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source: palm/trunk/SCRIPTS/palmrun @ 3401

Last change on this file since 3401 was 3393, checked in by knoop, 6 years ago
palmrun: added _stdout monitoring file and output filter for "STOP 1" in batch mode
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 3393 2018-10-22 16:22:55Z eckhard $
[3346]	29	# job_id is set for compatibility reasons with older versions of config files
	30	#
	31	# 3313 2018-10-06 15:22:48Z knoop
[3294]	32	# more detailed error message for outdated fileconnection file
	33	#
	34	# 3236 2018-09-10 09:07:06Z raasch
[3236]	35	# warning issued in case of file connection file version mismatch,
	36	# host_configuration renamed configuration_identifier,
	37	# "host identifier" in header output renamed "config. identifier",
	38	# jobname renamed run_identifier,
	39	# run_id renamed run_id_number
	40	# job_id renamed run_id
	41	# option -r renamed -i
	42	#
	43	# 3151 2018-07-19 08:45:38Z raasch
[3151]	44	# removed additional listing of files to be compiled, print PALM code revision
	45	# in header
	46	#
	47	# 3132 2018-07-16 11:44:58Z raasch
[3132]	48	# create consistent error messages in case of failed restarts,
	49	# check existence of remote job catalog
	50	#
	51	# 3043 2018-05-25 10:47:54Z raasch
[3043]	52	# check for setting of fast_io_catalog
	53	#
	54	# 3033 2018-05-23 15:26:19Z raasch
[3025]	55	# -T option not required for interactive runs (tasks per node =
	56	# total number of cores is assumed as default, if option is not given),
	57	# reformatting of a few messages,
	58	# bugfix: destination output directory is created if attribute "pe" is set in
	59	# .palm.iofiles
	60	#
	61	# 2718 2018-01-02 08:49:38Z maronga
[2993]	62	# bugfix of r2990
	63	#
	64	# 2718 2018-01-02 08:49:38Z maronga
[2990]	65	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	66	# not in the working directory from where palmrun is called
	67	#
	68	# 2718 2018-01-02 08:49:38Z maronga
[2957]	69	# svfout in the activation string will be replaced now by svfin in case of
	70	# automatic restarts
	71	#
	72	# 2718 2018-01-02 08:49:38Z maronga
[2906]	73	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	74	# the possible output or input of sky view factors
	75	#
	76	# 2718 2018-01-02 08:49:38Z maronga
[2834]	77	# "fname" renamed to "jobname"
	78	#
	79	# 2718 2018-01-02 08:49:38Z maronga
[2799]	80	# parameters are allowed in output commands (OC:)
	81	#
	82	# 2718 2018-01-02 08:49:38Z maronga
[2789]	83	# bugfix: exit if no queue has been given neither with option -q nor in the
	84	# configuration file
	85	#
	86	# 2718 2018-01-02 08:49:38Z maronga
[2762]	87	# file connection file from trunk/SCRIPTS is taken by default
	88	#
	89	# 2718 2018-01-02 08:49:38Z maronga
[2716]	90	# Corrected "Former revisions" section
	91	#
	92	# 2696 2017-12-14 17:12:51Z kanani
	93	# Change in file header (GPL part)
	94	#
	95	# 2693 2017-12-13 12:33:49Z raasch
[2693]	96	# replacement of variables given by {{<variable>}} in configuration file is now
	97	# done in a more general way, variable names are written in small letters
	98	#
	99	# 2670 2017-12-06 16:32:19Z raasch
[2670]	100	# test printouts removed
	101	#
	102	# 2669 2017-12-06 16:03:27Z raasch
[2669]	103	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	104	# removed,
	105	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	106	# files,
	107	# informative messages in case of missing optional input files shortened
	108	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	109	#
	110	# 2638 2017-11-23 12:44:23Z raasch
[2610]	111	# use of wildcards in file connection statements enabled
	112	#
	113	# 2605 2017-11-09 15:31:46Z raasch
[2605]	114	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	115	# will not be sent with the job file any more, but copied into the
[2610]	116	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	117	#
	118	# 2600 2017-11-01 14:11:20Z raasch
[2600]	119	# cycle numbers are made three digits wide
	120	#
	121	# 2566 2017-10-20 08:50:47Z raasch
[2566]	122	# execute command for combine_plot_fields added
	123	# "TEMPDIR" renamed "tempdir"
	124	# temporary working directory for local batch jobs is created immediately within
	125	# the user's palmrun call, due to a requirement of the "grid engine" batch
	126	# system, where the working directory is given with batch directive -wd and must
	127	# already exist when the job is submitted,
	128	# informative messages in non-trace mode reduced and partly reformatted
	129	#
	130	# 2551 2017-10-18 07:25:11Z raasch
[2551]	131	# TEMPDIR added as replacement string to be used in batch directives
	132	#
	133	# 2512 2017-10-04 08:26:59Z raasch
[2507]	134	# bugfix for determining cycle numbers of NetCDF input files
	135	#
	136	# 2506 2017-09-29 08:30:37Z raasch
[2506]	137	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	138	# host configuration added to SOURCES_FOR_RUN_... folder name
	139	# host_identifier renamed host_configuration
	140	# option -W added to allow for job dependencies
	141	#
	142	# 2501 2017-09-26 11:41:55Z raasch
[2501]	143	# default value for number of cores (option -X) set to 1
	144	# bugfix for mechanism which overwrites configuration file settings with values
	145	# provided by palmrun options
	146	#
	147	# 2499 2017-09-22 16:47:58Z kanani
[2499]	148	# option -h named configuration identifier
	149	#
	150	# 2480 2017-09-19 06:24:14Z maronga
[2480]	151	# bugfix for last revision
	152	#
	153	# 2479 2017-09-19 06:12:16Z raasch
[2479]	154	# option -A (project account number) added
	155	#
	156	# 2422 2017-09-08 08:25:41Z raasch
[2410]	157	# initial revision
[2380]	158	#
	159	#--------------------------------------------------------------------------------#
	160	# palmrun - script for running PALM jobs on local and remote hosts
	161	#--------------------------------------------------------------------------------#
	162
	163
	164
	165	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	166
	167	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	168	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	169	# (TOO MANY ARGUMENTS - PROBLEM)
	170	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	171
[2610]	172	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	173	typeset -i nr_of_output_files=0
[2380]	174	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	175	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	176	# SCRIPT-OPTION ARGUMENTS
	177	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	178	typeset -i icycle inode ival maxcycle mpi_tasks
	179	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	180
	181	activation_string_list=""
	182	AddFilenames=""
	183	combine_plot_fields=true
	184	compiler_name=""
	185	compiler_name_ser=""
	186	compiler_options=""
[3236]	187	configuration_identifier="default"
[2501]	188	cores=1
[2380]	189	cores_atmos=0
	190	cores_ocean=0
	191	coupled_dist=""
	192	cpp_options=""
	193	cpumax=0
[2506]	194	create_batch_job=false
[2380]	195	create_jobfile_only=false
	196	create_remote_batch_job=false
	197	dashes=" ----------------------------------------------------------------------------"
	198	defaultqueue=""
[2506]	199	delete_temporary_catalog=true
[2380]	200	do_compile=true
	201	do_trace=false
	202	executable=""
	203	execute_command=""
	204	execution_error=false
[2762]	205	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	206	global_revision=""
	207	hostfile=""
	208	hp=""
	209	keep_data_from_previous_run=false
	210	link_local_input=false
	211	link_local_output=false
[2388]	212	linker_options=""
[2385]	213	local_jobcatalog=""
[2380]	214	locat=normal
	215	makefile=""
	216	max_par_io_str=""
	217	prc=$0
	218	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	219	do
	220	prc=`echo $prc \| cut -f2- -d"/"`
	221	done
	222	module_calls=""
[2506]	223	palmrun_memory=""
[2380]	224	palmrun_script_name=$prc
	225	openmp=false
[2506]	226	previous_job=""
[2479]	227	project_account=""
[2380]	228	queue=none
[2906]	229	read_svf=""
[2380]	230	restart_run=false
	231	return_address=""
[2385]	232	remote_jobcatalog=""
[2380]	233	remote_username=""
	234	running_in_batch_mode=false
[3313]	235	running_in_test_mode=false
[2380]	236	run_coupled_model=false
	237	run_id=""
[3236]	238	run_id_number=""
	239	run_identifier=test
[2380]	240	silent=false
	241	source_list=""
	242	source_path=""
[2501]	243	tasks_per_node=0
[2380]	244	threads_per_task=1
	245	transfer_problems=false
[2384]	246	user_source_path=""
[2506]	247	use_existing_sources_folder=""
[2380]	248	use_openmp=false
[3033]	249	version="palmrun 1.0 Rev$Rev: 3393 $"
[2380]	250	working_directory=`pwd`
	251	write_binary=""
[2906]	252	write_svf=""
[2380]	253
	254
	255	# ERROR HANDLING IN CASE OF EXIT
[2404]	256	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	257	then
	258
	259	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	260	(( i = 0 ))
	261	while (( i < iec ))
	262	do
	263	(( i = i + 1 ))
	264	printf "\n *** Execution of ERROR-command:\n"
	265	printf " >>> ${err_command[$i]}\n"
	266	eval ${err_command[$i]}
	267	done
[2566]	268	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	269	printf "\n\n+++ palmrun crashed \n\n"
	270	exit 1
	271	elif [[ $locat != normal ]]
[2380]	272	then
[3312]	273	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	274	printf "\n+++ palmrun killed by \"^C\" \n\n"
	275	exit 2
	276	else
[2566]	277	printf "\n --> palmrun finished\n\n"
[3312]	278	exit 0
[2380]	279	fi' exit
	280
	281
	282	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	283	trap 'locat=control_c
	284	exit 1
[2380]	285	' 2
	286
	287
	288	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	289	# WHICH WILL BE USED TO START RESTART-JOBS
[3313]	290	while getopts :a:A:bBCd:FG:h:i:jkm:M:O:q:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
[2380]	291	do
	292	case $option in
	293	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	294	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	295	(b) create_batch_job=true; prc="$prc -b";;
	296	(B) delete_temporary_catalog=false; prc="$prc -B";;
	297	(C) restart_run=true; prc="$prc -C";;
[3236]	298	(d) run_identifier=$OPTARG; prc="$prc -d$OPTARG";;
[2380]	299	(F) create_jobfile_only=true;;
	300	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	301	(h) configuration_identifier=$OPTARG; prc="$prc -h$OPTARG";;
	302	(i) run_id_number=$OPTARG;;
[2380]	303	(j) running_in_batch_mode=true;;
	304	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	305	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	306	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	307	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	308	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	309	(R) return_address=$OPTARG;;
	310	(s) source_list=$OPTARG;;
[2501]	311	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	312	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	313	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	314	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	315	(v) silent=true; prc="$prc -v";;
[2506]	316	(V) use_existing_sources_folder="-V";;
[2380]	317	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	318	(W) previous_job=$OPTARG;;
[2380]	319	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	320	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	321	(y) ocean_file_appendix=true; prc="$prc -y";;
	322	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	323	(z) running_in_test_mode=true;;
[2380]	324	(Z) combine_plot_fields=false; prc="$prc -Z";;
	325	(\?) printf "\n +++ unknown option $OPTARG \n"
	326	printf "\n --> type \"$0 ?\" for available options \n"
	327	locat=parameter;exit;;
	328	esac
	329	done
	330
	331
	332	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	333	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	334	(( to_shift = $OPTIND - 1 ))
	335	shift $to_shift
	336
	337	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	338	if [[ "$1" = "?" ]]
	339	then
	340	(printf "\n *** Description of available palmrun options:\n"
	341	printf "\n Option Description Default-Value"
	342	printf "\n -a activation string list \"\" "
[2479]	343	printf "\n -A project account number ---"
[2380]	344	printf "\n -b batch-job on local machine ---"
	345	printf "\n -B do not delete temporary directory at end ---"
[3025]	346	printf "\n -d run identifier test"
[2380]	347	printf "\n -F create batch job file only ---"
[2506]	348	printf "\n -h host configuration \"default\" "
[2380]	349	printf "\n -k keep data from previous run"
	350	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	351	printf "\n -M Makefile name Makefile"
	352	printf "\n -O threads per openMP task ---"
	353	printf "\n -q queue \"$queue\" "
	354	printf "\n -s filenames of routines to be compiled \"\" "
	355	printf "\n must end with .f, .f90, .F, or .c !"
	356	printf "\n use \"..\" for more than one file and wildcards"
	357	printf "\n -s LM compiles all locally modified files"
	358	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	359	printf "\n -T tasks per node ---"
[2380]	360	printf "\n -u username on remote machine \"\" "
	361	printf "\n -v no prompt for confirmation ---"
[2506]	362	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	363	printf "\n -w maximum parallel io streams as given by -X"
[2506]	364	printf "\n -W name of job to wait for ---"
[2380]	365	printf "\n -x tracing of palmrun for debug purposes ---"
	366	printf "\n -X # of processors (on parallel machines) 1"
	367	printf "\n -y add appendix \"_O\" to all local output"
	368	printf "\n files (ocean precursor runs followed by"
	369	printf "\n coupled atmosphere-ocean runs) ---"
	370	printf "\n -Y run coupled model, \"#1 #2\" with"
	371	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	372	printf "\n -Z skip combine_plot_fields at the end of "
	373	printf "\n the simulation ---"
	374	printf "\n "
	375	printf "\n Possible values of positional parameter <modus>:"
	376	printf "\n \"?\" - this outline \n\n") \| more
	377	exit
	378	elif [[ "$1" != "" ]]
	379	then
	380	printf "\n +++ positional parameter $1 unknown \n"
	381	locat=parameter; exit
	382	fi
	383
	384
	385
	386	# SHORT STARTING MESSAGE
	387	printf "\n*** $version "
	388	printf "\n will be executed. Please wait ..."
	389
	390
[3236]	391	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLES
	392	export fname=$run_identifier
	393	export jobname=$run_identifier
[2834]	394
	395
[2506]	396	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	397	config_file=.palm.config.$configuration_identifier
	398	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	399
	400
	401	# CHECK, IF CONFIGURATION FILE EXISTS
	402	if [[ ! -f $config_file ]]
	403	then
	404	printf "\n\n +++ configuration file: "
	405	printf "\n $config_file"
	406	printf "\n does not exist"
	407	locat=connect; exit
	408	fi
	409
	410
[2762]	411	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	412	if [[ -f .palm.iofiles ]]
	413	then
[3236]	414
	415	# CHECK VERSION MISMATCH
	416	if [[ $running_in_batch_mode != true ]]
	417	then
	418	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	419	then
	420	printf "\n\n +++ WARNING: A file connection file has been found in your"
	421	printf "\n working directory, but its revision does not match"
	422	printf "\n the revision of the default (trunk) version."
[3294]	423	printf "\n You may need to update your connection file"
	424	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	425	fi
	426	fi
	427
[2762]	428	fileconnection_file=.palm.iofiles
[3236]	429
[2762]	430	fi
	431
	432
[2380]	433	# CHECK, IF FILE CONNECTION FILE EXISTS
	434	if [[ ! -f $fileconnection_file ]]
	435	then
	436	printf "\n\n +++ file connection file: "
	437	printf "\n $fileconnection_file"
	438	printf "\n does not exist"
	439	locat=connect; exit
	440	fi
	441
	442
[2404]	443	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	444	if [[ "$activation_string_list" = "" ]]
	445	then
	446	printf "\n\n +++ no activation string list given: "
	447	printf "\n please set palmrun option \"-a\" "
	448	locat=palmrun_option; exit
	449	fi
	450
	451
	452	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	453	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	454	then
	455	write_binary=true
	456	else
	457	write_binary=false
	458	fi
	459
[2906]	460	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	461	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	462	then
	463	write_svf=true
	464	else
	465	write_svf=false
	466	fi
[2404]	467
[2906]	468	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	469	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	470	then
	471	read_svf=true
	472	else
	473	read_svf=false
	474	fi
	475
	476
[2380]	477	# READ AND EVALUATE THE CONFIGURATION-FILE
	478	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	479
	480	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	481	while read line
	482	do
	483
	484	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	485	eval line=\"$line\"
	486
	487
	488	# INTERPRET THE LINE
	489	if [[ "$(echo $line)" = "" ]]
	490	then
	491
	492	# EMPTY LINE, NO ACTION
	493	continue
	494
	495	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	496	then
	497
	498	# LINE IS A COMMENT LINE
	499	continue
	500
	501	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	502	then
	503
	504	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	505	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	506	value=`echo $line \| cut -d" " -s -f2-`
	507
	508
	509	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	510	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	511	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	512	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	513	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	514	# CONFIGURATION-FILE.
	515	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	516	then
	517	eval export $var="\$value"
	518
	519	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	520	if [[ $do_trace = true ]]
	521	then
	522	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	523	fi
	524	fi
	525
	526	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	527	then
	528
	529	# LINE DEFINES BATCH-DIRECTIVE
	530	(( ibd = ibd + 1 ))
	531	line=$(echo $line \| cut -c4-)
	532	batch_directive[$ibd]="$line"
	533
	534	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	535	then
	536
	537	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	538	# REMOTE TO A LOCAL HOST
	539	(( ibdt = ibdt + 1 ))
	540	line=$(echo $line \| cut -c5-)
	541	batch_directive_transfer[$ibdt]="$line"
	542
	543	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	544	then
	545
	546	# LINE DEFINES ERROR-COMMAND
	547	(( iec = iec + 1 ))
	548	line=$(echo $line \| cut -c4-)
	549	err_command[$iec]="$line"
	550
	551	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	552	then
	553
	554	# LINE DEFINES INPUT-COMMAND
	555	(( iic = iic + 1 ))
	556	line=$(echo $line \| cut -c4-)
	557	in_command[$iic]="$line"
	558
	559	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	560	then
	561
	562	# LINE DEFINES OUTPUT-COMMAND
	563	(( ioc = ioc + 1 ))
	564	line=$(echo $line \| cut -c4-)
	565	out_command[$ioc]="$line"
	566
	567	else
	568
	569	# SKIP ALL OTHER LINES
	570	continue
	571
	572	fi
	573
	574	done < $config_file
	575
	576
	577	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	578	if [[ "$fast_io_catalog" = "" ]]
	579	then
	580	printf "\n +++ no fast_io_catalog found in $config_file"
	581	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	582	locat=config_file; exit
	583	fi
[2380]	584	if [[ "$compiler_name" = "" ]]
	585	then
	586	printf "\n +++ no compiler name found in $config_file"
	587	printf "\n Please add line \"compiler_name ...\" to that file."
	588	locat=config_file; exit
	589	fi
	590	if [[ "$compiler_name_ser" = "" ]]
	591	then
	592	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	593	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	594	locat=config_file; exit
	595	fi
	596	if [[ "$compiler_options" = "" ]]
	597	then
	598	printf "\n +++ no compiler options found in $config_file"
	599	printf "\n Please add line \"compiler_options ...\" to that file."
	600	locat=config_file; exit
	601	fi
[2388]	602	if [[ "$linker_options" = "" ]]
[2380]	603	then
[2388]	604	printf "\n +++ no linker options found in $config_file"
	605	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	606	locat=config_file; exit
	607	fi
	608	if [[ "$execute_command" = "" ]]
	609	then
	610	printf "\n +++ no execute command found in $config_file"
	611	printf "\n Please add line \"execute_command ...\" to that file."
	612	locat=config_file; exit
	613	fi
	614
	615	if [[ "$hostfile" != "" ]]
	616	then
	617	if [[ $hostfile != auto && ! -f $hostfile ]]
	618	then
	619	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	620	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	621	locat=config_file; exit
	622	fi
	623	fi
	624
	625
	626	# DETERMINE THE CALL STATUS
	627	if [[ "$return_address" != "" ]]
	628	then
	629
	630	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	631	# BATCH MODE AND ...
	632	running_on_remote=true
	633
	634	else
	635
	636	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	637	if [[ "$remote_ip" != "" ]]
	638	then
	639
	640	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	641	create_remote_batch_job=true
	642
[3132]	643	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	644	if [[ "$remote_jobcatalog" = "" ]]
	645	then
	646	printf "\n +++ no remote jobcatalog found in $config_file"
	647	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	648	locat=config_file; exit
	649	fi
	650
	651
[2380]	652	fi
	653	running_on_remote=false
	654	fi
	655
	656
	657
	658	# READ AND EVALUATE THE I/O-FILE LIST
	659	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	660
	661	# READ THE FILE CONNECTION FILE LINE BY LINE
	662	while read line
	663	do
	664
[2669]	665	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	666	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	667
	668	# INTERPRET THE LINE
	669	if [[ "$(echo $line)" = "" ]]
	670	then
	671	# EMPTY LINE, NO ACTION
	672	continue
	673
	674	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	675	then
	676
	677	# LINE IS A COMMENT LINE
	678	true
	679
	680	else
	681
	682	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	683	# s2a: in/out - field
[2669]	684	# s2b: action - field (optional)
	685	s1=`echo "$line" \| cut -d" " -f1`
	686	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	687	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	688	then
[2669]	689	s2a=$s2
[2380]	690	s2b=""
	691	else
[2669]	692	s2a=`echo $s2 \| cut -d":" -f1`
	693	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	694	fi
[2669]	695	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	696	s4=`echo "$line" \| cut -d" " -s -f4`
	697	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	698	s5=`echo "$line" \| cut -d" " -s -f5`
	699	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	700
	701
	702	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	703	# INPUT- OR OUTPUT-LIST.
	704	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	705	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	706	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	707	# IS NOT CHECKED AND STORED.
[2610]	708	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	709	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	710	then
	711	found=false
	712	for actual in $activation_string_list
	713	do
	714	for formal in $s3
	715	do
	716	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	717	done
	718	done
	719	if [[ $found = true ]]
	720	then
	721	(( iin = iin + 1 ))
[2669]	722	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	723	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	724	if [[ "$s2a" = inopt ]]
	725	then
	726	optin_pre[$iin]=yes
	727	else
	728	optin_pre[$iin]=no
	729	fi
[2605]	730
	731	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	732	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	733	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	734	then
[2610]	735	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	736	fi
	737
[2610]	738	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	739	# THE WILDCARD FROM THE ENDING
	740	if [[ "${s5: -1}" = "*" ]]
	741	then
[2669]	742	if [[ "$s2b" = "di" ]]
[2610]	743	then
	744	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	745	printf "\n see file \"$fileconnection_file\", line"
	746	printf "\n$line"
	747	locat=iofiles_file; exit
	748	fi
	749	multin[$iin]=true
	750	string=${endin_pre[$iin]}
	751	endin_pre[$iin]="${string%?}"
	752	else
	753	multin[$iin]=false
	754	fi
[2380]	755	fi
[2669]	756	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	757	then
	758	found=false
	759	for actual in $activation_string_list
	760	do
	761	for formal in $s3
	762	do
[2670]	763	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	764	done
	765	done
	766	if [[ $found = true ]]
	767	then
	768	(( iout = iout + 1 ))
[2669]	769	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	770	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	771
[2669]	772	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	773	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	774	if [[ $formal = wildcard ]]
	775	then
	776	warnout_pre[$iout]=false
	777	else
	778	warnout_pre[$iout]=true
	779	fi
	780
[2610]	781	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	782	# THE WILDCARD FROM THE LOCAL FILENAME
	783	if [[ "${s1: -1}" = "*" ]]
	784	then
[2669]	785	if [[ "$s2b" = "di" ]]
[2610]	786	then
	787	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	788	printf "\n see file \"$fileconnection_file\", line"
	789	printf "\n$line"
	790	locat=iofiles_file; exit
	791	fi
	792	multout[$iout]=true
	793	string=${localout_pre[$iout]}
	794	localout_pre[$iout]="${string%?}"
	795	else
	796	multout[$iout]=false
	797	fi
[2380]	798	fi
[2669]	799	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	800	then
[2669]	801	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	802	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	803	locat=connect; exit
	804	fi
	805	IFS="$IFSALT"
	806	fi
	807
	808	done < $fileconnection_file
	809
	810
	811
[2501]	812	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	813	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	814	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	815	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	816	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	817	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	818
	819
	820
[2380]	821	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	822	if [[ $run_coupled_model = true ]]
	823	then
	824
	825	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	826	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	827
	828	if (( $cores_ocean + $cores_atmos != $cores ))
	829	then
	830
	831	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	832	printf "\n PEs (total) : $cores"
	833	printf "\n PEs (atmosphere): $cores_atmos"
	834	printf "\n PEs (ocean) : $cores_ocean"
	835	locat=coupling; exit
	836
	837	fi
	838
	839	fi
	840
	841
	842	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	843	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	844	# FOLDER
	845	if [[ $running_in_batch_mode = true ]]
	846	then
	847
[2506]	848	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	849	then
[2506]	850	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	851	printf "\n Please check the output of the palmrun-call"
	852	printf "\n that you did on your local host."
	853	locat=SOURCES_FOR_RUN; exit
	854	fi
	855
	856	else
	857
	858	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	859	# AUTOMATIC RESTART RUN
	860	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	861	if [[ $restart_run = false ]]
	862	then
	863
	864	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	865	# THE LOCAL HOST
	866	if [[ ! -d $source_path ]]
	867	then
	868	printf "\n\n +++ source path \"$source_path\" on local host"
	869	printf "\n \"$(hostname)\" does not exist"
	870	locat=source_path; exit
	871	fi
	872
[2990]	873	rm -rf ${base_directory}/${sources_for_run_catalog}
	874	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	875
	876	if [[ "$source_list" = LM ]]
	877	then
	878
	879	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	880	source_list=""
	881	cd $source_path
	882
	883
[2512]	884	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	885	if [[ ! -d ../.svn ]]
[2380]	886	then
	887	printf "\n\n +++ source directory"
	888	printf "\n \"$source_path\" "
	889	printf "\n is not under control of \"subversion\"."
[2512]	890	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	891	fi
	892
	893
	894	# LIST ALL MODIFIED SOURCE CODE FILES
	895	Filenames=""
[2404]	896	svn status > tmp_svnstatus
[2380]	897	while read line
	898	do
	899	firstc=`echo $line \| cut -c1`
	900	if [[ $firstc = M \|\| $firstc = "?" ]]
	901	then
	902	Name=`echo "$line" \| cut -c8-`
	903	extension=`echo $Name \| cut -d. -f2`
	904	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	905	then
	906	Filenames="$Filenames "$Name
	907	fi
	908	fi
[2404]	909	done < tmp_svnstatus
	910	rm -rf tmp_svnstatus
[2380]	911
	912
	913	# COPY FILES TO SOURCES_FOR_RUN_...
	914	for filename in $Filenames
	915	do
[2990]	916	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	917	source_list=$source_list"$filename "
	918	done
	919
	920	cd - > /dev/null
	921
	922
	923	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	924	elif [[ "$source_list" != "" ]]
	925	then
	926
	927	cd $source_path
	928
	929	for filename in $source_list
	930	do
	931
	932	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	933	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	934	then
	935	printf "\n +++ source code file: $filename"
	936	printf "\n must not contain (\"/\") "
	937	locat=source; exit
	938	fi
	939
	940	if [[ ! -f $filename ]]
	941	then
	942	printf "\n +++ source code file: $filename"
	943	printf "\n does not exist"
	944	locat=source; exit
	945	else
[2990]	946	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	947	fi
	948
	949	done
	950
	951	cd - > /dev/null
	952
	953	fi
	954
	955	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	956	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	957	if [[ ! -f $makefile ]]
	958	then
	959	printf "\n +++ file \"$makefile\" does not exist"
	960	locat=make; exit
	961	else
[2990]	962	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	963	fi
	964
	965
	966	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	967	if [[ "$user_source_path" != "" ]]
[2380]	968	then
	969
	970	# DOES THE DIRECTORY EXIST?
[2384]	971	if [[ ! -d $user_source_path ]]
[2380]	972	then
	973
	974	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	975	printf "\n \"$user_source_path\" "
[2380]	976	printf "\n does not exist or is not a directory."
	977	printf "\n No source code will be used from this directory!\n"
[2384]	978	user_source_path=""
[2380]	979	if [[ $silent == false ]]
	980	then
	981	sleep 2
	982	fi
	983
	984	else
	985
[2384]	986	cd $user_source_path
[2380]	987
	988	Names=$(ls -1 *.f90 2>&1)
	989	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	990	Names=$(ls -1 *.F90 2>&1)
	991	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	992	Names=$(ls -1 *.F 2>&1)
	993	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	994	Names=$(ls -1 *.f 2>&1)
	995	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	996	Names=$(ls -1 *.c 2>&1)
	997	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	998
	999	cd - > /dev/null
[2990]	1000	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1001
	1002	# COPY MAKEFILE IF EXISTING
[2384]	1003	if [[ -f $user_source_path/Makefile ]]
[2380]	1004	then
	1005	printf "\n\n *** user Makefile from directory"
[2384]	1006	printf "\n \"$user_source_path\" is used \n"
[2380]	1007	if [[ $silent == false ]]
	1008	then
	1009	sleep 1
	1010	fi
[2384]	1011	cp $user_source_path/Makefile .
[2380]	1012	fi
	1013
	1014	for filename in $AddFilenames
	1015	do
	1016	if [[ -f $filename ]]
	1017	then
	1018	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1019	printf "\n source code directory \"$user_source_path\" "
[2380]	1020	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1021	printf "\n from directory \"$source_path\"."
	1022	locat=source; exit
	1023	fi
	1024
[2384]	1025	cp $user_source_path/$filename .
[2380]	1026	source_list="$source_list $filename"
	1027
	1028	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1029	if [[ $(grep -c $filename Makefile) = 0 ]]
	1030	then
	1031	printf "\n\n +++ user file \"$filename\" "
	1032	printf "\n is not listed in Makefile \n"
	1033	locat=source; exit
	1034	fi
	1035	done
	1036	cd - > /dev/null
	1037	fi
	1038	fi
	1039
	1040	# COPY CONFIGURATION FILES
[2990]	1041	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1042	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1043
	1044	# COPY SHELLSCRIPTS
[2990]	1045	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1046	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1047
	1048	fi
	1049
	1050	fi
	1051
[2605]	1052
[2380]	1053	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1054	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1055	if [[ "$global_revision" = "" ]]
	1056	then
	1057	global_revision=`svnversion $source_path 2>/dev/null`
	1058	global_revision="Rev: $global_revision"
	1059	fi
	1060
	1061
	1062	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1063	if [[ -n $cores ]]
	1064	then
	1065
	1066	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1067	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1068	if [[ $tasks_per_node = 0 ]]
[2380]	1069	then
[3025]	1070	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1071	then
	1072	printf "\n"
	1073	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1074	printf "\n set -T option or define tasks_per_node in the config file"
	1075	locat=tasks_per_node; (( iec = 0 )); exit
	1076	else
	1077	# DEFAULT FOR INTERACTIVE RUN
	1078	tasks_per_node=$cores
	1079	fi
[2380]	1080	fi
	1081
	1082	if (( cores < tasks_per_node ))
	1083	then
	1084	printf "\n"
	1085	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1086	printf "\n given values: -T $tasks_per_node -X $cores"
	1087	locat=tasks_per_node; (( iec = 0 )); exit
	1088	fi
	1089
	1090	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1091	(( mpi_tasks = cores / threads_per_task ))
	1092	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1093	(( ii = cores / tasks_per_node ))
	1094	(( remaining_cores = cores - ii * tasks_per_node ))
	1095	if (( remaining_cores > 0 ))
	1096	then
	1097	printf "\n"
	1098	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1099	printf "\n divisor of the total number of cores (option \"-X\")"
	1100	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1101	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1102	(( nodes = nodes + 1 ))
	1103	fi
	1104
	1105	fi
	1106
	1107
	1108	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1109	if [[ "$maximum_parallel_io_streams" = "" ]]
	1110	then
	1111	maximum_parallel_io_streams=$cores
	1112	fi
	1113
	1114
	1115	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1116	if [[ "$scp_port" != "" ]]
	1117	then
	1118	PORTOPT="-P $scp_port"
	1119	SSH_PORTOPT="-p $scp_port"
	1120	fi
	1121
	1122
	1123	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1124	# CONFIG-FILE
	1125	if [[ "$ssh_key" != "" ]]
	1126	then
	1127	ssh_key="-i $HOME/.ssh/$ssh_key"
	1128	fi
	1129
	1130
	1131	# SET QUEUE, IF NOT GIVEN
	1132	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1133	then
	1134
	1135	if [[ $queue = none && "$defaultqueue" = "" ]]
	1136	then
	1137	printf "\n"
	1138	printf "\n +++ no default queue given in configuration file and no queue"
	1139	printf "\n given with option -q"
[2789]	1140	locat=queue; exit
[2380]	1141	fi
	1142	if [[ $queue = none ]]
	1143	then
	1144	queue=$defaultqueue
	1145	fi
	1146
	1147	fi
	1148
	1149
	1150	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1151	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1152	(( i = 0 ))
[2610]	1153	(( nr_of_input_files = 0 ))
[2380]	1154	while (( i < iin ))
	1155	do
	1156	(( i = i + 1 ))
	1157
	1158	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1159	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1160	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1161	then
[2610]	1162	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1163	else
[3236]	1164	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1165	fi
	1166
[2610]	1167
[2380]	1168	# CHECK IF FILE EXISTS
	1169	if ! ls $filename* 1>/dev/null 2>&1
	1170	then
	1171
[2669]	1172	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1173	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1174	then
	1175	printf "\n\n +++ INPUT-file: "
[2610]	1176	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1177	then
	1178	printf "\n $filename"
	1179	else
[2610]	1180	printf "\n $filename.${extin_pre[$i]}"
[2380]	1181	fi
	1182	printf "\n does not exist\n"
	1183	locat=input; exit
	1184	else
[2610]	1185	(( nr_of_input_files = nr_of_input_files + 1 ))
	1186	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1187	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1188	actionin[$nr_of_input_files]="unavailable"
[2610]	1189	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1190	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1191	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1192	fi
[2605]	1193
[2380]	1194	else
	1195
[3236]	1196	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1197	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1198	# ENDINGS
[2610]	1199	if [[ "${multin[$i]}" = true ]]
	1200	then
	1201	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1202	ls -1 -d ${filename} > filelist 2>/dev/null
	1203	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1204	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1205
[2610]	1206	endings=""
	1207	while read line
	1208	do
	1209	# filename without path (i.e. after the last "/")
	1210	basefilename=$(basename ${line})
[2380]	1211
[2610]	1212	# check if there is an extension and remove it
	1213	ext=${basefilename##*.}
	1214	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1215	then
	1216	basefilename=${basefilename%.*}
	1217	fi
[2380]	1218
[2610]	1219	# check for an existing cycle number and remove it
	1220	cycle=${basefilename##*.}
	1221	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1222	then
	1223	basefilename=${basefilename%.*}
	1224	fi
[2600]	1225
[3236]	1226	# remove the run_identifier from the beginning
	1227	length_run_identifier=${#run_identifier}
	1228	ending=${basefilename:${length_run_identifier}}
[2610]	1229
	1230	# remove the ending given in the .iofiles from the beginning
	1231	endingstring="${endin_pre[$i]}"
	1232	length_ending=${#endingstring}
	1233	ending=${ending:${length_ending}}
	1234
	1235	if [[ "$ending" = "" ]]
[2600]	1236	then
[2610]	1237	# standard ending as given in the .iofiles
	1238	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1239	then
	1240	endings="$endings DEFAULT"
	1241	fi
[2600]	1242	else
[2610]	1243	# ending must start with "_", otherwise its a different file
	1244	if [[ "${ending:0:1}" = "_" ]]
	1245	then
	1246	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1247	then
	1248	endings="$endings $ending"
	1249	fi
	1250	fi
[2600]	1251	fi
[2610]	1252
	1253	done <filelist
[2380]	1254
[2610]	1255	rm filelist
[2380]	1256
[2600]	1257	else
[2610]	1258
	1259	# SINGLE NAME
	1260	endings=DEFAULT
	1261
[2600]	1262	fi
	1263
[2610]	1264	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1265	for ending in $endings
	1266	do
	1267
	1268	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1269	if [[ $ending = DEFAULT ]]
[2380]	1270	then
[2610]	1271	ending=""
	1272	fi
	1273
	1274	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1275	(( nr_of_input_files = nr_of_input_files + 1 ))
	1276	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1277	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1278	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1279	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1280	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1281	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1282
	1283
	1284	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1285	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1286	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1287	then
	1288	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1289	else
[3236]	1290	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1291	fi
[2610]	1292
	1293	# DETERMINE THE FILE'S CYCLE NUMBER
	1294	(( maxcycle = 0 ))
	1295	ls -1 -d $filename > filelist 2>/dev/null
	1296	ls -1 -d $filename.* >> filelist 2>/dev/null
	1297	while read line
	1298	do
	1299	# filename without path (i.e. after the last "/")
	1300	basefilename=$(basename ${line})
	1301
	1302	# check if there is an extension
	1303	extension=${basefilename##*.}
	1304	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1305	then
	1306	basefilename=${basefilename%.*}
	1307	fi
	1308
	1309	# check for an existing cycle number
	1310	cycle=${basefilename##*.}
	1311	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1312	then
[2669]	1313	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1314	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1315	(( icycle = $((10#$cycle)) ))
[2610]	1316	else
	1317	(( icycle = 0 ))
	1318	fi
	1319
	1320	if (( icycle > maxcycle ))
	1321	then
	1322	(( maxcycle = icycle ))
	1323
	1324	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1325	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1326	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1327	then
	1328	leading_zero=true
	1329	else
	1330	leading_zero=false
	1331	fi
	1332	fi
	1333
	1334	done <filelist
	1335	rm filelist
	1336
	1337	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1338	if [[ $leading_zero = true ]]
[2380]	1339	then
[2610]	1340	cyclestring=`printf "%03d" $maxcycle`
	1341	else
	1342	cyclestring=$maxcycle
[2380]	1343	fi
[2610]	1344
	1345	# APPEND CYCLE NUMBER TO FILENAME
	1346	if (( maxcycle > 0 ))
[2380]	1347	then
[2610]	1348	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1349	then
	1350	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1351	else
	1352	filename=${filename}.$cyclestring
	1353	fi
[2380]	1354	else
[2610]	1355	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1356	then
	1357	filename=${filename}.${extin[$nr_of_input_files]}
	1358	fi
[2380]	1359	fi
[2610]	1360
	1361	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1362	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1363	absnamein[$nr_of_input_files]=$filename
	1364	if (( maxcycle > 0 ))
[2380]	1365	then
[2610]	1366	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1367	then
	1368	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1369	else
[3236]	1370	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1371	fi
[2380]	1372	else
[2610]	1373	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1374	then
	1375	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1376	else
[3236]	1377	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1378	fi
[2380]	1379	fi
	1380
[2610]	1381	done
	1382
[2380]	1383	fi
[2610]	1384
[2380]	1385	done
	1386
[2610]	1387
[2380]	1388	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1389	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1390	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1391	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1392	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1393	# REMOTE HOST)
	1394	(( i = 0 ))
	1395	while (( i < iout ))
	1396	do
	1397	(( i = i + 1 ))
[2610]	1398	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1399	then
[2610]	1400	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1401	then
[2610]	1402	actionout_pre[$i]=""
	1403	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1404	then
[2610]	1405	actionout_pre[$i]=pe
	1406	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1407	then
[2610]	1408	actionout_pre[$i]=a
[2380]	1409	fi
	1410	(( maxcycle = 0 ))
[3236]	1411	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1412	eval catalogname=${pathout_pre[$i]}
[2380]	1413	if ! ls $filename* 1>/dev/null 2>&1
	1414	then
	1415
	1416	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1417	if cat /dev/null > $filename
	1418	then
	1419	rm $filename
	1420	else
	1421
	1422	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1423	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1424	if [[ ! -d $catalogname ]]
	1425	then
	1426	if mkdir -p $catalogname
	1427	then
	1428	printf "\n\n *** directory:"
	1429	printf "\n $catalogname"
	1430	printf "\n was created\n"
	1431	else
	1432	printf "\n\n +++ OUTPUT-file:"
	1433	printf "\n $filename"
	1434	printf "\n cannot be created, because directory does not exist"
	1435	printf "\n and cannot be created either"
	1436	printf "\n"
	1437	locat=output ; exit
	1438	fi 2>/dev/null
	1439	else
	1440	printf "\n\n +++ OUTPUT-file:"
	1441	printf "\n $filename"
	1442	printf "\n cannot be created, although directory exists"
	1443	printf "\n"
	1444	locat=output ; exit
	1445	fi
	1446	fi 2>/dev/null
	1447
	1448	fi
	1449
	1450	fi
	1451	done
	1452
	1453
	1454	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1455	if [[ $running_in_batch_mode = false ]]
	1456	then
[3236]	1457	run_id_number=$RANDOM
	1458	run_id=${run_identifier}.$run_id_number
[2380]	1459
[3236]	1460	tempdir=$fast_io_catalog/$run_id
[3346]	1461
	1462	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1463	export job_id=$run_id
	1464
[2380]	1465	fi
	1466
	1467
	1468	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1469	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1470	then
	1471
	1472	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1473	if [[ $ibd = 0 ]]
	1474	then
	1475	printf "\n"
	1476	printf "\n +++ no batch directives found in configuration file"
	1477	locat=config_file_batch_directives; (( iec = 0 )); exit
	1478	fi
	1479
	1480	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1481	done=false
[2384]	1482	cputime=$cpumax
[2380]	1483	while [[ $done = false ]]
	1484	do
[2384]	1485	if (( cputime == 0 ))
[2380]	1486	then
	1487	printf "\n +++ cpu-time is undefined"
	1488	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1489	printf "\n >>> "
[2384]	1490	read cputime 1>/dev/null 2>&1
[2380]	1491	else
	1492	done=true
	1493	fi
	1494	done
[2420]	1495	cpumax=$cputime
[2380]	1496
	1497	# CHECK THE MEMORY DEMAND
	1498	done=false
	1499	while [[ $done = false ]]
	1500	do
	1501	if (( memory == 0 ))
	1502	then
	1503	printf "\n +++ memory demand is undefined"
	1504	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1505	printf "\n >>> "
	1506	read memory 1>/dev/null 2>&1
	1507	else
	1508	done=true
	1509	fi
	1510	done
	1511
	1512	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1513	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1514	then
	1515	while [[ -z $remote_username ]]
	1516	do
[2420]	1517	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1518	printf "\n >>> Please type username:"
	1519	printf "\n >>> "
	1520	read remote_username
	1521	done
	1522	fi
	1523
	1524	else
	1525
[2420]	1526	if [[ $running_in_batch_mode = false ]]
	1527	then
	1528	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1529	cpumax=$cputime
	1530	else
	1531	cputime=$cpumax
	1532	fi
[2380]	1533
	1534	fi
	1535
	1536
	1537	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1538	(( cpu_hours = cputime / 3600 ))
	1539	(( resttime = cputime - cpu_hours * 3600 ))
	1540	(( cpu_minutes = resttime / 60 ))
	1541	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1542	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1543
	1544
	1545	# OUTPUT OF THE PALMRUN-HEADER
	1546	calltime=$(date)
	1547	printf "\n"
	1548	printf "#------------------------------------------------------------------------# \n"
	1549	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1550	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1551	printf "\| \| \n"
	1552	column1="called on:"; column2=$(hostname)
	1553	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1554	if [[ $create_remote_batch_job = true ]]
	1555	then
[3236]	1556	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1557	else
	1558	if [[ $running_on_remote = true ]]
	1559	then
[3236]	1560	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1561	else
[3236]	1562	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1563	fi
	1564	fi
	1565	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1566
	1567	column1="running in:"
	1568	if [[ $running_in_batch_mode = true ]]
	1569	then
	1570	column2="batch job mode"
	1571	else
	1572	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1573	then
	1574	column2="job creation mode"
	1575	else
	1576	column2="interactive run mode"
	1577	fi
	1578	fi
	1579	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1580
[2479]	1581	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1582	then
[2480]	1583	if [[ "$project_account" != "" ]]
[2479]	1584	then
	1585	column1="project account number:"
	1586	column2="$project_account"
	1587	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1588	fi
	1589	fi
	1590
[2380]	1591	if [[ -n $cores ]]
	1592	then
	1593	if [[ $run_coupled_model = false ]]
	1594	then
	1595	column1="number of cores:"; column2=$cores
	1596	else
	1597	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1598	fi
	1599	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1600	fi
	1601	if [[ -n $tasks_per_node ]]
	1602	then
	1603	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1604	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1605	if (( remaining_cores > 0 ))
	1606	then
	1607	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1608	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1609	fi
	1610	fi
	1611	if [[ $maximum_parallel_io_streams != $cores ]]
	1612	then
	1613	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1614	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1615	fi
	1616	if [[ $use_openmp = true ]]
	1617	then
	1618	column1="threads per task:"; column2="$threads_per_task"
	1619	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1620	fi
[2384]	1621	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1622	then
[2506]	1623	column1="memory demand / PE":; column2="$memory MB"
	1624	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1625	column1="job cpu time (h:m:s):"; column2="$timestring"
	1626	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1627	fi
[2380]	1628	printf "\| \| \n"
	1629	if [[ "$source_list" != "" ]]
	1630	then
	1631	if [[ "$make_options" != "" ]]
	1632	then
	1633	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1634	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1635	line=$(echo "$make_options" \| cut -c46-)
	1636	while [[ "$line" != "" ]]
	1637	do
	1638	column1=""
	1639	column2=$(echo "$line" \| cut -c-45)
	1640	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1641	line=$(echo "$line" \| cut -c46-)
	1642	done
	1643	fi
	1644	fi
	1645
	1646	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1647	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1648	line=$(echo "$cpp_options" \| cut -c46-)
	1649	while [[ "$line" != "" ]]
	1650	do
	1651	column1=""
	1652	column2=$(echo "$line" \| cut -c-45)
	1653	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1654	line=$(echo "$line" \| cut -c46-)
	1655	done
	1656
	1657	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1658	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1659	line=$(echo "$compiler_options" \| cut -c46-)
	1660	while [[ "$line" != "" ]]
	1661	do
	1662	column1=""
	1663	column2=$(echo "$line" \| cut -c-45)
	1664	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1665	line=$(echo "$line" \| cut -c46-)
	1666	done
	1667
[2388]	1668	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1669	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1670	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1671	while [[ "$line" != "" ]]
	1672	do
	1673	column1=""
	1674	column2=$(echo "$line" \| cut -c-45)
	1675	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1676	line=$(echo "$line" \| cut -c46-)
	1677	done
	1678
	1679	if [[ "$login_init_cmd" != "" ]]
	1680	then
	1681	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1682	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1683	line=$(echo "$login_init_cmd" \| cut -c46-)
	1684	while [[ "$line" != "" ]]
	1685	do
	1686	column1=""
	1687	column2=$(echo "$line" \| cut -c-45)
	1688	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1689	line=$(echo "$line" \| cut -c46-)
	1690	done
	1691	fi
	1692
	1693	if [[ "$module_commands" != "" ]]
	1694	then
	1695	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1696	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1697	line=$(echo "$module_commands" \| cut -c46-)
	1698	while [[ "$line" != "" ]]
	1699	do
	1700	column1=""
	1701	column2=$(echo "$line" \| cut -c-45)
	1702	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1703	line=$(echo "$line" \| cut -c46-)
	1704	done
	1705	fi
	1706	printf "\| \| \n"
[3236]	1707	column1="run identifier:"; column2=$run_identifier
[2380]	1708	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1709	column1="activation string list:"; column2=$(echo $activation_string_list)
	1710	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1711
	1712	if [[ "$ocean_file_appendix" = true ]]
	1713	then
	1714	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1715	fi
	1716
	1717	if [[ "$source_list" != "" ]]
	1718	then
	1719	printf "\| \| \n"
	1720	printf "\| Files to be compiled: \| \n"
	1721	line=$source_list
	1722	while [[ "$line" != "" ]]
	1723	do
	1724	linestart=$(echo $line \| cut -c-70)
	1725	printf "\| %-70s \| \n" "$linestart"
	1726	line=$(echo "$line" \| cut -c71-)
	1727	done
	1728	fi
	1729	printf "#------------------------------------------------------------------------#"
	1730
	1731
	1732
	1733	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1734	if [[ $do_trace = true ]]
	1735	then
	1736	(( i = 0 ))
[2610]	1737	while (( i < nr_of_input_files ))
[2380]	1738	do
	1739	(( i = i + 1 ))
	1740	if (( i == 1 ))
	1741	then
	1742	printf "\n\n >>> INPUT-file assignments:\n"
	1743	fi
	1744	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1745	done
	1746	(( i = 0 ))
	1747	while (( i < iout ))
	1748	do
	1749	(( i = i + 1 ))
	1750	if (( i == 1 ))
	1751	then
	1752	printf "\n\n >>> OUTPUT-file assignments:\n"
	1753	fi
	1754	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1755	done
	1756	(( i = 0 ))
	1757	while (( i < iic ))
	1758	do
	1759	(( i = i + 1 ))
	1760	if (( i == 1 ))
	1761	then
	1762	printf "\n\n >>> INPUT-commands:\n"
	1763	fi
	1764	printf "\n ${in_command[$i]}"
	1765	done
	1766	(( i = 0 ))
	1767	while (( i < ioc ))
	1768	do
	1769	(( i = i + 1 ))
	1770	if (( i == 1 ))
	1771	then
	1772	printf "\n\n >>> OUTPUT-commands:\n"
	1773	fi
	1774	printf "\n ${out_command[$i]}"
	1775	done
	1776	fi
	1777
	1778	# QUERY FOR CONTINUE
	1779	if [[ $silent = false && $running_in_batch_mode = false ]]
	1780	then
	1781	antwort=dummy
	1782	printf "\n\n"
	1783	printf " >>> everything o.k. (y/n) ? "
	1784	while read antwort
	1785	do
	1786	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1787	then
	1788	printf " >>> everything o.k. (y/n) ? "
	1789	else
	1790	break
	1791	fi
	1792	done
	1793	if [[ $antwort = n \|\| $antwort = N ]]
	1794	then
	1795	locat=user_abort; (( iec = 0 )); exit
	1796	fi
	1797	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1798	then
[2566]	1799	printf "\n *** batch-job will be created and submitted"
[2380]	1800	else
[2566]	1801	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1802	fi
	1803	fi
	1804
	1805
	1806
	1807	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1808	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1809	then
	1810
	1811	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1812	then
[2566]	1813	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1814	else
[2566]	1815	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1816	fi
	1817
[2422]	1818	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1819	# IT SHALL BE CREATED
	1820	ask_for_make_depository=false
	1821	if [[ $create_remote_batch_job = true ]]
	1822	then
	1823
	1824	line=`grep %base_directory $config_file`
[3236]	1825	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
	1826	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]	1827
[3236]	1828	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1829	then
	1830	printf "\n\n +++ make depository \"${make_depository}\""
	1831	printf "\n on remote host not found!"
	1832	ask_for_make_depository=true
	1833	fi
[3236]	1834	rm ${configuration_identifier}_last_make_protokoll
[2422]	1835
	1836	else
	1837
	1838	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1839	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1840	if [[ ! -d ${make_depository} ]]
	1841	then
	1842	printf "\n\n +++ make depository \"${make_depository}\""
	1843	printf "\n on local host not found!"
	1844	ask_for_make_depository=true
	1845	fi
	1846
	1847	fi
	1848
	1849	if [[ $ask_for_make_depository = true ]]
	1850	then
	1851
	1852	antwort=dummy
	1853	printf "\n\n"
	1854	printf " >>> Create a new one (y/n) ? "
	1855	while read antwort
	1856	do
	1857	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1858	then
	1859	printf " >>> Create a new one (y/n) ? "
	1860	else
	1861	break
	1862	fi
	1863	done
	1864	if [[ $antwort = n \|\| $antwort = N ]]
	1865	then
	1866	locat=user_abort; (( iec = 0 )); exit
	1867	fi
	1868
[2566]	1869	if [[ $do_trace = true ]]
	1870	then
[3236]	1871	palmbuild -h $configuration_identifier
[2566]	1872	else
[3236]	1873	palmbuild -v -h $configuration_identifier
[2566]	1874	fi
[2422]	1875
[3312]	1876	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1877	then
	1878
	1879	# ABORT IN CASE OF COMPILATION PROBLEMS
	1880	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1881	locat=make_depository
	1882	exit
	1883	else
	1884	echo " *** now continue with creating executable and other sources"
	1885	fi
	1886
	1887	fi
	1888
[2566]	1889	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3236]	1890	palmbuild -v $use_existing_sources_folder -h $configuration_identifier -d $run_identifier
[2380]	1891
[3312]	1892	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1893	then
	1894
	1895	# ABORT IN CASE OF COMPILATION PROBLEMS
	1896	printf "\n +++ error while creating executable and/or other sources"
	1897	locat=execution
[2990]	1898	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1899	exit
	1900
	1901	else
	1902
[2566]	1903	printf " *** executable and other sources created\n"
[2990]	1904	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1905
	1906	fi
	1907
	1908	fi
	1909
	1910
[2669]	1911	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1912	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1913	if [[ $create_remote_batch_job = true ]]
	1914	then
	1915	(( i = 0 ))
[2610]	1916	while (( i < nr_of_input_files ))
[2605]	1917	do
	1918	(( i = i + 1 ))
[2669]	1919	if [[ "${actionin[$i]}" = tr ]]
[2605]	1920	then
	1921	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1922	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1923	fi
	1924	done
	1925	if (( i > 0 ))
	1926	then
[3025]	1927	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1928	fi
	1929	fi
	1930
	1931
[2380]	1932	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1933	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1934	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1935	then
	1936
	1937	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1938	if [[ $running_in_batch_mode = false ]]
	1939	then
	1940	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1941	# FOLDER
[2566]	1942	mkdir -p $tempdir
	1943	chmod go+rx $tempdir
	1944	cd $tempdir
	1945	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1946	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1947
	1948	else
	1949
	1950	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1951	printf "\n *** running in temporary directory: $tempdir"
[2380]	1952
	1953	fi
	1954
	1955
	1956	# PROVIDE THE INPUT FILES
	1957	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1958	optional_files_missing=false
[2380]	1959	(( i = 0 ))
[2610]	1960	while (( i < nr_of_input_files ))
[2380]	1961	do
	1962	(( i = i + 1 ))
	1963	if (( i == 1 ))
	1964	then
	1965	printf "\n\n *** providing INPUT-files:\n$dashes"
	1966	fi
	1967
	1968
	1969	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1970	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1971	then
[2669]	1972	optional_files_missing=true
[2380]	1973	continue
	1974	fi
	1975
	1976	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1977	files_for_cores=false; filetype=file
	1978	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1979	then
	1980	files_for_cores=true; filetype=files
	1981	actionin[$i]=""
	1982	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1983	then
	1984	actionin[$i]=""
	1985	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1986	then
	1987	files_for_cores=true; filetype=files
	1988	actionin[$i]="ln"
	1989	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1990	then
	1991	actionin[$i]="ln"
	1992	fi
	1993
	1994	if [[ $files_for_cores = true ]]
	1995	then
	1996	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1997	else
	1998	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1999	fi
	2000
	2001	# INPUT-FILES TO BE LINKED
	2002	if [[ "${actionin[$i]}" = ln ]]
	2003	then
	2004
	2005	printf "\n $filetype will be linked"
	2006	if [[ $files_for_cores = false ]]
	2007	then
	2008	if [[ -f "${absnamein[$i]}" ]]
	2009	then
	2010	ln ${absnamein[$i]} ${localin[$i]}
	2011	got_tmp[$i]=true
	2012	fi
	2013	else
	2014	if [[ -d "${absnamein[$i]}" ]]
	2015	then
[2396]	2016	mkdir -p ${localin[$i]}
[2380]	2017	cd ${absnamein[$i]}
	2018	for file in $(ls *)
	2019	do
[2566]	2020	ln $file $tempdir/${localin[$i]}
[2380]	2021	done >\|/dev/null 2>&1
[2566]	2022	cd $tempdir
[2380]	2023	fi
	2024
	2025	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2026	if [[ ! -f "${localin[$i]}/_000000" ]]
	2027	then
	2028	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2029	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2030	fi
	2031
	2032	got_tmp[$i]=true
	2033	fi
	2034	fi
	2035
	2036	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2037	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2038	then
	2039
	2040	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2041	then
	2042
	2043	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2044	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2045	printf "\n file will be provided for $cores processors"
[2396]	2046	mkdir -p ${localin[$i]}
[2380]	2047	ival=$cores
	2048	(( ii = 0 ))
	2049	while (( ii <= ival-1 ))
	2050	do
	2051	if (( ii < 10 ))
	2052	then
	2053	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2054	elif (( ii < 100 ))
	2055	then
	2056	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2057	elif (( ii < 1000 ))
	2058	then
	2059	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2060	else
	2061	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2062	fi
	2063	(( ii = ii + 1 ))
	2064	done
	2065
	2066	else
	2067
	2068	if [[ $files_for_cores = true ]]
	2069	then
	2070
	2071	# PROVIDE FILES FOR EACH CORE
	2072	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2073	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2074	printf "\n providing $cores files for the respective cores"
[2396]	2075	mkdir -p ${localin[$i]}
[2380]	2076	if [[ $link_local_input = true ]]
	2077	then
	2078	printf " files will be linked\n"
	2079	cd ${absnamein[$i]}
	2080	for file in $(ls *)
	2081	do
	2082	ln -f $file ${localin[$i]}
	2083	done
[2566]	2084	cd $tempdir
[2380]	2085	fi
	2086
	2087	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2088	if [[ ! -f "${localin[$i]}/_000000" ]]
	2089	then
	2090	if [[ $link_local_input = true ]]
	2091	then
	2092	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2093	fi
	2094	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2095	fi
	2096
	2097	else
	2098
	2099	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2100	if [[ $link_local_input = true ]]
	2101	then
	2102	printf " file will be linked\n"
	2103	ln -f ${absnamein[$i]} ${localin[$i]}
	2104	fi
[2605]	2105	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2106	if [[ ! -f "${localin[$i]}" ]]
	2107	then
	2108	if [[ $link_local_input = true ]]
	2109	then
	2110	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2111	fi
[2669]	2112	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2113	then
	2114	mv ${absnamein[$i]} ${localin[$i]}
	2115	else
	2116	cp ${absnamein[$i]} ${localin[$i]}
	2117	fi
[2380]	2118	fi
	2119	fi
	2120	fi
	2121	fi
	2122
	2123	done
	2124	if (( i != 0 ))
	2125	then
[2669]	2126	if [[ $optional_files_missing = true ]]
	2127	then
	2128	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2129	fi
[2380]	2130	printf "\n$dashes\n *** all INPUT-files provided \n"
	2131	fi
	2132
	2133
	2134	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2135	(( i = 0 ))
	2136	while (( i < iic ))
	2137	do
	2138	(( i = i + 1 ))
	2139	if (( i == 1 ))
	2140	then
	2141	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2142	fi
	2143	printf "\n >>> ${in_command[$i]}"
	2144	eval ${in_command[$i]}
	2145	if (( i == iic ))
	2146	then
	2147	printf "\n$dashes\n"
	2148	fi
	2149	done
	2150
	2151
[3313]	2152	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2153	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2154	then
	2155	progress_bar_disabled=true
	2156	else
	2157	progress_bar_disabled=false
	2158	fi
	2159
	2160
[2380]	2161	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2162	# (FILE ENVPAR WILL BE READ BY PALM)
	2163	cat > ENVPAR << EOF
[3236]	2164	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2165	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2166	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2167	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2168	maximum_cpu_time_allowed = ${cpumax}.,
	2169	revision = '$global_revision',
[3313]	2170	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2171
	2172	EOF
	2173
	2174
	2175	# STARTING THE EXECUTABLE
	2176	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2177	PATH=$PATH:$tempdir
[2380]	2178
	2179
	2180	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2181	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2182	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2183	eval line=\"$line\"
	2184	execute_command="$line"
	2185
	2186
	2187	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2188	if [[ "$execute_command_for_combine" = "" ]]
	2189	then
	2190	eval line2=\"$line2\"
	2191	execute_command_for_combine="$line2"
	2192	fi
	2193
[2380]	2194
	2195
	2196	# PROVIDE A HOSTFILE, IF REQUIRED
	2197	if [[ "$hostfile" != "" ]]
	2198	then
	2199
	2200	if [[ $hostfile = auto ]]
	2201	then
	2202	# CREATE A NEW HOSTFILE
	2203	(( ii = 1 ))
	2204	while (( ii <= cores / threads_per_task ))
	2205	do
	2206	echo $(hostname) >> hostfile
	2207	(( ii = ii + 1 ))
	2208	done
	2209	if (( cores / threads_per_task == 0 ))
	2210	then
	2211	echo $(hostname) >> hostfile
	2212	fi
	2213
	2214	else
	2215	cp $hostfile hostfile
	2216	fi
	2217	eval line=\"`head -n $ii hostfile`\"
	2218	printf "\n *** running on: $line"
	2219	fi
	2220
	2221
	2222
	2223	# SET THE NUMBER OF OPENMP-THREADS
	2224	if [[ $use_openmp = true ]]
	2225	then
	2226	export OMP_NUM_THREADS=$threads_per_task
	2227	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2228	else
	2229	export OMP_NUM_THREADS=1
	2230	fi
	2231
	2232
[2610]	2233	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2234	if [[ $run_coupled_model = false ]]
	2235	then
	2236	if [[ "$ocean_file_appendix" = true ]]
	2237	then
	2238	echo "precursor_ocean" > coupling_steering
	2239	else
	2240	echo "precursor_atmos" > coupling_steering
	2241	fi
	2242	else
	2243	(( iia = $cores_atmos / $threads_per_task ))
	2244	(( iio = $cores_ocean / $threads_per_task ))
	2245	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2246	printf "\n\n"
	2247	echo "coupled_run $iia $iio" > coupling_steering
	2248	fi
	2249
	2250	printf "\n *** execute command:"
	2251	printf "\n \"$execute_command\" \n\n"
	2252
	2253
[3393]	2254	if [[ $progress_bar_disabled = true ]]
[2380]	2255	then
[3393]	2256	$execute_command < coupling_steering &> >(grep -v --line-buffered '^STOP 1$' &> >(tee STDOUT) )
	2257	exit_code=${PIPESTATUS[0]}
	2258	else
	2259	$execute_command < coupling_steering &> >(tee STDOUT)
	2260	exit_code=${PIPESTATUS[0]}
	2261	fi
[2380]	2262
[3393]	2263	if [[ ${exit_code} != 0 ]]
	2264	then
	2265
[2380]	2266	# ABORT IN CASE OF RUNTIME ERRORS
	2267	printf "\n +++ runtime error occured"
	2268	locat=execution
	2269	exit
	2270
	2271	else
	2272
	2273	printf "\n$dashes\n *** execution finished \n"
	2274
	2275	fi
	2276
	2277
	2278	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2279	# BY EACH CORE INTO ONE FILE
	2280	if [[ ! -f combine_plot_fields.x ]]
	2281	then
	2282
	2283	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2284	printf "\n 2d- and/or 3d-data may be incomplete!"
	2285	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2286
	2287	elif [[ "$combine_plot_fields" == true ]]
	2288	then
	2289
	2290	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2291	$execute_command_for_combine
	2292
	2293	else
	2294
	2295	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2296	# DATA OUTPUT
[2380]	2297	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2298	fi
	2299
	2300
	2301
	2302	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2303	(( i = 0 ))
	2304	while (( i < ioc ))
	2305	do
	2306	(( i = i + 1 ))
	2307	if (( i == 1 ))
	2308	then
	2309	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2310	fi
[2799]	2311
	2312	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2313	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2314
[2380]	2315	printf "\n >>> ${out_command[$i]}"
	2316	eval ${out_command[$i]}
	2317	if (( i == ioc ))
	2318	then
	2319	printf "\n$dashes\n"
	2320	fi
	2321	done
	2322
	2323
[2610]	2324	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2325	# WILDCARDS
[2380]	2326	(( i = 0 ))
[2610]	2327	(( nr_of_output_files = 0 ))
	2328
[2380]	2329	while (( i < iout ))
	2330	do
[2610]	2331
[2380]	2332	(( i = i + 1 ))
[2610]	2333
	2334	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2335	# CREATE A LIST FOR THE DETECTED ENDINGS
	2336	if [[ "${multout[$i]}" = true ]]
	2337	then
	2338	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2339	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2340	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2341
	2342	endings="DEFAULT"
	2343	while read line
	2344	do
	2345	# remove the local name from the beginning
	2346	localnamestring="${localout_pre[$i]}"
	2347	length_localname=${#localnamestring}
	2348	ending=${line:${length_localname}}
	2349
	2350	if [[ "$ending" != "" ]]
	2351	then
	2352	endings="$endings $ending"
	2353	fi
	2354
	2355	done <filelist
	2356
	2357	rm filelist
	2358
	2359	else
	2360
	2361	# SINGLE NAME
	2362	endings=DEFAULT
	2363
	2364	fi
	2365
	2366	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2367	for ending in $endings
	2368	do
	2369
	2370	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2371	if [[ $ending = DEFAULT ]]
	2372	then
	2373	ending=""
	2374	fi
	2375
	2376	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2377	(( nr_of_output_files = nr_of_output_files + 1 ))
	2378	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2379	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2380	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2381	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2382	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2383	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2384	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2385
	2386	done
	2387
	2388	done
	2389
	2390
	2391
	2392
	2393	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2394	(( i = 0 ))
	2395	while (( i < nr_of_output_files ))
	2396	do
	2397	(( i = i + 1 ))
[2380]	2398	if (( i == 1 ))
	2399	then
	2400	printf "\n\n *** saving OUTPUT-files:"
	2401
	2402	# GET RUN NUMBER ASSIGNED BY PALM
	2403	if [[ -f RUN_NUMBER ]]
	2404	then
	2405	read run_number < RUN_NUMBER
	2406	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2407	usecycle_option="-U $run_number"
	2408	else
	2409	run_number=0
	2410	usecycle_option=""
	2411	fi
	2412	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2413	then
[2404]	2414	printf "\n *** in case of SCP transfers to local host"
	2415	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2416	fi
	2417	printf "\n$dashes"
	2418	fi
	2419
	2420	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2421	then
	2422
[3236]	2423	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2424
	2425	# DETERMINE THE CYCLE NUMBER
	2426	ls -1 -d $filename > filelist 2>/dev/null
	2427	ls -1 -d $filename.* >> filelist 2>/dev/null
	2428	while read line
	2429	do
	2430
	2431	# filename without path (i.e. after the last "/")
	2432	basefilename=$(basename ${line})
	2433
	2434	# check if there is an extension
	2435	extension=${basefilename##*.}
	2436	if [[ "$extension" = "${extout[$i]}" ]]
	2437	then
	2438	basefilename=${basefilename%.*}
	2439	fi
	2440
	2441	# check for an existing cycle number
	2442	cycle=${basefilename##*.}
	2443	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2444	then
[2669]	2445	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2446	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2447	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2448	else
	2449	(( icycle = 1 ))
	2450	fi
	2451
	2452	if (( icycle > maxcycle ))
	2453	then
	2454	(( maxcycle = icycle ))
	2455	fi
	2456
	2457	done <filelist
	2458	rm filelist
	2459
	2460
	2461	# SET THE CYCLE NUMBER
	2462	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2463	if [[ "${actionout[$i]}" = a ]]
	2464	then
	2465	(( maxcycle = maxcycle - 1 ))
	2466	fi
	2467
	2468	(( cycnum[$i] = maxcycle ))
	2469	pathout[$i]=$filename
	2470
	2471
	2472	# ADD CYCLE NUMBER TO FILENAME
	2473	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2474	if [[ "${actionout[$i]}" != "a" ]]
	2475	then
	2476	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2477	# WITH AN EXISTING CYCLE NUMBER
	2478	if (( run_number >= cycnum[$i] ))
	2479	then
	2480	(( cycnum[$i] = run_number ))
	2481	else
	2482	if (( run_number > 0 ))
	2483	then
	2484	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2485	fi
	2486	fi
	2487	fi
	2488	if (( cycnum[$i] > 0 ))
	2489	then
[2600]	2490	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2491	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2492	fi
	2493	fi
	2494
	2495	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2496	files_for_cores=false; filetype=file
	2497	link_local_output=false
	2498	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2499	then
	2500	files_for_cores=true; filetype=directory
	2501	actionout[$i]=""
	2502	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2503	then
	2504	actionout[$i]=""
	2505	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2506	then
	2507	files_for_cores=true; filetype=directory
	2508	link_local_output=true
	2509	actionout[$i]=""
	2510	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2511	then
	2512	link_local_output
	2513	actionout[$i]=""
	2514	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2515	then
	2516	files_for_cores=true; filetype=directory
	2517	actionout[$i]="tr"
	2518	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2519	then
	2520	actionout[$i]="tr"
	2521	fi
	2522
	2523	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2524	then
[2669]	2525	if [[ ${warnout[$i]} = true ]]
	2526	then
	2527	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2528	fi
[2380]	2529	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2530	then
[2669]	2531	if [[ ${warnout[$i]} = true ]]
	2532	then
	2533	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2534	fi
[2380]	2535	else
	2536
	2537
	2538	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2539	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2540	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2541	then
	2542	if [[ $running_on_remote = true ]]
	2543	then
	2544
	2545	# SET OPTIONS FOR TRANSFER
	2546	if [[ "${actionout[$i]}" = tr ]]
	2547	then
	2548	if [[ $files_for_cores = false ]]
	2549	then
	2550	catalog_option=""
	2551	catalog_string=""
	2552	else
	2553	catalog_option="-c"
	2554	catalog_string="/"
	2555	fi
	2556	append_option=""
	2557	append_string=""
	2558	else
	2559	append_option="-A"
	2560	append_string="append"
	2561	fi
	2562
	2563	transfer_failed=false
	2564	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2565	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2566
	2567	# TRANSFER VIA SCP
	2568	if [[ "$remote_loginnode" != "" ]]
	2569	then
[3236]	2570	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]	2571	else
[3236]	2572	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]	2573	fi
[3312]	2574	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2575
	2576
	2577	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2578	if [[ $transfer_failed = true ]]
	2579	then
	2580	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2581	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2582
	2583	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2584	eval local_catalog=${pathout[$i]}
	2585	if [[ ! -d $local_catalog ]]
	2586	then
	2587	printf " *** local directory does not exist. Trying to create:\n"
	2588	printf " $local_catalog \n"
	2589	mkdir -p $local_catalog
	2590	fi
[3236]	2591	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2592	transfer_problems=true
	2593	fi
	2594
	2595	else
	2596
	2597	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2598	# BE COPIED OR APPENDED ON THIS MACHINE
	2599	if [[ "${actionout[$i]}" = tr ]]
	2600	then
	2601	actionout[$i]=""
	2602	else
	2603	actionout[$i]="a"
	2604	fi
	2605	fi
	2606	fi
	2607
	2608
	2609	# APPEND ON THIS MACHINE
	2610	if [[ "${actionout[$i]}" = "a" ]]
	2611	then
	2612	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2613	then
	2614	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2615	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2616	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2617	else
	2618	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2619	printf "\n ${pathout[$i]}\n"
	2620	cat ${localout[$i]} >> ${pathout[$i]}
	2621	fi
	2622	fi
	2623
	2624	# COPY ON THIS MACHINE
	2625	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2626	# ON DIFFERENT FILE-SYSTEMS
	2627	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2628	then
	2629
	2630	# COPY IN CASE OF RUNS ON SINGLE CORES
	2631	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2632	then
	2633	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2634	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2635	if [[ $link_local_output = true ]]
	2636	then
	2637	printf " file will be linked\n"
	2638	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2639	fi
	2640	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2641	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2642	then
	2643	if [[ $link_local_output = true ]]
	2644	then
	2645	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2646	fi
	2647	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2648	else
	2649	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2650	fi
	2651	else
	2652	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2653	printf "\n ${pathout[$i]}\n"
	2654	if [[ $link_local_output = true ]]
	2655	then
	2656	printf " file will be linked\n"
	2657	ln -f ${localout[$i]} ${pathout[$i]}
	2658	fi
	2659	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2660	if [[ ! -f "${pathout[$i]}" ]]
	2661	then
	2662	if [[ $link_local_output = true ]]
	2663	then
	2664	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2665	fi
	2666	cp ${localout[$i]} ${pathout[$i]}
	2667	else
	2668	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2669	fi
	2670	fi
	2671
	2672	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2673	then
	2674
	2675	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2676	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2677	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2678	printf "\n ${pathout[$i]}\n"
	2679	if [[ $link_local_output = true ]]
	2680	then
	2681	printf " files will be linked\n"
[2396]	2682	mkdir -p ${pathout[$i]}
[2380]	2683	cd ${localout[$i]}
	2684	for file in $(ls *)
	2685	do
	2686	ln -f $file ${pathout[$i]}
	2687	done >\|/dev/null 2>&1
[2566]	2688	cd $tempdir
[2380]	2689	fi
	2690
	2691	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2692	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2693	then
	2694	if [[ $link_local_output = true ]]
	2695	then
	2696	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2697	fi
[3025]	2698	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2699	cp -r ${localout[$i]}/* ${pathout[$i]}
	2700	fi
	2701
	2702	fi
	2703	fi
	2704	done
	2705
	2706	if (( i != 0 ))
	2707	then
	2708	if [[ $transfer_problems = true ]]
	2709	then
	2710	printf "\n$dashes\n *** OUTPUT-files saved"
	2711	printf "\n +++ WARNING: some data transfers failed! \n"
	2712	else
	2713	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2714	fi
	2715	fi
	2716
	2717
	2718	# IF REQUIRED, START A RESTART-JOB
	2719	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2720	if [[ -f CONTINUE_RUN ]]
	2721	then
	2722
	2723	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2724	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2725	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2726	# -b START A BATCH JOB
	2727	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2728	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2729	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2730
[2957]	2731	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2732	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2733	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2734	then
	2735	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2736	fi
[2380]	2737
	2738	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2739	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2740	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2741	then
[2381]	2742	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2743	fi
	2744
	2745
	2746	# START THE RESTART-JOB
	2747	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2748	echo " $prc"
	2749	printf "\n$dashes\n"
	2750	if [[ $running_on_remote = true ]]
	2751	then
	2752
	2753	echo "*** ssh will be used to initiate restart-runs!"
	2754	echo " return_address=\"$return_address\" "
	2755	echo " return_username=\"$local_username\" "
	2756
	2757	if [[ "$remote_loginnode" != "" ]]
	2758	then
[3132]	2759	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]	2760	else
[3132]	2761	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
[2380]	2762	fi
	2763
	2764	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2765	sleep 30
	2766
	2767	else
	2768
	2769	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2770	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2771	cd - > /dev/null
	2772
	2773	fi
	2774
[3132]	2775	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2776	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2777	then
	2778	printf "\n$dashes\n +++ creating restart run failed \n"
	2779	locat=create_restart
	2780	exit
	2781	rm palmrun_restart.log
	2782	else
	2783	printf "\n$dashes\n *** restart run initiated \n"
	2784	rm palmrun_restart.log
	2785	fi
[2380]	2786
[3132]	2787
[2380]	2788	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2789	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2790	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2791	# MAY BE VERY HUGE)
	2792	(( i = 0 ))
[2610]	2793	while (( i < nr_of_input_files ))
[2380]	2794	do
	2795	(( i = i + 1 ))
	2796	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2797	then
	2798	rm -r ${absnamein[$i]}
	2799	fi
	2800	done
	2801
	2802	fi
	2803
	2804
	2805	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2806	cd $HOME
[2566]	2807	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2808
	2809
	2810	else
	2811
	2812
	2813	# PREPARING ACTIONS,
	2814	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2815
	2816	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3236]	2817	palmrun_com="$palmrun_script_name -d $run_identifier -h $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2818	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2819	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2820	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2821	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2822	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2823	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2824	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2825	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2826	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2827	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2828	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2829	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2830	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2831	if [[ $create_remote_batch_job = true ]]
	2832	then
	2833	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2834	if [[ $do_trace = true ]]
	2835	then
	2836	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2837	fi
[2380]	2838	elif [[ $create_batch_job = true ]]
	2839	then
	2840	palmrun_com=${palmrun_com}" -j"
[2420]	2841	if [[ $do_trace = true ]]
	2842	then
	2843	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2844	fi
[2380]	2845	fi
	2846
	2847
	2848	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2849	# REMOTE HOST
[3236]	2850	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2851	job_protocol_file=$job_protocol_file_local
	2852	if [[ $create_remote_batch_job = true ]]
	2853	then
[3236]	2854	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2855	job_protocol_file=$job_protocol_file_remote
	2856	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2857	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2858	fi
	2859
	2860
	2861	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2862	jobfile=jobfile.$run_id_number
[2380]	2863
	2864
	2865	# FIRST CREATE THE BATCH DIRECTIVES
	2866	(( i = 0 ))
	2867	while (( i < ibd ))
	2868	do
	2869	(( i = i + 1 ))
[2693]	2870	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2871	eval line=\"$line\"
	2872	echo "$line" >> $jobfile
	2873	done
	2874	echo " " >> $jobfile
	2875
	2876
	2877	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2878	# PROTOCOL
	2879	if [[ $create_remote_batch_job = true ]]
	2880	then
[3236]	2881	echo "set +vx" >> $jobfile
	2882	echo "trap '" >> $jobfile
	2883	echo "set +vx" >> $jobfile
	2884	echo "cd ${remote_jobcatalog}" >> $jobfile
	2885	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2886
	2887	# ADD THE BATCH DIRECTIVES
	2888	(( i = 0 ))
	2889	while (( i < ibdt ))
	2890	do
	2891	(( i = i + 1 ))
[2693]	2892	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2893	eval line=\"$line\"
	2894	echo "$line" >> $jobfile
	2895	done
	2896	echo " " >> $jobfile
	2897
	2898	echo "set -x" >> $jobfile
[3236]	2899	echo "${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]	2900	echo "%%END%%" >> $jobfile
	2901	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2902	echo "$submit_command $scpjob_file" >> $jobfile
	2903	echo "rm $scpjob_file" >> $jobfile
[2404]	2904	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2905	echo "set -x" >> $jobfile
	2906	echo " ' exit" >> $jobfile
	2907	fi
	2908
	2909
	2910	# ACTIVATE ERROR-TRACEBACK
	2911	if [[ $do_trace = true ]]
	2912	then
	2913	echo "set -x" >> $jobfile
	2914	else
	2915	echo "set +vx" >> $jobfile
	2916	fi
	2917
	2918
	2919	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2920	if [[ "$login_init_cmd" != "" ]]
	2921	then
	2922	echo "$login_init_cmd" >> $jobfile
	2923	fi
	2924	if [[ "$module_commands" != "" ]]
	2925	then
	2926	echo "$module_commands" >> $jobfile
	2927	fi
	2928
	2929
	2930	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2931	if [[ $create_remote_batch_job = true ]]
	2932	then
	2933	echo "mkdir $tempdir" >> $jobfile
	2934	echo "chmod go+rx $tempdir" >> $jobfile
	2935	else
	2936	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2937	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2938	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2939	mkdir $tempdir
	2940	chmod go+rx $tempdir
	2941	fi
	2942	echo "cd $tempdir" >> $jobfile
	2943	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2944	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2945	echo "export PATH=.:\$PATH" >> $jobfile
	2946	echo "export execute_palmrun=true" >> $jobfile
	2947
	2948
	2949	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2950	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2951	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2952	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2953	echo "export LOCAL_PWD" >> $jobfile
	2954
	2955
	2956	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2957	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2958	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2959
	2960
	2961	# CALL PALMRUN WITHIN THE JOB
	2962	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2963	echo "set -x" >> $jobfile
	2964	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2965
	2966
	2967	# TRANSFER JOBFILE TO THE TARGET HOST
	2968	if [[ $create_jobfile_only = false ]]
	2969	then
	2970
	2971	if [[ $create_remote_batch_job = true ]]
	2972	then
	2973
[2420]	2974	echo " "
[2566]	2975	echo " *** transfer of job to remote host via scp"
[2420]	2976	if [[ $do_trace = true ]]
	2977	then
[3236]	2978	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	2979	fi
[3236]	2980	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	2981
[2566]	2982	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2983	if [[ $do_trace = true ]]
	2984	then
[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"
[2420]	2986	fi
[3236]	2987	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]	2988
	2989	elif [[ $create_batch_job = true ]]
	2990	then
	2991
[2385]	2992	eval local_jobcatalog=$local_jobcatalog
[3236]	2993	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	2994	cd $local_jobcatalog
[2380]	2995	echo " "
[2420]	2996	echo " *** submit the job"
	2997	if [[ $do_trace = true ]]
	2998	then
[3236]	2999	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3000	fi
[3236]	3001	$submit_command ${configuration_identifier}_${run_id}
	3002	rm ${configuration_identifier}_${run_id}
[2380]	3003	cd - > /dev/null
	3004
	3005	fi
	3006
	3007	rm -rf $jobfile
	3008
	3009	else
	3010
	3011	printf "\n *** jobfile created under name \"$jobfile\" "
	3012	printf "\n no batch-job has been sent!"
	3013
	3014	fi
	3015
	3016	fi # END OF REMOTE-PART

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