then
	2088	if [[ $link_local_input = true ]]
	2089	then
	2090	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2091	fi
	2092	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2093	fi
	2094
	2095	else
	2096
	2097	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2098	if [[ $link_local_input = true ]]
	2099	then
	2100	printf " file will be linked\n"
	2101	ln -f ${absnamein[$i]} ${localin[$i]}
	2102	fi
[2605]	2103	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2104	if [[ ! -f "${localin[$i]}" ]]
	2105	then
	2106	if [[ $link_local_input = true ]]
	2107	then
	2108	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2109	fi
[2669]	2110	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2111	then
	2112	mv ${absnamein[$i]} ${localin[$i]}
	2113	else
	2114	cp ${absnamein[$i]} ${localin[$i]}
	2115	fi
[2380]	2116	fi
	2117	fi
	2118	fi
	2119	fi
	2120
	2121	done
	2122	if (( i != 0 ))
	2123	then
[2669]	2124	if [[ $optional_files_missing = true ]]
	2125	then
	2126	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2127	fi
[2380]	2128	printf "\n$dashes\n *** all INPUT-files provided \n"
	2129	fi
	2130
	2131
	2132	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2133	(( i = 0 ))
	2134	while (( i < iic ))
	2135	do
	2136	(( i = i + 1 ))
	2137	if (( i == 1 ))
	2138	then
	2139	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2140	fi
	2141	printf "\n >>> ${in_command[$i]}"
	2142	eval ${in_command[$i]}
	2143	if (( i == iic ))
	2144	then
	2145	printf "\n$dashes\n"
	2146	fi
	2147	done
	2148
	2149
[3313]	2150	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2151	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2152	then
	2153	progress_bar_disabled=true
	2154	else
	2155	progress_bar_disabled=false
	2156	fi
	2157
	2158
[2380]	2159	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2160	# (FILE ENVPAR WILL BE READ BY PALM)
	2161	cat > ENVPAR << EOF
[3236]	2162	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2163	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2164	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2165	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2166	maximum_cpu_time_allowed = ${cpumax}.,
	2167	revision = '$global_revision',
[3313]	2168	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2169
	2170	EOF
	2171
	2172
	2173	# STARTING THE EXECUTABLE
	2174	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2175	PATH=$PATH:$tempdir
[2380]	2176
	2177
	2178	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2179	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2180	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2181	eval line=\"$line\"
	2182	execute_command="$line"
	2183
	2184
	2185	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2186	if [[ "$execute_command_for_combine" = "" ]]
	2187	then
	2188	eval line2=\"$line2\"
	2189	execute_command_for_combine="$line2"
	2190	fi
	2191
[2380]	2192
	2193
	2194	# PROVIDE A HOSTFILE, IF REQUIRED
	2195	if [[ "$hostfile" != "" ]]
	2196	then
	2197
	2198	if [[ $hostfile = auto ]]
	2199	then
	2200	# CREATE A NEW HOSTFILE
	2201	(( ii = 1 ))
	2202	while (( ii <= cores / threads_per_task ))
	2203	do
	2204	echo $(hostname) >> hostfile
	2205	(( ii = ii + 1 ))
	2206	done
	2207	if (( cores / threads_per_task == 0 ))
	2208	then
	2209	echo $(hostname) >> hostfile
	2210	fi
	2211
	2212	else
	2213	cp $hostfile hostfile
	2214	fi
	2215	eval line=\"`head -n $ii hostfile`\"
	2216	printf "\n *** running on: $line"
	2217	fi
	2218
	2219
	2220
	2221	# SET THE NUMBER OF OPENMP-THREADS
	2222	if [[ $use_openmp = true ]]
	2223	then
	2224	export OMP_NUM_THREADS=$threads_per_task
	2225	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2226	else
	2227	export OMP_NUM_THREADS=1
	2228	fi
	2229
	2230
[2610]	2231	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2232	if [[ $run_coupled_model = false ]]
	2233	then
	2234	if [[ "$ocean_file_appendix" = true ]]
	2235	then
	2236	echo "precursor_ocean" > coupling_steering
	2237	else
	2238	echo "precursor_atmos" > coupling_steering
	2239	fi
	2240	else
	2241	(( iia = $cores_atmos / $threads_per_task ))
	2242	(( iio = $cores_ocean / $threads_per_task ))
	2243	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2244	printf "\n\n"
	2245	echo "coupled_run $iia $iio" > coupling_steering
	2246	fi
	2247
	2248	printf "\n *** execute command:"
	2249	printf "\n \"$execute_command\" \n\n"
	2250
	2251
[3393]	2252	if [[ $progress_bar_disabled = true ]]
[2380]	2253	then
[3402]	2254	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2255	exit_code=${PIPESTATUS[0]}
	2256	else
	2257	$execute_command < coupling_steering &> >(tee STDOUT)
	2258	exit_code=${PIPESTATUS[0]}
	2259	fi
[2380]	2260
[3393]	2261	if [[ ${exit_code} != 0 ]]
	2262	then
	2263
[2380]	2264	# ABORT IN CASE OF RUNTIME ERRORS
	2265	printf "\n +++ runtime error occured"
	2266	locat=execution
	2267	exit
	2268
	2269	else
	2270
	2271	printf "\n$dashes\n *** execution finished \n"
	2272
	2273	fi
	2274
	2275
	2276	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2277	# BY EACH CORE INTO ONE FILE
	2278	if [[ ! -f combine_plot_fields.x ]]
	2279	then
	2280
	2281	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2282	printf "\n 2d- and/or 3d-data may be incomplete!"
	2283	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2284
	2285	elif [[ "$combine_plot_fields" == true ]]
	2286	then
	2287
	2288	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2289	$execute_command_for_combine
	2290
	2291	else
	2292
	2293	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2294	# DATA OUTPUT
[2380]	2295	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2296	fi
	2297
	2298
	2299
	2300	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2301	(( i = 0 ))
	2302	while (( i < ioc ))
	2303	do
	2304	(( i = i + 1 ))
	2305	if (( i == 1 ))
	2306	then
	2307	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2308	fi
[2799]	2309
	2310	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2311	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2312
[2380]	2313	printf "\n >>> ${out_command[$i]}"
	2314	eval ${out_command[$i]}
	2315	if (( i == ioc ))
	2316	then
	2317	printf "\n$dashes\n"
	2318	fi
	2319	done
	2320
	2321
[2610]	2322	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2323	# WILDCARDS
[2380]	2324	(( i = 0 ))
[2610]	2325	(( nr_of_output_files = 0 ))
	2326
[2380]	2327	while (( i < iout ))
	2328	do
[2610]	2329
[2380]	2330	(( i = i + 1 ))
[2610]	2331
	2332	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2333	# CREATE A LIST FOR THE DETECTED ENDINGS
	2334	if [[ "${multout[$i]}" = true ]]
	2335	then
	2336	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2337	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2338	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2339
	2340	endings="DEFAULT"
	2341	while read line
	2342	do
	2343	# remove the local name from the beginning
	2344	localnamestring="${localout_pre[$i]}"
	2345	length_localname=${#localnamestring}
	2346	ending=${line:${length_localname}}
	2347
	2348	if [[ "$ending" != "" ]]
	2349	then
	2350	endings="$endings $ending"
	2351	fi
	2352
	2353	done <filelist
	2354
	2355	rm filelist
	2356
	2357	else
	2358
	2359	# SINGLE NAME
	2360	endings=DEFAULT
	2361
	2362	fi
	2363
	2364	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2365	for ending in $endings
	2366	do
	2367
	2368	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2369	if [[ $ending = DEFAULT ]]
	2370	then
	2371	ending=""
	2372	fi
	2373
	2374	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2375	(( nr_of_output_files = nr_of_output_files + 1 ))
	2376	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2377	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2378	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2379	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2380	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2381	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2382	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2383
	2384	done
	2385
	2386	done
	2387
	2388
	2389
	2390
	2391	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2392	(( i = 0 ))
	2393	while (( i < nr_of_output_files ))
	2394	do
	2395	(( i = i + 1 ))
[2380]	2396	if (( i == 1 ))
	2397	then
	2398	printf "\n\n *** saving OUTPUT-files:"
	2399
	2400	# GET RUN NUMBER ASSIGNED BY PALM
	2401	if [[ -f RUN_NUMBER ]]
	2402	then
	2403	read run_number < RUN_NUMBER
	2404	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2405	usecycle_option="-U $run_number"
	2406	else
	2407	run_number=0
	2408	usecycle_option=""
	2409	fi
	2410	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2411	then
[2404]	2412	printf "\n *** in case of SCP transfers to local host"
	2413	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2414	fi
	2415	printf "\n$dashes"
	2416	fi
	2417
	2418	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2419	then
	2420
[3236]	2421	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2422
	2423	# DETERMINE THE CYCLE NUMBER
	2424	ls -1 -d $filename > filelist 2>/dev/null
	2425	ls -1 -d $filename.* >> filelist 2>/dev/null
	2426	while read line
	2427	do
	2428
	2429	# filename without path (i.e. after the last "/")
	2430	basefilename=$(basename ${line})
	2431
	2432	# check if there is an extension
	2433	extension=${basefilename##*.}
	2434	if [[ "$extension" = "${extout[$i]}" ]]
	2435	then
	2436	basefilename=${basefilename%.*}
	2437	fi
	2438
	2439	# check for an existing cycle number
	2440	cycle=${basefilename##*.}
	2441	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2442	then
[2669]	2443	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2444	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2445	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2446	else
	2447	(( icycle = 1 ))
	2448	fi
	2449
	2450	if (( icycle > maxcycle ))
	2451	then
	2452	(( maxcycle = icycle ))
	2453	fi
	2454
	2455	done <filelist
	2456	rm filelist
	2457
	2458
	2459	# SET THE CYCLE NUMBER
	2460	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2461	if [[ "${actionout[$i]}" = a ]]
	2462	then
	2463	(( maxcycle = maxcycle - 1 ))
	2464	fi
	2465
	2466	(( cycnum[$i] = maxcycle ))
	2467	pathout[$i]=$filename
	2468
	2469
	2470	# ADD CYCLE NUMBER TO FILENAME
	2471	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2472	if [[ "${actionout[$i]}" != "a" ]]
	2473	then
	2474	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2475	# WITH AN EXISTING CYCLE NUMBER
	2476	if (( run_number >= cycnum[$i] ))
	2477	then
	2478	(( cycnum[$i] = run_number ))
	2479	else
	2480	if (( run_number > 0 ))
	2481	then
	2482	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2483	fi
	2484	fi
	2485	fi
	2486	if (( cycnum[$i] > 0 ))
	2487	then
[2600]	2488	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2489	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2490	fi
	2491	fi
	2492
	2493	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2494	files_for_cores=false; filetype=file
	2495	link_local_output=false
	2496	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2497	then
	2498	files_for_cores=true; filetype=directory
	2499	actionout[$i]=""
	2500	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2501	then
	2502	actionout[$i]=""
	2503	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2504	then
	2505	files_for_cores=true; filetype=directory
	2506	link_local_output=true
	2507	actionout[$i]=""
	2508	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2509	then
	2510	link_local_output
	2511	actionout[$i]=""
	2512	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2513	then
	2514	files_for_cores=true; filetype=directory
	2515	actionout[$i]="tr"
	2516	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2517	then
	2518	actionout[$i]="tr"
	2519	fi
	2520
	2521	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2522	then
[2669]	2523	if [[ ${warnout[$i]} = true ]]
	2524	then
	2525	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2526	fi
[2380]	2527	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2528	then
[2669]	2529	if [[ ${warnout[$i]} = true ]]
	2530	then
	2531	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2532	fi
[2380]	2533	else
	2534
	2535
	2536	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2537	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2538	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2539	then
	2540	if [[ $running_on_remote = true ]]
	2541	then
	2542
	2543	# SET OPTIONS FOR TRANSFER
	2544	if [[ "${actionout[$i]}" = tr ]]
	2545	then
	2546	if [[ $files_for_cores = false ]]
	2547	then
	2548	catalog_option=""
	2549	catalog_string=""
	2550	else
	2551	catalog_option="-c"
	2552	catalog_string="/"
	2553	fi
	2554	append_option=""
	2555	append_string=""
	2556	else
	2557	append_option="-A"
	2558	append_string="append"
	2559	fi
	2560
	2561	transfer_failed=false
	2562	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2563	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2564
	2565	# TRANSFER VIA SCP
	2566	if [[ "$remote_loginnode" != "" ]]
	2567	then
[3236]	2568	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]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
[2380]	2569	else
[3236]	2570	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}
[2380]	2571	fi
[3312]	2572	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2573
	2574
	2575	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2576	if [[ $transfer_failed = true ]]
	2577	then
	2578	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2579	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2580
	2581	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2582	eval local_catalog=${pathout[$i]}
	2583	if [[ ! -d $local_catalog ]]
	2584	then
	2585	printf " *** local directory does not exist. Trying to create:\n"
	2586	printf " $local_catalog \n"
	2587	mkdir -p $local_catalog
	2588	fi
[3236]	2589	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2590	transfer_problems=true
	2591	fi
	2592
	2593	else
	2594
	2595	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2596	# BE COPIED OR APPENDED ON THIS MACHINE
	2597	if [[ "${actionout[$i]}" = tr ]]
	2598	then
	2599	actionout[$i]=""
	2600	else
	2601	actionout[$i]="a"
	2602	fi
	2603	fi
	2604	fi
	2605
	2606
	2607	# APPEND ON THIS MACHINE
	2608	if [[ "${actionout[$i]}" = "a" ]]
	2609	then
	2610	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2611	then
	2612	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2613	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2614	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2615	else
	2616	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2617	printf "\n ${pathout[$i]}\n"
	2618	cat ${localout[$i]} >> ${pathout[$i]}
	2619	fi
	2620	fi
	2621
	2622	# COPY ON THIS MACHINE
	2623	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2624	# ON DIFFERENT FILE-SYSTEMS
	2625	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2626	then
	2627
	2628	# COPY IN CASE OF RUNS ON SINGLE CORES
	2629	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2630	then
	2631	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2632	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2633	if [[ $link_local_output = true ]]
	2634	then
	2635	printf " file will be linked\n"
	2636	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2637	fi
	2638	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2639	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2640	then
	2641	if [[ $link_local_output = true ]]
	2642	then
	2643	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2644	fi
	2645	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2646	else
	2647	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2648	fi
	2649	else
	2650	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2651	printf "\n ${pathout[$i]}\n"
	2652	if [[ $link_local_output = true ]]
	2653	then
	2654	printf " file will be linked\n"
	2655	ln -f ${localout[$i]} ${pathout[$i]}
	2656	fi
	2657	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2658	if [[ ! -f "${pathout[$i]}" ]]
	2659	then
	2660	if [[ $link_local_output = true ]]
	2661	then
	2662	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2663	fi
	2664	cp ${localout[$i]} ${pathout[$i]}
	2665	else
	2666	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2667	fi
	2668	fi
	2669
	2670	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2671	then
	2672
	2673	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2674	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2675	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2676	printf "\n ${pathout[$i]}\n"
	2677	if [[ $link_local_output = true ]]
	2678	then
	2679	printf " files will be linked\n"
[2396]	2680	mkdir -p ${pathout[$i]}
[2380]	2681	cd ${localout[$i]}
	2682	for file in $(ls *)
	2683	do
	2684	ln -f $file ${pathout[$i]}
	2685	done >\|/dev/null 2>&1
[2566]	2686	cd $tempdir
[2380]	2687	fi
	2688
	2689	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2690	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2691	then
	2692	if [[ $link_local_output = true ]]
	2693	then
	2694	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2695	fi
[3025]	2696	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2697	cp -r ${localout[$i]}/* ${pathout[$i]}
	2698	fi
	2699
	2700	fi
	2701	fi
	2702	done
	2703
	2704	if (( i != 0 ))
	2705	then
	2706	if [[ $transfer_problems = true ]]
	2707	then
	2708	printf "\n$dashes\n *** OUTPUT-files saved"
	2709	printf "\n +++ WARNING: some data transfers failed! \n"
	2710	else
	2711	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2712	fi
	2713	fi
	2714
	2715
	2716	# IF REQUIRED, START A RESTART-JOB
	2717	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2718	if [[ -f CONTINUE_RUN ]]
	2719	then
	2720
	2721	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2722	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2723	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2724	# -b START A BATCH JOB
	2725	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2726	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2727	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2728
[2957]	2729	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2730	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2731	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2732	then
	2733	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2734	fi
[2380]	2735
	2736	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2737	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2738	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2739	then
[2381]	2740	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2741	fi
	2742
	2743
	2744	# START THE RESTART-JOB
	2745	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2746	echo " $prc"
	2747	printf "\n$dashes\n"
	2748	if [[ $running_on_remote = true ]]
	2749	then
	2750
	2751	echo "*** ssh will be used to initiate restart-runs!"
	2752	echo " return_address=\"$return_address\" "
	2753	echo " return_username=\"$local_username\" "
	2754
	2755	if [[ "$remote_loginnode" != "" ]]
	2756	then
[3132]	2757	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 \| tee palmrun_restart.log
[2380]	2758	else
[3132]	2759	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
[2380]	2760	fi
	2761
	2762	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2763	sleep 30
	2764
	2765	else
	2766
	2767	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2768	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2769	cd - > /dev/null
	2770
	2771	fi
	2772
[3132]	2773	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2774	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2775	then
	2776	printf "\n$dashes\n +++ creating restart run failed \n"
	2777	locat=create_restart
[3455]	2778	rm palmrun_restart.log
[3132]	2779	exit
	2780	else
	2781	printf "\n$dashes\n *** restart run initiated \n"
	2782	rm palmrun_restart.log
	2783	fi
[2380]	2784
[3132]	2785
[2380]	2786	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2787	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2788	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2789	# MAY BE VERY HUGE)
	2790	(( i = 0 ))
[2610]	2791	while (( i < nr_of_input_files ))
[2380]	2792	do
	2793	(( i = i + 1 ))
	2794	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2795	then
	2796	rm -r ${absnamein[$i]}
	2797	fi
	2798	done
	2799
	2800	fi
	2801
	2802
	2803	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2804	cd $HOME
[2566]	2805	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2806
	2807
	2808	else
	2809
	2810
	2811	# PREPARING ACTIONS,
	2812	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2813
	2814	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2815	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2816	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2817	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2818	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2819	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2820	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2821	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2822	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2823	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2824	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2825	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2826	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2827	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2828	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2829	if [[ $create_remote_batch_job = true ]]
	2830	then
	2831	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2832	if [[ $do_trace = true ]]
	2833	then
	2834	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2835	fi
[2380]	2836	elif [[ $create_batch_job = true ]]
	2837	then
	2838	palmrun_com=${palmrun_com}" -j"
[2420]	2839	if [[ $do_trace = true ]]
	2840	then
	2841	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2842	fi
[2380]	2843	fi
	2844
	2845
	2846	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2847	# REMOTE HOST
[3236]	2848	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2849	job_protocol_file=$job_protocol_file_local
	2850	if [[ $create_remote_batch_job = true ]]
	2851	then
[3236]	2852	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2853	job_protocol_file=$job_protocol_file_remote
	2854	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2855	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2856	fi
	2857
	2858
	2859	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2860	jobfile=jobfile.$run_id_number
[2380]	2861
	2862
	2863	# FIRST CREATE THE BATCH DIRECTIVES
	2864	(( i = 0 ))
	2865	while (( i < ibd ))
	2866	do
	2867	(( i = i + 1 ))
[2693]	2868	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2869	eval line=\"$line\"
	2870	echo "$line" >> $jobfile
	2871	done
	2872	echo " " >> $jobfile
	2873
	2874
	2875	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2876	# PROTOCOL
	2877	if [[ $create_remote_batch_job = true ]]
	2878	then
[3236]	2879	echo "set +vx" >> $jobfile
	2880	echo "trap '" >> $jobfile
	2881	echo "set +vx" >> $jobfile
	2882	echo "cd ${remote_jobcatalog}" >> $jobfile
	2883	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2884
	2885	# ADD THE BATCH DIRECTIVES
	2886	(( i = 0 ))
	2887	while (( i < ibdt ))
	2888	do
	2889	(( i = i + 1 ))
[2693]	2890	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2891	eval line=\"$line\"
	2892	echo "$line" >> $jobfile
	2893	done
	2894	echo " " >> $jobfile
	2895
	2896	echo "set -x" >> $jobfile
[3236]	2897	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${configuration_identifier}_${run_identifier}" >> $jobfile
[2380]	2898	echo "%%END%%" >> $jobfile
	2899	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2900	echo "$submit_command $scpjob_file" >> $jobfile
	2901	echo "rm $scpjob_file" >> $jobfile
[2404]	2902	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2903	echo "set -x" >> $jobfile
	2904	echo " ' exit" >> $jobfile
	2905	fi
	2906
	2907
	2908	# ACTIVATE ERROR-TRACEBACK
	2909	if [[ $do_trace = true ]]
	2910	then
	2911	echo "set -x" >> $jobfile
	2912	else
	2913	echo "set +vx" >> $jobfile
	2914	fi
	2915
	2916
	2917	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2918	if [[ "$login_init_cmd" != "" ]]
	2919	then
	2920	echo "$login_init_cmd" >> $jobfile
	2921	fi
	2922	if [[ "$module_commands" != "" ]]
	2923	then
	2924	echo "$module_commands" >> $jobfile
	2925	fi
	2926
	2927
	2928	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2929	if [[ $create_remote_batch_job = true ]]
	2930	then
	2931	echo "mkdir $tempdir" >> $jobfile
	2932	echo "chmod go+rx $tempdir" >> $jobfile
	2933	else
	2934	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2935	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2936	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2937	mkdir $tempdir
	2938	chmod go+rx $tempdir
	2939	fi
	2940	echo "cd $tempdir" >> $jobfile
	2941	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2942	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2943	echo "export PATH=.:\$PATH" >> $jobfile
	2944	echo "export execute_palmrun=true" >> $jobfile
	2945
	2946
	2947	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2948	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2949	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2950	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2951	echo "export LOCAL_PWD" >> $jobfile
	2952
	2953
	2954	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2955	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2956	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2957
	2958
	2959	# CALL PALMRUN WITHIN THE JOB
	2960	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2961	echo "set -x" >> $jobfile
	2962	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2963
	2964
	2965	# TRANSFER JOBFILE TO THE TARGET HOST
	2966	if [[ $create_jobfile_only = false ]]
	2967	then
	2968
	2969	if [[ $create_remote_batch_job = true ]]
	2970	then
	2971
[2420]	2972	echo " "
[2566]	2973	echo " *** transfer of job to remote host via scp"
[2420]	2974	if [[ $do_trace = true ]]
	2975	then
[3236]	2976	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	2977	fi
[3236]	2978	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	2979
[2566]	2980	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2981	if [[ $do_trace = true ]]
	2982	then
[3236]	2983	echo " cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
[2420]	2984	fi
[3236]	2985	echo "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
[2380]	2986
	2987	elif [[ $create_batch_job = true ]]
	2988	then
	2989
[2385]	2990	eval local_jobcatalog=$local_jobcatalog
[3236]	2991	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	2992	cd $local_jobcatalog
[2380]	2993	echo " "
[2420]	2994	echo " *** submit the job"
	2995	if [[ $do_trace = true ]]
	2996	then
[3236]	2997	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	2998	fi
[3236]	2999	$submit_command ${configuration_identifier}_${run_id}
	3000	rm ${configuration_identifier}_${run_id}
[2380]	3001	cd - > /dev/null
	3002
	3003	fi
	3004
	3005	rm -rf $jobfile
	3006
	3007	else
	3008
	3009	printf "\n *** jobfile created under name \"$jobfile\" "
	3010	printf "\n no batch-job has been sent!"
	3011
	3012	fi
	3013
	3014	fi # END OF REMOTE-PART

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