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source: palm/trunk/SCRIPTS/palmrun @ 3505

Last change on this file since 3505 was 3505, checked in by raasch, 5 years ago
job folders are created in case that they do not exist
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 101.4 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 3505 2018-11-08 09:14:30Z raasch $
[3505]	29	# job folders are created in case that they do not exist
	30	#
	31	# 3455 2018-10-30 14:12:31Z raasch
[3455]	32	# options -h and -d renamed -c and -r, respectively
	33	#
	34	# 3402 2018-10-23 11:49:24Z knoop
[3346]	35	# job_id is set for compatibility reasons with older versions of config files
	36	#
	37	# 3313 2018-10-06 15:22:48Z knoop
[3294]	38	# more detailed error message for outdated fileconnection file
	39	#
	40	# 3236 2018-09-10 09:07:06Z raasch
[3236]	41	# warning issued in case of file connection file version mismatch,
	42	# host_configuration renamed configuration_identifier,
	43	# "host identifier" in header output renamed "config. identifier",
	44	# jobname renamed run_identifier,
	45	# run_id renamed run_id_number
	46	# job_id renamed run_id
	47	# option -r renamed -i
	48	#
	49	# 3151 2018-07-19 08:45:38Z raasch
[3151]	50	# removed additional listing of files to be compiled, print PALM code revision
	51	# in header
	52	#
	53	# 3132 2018-07-16 11:44:58Z raasch
[3132]	54	# create consistent error messages in case of failed restarts,
	55	# check existence of remote job catalog
	56	#
	57	# 3043 2018-05-25 10:47:54Z raasch
[3043]	58	# check for setting of fast_io_catalog
	59	#
	60	# 3033 2018-05-23 15:26:19Z raasch
[3025]	61	# -T option not required for interactive runs (tasks per node =
	62	# total number of cores is assumed as default, if option is not given),
	63	# reformatting of a few messages,
	64	# bugfix: destination output directory is created if attribute "pe" is set in
	65	# .palm.iofiles
	66	#
	67	# 2718 2018-01-02 08:49:38Z maronga
[2993]	68	# bugfix of r2990
	69	#
	70	# 2718 2018-01-02 08:49:38Z maronga
[2990]	71	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	72	# not in the working directory from where palmrun is called
	73	#
	74	# 2718 2018-01-02 08:49:38Z maronga
[2957]	75	# svfout in the activation string will be replaced now by svfin in case of
	76	# automatic restarts
	77	#
	78	# 2718 2018-01-02 08:49:38Z maronga
[2906]	79	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	80	# the possible output or input of sky view factors
	81	#
	82	# 2718 2018-01-02 08:49:38Z maronga
[2834]	83	# "fname" renamed to "jobname"
	84	#
	85	# 2718 2018-01-02 08:49:38Z maronga
[2799]	86	# parameters are allowed in output commands (OC:)
	87	#
	88	# 2718 2018-01-02 08:49:38Z maronga
[2789]	89	# bugfix: exit if no queue has been given neither with option -q nor in the
	90	# configuration file
	91	#
	92	# 2718 2018-01-02 08:49:38Z maronga
[2762]	93	# file connection file from trunk/SCRIPTS is taken by default
	94	#
	95	# 2718 2018-01-02 08:49:38Z maronga
[2716]	96	# Corrected "Former revisions" section
	97	#
	98	# 2696 2017-12-14 17:12:51Z kanani
	99	# Change in file header (GPL part)
	100	#
	101	# 2693 2017-12-13 12:33:49Z raasch
[2693]	102	# replacement of variables given by {{<variable>}} in configuration file is now
	103	# done in a more general way, variable names are written in small letters
	104	#
	105	# 2670 2017-12-06 16:32:19Z raasch
[2670]	106	# test printouts removed
	107	#
	108	# 2669 2017-12-06 16:03:27Z raasch
[2669]	109	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	110	# removed,
	111	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	112	# files,
	113	# informative messages in case of missing optional input files shortened
	114	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	115	#
	116	# 2638 2017-11-23 12:44:23Z raasch
[2610]	117	# use of wildcards in file connection statements enabled
	118	#
	119	# 2605 2017-11-09 15:31:46Z raasch
[2605]	120	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	121	# will not be sent with the job file any more, but copied into the
[2610]	122	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	123	#
	124	# 2600 2017-11-01 14:11:20Z raasch
[2600]	125	# cycle numbers are made three digits wide
	126	#
	127	# 2566 2017-10-20 08:50:47Z raasch
[2566]	128	# execute command for combine_plot_fields added
	129	# "TEMPDIR" renamed "tempdir"
	130	# temporary working directory for local batch jobs is created immediately within
	131	# the user's palmrun call, due to a requirement of the "grid engine" batch
	132	# system, where the working directory is given with batch directive -wd and must
	133	# already exist when the job is submitted,
	134	# informative messages in non-trace mode reduced and partly reformatted
	135	#
	136	# 2551 2017-10-18 07:25:11Z raasch
[2551]	137	# TEMPDIR added as replacement string to be used in batch directives
	138	#
	139	# 2512 2017-10-04 08:26:59Z raasch
[2507]	140	# bugfix for determining cycle numbers of NetCDF input files
	141	#
	142	# 2506 2017-09-29 08:30:37Z raasch
[2506]	143	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	144	# host configuration added to SOURCES_FOR_RUN_... folder name
	145	# host_identifier renamed host_configuration
	146	# option -W added to allow for job dependencies
	147	#
	148	# 2501 2017-09-26 11:41:55Z raasch
[2501]	149	# default value for number of cores (option -X) set to 1
	150	# bugfix for mechanism which overwrites configuration file settings with values
	151	# provided by palmrun options
	152	#
	153	# 2499 2017-09-22 16:47:58Z kanani
[2499]	154	# option -h named configuration identifier
	155	#
	156	# 2480 2017-09-19 06:24:14Z maronga
[2480]	157	# bugfix for last revision
	158	#
	159	# 2479 2017-09-19 06:12:16Z raasch
[2479]	160	# option -A (project account number) added
	161	#
	162	# 2422 2017-09-08 08:25:41Z raasch
[2410]	163	# initial revision
[2380]	164	#
	165	#--------------------------------------------------------------------------------#
	166	# palmrun - script for running PALM jobs on local and remote hosts
	167	#--------------------------------------------------------------------------------#
	168
	169
	170
	171	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	172
	173	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	174	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	175	# (TOO MANY ARGUMENTS - PROBLEM)
	176	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	177
[2610]	178	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	179	typeset -i nr_of_output_files=0
[2380]	180	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	181	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	182	# SCRIPT-OPTION ARGUMENTS
	183	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	184	typeset -i icycle inode ival maxcycle mpi_tasks
	185	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	186
	187	activation_string_list=""
	188	AddFilenames=""
	189	combine_plot_fields=true
	190	compiler_name=""
	191	compiler_name_ser=""
	192	compiler_options=""
[3236]	193	configuration_identifier="default"
[2501]	194	cores=1
[2380]	195	cores_atmos=0
	196	cores_ocean=0
	197	coupled_dist=""
	198	cpp_options=""
	199	cpumax=0
[2506]	200	create_batch_job=false
[2380]	201	create_jobfile_only=false
	202	create_remote_batch_job=false
	203	dashes=" ----------------------------------------------------------------------------"
	204	defaultqueue=""
[2506]	205	delete_temporary_catalog=true
[2380]	206	do_compile=true
	207	do_trace=false
	208	executable=""
	209	execute_command=""
	210	execution_error=false
[2762]	211	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	212	global_revision=""
	213	hostfile=""
	214	hp=""
	215	keep_data_from_previous_run=false
	216	link_local_input=false
	217	link_local_output=false
[2388]	218	linker_options=""
[2385]	219	local_jobcatalog=""
[2380]	220	locat=normal
	221	makefile=""
	222	max_par_io_str=""
	223	prc=$0
	224	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	225	do
	226	prc=`echo $prc \| cut -f2- -d"/"`
	227	done
	228	module_calls=""
[2506]	229	palmrun_memory=""
[2380]	230	palmrun_script_name=$prc
	231	openmp=false
[2506]	232	previous_job=""
[2479]	233	project_account=""
[2380]	234	queue=none
[2906]	235	read_svf=""
[2380]	236	restart_run=false
	237	return_address=""
[2385]	238	remote_jobcatalog=""
[2380]	239	remote_username=""
	240	running_in_batch_mode=false
[3313]	241	running_in_test_mode=false
[2380]	242	run_coupled_model=false
	243	run_id=""
[3236]	244	run_id_number=""
	245	run_identifier=test
[2380]	246	silent=false
	247	source_list=""
	248	source_path=""
[2501]	249	tasks_per_node=0
[2380]	250	threads_per_task=1
	251	transfer_problems=false
[2384]	252	user_source_path=""
[2506]	253	use_existing_sources_folder=""
[2380]	254	use_openmp=false
[3033]	255	version="palmrun 1.0 Rev$Rev: 3505 $"
[2380]	256	working_directory=`pwd`
	257	write_binary=""
[2906]	258	write_svf=""
[2380]	259
	260
	261	# ERROR HANDLING IN CASE OF EXIT
[2404]	262	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	263	then
	264
	265	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	266	(( i = 0 ))
	267	while (( i < iec ))
	268	do
	269	(( i = i + 1 ))
	270	printf "\n *** Execution of ERROR-command:\n"
	271	printf " >>> ${err_command[$i]}\n"
	272	eval ${err_command[$i]}
	273	done
[2566]	274	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	275	printf "\n\n+++ palmrun crashed \n\n"
	276	exit 1
	277	elif [[ $locat != normal ]]
[2380]	278	then
[3312]	279	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	280	printf "\n+++ palmrun killed by \"^C\" \n\n"
	281	exit 2
	282	else
[2566]	283	printf "\n --> palmrun finished\n\n"
[3312]	284	exit 0
[2380]	285	fi' exit
	286
	287
	288	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	289	trap 'locat=control_c
	290	exit 1
[2380]	291	' 2
	292
	293
	294	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	295	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	296	while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
[2380]	297	do
	298	case $option in
	299	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	300	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	301	(b) create_batch_job=true; prc="$prc -b";;
	302	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	303	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	304	(C) restart_run=true; prc="$prc -C";;
	305	(F) create_jobfile_only=true;;
	306	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	307	(i) run_id_number=$OPTARG;;
[2380]	308	(j) running_in_batch_mode=true;;
	309	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	310	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	311	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	312	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	313	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	314	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	315	(R) return_address=$OPTARG;;
	316	(s) source_list=$OPTARG;;
[2501]	317	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	318	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	319	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	320	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	321	(v) silent=true; prc="$prc -v";;
[2506]	322	(V) use_existing_sources_folder="-V";;
[2380]	323	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	324	(W) previous_job=$OPTARG;;
[2380]	325	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	326	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	327	(y) ocean_file_appendix=true; prc="$prc -y";;
	328	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	329	(z) running_in_test_mode=true;;
[2380]	330	(Z) combine_plot_fields=false; prc="$prc -Z";;
	331	(\?) printf "\n +++ unknown option $OPTARG \n"
	332	printf "\n --> type \"$0 ?\" for available options \n"
	333	locat=parameter;exit;;
	334	esac
	335	done
	336
	337
	338	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	339	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	340	(( to_shift = $OPTIND - 1 ))
	341	shift $to_shift
	342
	343	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	344	if [[ "$1" = "?" ]]
	345	then
	346	(printf "\n *** Description of available palmrun options:\n"
	347	printf "\n Option Description Default-Value"
	348	printf "\n -a activation string list \"\" "
[2479]	349	printf "\n -A project account number ---"
[2380]	350	printf "\n -b batch-job on local machine ---"
	351	printf "\n -B do not delete temporary directory at end ---"
[3455]	352	printf "\n -c configuration identifier \"default\" "
[2380]	353	printf "\n -F create batch job file only ---"
	354	printf "\n -k keep data from previous run"
	355	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	356	printf "\n -M Makefile name Makefile"
	357	printf "\n -O threads per openMP task ---"
	358	printf "\n -q queue \"$queue\" "
[3455]	359	printf "\n -r run identifier test"
[2380]	360	printf "\n -s filenames of routines to be compiled \"\" "
	361	printf "\n must end with .f, .f90, .F, or .c !"
	362	printf "\n use \"..\" for more than one file and wildcards"
	363	printf "\n -s LM compiles all locally modified files"
	364	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	365	printf "\n -T tasks per node ---"
[2380]	366	printf "\n -u username on remote machine \"\" "
	367	printf "\n -v no prompt for confirmation ---"
[2506]	368	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	369	printf "\n -w maximum parallel io streams as given by -X"
[2506]	370	printf "\n -W name of job to wait for ---"
[2380]	371	printf "\n -x tracing of palmrun for debug purposes ---"
	372	printf "\n -X # of processors (on parallel machines) 1"
	373	printf "\n -y add appendix \"_O\" to all local output"
	374	printf "\n files (ocean precursor runs followed by"
	375	printf "\n coupled atmosphere-ocean runs) ---"
	376	printf "\n -Y run coupled model, \"#1 #2\" with"
	377	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	378	printf "\n -Z skip combine_plot_fields at the end of "
	379	printf "\n the simulation ---"
	380	printf "\n "
	381	printf "\n Possible values of positional parameter <modus>:"
	382	printf "\n \"?\" - this outline \n\n") \| more
	383	exit
	384	elif [[ "$1" != "" ]]
	385	then
	386	printf "\n +++ positional parameter $1 unknown \n"
	387	locat=parameter; exit
	388	fi
	389
	390
	391
	392	# SHORT STARTING MESSAGE
	393	printf "\n*** $version "
	394	printf "\n will be executed. Please wait ..."
	395
	396
[2506]	397	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	398	config_file=.palm.config.$configuration_identifier
	399	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	400
	401
	402	# CHECK, IF CONFIGURATION FILE EXISTS
	403	if [[ ! -f $config_file ]]
	404	then
	405	printf "\n\n +++ configuration file: "
	406	printf "\n $config_file"
	407	printf "\n does not exist"
	408	locat=connect; exit
	409	fi
	410
	411
[2762]	412	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	413	if [[ -f .palm.iofiles ]]
	414	then
[3236]	415
	416	# CHECK VERSION MISMATCH
	417	if [[ $running_in_batch_mode != true ]]
	418	then
	419	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	420	then
	421	printf "\n\n +++ WARNING: A file connection file has been found in your"
	422	printf "\n working directory, but its revision does not match"
	423	printf "\n the revision of the default (trunk) version."
[3294]	424	printf "\n You may need to update your connection file"
	425	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	426	fi
	427	fi
	428
[2762]	429	fileconnection_file=.palm.iofiles
[3236]	430
[2762]	431	fi
	432
	433
[2380]	434	# CHECK, IF FILE CONNECTION FILE EXISTS
	435	if [[ ! -f $fileconnection_file ]]
	436	then
	437	printf "\n\n +++ file connection file: "
	438	printf "\n $fileconnection_file"
	439	printf "\n does not exist"
	440	locat=connect; exit
	441	fi
	442
	443
[2404]	444	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	445	if [[ "$activation_string_list" = "" ]]
	446	then
	447	printf "\n\n +++ no activation string list given: "
	448	printf "\n please set palmrun option \"-a\" "
	449	locat=palmrun_option; exit
	450	fi
	451
	452
	453	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	454	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	455	then
	456	write_binary=true
	457	else
	458	write_binary=false
	459	fi
	460
[2906]	461	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	462	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	463	then
	464	write_svf=true
	465	else
	466	write_svf=false
	467	fi
[2404]	468
[2906]	469	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	470	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	471	then
	472	read_svf=true
	473	else
	474	read_svf=false
	475	fi
	476
	477
[2380]	478	# READ AND EVALUATE THE CONFIGURATION-FILE
	479	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	480
	481	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	482	while read line
	483	do
	484
	485	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	486	eval line=\"$line\"
	487
	488
	489	# INTERPRET THE LINE
	490	if [[ "$(echo $line)" = "" ]]
	491	then
	492
	493	# EMPTY LINE, NO ACTION
	494	continue
	495
	496	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	497	then
	498
	499	# LINE IS A COMMENT LINE
	500	continue
	501
	502	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	503	then
	504
	505	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	506	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	507	value=`echo $line \| cut -d" " -s -f2-`
	508
	509
	510	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	511	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	512	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	513	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	514	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	515	# CONFIGURATION-FILE.
	516	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	517	then
	518	eval export $var="\$value"
	519
	520	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	521	if [[ $do_trace = true ]]
	522	then
	523	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	524	fi
	525	fi
	526
	527	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	528	then
	529
	530	# LINE DEFINES BATCH-DIRECTIVE
	531	(( ibd = ibd + 1 ))
	532	line=$(echo $line \| cut -c4-)
	533	batch_directive[$ibd]="$line"
	534
	535	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	536	then
	537
	538	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	539	# REMOTE TO A LOCAL HOST
	540	(( ibdt = ibdt + 1 ))
	541	line=$(echo $line \| cut -c5-)
	542	batch_directive_transfer[$ibdt]="$line"
	543
	544	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	545	then
	546
	547	# LINE DEFINES ERROR-COMMAND
	548	(( iec = iec + 1 ))
	549	line=$(echo $line \| cut -c4-)
	550	err_command[$iec]="$line"
	551
	552	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	553	then
	554
	555	# LINE DEFINES INPUT-COMMAND
	556	(( iic = iic + 1 ))
	557	line=$(echo $line \| cut -c4-)
	558	in_command[$iic]="$line"
	559
	560	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	561	then
	562
	563	# LINE DEFINES OUTPUT-COMMAND
	564	(( ioc = ioc + 1 ))
	565	line=$(echo $line \| cut -c4-)
	566	out_command[$ioc]="$line"
	567
	568	else
	569
	570	# SKIP ALL OTHER LINES
	571	continue
	572
	573	fi
	574
	575	done < $config_file
	576
	577
	578	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	579	if [[ "$fast_io_catalog" = "" ]]
	580	then
	581	printf "\n +++ no fast_io_catalog found in $config_file"
	582	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	583	locat=config_file; exit
	584	fi
[2380]	585	if [[ "$compiler_name" = "" ]]
	586	then
	587	printf "\n +++ no compiler name found in $config_file"
	588	printf "\n Please add line \"compiler_name ...\" to that file."
	589	locat=config_file; exit
	590	fi
	591	if [[ "$compiler_name_ser" = "" ]]
	592	then
	593	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	594	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	595	locat=config_file; exit
	596	fi
	597	if [[ "$compiler_options" = "" ]]
	598	then
	599	printf "\n +++ no compiler options found in $config_file"
	600	printf "\n Please add line \"compiler_options ...\" to that file."
	601	locat=config_file; exit
	602	fi
[2388]	603	if [[ "$linker_options" = "" ]]
[2380]	604	then
[2388]	605	printf "\n +++ no linker options found in $config_file"
	606	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	607	locat=config_file; exit
	608	fi
	609	if [[ "$execute_command" = "" ]]
	610	then
	611	printf "\n +++ no execute command found in $config_file"
	612	printf "\n Please add line \"execute_command ...\" to that file."
	613	locat=config_file; exit
	614	fi
	615
	616	if [[ "$hostfile" != "" ]]
	617	then
	618	if [[ $hostfile != auto && ! -f $hostfile ]]
	619	then
	620	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	621	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	622	locat=config_file; exit
	623	fi
	624	fi
	625
	626
	627	# DETERMINE THE CALL STATUS
	628	if [[ "$return_address" != "" ]]
	629	then
	630
	631	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	632	# BATCH MODE AND ...
	633	running_on_remote=true
	634
	635	else
	636
	637	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	638	if [[ "$remote_ip" != "" ]]
	639	then
	640
	641	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	642	create_remote_batch_job=true
	643
[3132]	644	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	645	if [[ "$remote_jobcatalog" = "" ]]
	646	then
	647	printf "\n +++ no remote jobcatalog found in $config_file"
	648	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	649	locat=config_file; exit
	650	fi
	651
	652
[2380]	653	fi
	654	running_on_remote=false
	655	fi
	656
	657
	658
	659	# READ AND EVALUATE THE I/O-FILE LIST
	660	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	661
	662	# READ THE FILE CONNECTION FILE LINE BY LINE
	663	while read line
	664	do
	665
[2669]	666	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	667	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	668
	669	# INTERPRET THE LINE
	670	if [[ "$(echo $line)" = "" ]]
	671	then
	672	# EMPTY LINE, NO ACTION
	673	continue
	674
	675	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	676	then
	677
	678	# LINE IS A COMMENT LINE
	679	true
	680
	681	else
	682
	683	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	684	# s2a: in/out - field
[2669]	685	# s2b: action - field (optional)
	686	s1=`echo "$line" \| cut -d" " -f1`
	687	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	688	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	689	then
[2669]	690	s2a=$s2
[2380]	691	s2b=""
	692	else
[2669]	693	s2a=`echo $s2 \| cut -d":" -f1`
	694	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	695	fi
[2669]	696	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	697	s4=`echo "$line" \| cut -d" " -s -f4`
	698	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	699	s5=`echo "$line" \| cut -d" " -s -f5`
	700	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	701
	702
	703	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	704	# INPUT- OR OUTPUT-LIST.
	705	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	706	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	707	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	708	# IS NOT CHECKED AND STORED.
[2610]	709	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	710	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	711	then
	712	found=false
	713	for actual in $activation_string_list
	714	do
	715	for formal in $s3
	716	do
	717	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	718	done
	719	done
	720	if [[ $found = true ]]
	721	then
	722	(( iin = iin + 1 ))
[2669]	723	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	724	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	725	if [[ "$s2a" = inopt ]]
	726	then
	727	optin_pre[$iin]=yes
	728	else
	729	optin_pre[$iin]=no
	730	fi
[2605]	731
	732	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	733	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	734	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	735	then
[2610]	736	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	737	fi
	738
[2610]	739	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	740	# THE WILDCARD FROM THE ENDING
	741	if [[ "${s5: -1}" = "*" ]]
	742	then
[2669]	743	if [[ "$s2b" = "di" ]]
[2610]	744	then
	745	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	746	printf "\n see file \"$fileconnection_file\", line"
	747	printf "\n$line"
	748	locat=iofiles_file; exit
	749	fi
	750	multin[$iin]=true
	751	string=${endin_pre[$iin]}
	752	endin_pre[$iin]="${string%?}"
	753	else
	754	multin[$iin]=false
	755	fi
[2380]	756	fi
[2669]	757	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	758	then
	759	found=false
	760	for actual in $activation_string_list
	761	do
	762	for formal in $s3
	763	do
[2670]	764	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	765	done
	766	done
	767	if [[ $found = true ]]
	768	then
	769	(( iout = iout + 1 ))
[2669]	770	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	771	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	772
[2669]	773	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	774	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	775	if [[ $formal = wildcard ]]
	776	then
	777	warnout_pre[$iout]=false
	778	else
	779	warnout_pre[$iout]=true
	780	fi
	781
[2610]	782	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	783	# THE WILDCARD FROM THE LOCAL FILENAME
	784	if [[ "${s1: -1}" = "*" ]]
	785	then
[2669]	786	if [[ "$s2b" = "di" ]]
[2610]	787	then
	788	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	789	printf "\n see file \"$fileconnection_file\", line"
	790	printf "\n$line"
	791	locat=iofiles_file; exit
	792	fi
	793	multout[$iout]=true
	794	string=${localout_pre[$iout]}
	795	localout_pre[$iout]="${string%?}"
	796	else
	797	multout[$iout]=false
	798	fi
[2380]	799	fi
[2669]	800	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	801	then
[2669]	802	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	803	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	804	locat=connect; exit
	805	fi
	806	IFS="$IFSALT"
	807	fi
	808
	809	done < $fileconnection_file
	810
	811
	812
[2501]	813	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	814	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	815	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	816	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	817	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	818	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	819
	820
	821
[2380]	822	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	823	if [[ $run_coupled_model = true ]]
	824	then
	825
	826	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	827	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	828
	829	if (( $cores_ocean + $cores_atmos != $cores ))
	830	then
	831
	832	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	833	printf "\n PEs (total) : $cores"
	834	printf "\n PEs (atmosphere): $cores_atmos"
	835	printf "\n PEs (ocean) : $cores_ocean"
	836	locat=coupling; exit
	837
	838	fi
	839
	840	fi
	841
	842
	843	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	844	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	845	# FOLDER
	846	if [[ $running_in_batch_mode = true ]]
	847	then
	848
[2506]	849	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	850	then
[2506]	851	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	852	printf "\n Please check the output of the palmrun-call"
	853	printf "\n that you did on your local host."
	854	locat=SOURCES_FOR_RUN; exit
	855	fi
	856
	857	else
	858
	859	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	860	# AUTOMATIC RESTART RUN
	861	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	862	if [[ $restart_run = false ]]
	863	then
	864
	865	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	866	# THE LOCAL HOST
	867	if [[ ! -d $source_path ]]
	868	then
	869	printf "\n\n +++ source path \"$source_path\" on local host"
	870	printf "\n \"$(hostname)\" does not exist"
	871	locat=source_path; exit
	872	fi
	873
[2990]	874	rm -rf ${base_directory}/${sources_for_run_catalog}
	875	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	876
	877	if [[ "$source_list" = LM ]]
	878	then
	879
	880	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	881	source_list=""
	882	cd $source_path
	883
	884
[2512]	885	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	886	if [[ ! -d ../.svn ]]
[2380]	887	then
	888	printf "\n\n +++ source directory"
	889	printf "\n \"$source_path\" "
	890	printf "\n is not under control of \"subversion\"."
[2512]	891	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	892	fi
	893
	894
	895	# LIST ALL MODIFIED SOURCE CODE FILES
	896	Filenames=""
[2404]	897	svn status > tmp_svnstatus
[2380]	898	while read line
	899	do
	900	firstc=`echo $line \| cut -c1`
	901	if [[ $firstc = M \|\| $firstc = "?" ]]
	902	then
	903	Name=`echo "$line" \| cut -c8-`
	904	extension=`echo $Name \| cut -d. -f2`
	905	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	906	then
	907	Filenames="$Filenames "$Name
	908	fi
	909	fi
[2404]	910	done < tmp_svnstatus
	911	rm -rf tmp_svnstatus
[2380]	912
	913
	914	# COPY FILES TO SOURCES_FOR_RUN_...
	915	for filename in $Filenames
	916	do
[2990]	917	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	918	source_list=$source_list"$filename "
	919	done
	920
	921	cd - > /dev/null
	922
	923
	924	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	925	elif [[ "$source_list" != "" ]]
	926	then
	927
	928	cd $source_path
	929
	930	for filename in $source_list
	931	do
	932
	933	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	934	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	935	then
	936	printf "\n +++ source code file: $filename"
	937	printf "\n must not contain (\"/\") "
	938	locat=source; exit
	939	fi
	940
	941	if [[ ! -f $filename ]]
	942	then
	943	printf "\n +++ source code file: $filename"
	944	printf "\n does not exist"
	945	locat=source; exit
	946	else
[2990]	947	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	948	fi
	949
	950	done
	951
	952	cd - > /dev/null
	953
	954	fi
	955
	956	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	957	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	958	if [[ ! -f $makefile ]]
	959	then
	960	printf "\n +++ file \"$makefile\" does not exist"
	961	locat=make; exit
	962	else
[2990]	963	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	964	fi
	965
	966
	967	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	968	if [[ "$user_source_path" != "" ]]
[2380]	969	then
	970
	971	# DOES THE DIRECTORY EXIST?
[2384]	972	if [[ ! -d $user_source_path ]]
[2380]	973	then
	974
	975	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	976	printf "\n \"$user_source_path\" "
[2380]	977	printf "\n does not exist or is not a directory."
	978	printf "\n No source code will be used from this directory!\n"
[2384]	979	user_source_path=""
[2380]	980	if [[ $silent == false ]]
	981	then
	982	sleep 2
	983	fi
	984
	985	else
	986
[2384]	987	cd $user_source_path
[2380]	988
	989	Names=$(ls -1 *.f90 2>&1)
	990	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	991	Names=$(ls -1 *.F90 2>&1)
	992	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	993	Names=$(ls -1 *.F 2>&1)
	994	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	995	Names=$(ls -1 *.f 2>&1)
	996	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	997	Names=$(ls -1 *.c 2>&1)
	998	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	999
	1000	cd - > /dev/null
[2990]	1001	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1002
	1003	# COPY MAKEFILE IF EXISTING
[2384]	1004	if [[ -f $user_source_path/Makefile ]]
[2380]	1005	then
	1006	printf "\n\n *** user Makefile from directory"
[2384]	1007	printf "\n \"$user_source_path\" is used \n"
[2380]	1008	if [[ $silent == false ]]
	1009	then
	1010	sleep 1
	1011	fi
[2384]	1012	cp $user_source_path/Makefile .
[2380]	1013	fi
	1014
	1015	for filename in $AddFilenames
	1016	do
	1017	if [[ -f $filename ]]
	1018	then
	1019	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1020	printf "\n source code directory \"$user_source_path\" "
[2380]	1021	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1022	printf "\n from directory \"$source_path\"."
	1023	locat=source; exit
	1024	fi
	1025
[2384]	1026	cp $user_source_path/$filename .
[2380]	1027	source_list="$source_list $filename"
	1028
	1029	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1030	if [[ $(grep -c $filename Makefile) = 0 ]]
	1031	then
	1032	printf "\n\n +++ user file \"$filename\" "
	1033	printf "\n is not listed in Makefile \n"
	1034	locat=source; exit
	1035	fi
	1036	done
	1037	cd - > /dev/null
	1038	fi
	1039	fi
	1040
	1041	# COPY CONFIGURATION FILES
[2990]	1042	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1043	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1044
	1045	# COPY SHELLSCRIPTS
[2990]	1046	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1047	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1048
	1049	fi
	1050
	1051	fi
	1052
[2605]	1053
[2380]	1054	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1055	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1056	if [[ "$global_revision" = "" ]]
	1057	then
	1058	global_revision=`svnversion $source_path 2>/dev/null`
	1059	global_revision="Rev: $global_revision"
	1060	fi
	1061
	1062
	1063	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1064	if [[ -n $cores ]]
	1065	then
	1066
	1067	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1068	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1069	if [[ $tasks_per_node = 0 ]]
[2380]	1070	then
[3025]	1071	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1072	then
	1073	printf "\n"
	1074	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1075	printf "\n set -T option or define tasks_per_node in the config file"
	1076	locat=tasks_per_node; (( iec = 0 )); exit
	1077	else
	1078	# DEFAULT FOR INTERACTIVE RUN
	1079	tasks_per_node=$cores
	1080	fi
[2380]	1081	fi
	1082
	1083	if (( cores < tasks_per_node ))
	1084	then
	1085	printf "\n"
	1086	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1087	printf "\n given values: -T $tasks_per_node -X $cores"
	1088	locat=tasks_per_node; (( iec = 0 )); exit
	1089	fi
	1090
	1091	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1092	(( mpi_tasks = cores / threads_per_task ))
	1093	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1094	(( ii = cores / tasks_per_node ))
	1095	(( remaining_cores = cores - ii * tasks_per_node ))
	1096	if (( remaining_cores > 0 ))
	1097	then
	1098	printf "\n"
	1099	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1100	printf "\n divisor of the total number of cores (option \"-X\")"
	1101	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1102	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1103	(( nodes = nodes + 1 ))
	1104	fi
	1105
	1106	fi
	1107
	1108
	1109	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1110	if [[ "$maximum_parallel_io_streams" = "" ]]
	1111	then
	1112	maximum_parallel_io_streams=$cores
	1113	fi
	1114
	1115
	1116	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1117	if [[ "$scp_port" != "" ]]
	1118	then
	1119	PORTOPT="-P $scp_port"
	1120	SSH_PORTOPT="-p $scp_port"
	1121	fi
	1122
	1123
	1124	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1125	# CONFIG-FILE
	1126	if [[ "$ssh_key" != "" ]]
	1127	then
	1128	ssh_key="-i $HOME/.ssh/$ssh_key"
	1129	fi
	1130
	1131
	1132	# SET QUEUE, IF NOT GIVEN
	1133	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1134	then
	1135
	1136	if [[ $queue = none && "$defaultqueue" = "" ]]
	1137	then
	1138	printf "\n"
	1139	printf "\n +++ no default queue given in configuration file and no queue"
	1140	printf "\n given with option -q"
[2789]	1141	locat=queue; exit
[2380]	1142	fi
	1143	if [[ $queue = none ]]
	1144	then
	1145	queue=$defaultqueue
	1146	fi
	1147
	1148	fi
	1149
	1150
	1151	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1152	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1153	(( i = 0 ))
[2610]	1154	(( nr_of_input_files = 0 ))
[2380]	1155	while (( i < iin ))
	1156	do
	1157	(( i = i + 1 ))
	1158
	1159	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1160	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1161	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1162	then
[2610]	1163	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1164	else
[3236]	1165	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1166	fi
	1167
[2610]	1168
[2380]	1169	# CHECK IF FILE EXISTS
	1170	if ! ls $filename* 1>/dev/null 2>&1
	1171	then
	1172
[2669]	1173	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1174	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1175	then
	1176	printf "\n\n +++ INPUT-file: "
[2610]	1177	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1178	then
	1179	printf "\n $filename"
	1180	else
[2610]	1181	printf "\n $filename.${extin_pre[$i]}"
[2380]	1182	fi
	1183	printf "\n does not exist\n"
	1184	locat=input; exit
	1185	else
[2610]	1186	(( nr_of_input_files = nr_of_input_files + 1 ))
	1187	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1188	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1189	actionin[$nr_of_input_files]="unavailable"
[2610]	1190	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1191	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1192	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1193	fi
[2605]	1194
[2380]	1195	else
	1196
[3236]	1197	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1198	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1199	# ENDINGS
[2610]	1200	if [[ "${multin[$i]}" = true ]]
	1201	then
	1202	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1203	ls -1 -d ${filename} > filelist 2>/dev/null
	1204	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1205	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1206
[2610]	1207	endings=""
	1208	while read line
	1209	do
	1210	# filename without path (i.e. after the last "/")
	1211	basefilename=$(basename ${line})
[2380]	1212
[2610]	1213	# check if there is an extension and remove it
	1214	ext=${basefilename##*.}
	1215	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1216	then
	1217	basefilename=${basefilename%.*}
	1218	fi
[2380]	1219
[2610]	1220	# check for an existing cycle number and remove it
	1221	cycle=${basefilename##*.}
	1222	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1223	then
	1224	basefilename=${basefilename%.*}
	1225	fi
[2600]	1226
[3236]	1227	# remove the run_identifier from the beginning
	1228	length_run_identifier=${#run_identifier}
	1229	ending=${basefilename:${length_run_identifier}}
[2610]	1230
	1231	# remove the ending given in the .iofiles from the beginning
	1232	endingstring="${endin_pre[$i]}"
	1233	length_ending=${#endingstring}
	1234	ending=${ending:${length_ending}}
	1235
	1236	if [[ "$ending" = "" ]]
[2600]	1237	then
[2610]	1238	# standard ending as given in the .iofiles
	1239	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1240	then
	1241	endings="$endings DEFAULT"
	1242	fi
[2600]	1243	else
[2610]	1244	# ending must start with "_", otherwise its a different file
	1245	if [[ "${ending:0:1}" = "_" ]]
	1246	then
	1247	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1248	then
	1249	endings="$endings $ending"
	1250	fi
	1251	fi
[2600]	1252	fi
[2610]	1253
	1254	done <filelist
[2380]	1255
[2610]	1256	rm filelist
[2380]	1257
[2600]	1258	else
[2610]	1259
	1260	# SINGLE NAME
	1261	endings=DEFAULT
	1262
[2600]	1263	fi
	1264
[2610]	1265	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1266	for ending in $endings
	1267	do
	1268
	1269	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1270	if [[ $ending = DEFAULT ]]
[2380]	1271	then
[2610]	1272	ending=""
	1273	fi
	1274
	1275	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1276	(( nr_of_input_files = nr_of_input_files + 1 ))
	1277	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1278	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1279	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1280	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1281	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1282	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1283
	1284
	1285	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1286	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1287	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1288	then
	1289	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1290	else
[3236]	1291	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1292	fi
[2610]	1293
	1294	# DETERMINE THE FILE'S CYCLE NUMBER
	1295	(( maxcycle = 0 ))
	1296	ls -1 -d $filename > filelist 2>/dev/null
	1297	ls -1 -d $filename.* >> filelist 2>/dev/null
	1298	while read line
	1299	do
	1300	# filename without path (i.e. after the last "/")
	1301	basefilename=$(basename ${line})
	1302
	1303	# check if there is an extension
	1304	extension=${basefilename##*.}
	1305	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1306	then
	1307	basefilename=${basefilename%.*}
	1308	fi
	1309
	1310	# check for an existing cycle number
	1311	cycle=${basefilename##*.}
	1312	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1313	then
[2669]	1314	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1315	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1316	(( icycle = $((10#$cycle)) ))
[2610]	1317	else
	1318	(( icycle = 0 ))
	1319	fi
	1320
	1321	if (( icycle > maxcycle ))
	1322	then
	1323	(( maxcycle = icycle ))
	1324
	1325	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1326	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1327	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1328	then
	1329	leading_zero=true
	1330	else
	1331	leading_zero=false
	1332	fi
	1333	fi
	1334
	1335	done <filelist
	1336	rm filelist
	1337
	1338	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1339	if [[ $leading_zero = true ]]
[2380]	1340	then
[2610]	1341	cyclestring=`printf "%03d" $maxcycle`
	1342	else
	1343	cyclestring=$maxcycle
[2380]	1344	fi
[2610]	1345
	1346	# APPEND CYCLE NUMBER TO FILENAME
	1347	if (( maxcycle > 0 ))
[2380]	1348	then
[2610]	1349	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1350	then
	1351	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1352	else
	1353	filename=${filename}.$cyclestring
	1354	fi
[2380]	1355	else
[2610]	1356	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1357	then
	1358	filename=${filename}.${extin[$nr_of_input_files]}
	1359	fi
[2380]	1360	fi
[2610]	1361
	1362	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1363	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1364	absnamein[$nr_of_input_files]=$filename
	1365	if (( maxcycle > 0 ))
[2380]	1366	then
[2610]	1367	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1368	then
	1369	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1370	else
[3236]	1371	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1372	fi
[2380]	1373	else
[2610]	1374	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1375	then
	1376	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1377	else
[3236]	1378	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1379	fi
[2380]	1380	fi
	1381
[2610]	1382	done
	1383
[2380]	1384	fi
[2610]	1385
[2380]	1386	done
	1387
[2610]	1388
[2380]	1389	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1390	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1391	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1392	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1393	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1394	# REMOTE HOST)
	1395	(( i = 0 ))
	1396	while (( i < iout ))
	1397	do
	1398	(( i = i + 1 ))
[2610]	1399	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1400	then
[2610]	1401	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1402	then
[2610]	1403	actionout_pre[$i]=""
	1404	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1405	then
[2610]	1406	actionout_pre[$i]=pe
	1407	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1408	then
[2610]	1409	actionout_pre[$i]=a
[2380]	1410	fi
	1411	(( maxcycle = 0 ))
[3236]	1412	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1413	eval catalogname=${pathout_pre[$i]}
[2380]	1414	if ! ls $filename* 1>/dev/null 2>&1
	1415	then
	1416
	1417	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1418	if cat /dev/null > $filename
	1419	then
	1420	rm $filename
	1421	else
	1422
	1423	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1424	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1425	if [[ ! -d $catalogname ]]
	1426	then
	1427	if mkdir -p $catalogname
	1428	then
	1429	printf "\n\n *** directory:"
	1430	printf "\n $catalogname"
	1431	printf "\n was created\n"
	1432	else
	1433	printf "\n\n +++ OUTPUT-file:"
	1434	printf "\n $filename"
	1435	printf "\n cannot be created, because directory does not exist"
	1436	printf "\n and cannot be created either"
	1437	printf "\n"
	1438	locat=output ; exit
	1439	fi 2>/dev/null
	1440	else
	1441	printf "\n\n +++ OUTPUT-file:"
	1442	printf "\n $filename"
	1443	printf "\n cannot be created, although directory exists"
	1444	printf "\n"
	1445	locat=output ; exit
	1446	fi
	1447	fi 2>/dev/null
	1448
	1449	fi
	1450
	1451	fi
	1452	done
	1453
	1454
	1455	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1456	if [[ $running_in_batch_mode = false ]]
	1457	then
[3236]	1458	run_id_number=$RANDOM
	1459	run_id=${run_identifier}.$run_id_number
[2380]	1460
[3236]	1461	tempdir=$fast_io_catalog/$run_id
[3346]	1462
	1463	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1464	export job_id=$run_id
	1465
[2380]	1466	fi
	1467
	1468
	1469	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1470	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1471	then
	1472
	1473	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1474	if [[ $ibd = 0 ]]
	1475	then
	1476	printf "\n"
	1477	printf "\n +++ no batch directives found in configuration file"
	1478	locat=config_file_batch_directives; (( iec = 0 )); exit
	1479	fi
	1480
	1481	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1482	done=false
[2384]	1483	cputime=$cpumax
[2380]	1484	while [[ $done = false ]]
	1485	do
[2384]	1486	if (( cputime == 0 ))
[2380]	1487	then
	1488	printf "\n +++ cpu-time is undefined"
	1489	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1490	printf "\n >>> "
[2384]	1491	read cputime 1>/dev/null 2>&1
[2380]	1492	else
	1493	done=true
	1494	fi
	1495	done
[2420]	1496	cpumax=$cputime
[2380]	1497
	1498	# CHECK THE MEMORY DEMAND
	1499	done=false
	1500	while [[ $done = false ]]
	1501	do
	1502	if (( memory == 0 ))
	1503	then
	1504	printf "\n +++ memory demand is undefined"
	1505	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1506	printf "\n >>> "
	1507	read memory 1>/dev/null 2>&1
	1508	else
	1509	done=true
	1510	fi
	1511	done
	1512
	1513	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1514	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1515	then
	1516	while [[ -z $remote_username ]]
	1517	do
[2420]	1518	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1519	printf "\n >>> Please type username:"
	1520	printf "\n >>> "
	1521	read remote_username
	1522	done
	1523	fi
	1524
	1525	else
	1526
[2420]	1527	if [[ $running_in_batch_mode = false ]]
	1528	then
	1529	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1530	cpumax=$cputime
	1531	else
	1532	cputime=$cpumax
	1533	fi
[2380]	1534
	1535	fi
	1536
	1537
	1538	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1539	(( cpu_hours = cputime / 3600 ))
	1540	(( resttime = cputime - cpu_hours * 3600 ))
	1541	(( cpu_minutes = resttime / 60 ))
	1542	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1543	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1544
	1545
	1546	# OUTPUT OF THE PALMRUN-HEADER
	1547	calltime=$(date)
	1548	printf "\n"
	1549	printf "#------------------------------------------------------------------------# \n"
	1550	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1551	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1552	printf "\| \| \n"
	1553	column1="called on:"; column2=$(hostname)
	1554	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1555	if [[ $create_remote_batch_job = true ]]
	1556	then
[3236]	1557	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1558	else
	1559	if [[ $running_on_remote = true ]]
	1560	then
[3236]	1561	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1562	else
[3236]	1563	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1564	fi
	1565	fi
	1566	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1567
	1568	column1="running in:"
	1569	if [[ $running_in_batch_mode = true ]]
	1570	then
	1571	column2="batch job mode"
	1572	else
	1573	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1574	then
	1575	column2="job creation mode"
	1576	else
	1577	column2="interactive run mode"
	1578	fi
	1579	fi
	1580	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1581
[2479]	1582	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1583	then
[2480]	1584	if [[ "$project_account" != "" ]]
[2479]	1585	then
	1586	column1="project account number:"
	1587	column2="$project_account"
	1588	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1589	fi
	1590	fi
	1591
[2380]	1592	if [[ -n $cores ]]
	1593	then
	1594	if [[ $run_coupled_model = false ]]
	1595	then
	1596	column1="number of cores:"; column2=$cores
	1597	else
	1598	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1599	fi
	1600	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1601	fi
	1602	if [[ -n $tasks_per_node ]]
	1603	then
	1604	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1605	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1606	if (( remaining_cores > 0 ))
	1607	then
	1608	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1609	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1610	fi
	1611	fi
	1612	if [[ $maximum_parallel_io_streams != $cores ]]
	1613	then
	1614	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1616	fi
	1617	if [[ $use_openmp = true ]]
	1618	then
	1619	column1="threads per task:"; column2="$threads_per_task"
	1620	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1621	fi
[2384]	1622	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1623	then
[2506]	1624	column1="memory demand / PE":; column2="$memory MB"
	1625	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1626	column1="job cpu time (h:m:s):"; column2="$timestring"
	1627	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1628	fi
[2380]	1629	printf "\| \| \n"
	1630	if [[ "$source_list" != "" ]]
	1631	then
	1632	if [[ "$make_options" != "" ]]
	1633	then
	1634	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1635	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1636	line=$(echo "$make_options" \| cut -c46-)
	1637	while [[ "$line" != "" ]]
	1638	do
	1639	column1=""
	1640	column2=$(echo "$line" \| cut -c-45)
	1641	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1642	line=$(echo "$line" \| cut -c46-)
	1643	done
	1644	fi
	1645	fi
	1646
	1647	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1648	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1649	line=$(echo "$cpp_options" \| cut -c46-)
	1650	while [[ "$line" != "" ]]
	1651	do
	1652	column1=""
	1653	column2=$(echo "$line" \| cut -c-45)
	1654	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1655	line=$(echo "$line" \| cut -c46-)
	1656	done
	1657
	1658	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1659	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1660	line=$(echo "$compiler_options" \| cut -c46-)
	1661	while [[ "$line" != "" ]]
	1662	do
	1663	column1=""
	1664	column2=$(echo "$line" \| cut -c-45)
	1665	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1666	line=$(echo "$line" \| cut -c46-)
	1667	done
	1668
[2388]	1669	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1670	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1671	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1672	while [[ "$line" != "" ]]
	1673	do
	1674	column1=""
	1675	column2=$(echo "$line" \| cut -c-45)
	1676	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1677	line=$(echo "$line" \| cut -c46-)
	1678	done
	1679
	1680	if [[ "$login_init_cmd" != "" ]]
	1681	then
	1682	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1683	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1684	line=$(echo "$login_init_cmd" \| cut -c46-)
	1685	while [[ "$line" != "" ]]
	1686	do
	1687	column1=""
	1688	column2=$(echo "$line" \| cut -c-45)
	1689	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1690	line=$(echo "$line" \| cut -c46-)
	1691	done
	1692	fi
	1693
	1694	if [[ "$module_commands" != "" ]]
	1695	then
	1696	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1697	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1698	line=$(echo "$module_commands" \| cut -c46-)
	1699	while [[ "$line" != "" ]]
	1700	do
	1701	column1=""
	1702	column2=$(echo "$line" \| cut -c-45)
	1703	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1704	line=$(echo "$line" \| cut -c46-)
	1705	done
	1706	fi
	1707	printf "\| \| \n"
[3236]	1708	column1="run identifier:"; column2=$run_identifier
[2380]	1709	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1710	column1="activation string list:"; column2=$(echo $activation_string_list)
	1711	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1712
	1713	if [[ "$ocean_file_appendix" = true ]]
	1714	then
	1715	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1716	fi
	1717
	1718	if [[ "$source_list" != "" ]]
	1719	then
	1720	printf "\| \| \n"
	1721	printf "\| Files to be compiled: \| \n"
	1722	line=$source_list
	1723	while [[ "$line" != "" ]]
	1724	do
	1725	linestart=$(echo $line \| cut -c-70)
	1726	printf "\| %-70s \| \n" "$linestart"
	1727	line=$(echo "$line" \| cut -c71-)
	1728	done
	1729	fi
	1730	printf "#------------------------------------------------------------------------#"
	1731
	1732
	1733
	1734	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1735	if [[ $do_trace = true ]]
	1736	then
	1737	(( i = 0 ))
[2610]	1738	while (( i < nr_of_input_files ))
[2380]	1739	do
	1740	(( i = i + 1 ))
	1741	if (( i == 1 ))
	1742	then
	1743	printf "\n\n >>> INPUT-file assignments:\n"
	1744	fi
	1745	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1746	done
	1747	(( i = 0 ))
	1748	while (( i < iout ))
	1749	do
	1750	(( i = i + 1 ))
	1751	if (( i == 1 ))
	1752	then
	1753	printf "\n\n >>> OUTPUT-file assignments:\n"
	1754	fi
	1755	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1756	done
	1757	(( i = 0 ))
	1758	while (( i < iic ))
	1759	do
	1760	(( i = i + 1 ))
	1761	if (( i == 1 ))
	1762	then
	1763	printf "\n\n >>> INPUT-commands:\n"
	1764	fi
	1765	printf "\n ${in_command[$i]}"
	1766	done
	1767	(( i = 0 ))
	1768	while (( i < ioc ))
	1769	do
	1770	(( i = i + 1 ))
	1771	if (( i == 1 ))
	1772	then
	1773	printf "\n\n >>> OUTPUT-commands:\n"
	1774	fi
	1775	printf "\n ${out_command[$i]}"
	1776	done
	1777	fi
	1778
	1779	# QUERY FOR CONTINUE
	1780	if [[ $silent = false && $running_in_batch_mode = false ]]
	1781	then
	1782	antwort=dummy
	1783	printf "\n\n"
	1784	printf " >>> everything o.k. (y/n) ? "
	1785	while read antwort
	1786	do
	1787	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1788	then
	1789	printf " >>> everything o.k. (y/n) ? "
	1790	else
	1791	break
	1792	fi
	1793	done
	1794	if [[ $antwort = n \|\| $antwort = N ]]
	1795	then
	1796	locat=user_abort; (( iec = 0 )); exit
	1797	fi
	1798	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1799	then
[2566]	1800	printf "\n *** batch-job will be created and submitted"
[2380]	1801	else
[2566]	1802	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1803	fi
	1804	fi
	1805
	1806
	1807
	1808	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1809	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1810	then
	1811
	1812	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1813	then
[2566]	1814	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1815	else
[2566]	1816	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1817	fi
	1818
[2422]	1819	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1820	# IT SHALL BE CREATED
	1821	ask_for_make_depository=false
	1822	if [[ $create_remote_batch_job = true ]]
	1823	then
	1824
	1825	line=`grep %base_directory $config_file`
[3236]	1826	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
	1827	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]	1828
[3236]	1829	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1830	then
	1831	printf "\n\n +++ make depository \"${make_depository}\""
	1832	printf "\n on remote host not found!"
	1833	ask_for_make_depository=true
	1834	fi
[3236]	1835	rm ${configuration_identifier}_last_make_protokoll
[2422]	1836
	1837	else
	1838
	1839	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1840	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1841	if [[ ! -d ${make_depository} ]]
	1842	then
	1843	printf "\n\n +++ make depository \"${make_depository}\""
	1844	printf "\n on local host not found!"
	1845	ask_for_make_depository=true
	1846	fi
	1847
	1848	fi
	1849
	1850	if [[ $ask_for_make_depository = true ]]
	1851	then
	1852
	1853	antwort=dummy
	1854	printf "\n\n"
	1855	printf " >>> Create a new one (y/n) ? "
	1856	while read antwort
	1857	do
	1858	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1859	then
	1860	printf " >>> Create a new one (y/n) ? "
	1861	else
	1862	break
	1863	fi
	1864	done
	1865	if [[ $antwort = n \|\| $antwort = N ]]
	1866	then
	1867	locat=user_abort; (( iec = 0 )); exit
	1868	fi
	1869
[2566]	1870	if [[ $do_trace = true ]]
	1871	then
[3455]	1872	palmbuild -c $configuration_identifier
[2566]	1873	else
[3455]	1874	palmbuild -v -c $configuration_identifier
[2566]	1875	fi
[2422]	1876
[3312]	1877	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1878	then
	1879
	1880	# ABORT IN CASE OF COMPILATION PROBLEMS
	1881	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1882	locat=make_depository
	1883	exit
	1884	else
	1885	echo " *** now continue with creating executable and other sources"
	1886	fi
	1887
	1888	fi
	1889
[2566]	1890	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1891	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1892
[3312]	1893	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1894	then
	1895
	1896	# ABORT IN CASE OF COMPILATION PROBLEMS
	1897	printf "\n +++ error while creating executable and/or other sources"
	1898	locat=execution
[2990]	1899	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1900	exit
	1901
	1902	else
	1903
[2566]	1904	printf " *** executable and other sources created\n"
[2990]	1905	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1906
	1907	fi
	1908
	1909	fi
	1910
	1911
[2669]	1912	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1913	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1914	if [[ $create_remote_batch_job = true ]]
	1915	then
	1916	(( i = 0 ))
[2610]	1917	while (( i < nr_of_input_files ))
[2605]	1918	do
	1919	(( i = i + 1 ))
[2669]	1920	if [[ "${actionin[$i]}" = tr ]]
[2605]	1921	then
	1922	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1923	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1924	fi
	1925	done
	1926	if (( i > 0 ))
	1927	then
[3025]	1928	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1929	fi
	1930	fi
	1931
	1932
[2380]	1933	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1934	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1935	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1936	then
	1937
	1938	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1939	if [[ $running_in_batch_mode = false ]]
	1940	then
	1941	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1942	# FOLDER
[2566]	1943	mkdir -p $tempdir
	1944	chmod go+rx $tempdir
	1945	cd $tempdir
	1946	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1947	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1948
	1949	else
	1950
	1951	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1952	printf "\n *** running in temporary directory: $tempdir"
[2380]	1953
	1954	fi
	1955
	1956
	1957	# PROVIDE THE INPUT FILES
	1958	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1959	optional_files_missing=false
[2380]	1960	(( i = 0 ))
[2610]	1961	while (( i < nr_of_input_files ))
[2380]	1962	do
	1963	(( i = i + 1 ))
	1964	if (( i == 1 ))
	1965	then
	1966	printf "\n\n *** providing INPUT-files:\n$dashes"
	1967	fi
	1968
	1969
	1970	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1971	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1972	then
[2669]	1973	optional_files_missing=true
[2380]	1974	continue
	1975	fi
	1976
	1977	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1978	files_for_cores=false; filetype=file
	1979	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1980	then
	1981	files_for_cores=true; filetype=files
	1982	actionin[$i]=""
	1983	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1984	then
	1985	actionin[$i]=""
	1986	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1987	then
	1988	files_for_cores=true; filetype=files
	1989	actionin[$i]="ln"
	1990	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1991	then
	1992	actionin[$i]="ln"
	1993	fi
	1994
	1995	if [[ $files_for_cores = true ]]
	1996	then
	1997	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1998	else
	1999	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2000	fi
	2001
	2002	# INPUT-FILES TO BE LINKED
	2003	if [[ "${actionin[$i]}" = ln ]]
	2004	then
	2005
	2006	printf "\n $filetype will be linked"
	2007	if [[ $files_for_cores = false ]]
	2008	then
	2009	if [[ -f "${absnamein[$i]}" ]]
	2010	then
	2011	ln ${absnamein[$i]} ${localin[$i]}
	2012	got_tmp[$i]=true
	2013	fi
	2014	else
	2015	if [[ -d "${absnamein[$i]}" ]]
	2016	then
[2396]	2017	mkdir -p ${localin[$i]}
[2380]	2018	cd ${absnamein[$i]}
	2019	for file in $(ls *)
	2020	do
[2566]	2021	ln $file $tempdir/${localin[$i]}
[2380]	2022	done >\|/dev/null 2>&1
[2566]	2023	cd $tempdir
[2380]	2024	fi
	2025
	2026	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2027	if [[ ! -f "${localin[$i]}/_000000" ]]
	2028	then
	2029	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2030	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2031	fi
	2032
	2033	got_tmp[$i]=true
	2034	fi
	2035	fi
	2036
	2037	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2038	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2039	then
	2040
	2041	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2042	then
	2043
	2044	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2045	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2046	printf "\n file will be provided for $cores processors"
[2396]	2047	mkdir -p ${localin[$i]}
[2380]	2048	ival=$cores
	2049	(( ii = 0 ))
	2050	while (( ii <= ival-1 ))
	2051	do
	2052	if (( ii < 10 ))
	2053	then
	2054	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2055	elif (( ii < 100 ))
	2056	then
	2057	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2058	elif (( ii < 1000 ))
	2059	then
	2060	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2061	else
	2062	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2063	fi
	2064	(( ii = ii + 1 ))
	2065	done
	2066
	2067	else
	2068
	2069	if [[ $files_for_cores = true ]]
	2070	then
	2071
	2072	# PROVIDE FILES FOR EACH CORE
	2073	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2074	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2075	printf "\n providing $cores files for the respective cores"
[2396]	2076	mkdir -p ${localin[$i]}
[2380]	2077	if [[ $link_local_input = true ]]
	2078	then
	2079	printf " files will be linked\n"
	2080	cd ${absnamein[$i]}
	2081	for file in $(ls *)
	2082	do
	2083	ln -f $file ${localin[$i]}
	2084	done
[2566]	2085	cd $tempdir
[2380]	2086	fi
	2087
	2088	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2089	if [[ ! -f "${localin[$i]}/_000000" ]]
	2090	then
	2091	if [[ $link_local_input = true ]]
	2092	then
	2093	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2094	fi
	2095	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2096	fi
	2097
	2098	else
	2099
	2100	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2101	if [[ $link_local_input = true ]]
	2102	then
	2103	printf " file will be linked\n"
	2104	ln -f ${absnamein[$i]} ${localin[$i]}
	2105	fi
[2605]	2106	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2107	if [[ ! -f "${localin[$i]}" ]]
	2108	then
	2109	if [[ $link_local_input = true ]]
	2110	then
	2111	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2112	fi
[2669]	2113	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2114	then
	2115	mv ${absnamein[$i]} ${localin[$i]}
	2116	else
	2117	cp ${absnamein[$i]} ${localin[$i]}
	2118	fi
[2380]	2119	fi
	2120	fi
	2121	fi
	2122	fi
	2123
	2124	done
	2125	if (( i != 0 ))
	2126	then
[2669]	2127	if [[ $optional_files_missing = true ]]
	2128	then
	2129	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2130	fi
[2380]	2131	printf "\n$dashes\n *** all INPUT-files provided \n"
	2132	fi
	2133
	2134
	2135	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2136	(( i = 0 ))
	2137	while (( i < iic ))
	2138	do
	2139	(( i = i + 1 ))
	2140	if (( i == 1 ))
	2141	then
	2142	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2143	fi
	2144	printf "\n >>> ${in_command[$i]}"
	2145	eval ${in_command[$i]}
	2146	if (( i == iic ))
	2147	then
	2148	printf "\n$dashes\n"
	2149	fi
	2150	done
	2151
	2152
[3313]	2153	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2154	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2155	then
	2156	progress_bar_disabled=true
	2157	else
	2158	progress_bar_disabled=false
	2159	fi
	2160
	2161
[2380]	2162	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2163	# (FILE ENVPAR WILL BE READ BY PALM)
	2164	cat > ENVPAR << EOF
[3236]	2165	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2166	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2167	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2168	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2169	maximum_cpu_time_allowed = ${cpumax}.,
	2170	revision = '$global_revision',
[3313]	2171	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2172
	2173	EOF
	2174
	2175
	2176	# STARTING THE EXECUTABLE
	2177	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2178	PATH=$PATH:$tempdir
[2380]	2179
	2180
	2181	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2182	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2183	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2184	eval line=\"$line\"
	2185	execute_command="$line"
	2186
	2187
	2188	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2189	if [[ "$execute_command_for_combine" = "" ]]
	2190	then
	2191	eval line2=\"$line2\"
	2192	execute_command_for_combine="$line2"
	2193	fi
	2194
[2380]	2195
	2196
	2197	# PROVIDE A HOSTFILE, IF REQUIRED
	2198	if [[ "$hostfile" != "" ]]
	2199	then
	2200
	2201	if [[ $hostfile = auto ]]
	2202	then
	2203	# CREATE A NEW HOSTFILE
	2204	(( ii = 1 ))
	2205	while (( ii <= cores / threads_per_task ))
	2206	do
	2207	echo $(hostname) >> hostfile
	2208	(( ii = ii + 1 ))
	2209	done
	2210	if (( cores / threads_per_task == 0 ))
	2211	then
	2212	echo $(hostname) >> hostfile
	2213	fi
	2214
	2215	else
	2216	cp $hostfile hostfile
	2217	fi
	2218	eval line=\"`head -n $ii hostfile`\"
	2219	printf "\n *** running on: $line"
	2220	fi
	2221
	2222
	2223
	2224	# SET THE NUMBER OF OPENMP-THREADS
	2225	if [[ $use_openmp = true ]]
	2226	then
	2227	export OMP_NUM_THREADS=$threads_per_task
	2228	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2229	else
	2230	export OMP_NUM_THREADS=1
	2231	fi
	2232
	2233
[2610]	2234	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2235	if [[ $run_coupled_model = false ]]
	2236	then
	2237	if [[ "$ocean_file_appendix" = true ]]
	2238	then
	2239	echo "precursor_ocean" > coupling_steering
	2240	else
	2241	echo "precursor_atmos" > coupling_steering
	2242	fi
	2243	else
	2244	(( iia = $cores_atmos / $threads_per_task ))
	2245	(( iio = $cores_ocean / $threads_per_task ))
	2246	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2247	printf "\n\n"
	2248	echo "coupled_run $iia $iio" > coupling_steering
	2249	fi
	2250
	2251	printf "\n *** execute command:"
	2252	printf "\n \"$execute_command\" \n\n"
	2253
	2254
[3393]	2255	if [[ $progress_bar_disabled = true ]]
[2380]	2256	then
[3402]	2257	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2258	exit_code=${PIPESTATUS[0]}
	2259	else
	2260	$execute_command < coupling_steering &> >(tee STDOUT)
	2261	exit_code=${PIPESTATUS[0]}
	2262	fi
[2380]	2263
[3393]	2264	if [[ ${exit_code} != 0 ]]
	2265	then
	2266
[2380]	2267	# ABORT IN CASE OF RUNTIME ERRORS
	2268	printf "\n +++ runtime error occured"
	2269	locat=execution
	2270	exit
	2271
	2272	else
	2273
	2274	printf "\n$dashes\n *** execution finished \n"
	2275
	2276	fi
	2277
	2278
	2279	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2280	# BY EACH CORE INTO ONE FILE
	2281	if [[ ! -f combine_plot_fields.x ]]
	2282	then
	2283
	2284	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2285	printf "\n 2d- and/or 3d-data may be incomplete!"
	2286	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2287
	2288	elif [[ "$combine_plot_fields" == true ]]
	2289	then
	2290
	2291	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2292	$execute_command_for_combine
	2293
	2294	else
	2295
	2296	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2297	# DATA OUTPUT
[2380]	2298	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2299	fi
	2300
	2301
	2302
	2303	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2304	(( i = 0 ))
	2305	while (( i < ioc ))
	2306	do
	2307	(( i = i + 1 ))
	2308	if (( i == 1 ))
	2309	then
	2310	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2311	fi
[2799]	2312
	2313	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2314	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2315
[2380]	2316	printf "\n >>> ${out_command[$i]}"
	2317	eval ${out_command[$i]}
	2318	if (( i == ioc ))
	2319	then
	2320	printf "\n$dashes\n"
	2321	fi
	2322	done
	2323
	2324
[2610]	2325	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2326	# WILDCARDS
[2380]	2327	(( i = 0 ))
[2610]	2328	(( nr_of_output_files = 0 ))
	2329
[2380]	2330	while (( i < iout ))
	2331	do
[2610]	2332
[2380]	2333	(( i = i + 1 ))
[2610]	2334
	2335	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2336	# CREATE A LIST FOR THE DETECTED ENDINGS
	2337	if [[ "${multout[$i]}" = true ]]
	2338	then
	2339	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2340	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2341	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2342
	2343	endings="DEFAULT"
	2344	while read line
	2345	do
	2346	# remove the local name from the beginning
	2347	localnamestring="${localout_pre[$i]}"
	2348	length_localname=${#localnamestring}
	2349	ending=${line:${length_localname}}
	2350
	2351	if [[ "$ending" != "" ]]
	2352	then
	2353	endings="$endings $ending"
	2354	fi
	2355
	2356	done <filelist
	2357
	2358	rm filelist
	2359
	2360	else
	2361
	2362	# SINGLE NAME
	2363	endings=DEFAULT
	2364
	2365	fi
	2366
	2367	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2368	for ending in $endings
	2369	do
	2370
	2371	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2372	if [[ $ending = DEFAULT ]]
	2373	then
	2374	ending=""
	2375	fi
	2376
	2377	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2378	(( nr_of_output_files = nr_of_output_files + 1 ))
	2379	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2380	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2381	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2382	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2383	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2384	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2385	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2386
	2387	done
	2388
	2389	done
	2390
	2391
	2392
	2393
	2394	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2395	(( i = 0 ))
	2396	while (( i < nr_of_output_files ))
	2397	do
	2398	(( i = i + 1 ))
[2380]	2399	if (( i == 1 ))
	2400	then
	2401	printf "\n\n *** saving OUTPUT-files:"
	2402
	2403	# GET RUN NUMBER ASSIGNED BY PALM
	2404	if [[ -f RUN_NUMBER ]]
	2405	then
	2406	read run_number < RUN_NUMBER
	2407	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2408	usecycle_option="-U $run_number"
	2409	else
	2410	run_number=0
	2411	usecycle_option=""
	2412	fi
	2413	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2414	then
[2404]	2415	printf "\n *** in case of SCP transfers to local host"
	2416	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2417	fi
	2418	printf "\n$dashes"
	2419	fi
	2420
	2421	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2422	then
	2423
[3236]	2424	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2425
	2426	# DETERMINE THE CYCLE NUMBER
	2427	ls -1 -d $filename > filelist 2>/dev/null
	2428	ls -1 -d $filename.* >> filelist 2>/dev/null
	2429	while read line
	2430	do
	2431
	2432	# filename without path (i.e. after the last "/")
	2433	basefilename=$(basename ${line})
	2434
	2435	# check if there is an extension
	2436	extension=${basefilename##*.}
	2437	if [[ "$extension" = "${extout[$i]}" ]]
	2438	then
	2439	basefilename=${basefilename%.*}
	2440	fi
	2441
	2442	# check for an existing cycle number
	2443	cycle=${basefilename##*.}
	2444	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2445	then
[2669]	2446	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2447	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2448	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2449	else
	2450	(( icycle = 1 ))
	2451	fi
	2452
	2453	if (( icycle > maxcycle ))
	2454	then
	2455	(( maxcycle = icycle ))
	2456	fi
	2457
	2458	done <filelist
	2459	rm filelist
	2460
	2461
	2462	# SET THE CYCLE NUMBER
	2463	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2464	if [[ "${actionout[$i]}" = a ]]
	2465	then
	2466	(( maxcycle = maxcycle - 1 ))
	2467	fi
	2468
	2469	(( cycnum[$i] = maxcycle ))
	2470	pathout[$i]=$filename
	2471
	2472
	2473	# ADD CYCLE NUMBER TO FILENAME
	2474	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2475	if [[ "${actionout[$i]}" != "a" ]]
	2476	then
	2477	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2478	# WITH AN EXISTING CYCLE NUMBER
	2479	if (( run_number >= cycnum[$i] ))
	2480	then
	2481	(( cycnum[$i] = run_number ))
	2482	else
	2483	if (( run_number > 0 ))
	2484	then
	2485	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2486	fi
	2487	fi
	2488	fi
	2489	if (( cycnum[$i] > 0 ))
	2490	then
[2600]	2491	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2492	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2493	fi
	2494	fi
	2495
	2496	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2497	files_for_cores=false; filetype=file
	2498	link_local_output=false
	2499	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2500	then
	2501	files_for_cores=true; filetype=directory
	2502	actionout[$i]=""
	2503	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2504	then
	2505	actionout[$i]=""
	2506	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2507	then
	2508	files_for_cores=true; filetype=directory
	2509	link_local_output=true
	2510	actionout[$i]=""
	2511	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2512	then
	2513	link_local_output
	2514	actionout[$i]=""
	2515	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2516	then
	2517	files_for_cores=true; filetype=directory
	2518	actionout[$i]="tr"
	2519	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2520	then
	2521	actionout[$i]="tr"
	2522	fi
	2523
	2524	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2525	then
[2669]	2526	if [[ ${warnout[$i]} = true ]]
	2527	then
	2528	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2529	fi
[2380]	2530	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2531	then
[2669]	2532	if [[ ${warnout[$i]} = true ]]
	2533	then
	2534	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2535	fi
[2380]	2536	else
	2537
	2538
	2539	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2540	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2541	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2542	then
	2543	if [[ $running_on_remote = true ]]
	2544	then
	2545
	2546	# SET OPTIONS FOR TRANSFER
	2547	if [[ "${actionout[$i]}" = tr ]]
	2548	then
	2549	if [[ $files_for_cores = false ]]
	2550	then
	2551	catalog_option=""
	2552	catalog_string=""
	2553	else
	2554	catalog_option="-c"
	2555	catalog_string="/"
	2556	fi
	2557	append_option=""
	2558	append_string=""
	2559	else
	2560	append_option="-A"
	2561	append_string="append"
	2562	fi
	2563
	2564	transfer_failed=false
	2565	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2566	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2567
	2568	# TRANSFER VIA SCP
	2569	if [[ "$remote_loginnode" != "" ]]
	2570	then
[3236]	2571	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]	2572	else
[3236]	2573	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]	2574	fi
[3312]	2575	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2576
	2577
	2578	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2579	if [[ $transfer_failed = true ]]
	2580	then
	2581	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2582	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2583
	2584	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2585	eval local_catalog=${pathout[$i]}
	2586	if [[ ! -d $local_catalog ]]
	2587	then
	2588	printf " *** local directory does not exist. Trying to create:\n"
	2589	printf " $local_catalog \n"
	2590	mkdir -p $local_catalog
	2591	fi
[3236]	2592	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2593	transfer_problems=true
	2594	fi
	2595
	2596	else
	2597
	2598	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2599	# BE COPIED OR APPENDED ON THIS MACHINE
	2600	if [[ "${actionout[$i]}" = tr ]]
	2601	then
	2602	actionout[$i]=""
	2603	else
	2604	actionout[$i]="a"
	2605	fi
	2606	fi
	2607	fi
	2608
	2609
	2610	# APPEND ON THIS MACHINE
	2611	if [[ "${actionout[$i]}" = "a" ]]
	2612	then
	2613	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2614	then
	2615	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2616	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2617	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2618	else
	2619	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2620	printf "\n ${pathout[$i]}\n"
	2621	cat ${localout[$i]} >> ${pathout[$i]}
	2622	fi
	2623	fi
	2624
	2625	# COPY ON THIS MACHINE
	2626	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2627	# ON DIFFERENT FILE-SYSTEMS
	2628	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2629	then
	2630
	2631	# COPY IN CASE OF RUNS ON SINGLE CORES
	2632	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2633	then
	2634	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2635	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2636	if [[ $link_local_output = true ]]
	2637	then
	2638	printf " file will be linked\n"
	2639	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2640	fi
	2641	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2642	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2643	then
	2644	if [[ $link_local_output = true ]]
	2645	then
	2646	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2647	fi
	2648	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2649	else
	2650	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2651	fi
	2652	else
	2653	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2654	printf "\n ${pathout[$i]}\n"
	2655	if [[ $link_local_output = true ]]
	2656	then
	2657	printf " file will be linked\n"
	2658	ln -f ${localout[$i]} ${pathout[$i]}
	2659	fi
	2660	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2661	if [[ ! -f "${pathout[$i]}" ]]
	2662	then
	2663	if [[ $link_local_output = true ]]
	2664	then
	2665	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2666	fi
	2667	cp ${localout[$i]} ${pathout[$i]}
	2668	else
	2669	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2670	fi
	2671	fi
	2672
	2673	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2674	then
	2675
	2676	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2677	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2678	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2679	printf "\n ${pathout[$i]}\n"
	2680	if [[ $link_local_output = true ]]
	2681	then
	2682	printf " files will be linked\n"
[2396]	2683	mkdir -p ${pathout[$i]}
[2380]	2684	cd ${localout[$i]}
	2685	for file in $(ls *)
	2686	do
	2687	ln -f $file ${pathout[$i]}
	2688	done >\|/dev/null 2>&1
[2566]	2689	cd $tempdir
[2380]	2690	fi
	2691
	2692	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2693	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2694	then
	2695	if [[ $link_local_output = true ]]
	2696	then
	2697	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2698	fi
[3025]	2699	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2700	cp -r ${localout[$i]}/* ${pathout[$i]}
	2701	fi
	2702
	2703	fi
	2704	fi
	2705	done
	2706
	2707	if (( i != 0 ))
	2708	then
	2709	if [[ $transfer_problems = true ]]
	2710	then
	2711	printf "\n$dashes\n *** OUTPUT-files saved"
	2712	printf "\n +++ WARNING: some data transfers failed! \n"
	2713	else
	2714	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2715	fi
	2716	fi
	2717
	2718
	2719	# IF REQUIRED, START A RESTART-JOB
	2720	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2721	if [[ -f CONTINUE_RUN ]]
	2722	then
	2723
	2724	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2725	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2726	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2727	# -b START A BATCH JOB
	2728	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2729	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2730	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2731
[2957]	2732	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2733	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2734	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2735	then
	2736	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2737	fi
[2380]	2738
	2739	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2740	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2741	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2742	then
[2381]	2743	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2744	fi
	2745
	2746
	2747	# START THE RESTART-JOB
	2748	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2749	echo " $prc"
	2750	printf "\n$dashes\n"
	2751	if [[ $running_on_remote = true ]]
	2752	then
	2753
	2754	echo "*** ssh will be used to initiate restart-runs!"
	2755	echo " return_address=\"$return_address\" "
	2756	echo " return_username=\"$local_username\" "
	2757
	2758	if [[ "$remote_loginnode" != "" ]]
	2759	then
[3132]	2760	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]	2761	else
[3132]	2762	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
[2380]	2763	fi
	2764
	2765	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2766	sleep 30
	2767
	2768	else
	2769
	2770	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2771	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2772	cd - > /dev/null
	2773
	2774	fi
	2775
[3132]	2776	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2777	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2778	then
	2779	printf "\n$dashes\n +++ creating restart run failed \n"
	2780	locat=create_restart
[3455]	2781	rm palmrun_restart.log
[3132]	2782	exit
	2783	else
	2784	printf "\n$dashes\n *** restart run initiated \n"
	2785	rm palmrun_restart.log
	2786	fi
[2380]	2787
[3132]	2788
[2380]	2789	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2790	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2791	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2792	# MAY BE VERY HUGE)
	2793	(( i = 0 ))
[2610]	2794	while (( i < nr_of_input_files ))
[2380]	2795	do
	2796	(( i = i + 1 ))
	2797	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2798	then
	2799	rm -r ${absnamein[$i]}
	2800	fi
	2801	done
	2802
	2803	fi
	2804
	2805
	2806	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2807	cd $HOME
[2566]	2808	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2809
	2810
	2811	else
	2812
	2813
	2814	# PREPARING ACTIONS,
	2815	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2816
	2817	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2818	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2819	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2820	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2821	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2822	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2823	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2824	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2825	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2826	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2827	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2828	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2829	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2830	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2831	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2832	if [[ $create_remote_batch_job = true ]]
	2833	then
	2834	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2835	if [[ $do_trace = true ]]
	2836	then
	2837	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2838	fi
[2380]	2839	elif [[ $create_batch_job = true ]]
	2840	then
	2841	palmrun_com=${palmrun_com}" -j"
[2420]	2842	if [[ $do_trace = true ]]
	2843	then
	2844	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2845	fi
[2380]	2846	fi
	2847
	2848
	2849	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2850	# REMOTE HOST
[3236]	2851	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2852	job_protocol_file=$job_protocol_file_local
	2853	if [[ $create_remote_batch_job = true ]]
	2854	then
[3236]	2855	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2856	job_protocol_file=$job_protocol_file_remote
	2857	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2858	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2859	fi
	2860
	2861
	2862	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2863	jobfile=jobfile.$run_id_number
[2380]	2864
	2865
	2866	# FIRST CREATE THE BATCH DIRECTIVES
	2867	(( i = 0 ))
	2868	while (( i < ibd ))
	2869	do
	2870	(( i = i + 1 ))
[2693]	2871	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2872	eval line=\"$line\"
	2873	echo "$line" >> $jobfile
	2874	done
	2875	echo " " >> $jobfile
	2876
	2877
	2878	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2879	# PROTOCOL
	2880	if [[ $create_remote_batch_job = true ]]
	2881	then
[3236]	2882	echo "set +vx" >> $jobfile
	2883	echo "trap '" >> $jobfile
	2884	echo "set +vx" >> $jobfile
	2885	echo "cd ${remote_jobcatalog}" >> $jobfile
	2886	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2887
	2888	# ADD THE BATCH DIRECTIVES
	2889	(( i = 0 ))
	2890	while (( i < ibdt ))
	2891	do
	2892	(( i = i + 1 ))
[2693]	2893	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2894	eval line=\"$line\"
	2895	echo "$line" >> $jobfile
	2896	done
	2897	echo " " >> $jobfile
	2898
	2899	echo "set -x" >> $jobfile
[3236]	2900	echo "${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]	2901	echo "%%END%%" >> $jobfile
	2902	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2903	echo "$submit_command $scpjob_file" >> $jobfile
	2904	echo "rm $scpjob_file" >> $jobfile
[2404]	2905	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2906	echo "set -x" >> $jobfile
	2907	echo " ' exit" >> $jobfile
	2908	fi
	2909
	2910
	2911	# ACTIVATE ERROR-TRACEBACK
	2912	if [[ $do_trace = true ]]
	2913	then
	2914	echo "set -x" >> $jobfile
	2915	else
	2916	echo "set +vx" >> $jobfile
	2917	fi
	2918
	2919
	2920	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2921	if [[ "$login_init_cmd" != "" ]]
	2922	then
	2923	echo "$login_init_cmd" >> $jobfile
	2924	fi
	2925	if [[ "$module_commands" != "" ]]
	2926	then
	2927	echo "$module_commands" >> $jobfile
	2928	fi
	2929
	2930
	2931	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2932	if [[ $create_remote_batch_job = true ]]
	2933	then
	2934	echo "mkdir $tempdir" >> $jobfile
	2935	echo "chmod go+rx $tempdir" >> $jobfile
	2936	else
	2937	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2938	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2939	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2940	mkdir $tempdir
	2941	chmod go+rx $tempdir
	2942	fi
	2943	echo "cd $tempdir" >> $jobfile
	2944	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2945	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2946	echo "export PATH=.:\$PATH" >> $jobfile
	2947	echo "export execute_palmrun=true" >> $jobfile
	2948
	2949
	2950	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2951	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2952	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2953	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2954	echo "export LOCAL_PWD" >> $jobfile
	2955
	2956
	2957	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2958	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2959	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2960
	2961
	2962	# CALL PALMRUN WITHIN THE JOB
	2963	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2964	echo "set -x" >> $jobfile
	2965	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2966
	2967
	2968	# TRANSFER JOBFILE TO THE TARGET HOST
	2969	if [[ $create_jobfile_only = false ]]
	2970	then
	2971
[3505]	2972	# CREATE LOCAL JOB FOLDER
	2973	eval local_jobcatalog=$local_jobcatalog
	2974	if [[ ! -d $local_jobcatalog ]]
	2975	then
	2976	echo " "
	2977	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	2978	mkdir $local_jobcatalog
	2979	fi
	2980
[2380]	2981	if [[ $create_remote_batch_job = true ]]
	2982	then
	2983
[2420]	2984	echo " "
[2566]	2985	echo " *** transfer of job to remote host via scp"
[3505]	2986
	2987	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
	2988	echo "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
	2989
	2990	# COPY THE JOB FILE
[2420]	2991	if [[ $do_trace = true ]]
	2992	then
[3236]	2993	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	2994	fi
[3236]	2995	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	2996
[3505]	2997	# SUBMIT THE JOB
[2566]	2998	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2999	if [[ $do_trace = true ]]
	3000	then
[3236]	3001	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]	3002	fi
[3236]	3003	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]	3004
	3005	elif [[ $create_batch_job = true ]]
	3006	then
	3007
[2385]	3008	eval local_jobcatalog=$local_jobcatalog
[3236]	3009	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3010	cd $local_jobcatalog
[2380]	3011	echo " "
[2420]	3012	echo " *** submit the job"
	3013	if [[ $do_trace = true ]]
	3014	then
[3236]	3015	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3016	fi
[3236]	3017	$submit_command ${configuration_identifier}_${run_id}
	3018	rm ${configuration_identifier}_${run_id}
[2380]	3019	cd - > /dev/null
	3020
	3021	fi
	3022
	3023	rm -rf $jobfile
	3024
	3025	else
	3026
	3027	printf "\n *** jobfile created under name \"$jobfile\" "
	3028	printf "\n no batch-job has been sent!"
	3029
	3030	fi
	3031
	3032	fi # END OF REMOTE-PART

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