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source: palm/trunk/SCRIPTS/palmrun @ 3313

Last change on this file since 3313 was 3313, checked in by knoop, 6 years ago
Added test mode to palmrun
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 100.3 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 3313 2018-10-06 15:22:48Z knoop $
[3294]	29	# more detailed error message for outdated fileconnection file
	30	#
	31	# 3236 2018-09-10 09:07:06Z raasch
[3236]	32	# warning issued in case of file connection file version mismatch,
	33	# host_configuration renamed configuration_identifier,
	34	# "host identifier" in header output renamed "config. identifier",
	35	# jobname renamed run_identifier,
	36	# run_id renamed run_id_number
	37	# job_id renamed run_id
	38	# option -r renamed -i
	39	#
	40	# 3151 2018-07-19 08:45:38Z raasch
[3151]	41	# removed additional listing of files to be compiled, print PALM code revision
	42	# in header
	43	#
	44	# 3132 2018-07-16 11:44:58Z raasch
[3132]	45	# create consistent error messages in case of failed restarts,
	46	# check existence of remote job catalog
	47	#
	48	# 3043 2018-05-25 10:47:54Z raasch
[3043]	49	# check for setting of fast_io_catalog
	50	#
	51	# 3033 2018-05-23 15:26:19Z raasch
[3025]	52	# -T option not required for interactive runs (tasks per node =
	53	# total number of cores is assumed as default, if option is not given),
	54	# reformatting of a few messages,
	55	# bugfix: destination output directory is created if attribute "pe" is set in
	56	# .palm.iofiles
	57	#
	58	# 2718 2018-01-02 08:49:38Z maronga
[2993]	59	# bugfix of r2990
	60	#
	61	# 2718 2018-01-02 08:49:38Z maronga
[2990]	62	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	63	# not in the working directory from where palmrun is called
	64	#
	65	# 2718 2018-01-02 08:49:38Z maronga
[2957]	66	# svfout in the activation string will be replaced now by svfin in case of
	67	# automatic restarts
	68	#
	69	# 2718 2018-01-02 08:49:38Z maronga
[2906]	70	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	71	# the possible output or input of sky view factors
	72	#
	73	# 2718 2018-01-02 08:49:38Z maronga
[2834]	74	# "fname" renamed to "jobname"
	75	#
	76	# 2718 2018-01-02 08:49:38Z maronga
[2799]	77	# parameters are allowed in output commands (OC:)
	78	#
	79	# 2718 2018-01-02 08:49:38Z maronga
[2789]	80	# bugfix: exit if no queue has been given neither with option -q nor in the
	81	# configuration file
	82	#
	83	# 2718 2018-01-02 08:49:38Z maronga
[2762]	84	# file connection file from trunk/SCRIPTS is taken by default
	85	#
	86	# 2718 2018-01-02 08:49:38Z maronga
[2716]	87	# Corrected "Former revisions" section
	88	#
	89	# 2696 2017-12-14 17:12:51Z kanani
	90	# Change in file header (GPL part)
	91	#
	92	# 2693 2017-12-13 12:33:49Z raasch
[2693]	93	# replacement of variables given by {{<variable>}} in configuration file is now
	94	# done in a more general way, variable names are written in small letters
	95	#
	96	# 2670 2017-12-06 16:32:19Z raasch
[2670]	97	# test printouts removed
	98	#
	99	# 2669 2017-12-06 16:03:27Z raasch
[2669]	100	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	101	# removed,
	102	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	103	# files,
	104	# informative messages in case of missing optional input files shortened
	105	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	106	#
	107	# 2638 2017-11-23 12:44:23Z raasch
[2610]	108	# use of wildcards in file connection statements enabled
	109	#
	110	# 2605 2017-11-09 15:31:46Z raasch
[2605]	111	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	112	# will not be sent with the job file any more, but copied into the
[2610]	113	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	114	#
	115	# 2600 2017-11-01 14:11:20Z raasch
[2600]	116	# cycle numbers are made three digits wide
	117	#
	118	# 2566 2017-10-20 08:50:47Z raasch
[2566]	119	# execute command for combine_plot_fields added
	120	# "TEMPDIR" renamed "tempdir"
	121	# temporary working directory for local batch jobs is created immediately within
	122	# the user's palmrun call, due to a requirement of the "grid engine" batch
	123	# system, where the working directory is given with batch directive -wd and must
	124	# already exist when the job is submitted,
	125	# informative messages in non-trace mode reduced and partly reformatted
	126	#
	127	# 2551 2017-10-18 07:25:11Z raasch
[2551]	128	# TEMPDIR added as replacement string to be used in batch directives
	129	#
	130	# 2512 2017-10-04 08:26:59Z raasch
[2507]	131	# bugfix for determining cycle numbers of NetCDF input files
	132	#
	133	# 2506 2017-09-29 08:30:37Z raasch
[2506]	134	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	135	# host configuration added to SOURCES_FOR_RUN_... folder name
	136	# host_identifier renamed host_configuration
	137	# option -W added to allow for job dependencies
	138	#
	139	# 2501 2017-09-26 11:41:55Z raasch
[2501]	140	# default value for number of cores (option -X) set to 1
	141	# bugfix for mechanism which overwrites configuration file settings with values
	142	# provided by palmrun options
	143	#
	144	# 2499 2017-09-22 16:47:58Z kanani
[2499]	145	# option -h named configuration identifier
	146	#
	147	# 2480 2017-09-19 06:24:14Z maronga
[2480]	148	# bugfix for last revision
	149	#
	150	# 2479 2017-09-19 06:12:16Z raasch
[2479]	151	# option -A (project account number) added
	152	#
	153	# 2422 2017-09-08 08:25:41Z raasch
[2410]	154	# initial revision
[2380]	155	#
	156	#--------------------------------------------------------------------------------#
	157	# palmrun - script for running PALM jobs on local and remote hosts
	158	#--------------------------------------------------------------------------------#
	159
	160
	161
	162	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	163
	164	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	165	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	166	# (TOO MANY ARGUMENTS - PROBLEM)
	167	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	168
[2610]	169	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	170	typeset -i nr_of_output_files=0
[2380]	171	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	172	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	173	# SCRIPT-OPTION ARGUMENTS
	174	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	175	typeset -i icycle inode ival maxcycle mpi_tasks
	176	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	177
	178	activation_string_list=""
	179	AddFilenames=""
	180	combine_plot_fields=true
	181	compiler_name=""
	182	compiler_name_ser=""
	183	compiler_options=""
[3236]	184	configuration_identifier="default"
[2501]	185	cores=1
[2380]	186	cores_atmos=0
	187	cores_ocean=0
	188	coupled_dist=""
	189	cpp_options=""
	190	cpumax=0
[2506]	191	create_batch_job=false
[2380]	192	create_jobfile_only=false
	193	create_remote_batch_job=false
	194	dashes=" ----------------------------------------------------------------------------"
	195	defaultqueue=""
[2506]	196	delete_temporary_catalog=true
[2380]	197	do_compile=true
	198	do_trace=false
	199	executable=""
	200	execute_command=""
	201	execution_error=false
[2762]	202	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	203	global_revision=""
	204	hostfile=""
	205	hp=""
	206	keep_data_from_previous_run=false
	207	link_local_input=false
	208	link_local_output=false
[2388]	209	linker_options=""
[2385]	210	local_jobcatalog=""
[2380]	211	locat=normal
	212	makefile=""
	213	max_par_io_str=""
	214	prc=$0
	215	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	216	do
	217	prc=`echo $prc \| cut -f2- -d"/"`
	218	done
	219	module_calls=""
[2506]	220	palmrun_memory=""
[2380]	221	palmrun_script_name=$prc
	222	openmp=false
[2506]	223	previous_job=""
[2479]	224	project_account=""
[2380]	225	queue=none
[2906]	226	read_svf=""
[2380]	227	restart_run=false
	228	return_address=""
[2385]	229	remote_jobcatalog=""
[2380]	230	remote_username=""
	231	running_in_batch_mode=false
[3313]	232	running_in_test_mode=false
[2380]	233	run_coupled_model=false
	234	run_id=""
[3236]	235	run_id_number=""
	236	run_identifier=test
[2380]	237	silent=false
	238	source_list=""
	239	source_path=""
[2501]	240	tasks_per_node=0
[2380]	241	threads_per_task=1
	242	transfer_problems=false
[2384]	243	user_source_path=""
[2506]	244	use_existing_sources_folder=""
[2380]	245	use_openmp=false
[3033]	246	version="palmrun 1.0 Rev$Rev: 3313 $"
[2380]	247	working_directory=`pwd`
	248	write_binary=""
[2906]	249	write_svf=""
[2380]	250
	251
	252	# ERROR HANDLING IN CASE OF EXIT
[2404]	253	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	254	then
	255
	256	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	257	(( i = 0 ))
	258	while (( i < iec ))
	259	do
	260	(( i = i + 1 ))
	261	printf "\n *** Execution of ERROR-command:\n"
	262	printf " >>> ${err_command[$i]}\n"
	263	eval ${err_command[$i]}
	264	done
[2566]	265	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	266	printf "\n\n+++ palmrun crashed \n\n"
	267	exit 1
	268	elif [[ $locat != normal ]]
[2380]	269	then
[3312]	270	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	271	printf "\n+++ palmrun killed by \"^C\" \n\n"
	272	exit 2
	273	else
[2566]	274	printf "\n --> palmrun finished\n\n"
[3312]	275	exit 0
[2380]	276	fi' exit
	277
	278
	279	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	280	trap 'locat=control_c
	281	exit 1
[2380]	282	' 2
	283
	284
	285	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	286	# WHICH WILL BE USED TO START RESTART-JOBS
[3313]	287	while getopts :a:A:bBCd:FG:h:i:jkm:M:O:q:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
[2380]	288	do
	289	case $option in
	290	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	291	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	292	(b) create_batch_job=true; prc="$prc -b";;
	293	(B) delete_temporary_catalog=false; prc="$prc -B";;
	294	(C) restart_run=true; prc="$prc -C";;
[3236]	295	(d) run_identifier=$OPTARG; prc="$prc -d$OPTARG";;
[2380]	296	(F) create_jobfile_only=true;;
	297	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	298	(h) configuration_identifier=$OPTARG; prc="$prc -h$OPTARG";;
	299	(i) run_id_number=$OPTARG;;
[2380]	300	(j) running_in_batch_mode=true;;
	301	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	302	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	303	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	304	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	305	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	306	(R) return_address=$OPTARG;;
	307	(s) source_list=$OPTARG;;
[2501]	308	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	309	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	310	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	311	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	312	(v) silent=true; prc="$prc -v";;
[2506]	313	(V) use_existing_sources_folder="-V";;
[2380]	314	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	315	(W) previous_job=$OPTARG;;
[2380]	316	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	317	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	318	(y) ocean_file_appendix=true; prc="$prc -y";;
	319	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	320	(z) running_in_test_mode=true;;
[2380]	321	(Z) combine_plot_fields=false; prc="$prc -Z";;
	322	(\?) printf "\n +++ unknown option $OPTARG \n"
	323	printf "\n --> type \"$0 ?\" for available options \n"
	324	locat=parameter;exit;;
	325	esac
	326	done
	327
	328
	329	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	330	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	331	(( to_shift = $OPTIND - 1 ))
	332	shift $to_shift
	333
	334	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	335	if [[ "$1" = "?" ]]
	336	then
	337	(printf "\n *** Description of available palmrun options:\n"
	338	printf "\n Option Description Default-Value"
	339	printf "\n -a activation string list \"\" "
[2479]	340	printf "\n -A project account number ---"
[2380]	341	printf "\n -b batch-job on local machine ---"
	342	printf "\n -B do not delete temporary directory at end ---"
[3025]	343	printf "\n -d run identifier test"
[2380]	344	printf "\n -F create batch job file only ---"
[2506]	345	printf "\n -h host configuration \"default\" "
[2380]	346	printf "\n -k keep data from previous run"
	347	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	348	printf "\n -M Makefile name Makefile"
	349	printf "\n -O threads per openMP task ---"
	350	printf "\n -q queue \"$queue\" "
	351	printf "\n -s filenames of routines to be compiled \"\" "
	352	printf "\n must end with .f, .f90, .F, or .c !"
	353	printf "\n use \"..\" for more than one file and wildcards"
	354	printf "\n -s LM compiles all locally modified files"
	355	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	356	printf "\n -T tasks per node ---"
[2380]	357	printf "\n -u username on remote machine \"\" "
	358	printf "\n -v no prompt for confirmation ---"
[2506]	359	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	360	printf "\n -w maximum parallel io streams as given by -X"
[2506]	361	printf "\n -W name of job to wait for ---"
[2380]	362	printf "\n -x tracing of palmrun for debug purposes ---"
	363	printf "\n -X # of processors (on parallel machines) 1"
	364	printf "\n -y add appendix \"_O\" to all local output"
	365	printf "\n files (ocean precursor runs followed by"
	366	printf "\n coupled atmosphere-ocean runs) ---"
	367	printf "\n -Y run coupled model, \"#1 #2\" with"
	368	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	369	printf "\n -Z skip combine_plot_fields at the end of "
	370	printf "\n the simulation ---"
	371	printf "\n "
	372	printf "\n Possible values of positional parameter <modus>:"
	373	printf "\n \"?\" - this outline \n\n") \| more
	374	exit
	375	elif [[ "$1" != "" ]]
	376	then
	377	printf "\n +++ positional parameter $1 unknown \n"
	378	locat=parameter; exit
	379	fi
	380
	381
	382
	383	# SHORT STARTING MESSAGE
	384	printf "\n*** $version "
	385	printf "\n will be executed. Please wait ..."
	386
	387
[3236]	388	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLES
	389	export fname=$run_identifier
	390	export jobname=$run_identifier
[2834]	391
	392
[2506]	393	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	394	config_file=.palm.config.$configuration_identifier
	395	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	396
	397
	398	# CHECK, IF CONFIGURATION FILE EXISTS
	399	if [[ ! -f $config_file ]]
	400	then
	401	printf "\n\n +++ configuration file: "
	402	printf "\n $config_file"
	403	printf "\n does not exist"
	404	locat=connect; exit
	405	fi
	406
	407
[2762]	408	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	409	if [[ -f .palm.iofiles ]]
	410	then
[3236]	411
	412	# CHECK VERSION MISMATCH
	413	if [[ $running_in_batch_mode != true ]]
	414	then
	415	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	416	then
	417	printf "\n\n +++ WARNING: A file connection file has been found in your"
	418	printf "\n working directory, but its revision does not match"
	419	printf "\n the revision of the default (trunk) version."
[3294]	420	printf "\n You may need to update your connection file"
	421	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	422	fi
	423	fi
	424
[2762]	425	fileconnection_file=.palm.iofiles
[3236]	426
[2762]	427	fi
	428
	429
[2380]	430	# CHECK, IF FILE CONNECTION FILE EXISTS
	431	if [[ ! -f $fileconnection_file ]]
	432	then
	433	printf "\n\n +++ file connection file: "
	434	printf "\n $fileconnection_file"
	435	printf "\n does not exist"
	436	locat=connect; exit
	437	fi
	438
	439
[2404]	440	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	441	if [[ "$activation_string_list" = "" ]]
	442	then
	443	printf "\n\n +++ no activation string list given: "
	444	printf "\n please set palmrun option \"-a\" "
	445	locat=palmrun_option; exit
	446	fi
	447
	448
	449	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	450	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	451	then
	452	write_binary=true
	453	else
	454	write_binary=false
	455	fi
	456
[2906]	457	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	458	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	459	then
	460	write_svf=true
	461	else
	462	write_svf=false
	463	fi
[2404]	464
[2906]	465	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	466	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	467	then
	468	read_svf=true
	469	else
	470	read_svf=false
	471	fi
	472
	473
[2380]	474	# READ AND EVALUATE THE CONFIGURATION-FILE
	475	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	476
	477	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	478	while read line
	479	do
	480
	481	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	482	eval line=\"$line\"
	483
	484
	485	# INTERPRET THE LINE
	486	if [[ "$(echo $line)" = "" ]]
	487	then
	488
	489	# EMPTY LINE, NO ACTION
	490	continue
	491
	492	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	493	then
	494
	495	# LINE IS A COMMENT LINE
	496	continue
	497
	498	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	499	then
	500
	501	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	502	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	503	value=`echo $line \| cut -d" " -s -f2-`
	504
	505
	506	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	507	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	508	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	509	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	510	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	511	# CONFIGURATION-FILE.
	512	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	513	then
	514	eval export $var="\$value"
	515
	516	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	517	if [[ $do_trace = true ]]
	518	then
	519	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	520	fi
	521	fi
	522
	523	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	524	then
	525
	526	# LINE DEFINES BATCH-DIRECTIVE
	527	(( ibd = ibd + 1 ))
	528	line=$(echo $line \| cut -c4-)
	529	batch_directive[$ibd]="$line"
	530
	531	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	532	then
	533
	534	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	535	# REMOTE TO A LOCAL HOST
	536	(( ibdt = ibdt + 1 ))
	537	line=$(echo $line \| cut -c5-)
	538	batch_directive_transfer[$ibdt]="$line"
	539
	540	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	541	then
	542
	543	# LINE DEFINES ERROR-COMMAND
	544	(( iec = iec + 1 ))
	545	line=$(echo $line \| cut -c4-)
	546	err_command[$iec]="$line"
	547
	548	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	549	then
	550
	551	# LINE DEFINES INPUT-COMMAND
	552	(( iic = iic + 1 ))
	553	line=$(echo $line \| cut -c4-)
	554	in_command[$iic]="$line"
	555
	556	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	557	then
	558
	559	# LINE DEFINES OUTPUT-COMMAND
	560	(( ioc = ioc + 1 ))
	561	line=$(echo $line \| cut -c4-)
	562	out_command[$ioc]="$line"
	563
	564	else
	565
	566	# SKIP ALL OTHER LINES
	567	continue
	568
	569	fi
	570
	571	done < $config_file
	572
	573
	574	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	575	if [[ "$fast_io_catalog" = "" ]]
	576	then
	577	printf "\n +++ no fast_io_catalog found in $config_file"
	578	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	579	locat=config_file; exit
	580	fi
[2380]	581	if [[ "$compiler_name" = "" ]]
	582	then
	583	printf "\n +++ no compiler name found in $config_file"
	584	printf "\n Please add line \"compiler_name ...\" to that file."
	585	locat=config_file; exit
	586	fi
	587	if [[ "$compiler_name_ser" = "" ]]
	588	then
	589	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	590	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	591	locat=config_file; exit
	592	fi
	593	if [[ "$compiler_options" = "" ]]
	594	then
	595	printf "\n +++ no compiler options found in $config_file"
	596	printf "\n Please add line \"compiler_options ...\" to that file."
	597	locat=config_file; exit
	598	fi
[2388]	599	if [[ "$linker_options" = "" ]]
[2380]	600	then
[2388]	601	printf "\n +++ no linker options found in $config_file"
	602	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	603	locat=config_file; exit
	604	fi
	605	if [[ "$execute_command" = "" ]]
	606	then
	607	printf "\n +++ no execute command found in $config_file"
	608	printf "\n Please add line \"execute_command ...\" to that file."
	609	locat=config_file; exit
	610	fi
	611
	612	if [[ "$hostfile" != "" ]]
	613	then
	614	if [[ $hostfile != auto && ! -f $hostfile ]]
	615	then
	616	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	617	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	618	locat=config_file; exit
	619	fi
	620	fi
	621
	622
	623	# DETERMINE THE CALL STATUS
	624	if [[ "$return_address" != "" ]]
	625	then
	626
	627	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	628	# BATCH MODE AND ...
	629	running_on_remote=true
	630
	631	else
	632
	633	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	634	if [[ "$remote_ip" != "" ]]
	635	then
	636
	637	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	638	create_remote_batch_job=true
	639
[3132]	640	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	641	if [[ "$remote_jobcatalog" = "" ]]
	642	then
	643	printf "\n +++ no remote jobcatalog found in $config_file"
	644	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	645	locat=config_file; exit
	646	fi
	647
	648
[2380]	649	fi
	650	running_on_remote=false
	651	fi
	652
	653
	654
	655	# READ AND EVALUATE THE I/O-FILE LIST
	656	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	657
	658	# READ THE FILE CONNECTION FILE LINE BY LINE
	659	while read line
	660	do
	661
[2669]	662	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	663	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	664
	665	# INTERPRET THE LINE
	666	if [[ "$(echo $line)" = "" ]]
	667	then
	668	# EMPTY LINE, NO ACTION
	669	continue
	670
	671	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	672	then
	673
	674	# LINE IS A COMMENT LINE
	675	true
	676
	677	else
	678
	679	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	680	# s2a: in/out - field
[2669]	681	# s2b: action - field (optional)
	682	s1=`echo "$line" \| cut -d" " -f1`
	683	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	684	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	685	then
[2669]	686	s2a=$s2
[2380]	687	s2b=""
	688	else
[2669]	689	s2a=`echo $s2 \| cut -d":" -f1`
	690	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	691	fi
[2669]	692	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	693	s4=`echo "$line" \| cut -d" " -s -f4`
	694	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	695	s5=`echo "$line" \| cut -d" " -s -f5`
	696	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	697
	698
	699	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	700	# INPUT- OR OUTPUT-LIST.
	701	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	702	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	703	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	704	# IS NOT CHECKED AND STORED.
[2610]	705	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	706	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	707	then
	708	found=false
	709	for actual in $activation_string_list
	710	do
	711	for formal in $s3
	712	do
	713	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	714	done
	715	done
	716	if [[ $found = true ]]
	717	then
	718	(( iin = iin + 1 ))
[2669]	719	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	720	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	721	if [[ "$s2a" = inopt ]]
	722	then
	723	optin_pre[$iin]=yes
	724	else
	725	optin_pre[$iin]=no
	726	fi
[2605]	727
	728	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	729	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	730	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	731	then
[2610]	732	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	733	fi
	734
[2610]	735	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	736	# THE WILDCARD FROM THE ENDING
	737	if [[ "${s5: -1}" = "*" ]]
	738	then
[2669]	739	if [[ "$s2b" = "di" ]]
[2610]	740	then
	741	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	742	printf "\n see file \"$fileconnection_file\", line"
	743	printf "\n$line"
	744	locat=iofiles_file; exit
	745	fi
	746	multin[$iin]=true
	747	string=${endin_pre[$iin]}
	748	endin_pre[$iin]="${string%?}"
	749	else
	750	multin[$iin]=false
	751	fi
[2380]	752	fi
[2669]	753	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	754	then
	755	found=false
	756	for actual in $activation_string_list
	757	do
	758	for formal in $s3
	759	do
[2670]	760	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	761	done
	762	done
	763	if [[ $found = true ]]
	764	then
	765	(( iout = iout + 1 ))
[2669]	766	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	767	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	768
[2669]	769	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	770	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	771	if [[ $formal = wildcard ]]
	772	then
	773	warnout_pre[$iout]=false
	774	else
	775	warnout_pre[$iout]=true
	776	fi
	777
[2610]	778	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	779	# THE WILDCARD FROM THE LOCAL FILENAME
	780	if [[ "${s1: -1}" = "*" ]]
	781	then
[2669]	782	if [[ "$s2b" = "di" ]]
[2610]	783	then
	784	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	785	printf "\n see file \"$fileconnection_file\", line"
	786	printf "\n$line"
	787	locat=iofiles_file; exit
	788	fi
	789	multout[$iout]=true
	790	string=${localout_pre[$iout]}
	791	localout_pre[$iout]="${string%?}"
	792	else
	793	multout[$iout]=false
	794	fi
[2380]	795	fi
[2669]	796	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	797	then
[2669]	798	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	799	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	800	locat=connect; exit
	801	fi
	802	IFS="$IFSALT"
	803	fi
	804
	805	done < $fileconnection_file
	806
	807
	808
[2501]	809	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	810	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	811	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	812	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	813	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	814	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	815
	816
	817
[2380]	818	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	819	if [[ $run_coupled_model = true ]]
	820	then
	821
	822	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	823	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	824
	825	if (( $cores_ocean + $cores_atmos != $cores ))
	826	then
	827
	828	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	829	printf "\n PEs (total) : $cores"
	830	printf "\n PEs (atmosphere): $cores_atmos"
	831	printf "\n PEs (ocean) : $cores_ocean"
	832	locat=coupling; exit
	833
	834	fi
	835
	836	fi
	837
	838
	839	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	840	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	841	# FOLDER
	842	if [[ $running_in_batch_mode = true ]]
	843	then
	844
[2506]	845	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	846	then
[2506]	847	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	848	printf "\n Please check the output of the palmrun-call"
	849	printf "\n that you did on your local host."
	850	locat=SOURCES_FOR_RUN; exit
	851	fi
	852
	853	else
	854
	855	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	856	# AUTOMATIC RESTART RUN
	857	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	858	if [[ $restart_run = false ]]
	859	then
	860
	861	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	862	# THE LOCAL HOST
	863	if [[ ! -d $source_path ]]
	864	then
	865	printf "\n\n +++ source path \"$source_path\" on local host"
	866	printf "\n \"$(hostname)\" does not exist"
	867	locat=source_path; exit
	868	fi
	869
[2990]	870	rm -rf ${base_directory}/${sources_for_run_catalog}
	871	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	872
	873	if [[ "$source_list" = LM ]]
	874	then
	875
	876	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	877	source_list=""
	878	cd $source_path
	879
	880
[2512]	881	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	882	if [[ ! -d ../.svn ]]
[2380]	883	then
	884	printf "\n\n +++ source directory"
	885	printf "\n \"$source_path\" "
	886	printf "\n is not under control of \"subversion\"."
[2512]	887	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	888	fi
	889
	890
	891	# LIST ALL MODIFIED SOURCE CODE FILES
	892	Filenames=""
[2404]	893	svn status > tmp_svnstatus
[2380]	894	while read line
	895	do
	896	firstc=`echo $line \| cut -c1`
	897	if [[ $firstc = M \|\| $firstc = "?" ]]
	898	then
	899	Name=`echo "$line" \| cut -c8-`
	900	extension=`echo $Name \| cut -d. -f2`
	901	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	902	then
	903	Filenames="$Filenames "$Name
	904	fi
	905	fi
[2404]	906	done < tmp_svnstatus
	907	rm -rf tmp_svnstatus
[2380]	908
	909
	910	# COPY FILES TO SOURCES_FOR_RUN_...
	911	for filename in $Filenames
	912	do
[2990]	913	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	914	source_list=$source_list"$filename "
	915	done
	916
	917	cd - > /dev/null
	918
	919
	920	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	921	elif [[ "$source_list" != "" ]]
	922	then
	923
	924	cd $source_path
	925
	926	for filename in $source_list
	927	do
	928
	929	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	930	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	931	then
	932	printf "\n +++ source code file: $filename"
	933	printf "\n must not contain (\"/\") "
	934	locat=source; exit
	935	fi
	936
	937	if [[ ! -f $filename ]]
	938	then
	939	printf "\n +++ source code file: $filename"
	940	printf "\n does not exist"
	941	locat=source; exit
	942	else
[2990]	943	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	944	fi
	945
	946	done
	947
	948	cd - > /dev/null
	949
	950	fi
	951
	952	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	953	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	954	if [[ ! -f $makefile ]]
	955	then
	956	printf "\n +++ file \"$makefile\" does not exist"
	957	locat=make; exit
	958	else
[2990]	959	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	960	fi
	961
	962
	963	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	964	if [[ "$user_source_path" != "" ]]
[2380]	965	then
	966
	967	# DOES THE DIRECTORY EXIST?
[2384]	968	if [[ ! -d $user_source_path ]]
[2380]	969	then
	970
	971	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	972	printf "\n \"$user_source_path\" "
[2380]	973	printf "\n does not exist or is not a directory."
	974	printf "\n No source code will be used from this directory!\n"
[2384]	975	user_source_path=""
[2380]	976	if [[ $silent == false ]]
	977	then
	978	sleep 2
	979	fi
	980
	981	else
	982
[2384]	983	cd $user_source_path
[2380]	984
	985	Names=$(ls -1 *.f90 2>&1)
	986	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	987	Names=$(ls -1 *.F90 2>&1)
	988	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	989	Names=$(ls -1 *.F 2>&1)
	990	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	991	Names=$(ls -1 *.f 2>&1)
	992	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	993	Names=$(ls -1 *.c 2>&1)
	994	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	995
	996	cd - > /dev/null
[2990]	997	cd ${base_directory}/${sources_for_run_catalog}
[2380]	998
	999	# COPY MAKEFILE IF EXISTING
[2384]	1000	if [[ -f $user_source_path/Makefile ]]
[2380]	1001	then
	1002	printf "\n\n *** user Makefile from directory"
[2384]	1003	printf "\n \"$user_source_path\" is used \n"
[2380]	1004	if [[ $silent == false ]]
	1005	then
	1006	sleep 1
	1007	fi
[2384]	1008	cp $user_source_path/Makefile .
[2380]	1009	fi
	1010
	1011	for filename in $AddFilenames
	1012	do
	1013	if [[ -f $filename ]]
	1014	then
	1015	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1016	printf "\n source code directory \"$user_source_path\" "
[2380]	1017	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1018	printf "\n from directory \"$source_path\"."
	1019	locat=source; exit
	1020	fi
	1021
[2384]	1022	cp $user_source_path/$filename .
[2380]	1023	source_list="$source_list $filename"
	1024
	1025	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1026	if [[ $(grep -c $filename Makefile) = 0 ]]
	1027	then
	1028	printf "\n\n +++ user file \"$filename\" "
	1029	printf "\n is not listed in Makefile \n"
	1030	locat=source; exit
	1031	fi
	1032	done
	1033	cd - > /dev/null
	1034	fi
	1035	fi
	1036
	1037	# COPY CONFIGURATION FILES
[2990]	1038	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1039	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1040
	1041	# COPY SHELLSCRIPTS
[2990]	1042	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1043	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1044
	1045	fi
	1046
	1047	fi
	1048
[2605]	1049
[2380]	1050	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1051	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1052	if [[ "$global_revision" = "" ]]
	1053	then
	1054	global_revision=`svnversion $source_path 2>/dev/null`
	1055	global_revision="Rev: $global_revision"
	1056	fi
	1057
	1058
	1059	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1060	if [[ -n $cores ]]
	1061	then
	1062
	1063	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1064	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1065	if [[ $tasks_per_node = 0 ]]
[2380]	1066	then
[3025]	1067	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1068	then
	1069	printf "\n"
	1070	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1071	printf "\n set -T option or define tasks_per_node in the config file"
	1072	locat=tasks_per_node; (( iec = 0 )); exit
	1073	else
	1074	# DEFAULT FOR INTERACTIVE RUN
	1075	tasks_per_node=$cores
	1076	fi
[2380]	1077	fi
	1078
	1079	if (( cores < tasks_per_node ))
	1080	then
	1081	printf "\n"
	1082	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1083	printf "\n given values: -T $tasks_per_node -X $cores"
	1084	locat=tasks_per_node; (( iec = 0 )); exit
	1085	fi
	1086
	1087	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1088	(( mpi_tasks = cores / threads_per_task ))
	1089	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1090	(( ii = cores / tasks_per_node ))
	1091	(( remaining_cores = cores - ii * tasks_per_node ))
	1092	if (( remaining_cores > 0 ))
	1093	then
	1094	printf "\n"
	1095	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1096	printf "\n divisor of the total number of cores (option \"-X\")"
	1097	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1098	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1099	(( nodes = nodes + 1 ))
	1100	fi
	1101
	1102	fi
	1103
	1104
	1105	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1106	if [[ "$maximum_parallel_io_streams" = "" ]]
	1107	then
	1108	maximum_parallel_io_streams=$cores
	1109	fi
	1110
	1111
	1112	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1113	if [[ "$scp_port" != "" ]]
	1114	then
	1115	PORTOPT="-P $scp_port"
	1116	SSH_PORTOPT="-p $scp_port"
	1117	fi
	1118
	1119
	1120	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1121	# CONFIG-FILE
	1122	if [[ "$ssh_key" != "" ]]
	1123	then
	1124	ssh_key="-i $HOME/.ssh/$ssh_key"
	1125	fi
	1126
	1127
	1128	# SET QUEUE, IF NOT GIVEN
	1129	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1130	then
	1131
	1132	if [[ $queue = none && "$defaultqueue" = "" ]]
	1133	then
	1134	printf "\n"
	1135	printf "\n +++ no default queue given in configuration file and no queue"
	1136	printf "\n given with option -q"
[2789]	1137	locat=queue; exit
[2380]	1138	fi
	1139	if [[ $queue = none ]]
	1140	then
	1141	queue=$defaultqueue
	1142	fi
	1143
	1144	fi
	1145
	1146
	1147	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1148	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1149	(( i = 0 ))
[2610]	1150	(( nr_of_input_files = 0 ))
[2380]	1151	while (( i < iin ))
	1152	do
	1153	(( i = i + 1 ))
	1154
	1155	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1156	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1157	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1158	then
[2610]	1159	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1160	else
[3236]	1161	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1162	fi
	1163
[2610]	1164
[2380]	1165	# CHECK IF FILE EXISTS
	1166	if ! ls $filename* 1>/dev/null 2>&1
	1167	then
	1168
[2669]	1169	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1170	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1171	then
	1172	printf "\n\n +++ INPUT-file: "
[2610]	1173	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1174	then
	1175	printf "\n $filename"
	1176	else
[2610]	1177	printf "\n $filename.${extin_pre[$i]}"
[2380]	1178	fi
	1179	printf "\n does not exist\n"
	1180	locat=input; exit
	1181	else
[2610]	1182	(( nr_of_input_files = nr_of_input_files + 1 ))
	1183	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1184	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1185	actionin[$nr_of_input_files]="unavailable"
[2610]	1186	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1187	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1188	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1189	fi
[2605]	1190
[2380]	1191	else
	1192
[3236]	1193	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1194	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1195	# ENDINGS
[2610]	1196	if [[ "${multin[$i]}" = true ]]
	1197	then
	1198	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1199	ls -1 -d ${filename} > filelist 2>/dev/null
	1200	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1201	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1202
[2610]	1203	endings=""
	1204	while read line
	1205	do
	1206	# filename without path (i.e. after the last "/")
	1207	basefilename=$(basename ${line})
[2380]	1208
[2610]	1209	# check if there is an extension and remove it
	1210	ext=${basefilename##*.}
	1211	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1212	then
	1213	basefilename=${basefilename%.*}
	1214	fi
[2380]	1215
[2610]	1216	# check for an existing cycle number and remove it
	1217	cycle=${basefilename##*.}
	1218	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1219	then
	1220	basefilename=${basefilename%.*}
	1221	fi
[2600]	1222
[3236]	1223	# remove the run_identifier from the beginning
	1224	length_run_identifier=${#run_identifier}
	1225	ending=${basefilename:${length_run_identifier}}
[2610]	1226
	1227	# remove the ending given in the .iofiles from the beginning
	1228	endingstring="${endin_pre[$i]}"
	1229	length_ending=${#endingstring}
	1230	ending=${ending:${length_ending}}
	1231
	1232	if [[ "$ending" = "" ]]
[2600]	1233	then
[2610]	1234	# standard ending as given in the .iofiles
	1235	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1236	then
	1237	endings="$endings DEFAULT"
	1238	fi
[2600]	1239	else
[2610]	1240	# ending must start with "_", otherwise its a different file
	1241	if [[ "${ending:0:1}" = "_" ]]
	1242	then
	1243	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1244	then
	1245	endings="$endings $ending"
	1246	fi
	1247	fi
[2600]	1248	fi
[2610]	1249
	1250	done <filelist
[2380]	1251
[2610]	1252	rm filelist
[2380]	1253
[2600]	1254	else
[2610]	1255
	1256	# SINGLE NAME
	1257	endings=DEFAULT
	1258
[2600]	1259	fi
	1260
[2610]	1261	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1262	for ending in $endings
	1263	do
	1264
	1265	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1266	if [[ $ending = DEFAULT ]]
[2380]	1267	then
[2610]	1268	ending=""
	1269	fi
	1270
	1271	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1272	(( nr_of_input_files = nr_of_input_files + 1 ))
	1273	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1274	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1275	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1276	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1277	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1278	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1279
	1280
	1281	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1282	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1283	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1284	then
	1285	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1286	else
[3236]	1287	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1288	fi
[2610]	1289
	1290	# DETERMINE THE FILE'S CYCLE NUMBER
	1291	(( maxcycle = 0 ))
	1292	ls -1 -d $filename > filelist 2>/dev/null
	1293	ls -1 -d $filename.* >> filelist 2>/dev/null
	1294	while read line
	1295	do
	1296	# filename without path (i.e. after the last "/")
	1297	basefilename=$(basename ${line})
	1298
	1299	# check if there is an extension
	1300	extension=${basefilename##*.}
	1301	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1302	then
	1303	basefilename=${basefilename%.*}
	1304	fi
	1305
	1306	# check for an existing cycle number
	1307	cycle=${basefilename##*.}
	1308	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1309	then
[2669]	1310	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1311	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1312	(( icycle = $((10#$cycle)) ))
[2610]	1313	else
	1314	(( icycle = 0 ))
	1315	fi
	1316
	1317	if (( icycle > maxcycle ))
	1318	then
	1319	(( maxcycle = icycle ))
	1320
	1321	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1322	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1323	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1324	then
	1325	leading_zero=true
	1326	else
	1327	leading_zero=false
	1328	fi
	1329	fi
	1330
	1331	done <filelist
	1332	rm filelist
	1333
	1334	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1335	if [[ $leading_zero = true ]]
[2380]	1336	then
[2610]	1337	cyclestring=`printf "%03d" $maxcycle`
	1338	else
	1339	cyclestring=$maxcycle
[2380]	1340	fi
[2610]	1341
	1342	# APPEND CYCLE NUMBER TO FILENAME
	1343	if (( maxcycle > 0 ))
[2380]	1344	then
[2610]	1345	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1346	then
	1347	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1348	else
	1349	filename=${filename}.$cyclestring
	1350	fi
[2380]	1351	else
[2610]	1352	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1353	then
	1354	filename=${filename}.${extin[$nr_of_input_files]}
	1355	fi
[2380]	1356	fi
[2610]	1357
	1358	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1359	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1360	absnamein[$nr_of_input_files]=$filename
	1361	if (( maxcycle > 0 ))
[2380]	1362	then
[2610]	1363	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1364	then
	1365	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1366	else
[3236]	1367	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1368	fi
[2380]	1369	else
[2610]	1370	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1371	then
	1372	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1373	else
[3236]	1374	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1375	fi
[2380]	1376	fi
	1377
[2610]	1378	done
	1379
[2380]	1380	fi
[2610]	1381
[2380]	1382	done
	1383
[2610]	1384
[2380]	1385	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1386	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1387	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1388	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1389	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1390	# REMOTE HOST)
	1391	(( i = 0 ))
	1392	while (( i < iout ))
	1393	do
	1394	(( i = i + 1 ))
[2610]	1395	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1396	then
[2610]	1397	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1398	then
[2610]	1399	actionout_pre[$i]=""
	1400	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1401	then
[2610]	1402	actionout_pre[$i]=pe
	1403	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1404	then
[2610]	1405	actionout_pre[$i]=a
[2380]	1406	fi
	1407	(( maxcycle = 0 ))
[3236]	1408	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1409	eval catalogname=${pathout_pre[$i]}
[2380]	1410	if ! ls $filename* 1>/dev/null 2>&1
	1411	then
	1412
	1413	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1414	if cat /dev/null > $filename
	1415	then
	1416	rm $filename
	1417	else
	1418
	1419	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1420	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1421	if [[ ! -d $catalogname ]]
	1422	then
	1423	if mkdir -p $catalogname
	1424	then
	1425	printf "\n\n *** directory:"
	1426	printf "\n $catalogname"
	1427	printf "\n was created\n"
	1428	else
	1429	printf "\n\n +++ OUTPUT-file:"
	1430	printf "\n $filename"
	1431	printf "\n cannot be created, because directory does not exist"
	1432	printf "\n and cannot be created either"
	1433	printf "\n"
	1434	locat=output ; exit
	1435	fi 2>/dev/null
	1436	else
	1437	printf "\n\n +++ OUTPUT-file:"
	1438	printf "\n $filename"
	1439	printf "\n cannot be created, although directory exists"
	1440	printf "\n"
	1441	locat=output ; exit
	1442	fi
	1443	fi 2>/dev/null
	1444
	1445	fi
	1446
	1447	fi
	1448	done
	1449
	1450
	1451	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1452	if [[ $running_in_batch_mode = false ]]
	1453	then
[3236]	1454	run_id_number=$RANDOM
	1455	run_id=${run_identifier}.$run_id_number
[2380]	1456
[3236]	1457	tempdir=$fast_io_catalog/$run_id
[2380]	1458	fi
	1459
	1460
	1461	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1462	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1463	then
	1464
	1465	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1466	if [[ $ibd = 0 ]]
	1467	then
	1468	printf "\n"
	1469	printf "\n +++ no batch directives found in configuration file"
	1470	locat=config_file_batch_directives; (( iec = 0 )); exit
	1471	fi
	1472
	1473	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1474	done=false
[2384]	1475	cputime=$cpumax
[2380]	1476	while [[ $done = false ]]
	1477	do
[2384]	1478	if (( cputime == 0 ))
[2380]	1479	then
	1480	printf "\n +++ cpu-time is undefined"
	1481	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1482	printf "\n >>> "
[2384]	1483	read cputime 1>/dev/null 2>&1
[2380]	1484	else
	1485	done=true
	1486	fi
	1487	done
[2420]	1488	cpumax=$cputime
[2380]	1489
	1490	# CHECK THE MEMORY DEMAND
	1491	done=false
	1492	while [[ $done = false ]]
	1493	do
	1494	if (( memory == 0 ))
	1495	then
	1496	printf "\n +++ memory demand is undefined"
	1497	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1498	printf "\n >>> "
	1499	read memory 1>/dev/null 2>&1
	1500	else
	1501	done=true
	1502	fi
	1503	done
	1504
	1505	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1506	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1507	then
	1508	while [[ -z $remote_username ]]
	1509	do
[2420]	1510	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1511	printf "\n >>> Please type username:"
	1512	printf "\n >>> "
	1513	read remote_username
	1514	done
	1515	fi
	1516
	1517	else
	1518
[2420]	1519	if [[ $running_in_batch_mode = false ]]
	1520	then
	1521	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1522	cpumax=$cputime
	1523	else
	1524	cputime=$cpumax
	1525	fi
[2380]	1526
	1527	fi
	1528
	1529
	1530	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1531	(( cpu_hours = cputime / 3600 ))
	1532	(( resttime = cputime - cpu_hours * 3600 ))
	1533	(( cpu_minutes = resttime / 60 ))
	1534	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1535	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1536
	1537
	1538	# OUTPUT OF THE PALMRUN-HEADER
	1539	calltime=$(date)
	1540	printf "\n"
	1541	printf "#------------------------------------------------------------------------# \n"
	1542	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1543	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1544	printf "\| \| \n"
	1545	column1="called on:"; column2=$(hostname)
	1546	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1547	if [[ $create_remote_batch_job = true ]]
	1548	then
[3236]	1549	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1550	else
	1551	if [[ $running_on_remote = true ]]
	1552	then
[3236]	1553	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1554	else
[3236]	1555	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1556	fi
	1557	fi
	1558	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1559
	1560	column1="running in:"
	1561	if [[ $running_in_batch_mode = true ]]
	1562	then
	1563	column2="batch job mode"
	1564	else
	1565	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1566	then
	1567	column2="job creation mode"
	1568	else
	1569	column2="interactive run mode"
	1570	fi
	1571	fi
	1572	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1573
[2479]	1574	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1575	then
[2480]	1576	if [[ "$project_account" != "" ]]
[2479]	1577	then
	1578	column1="project account number:"
	1579	column2="$project_account"
	1580	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1581	fi
	1582	fi
	1583
[2380]	1584	if [[ -n $cores ]]
	1585	then
	1586	if [[ $run_coupled_model = false ]]
	1587	then
	1588	column1="number of cores:"; column2=$cores
	1589	else
	1590	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1591	fi
	1592	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1593	fi
	1594	if [[ -n $tasks_per_node ]]
	1595	then
	1596	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1597	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1598	if (( remaining_cores > 0 ))
	1599	then
	1600	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1601	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1602	fi
	1603	fi
	1604	if [[ $maximum_parallel_io_streams != $cores ]]
	1605	then
	1606	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1607	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1608	fi
	1609	if [[ $use_openmp = true ]]
	1610	then
	1611	column1="threads per task:"; column2="$threads_per_task"
	1612	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1613	fi
[2384]	1614	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1615	then
[2506]	1616	column1="memory demand / PE":; column2="$memory MB"
	1617	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1618	column1="job cpu time (h:m:s):"; column2="$timestring"
	1619	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1620	fi
[2380]	1621	printf "\| \| \n"
	1622	if [[ "$source_list" != "" ]]
	1623	then
	1624	if [[ "$make_options" != "" ]]
	1625	then
	1626	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1627	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1628	line=$(echo "$make_options" \| cut -c46-)
	1629	while [[ "$line" != "" ]]
	1630	do
	1631	column1=""
	1632	column2=$(echo "$line" \| cut -c-45)
	1633	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1634	line=$(echo "$line" \| cut -c46-)
	1635	done
	1636	fi
	1637	fi
	1638
	1639	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1640	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1641	line=$(echo "$cpp_options" \| cut -c46-)
	1642	while [[ "$line" != "" ]]
	1643	do
	1644	column1=""
	1645	column2=$(echo "$line" \| cut -c-45)
	1646	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1647	line=$(echo "$line" \| cut -c46-)
	1648	done
	1649
	1650	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1651	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1652	line=$(echo "$compiler_options" \| cut -c46-)
	1653	while [[ "$line" != "" ]]
	1654	do
	1655	column1=""
	1656	column2=$(echo "$line" \| cut -c-45)
	1657	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1658	line=$(echo "$line" \| cut -c46-)
	1659	done
	1660
[2388]	1661	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1662	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1663	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1664	while [[ "$line" != "" ]]
	1665	do
	1666	column1=""
	1667	column2=$(echo "$line" \| cut -c-45)
	1668	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1669	line=$(echo "$line" \| cut -c46-)
	1670	done
	1671
	1672	if [[ "$login_init_cmd" != "" ]]
	1673	then
	1674	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1675	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1676	line=$(echo "$login_init_cmd" \| cut -c46-)
	1677	while [[ "$line" != "" ]]
	1678	do
	1679	column1=""
	1680	column2=$(echo "$line" \| cut -c-45)
	1681	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1682	line=$(echo "$line" \| cut -c46-)
	1683	done
	1684	fi
	1685
	1686	if [[ "$module_commands" != "" ]]
	1687	then
	1688	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1689	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1690	line=$(echo "$module_commands" \| cut -c46-)
	1691	while [[ "$line" != "" ]]
	1692	do
	1693	column1=""
	1694	column2=$(echo "$line" \| cut -c-45)
	1695	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1696	line=$(echo "$line" \| cut -c46-)
	1697	done
	1698	fi
	1699	printf "\| \| \n"
[3236]	1700	column1="run identifier:"; column2=$run_identifier
[2380]	1701	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1702	column1="activation string list:"; column2=$(echo $activation_string_list)
	1703	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1704
	1705	if [[ "$ocean_file_appendix" = true ]]
	1706	then
	1707	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1708	fi
	1709
	1710	if [[ "$source_list" != "" ]]
	1711	then
	1712	printf "\| \| \n"
	1713	printf "\| Files to be compiled: \| \n"
	1714	line=$source_list
	1715	while [[ "$line" != "" ]]
	1716	do
	1717	linestart=$(echo $line \| cut -c-70)
	1718	printf "\| %-70s \| \n" "$linestart"
	1719	line=$(echo "$line" \| cut -c71-)
	1720	done
	1721	fi
	1722	printf "#------------------------------------------------------------------------#"
	1723
	1724
	1725
	1726	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1727	if [[ $do_trace = true ]]
	1728	then
	1729	(( i = 0 ))
[2610]	1730	while (( i < nr_of_input_files ))
[2380]	1731	do
	1732	(( i = i + 1 ))
	1733	if (( i == 1 ))
	1734	then
	1735	printf "\n\n >>> INPUT-file assignments:\n"
	1736	fi
	1737	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1738	done
	1739	(( i = 0 ))
	1740	while (( i < iout ))
	1741	do
	1742	(( i = i + 1 ))
	1743	if (( i == 1 ))
	1744	then
	1745	printf "\n\n >>> OUTPUT-file assignments:\n"
	1746	fi
	1747	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1748	done
	1749	(( i = 0 ))
	1750	while (( i < iic ))
	1751	do
	1752	(( i = i + 1 ))
	1753	if (( i == 1 ))
	1754	then
	1755	printf "\n\n >>> INPUT-commands:\n"
	1756	fi
	1757	printf "\n ${in_command[$i]}"
	1758	done
	1759	(( i = 0 ))
	1760	while (( i < ioc ))
	1761	do
	1762	(( i = i + 1 ))
	1763	if (( i == 1 ))
	1764	then
	1765	printf "\n\n >>> OUTPUT-commands:\n"
	1766	fi
	1767	printf "\n ${out_command[$i]}"
	1768	done
	1769	fi
	1770
	1771	# QUERY FOR CONTINUE
	1772	if [[ $silent = false && $running_in_batch_mode = false ]]
	1773	then
	1774	antwort=dummy
	1775	printf "\n\n"
	1776	printf " >>> everything o.k. (y/n) ? "
	1777	while read antwort
	1778	do
	1779	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1780	then
	1781	printf " >>> everything o.k. (y/n) ? "
	1782	else
	1783	break
	1784	fi
	1785	done
	1786	if [[ $antwort = n \|\| $antwort = N ]]
	1787	then
	1788	locat=user_abort; (( iec = 0 )); exit
	1789	fi
	1790	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1791	then
[2566]	1792	printf "\n *** batch-job will be created and submitted"
[2380]	1793	else
[2566]	1794	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1795	fi
	1796	fi
	1797
	1798
	1799
	1800	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1801	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1802	then
	1803
	1804	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1805	then
[2566]	1806	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1807	else
[2566]	1808	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1809	fi
	1810
[2422]	1811	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1812	# IT SHALL BE CREATED
	1813	ask_for_make_depository=false
	1814	if [[ $create_remote_batch_job = true ]]
	1815	then
	1816
	1817	line=`grep %base_directory $config_file`
[3236]	1818	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
	1819	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]	1820
[3236]	1821	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1822	then
	1823	printf "\n\n +++ make depository \"${make_depository}\""
	1824	printf "\n on remote host not found!"
	1825	ask_for_make_depository=true
	1826	fi
[3236]	1827	rm ${configuration_identifier}_last_make_protokoll
[2422]	1828
	1829	else
	1830
	1831	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1832	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1833	if [[ ! -d ${make_depository} ]]
	1834	then
	1835	printf "\n\n +++ make depository \"${make_depository}\""
	1836	printf "\n on local host not found!"
	1837	ask_for_make_depository=true
	1838	fi
	1839
	1840	fi
	1841
	1842	if [[ $ask_for_make_depository = true ]]
	1843	then
	1844
	1845	antwort=dummy
	1846	printf "\n\n"
	1847	printf " >>> Create a new one (y/n) ? "
	1848	while read antwort
	1849	do
	1850	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1851	then
	1852	printf " >>> Create a new one (y/n) ? "
	1853	else
	1854	break
	1855	fi
	1856	done
	1857	if [[ $antwort = n \|\| $antwort = N ]]
	1858	then
	1859	locat=user_abort; (( iec = 0 )); exit
	1860	fi
	1861
[2566]	1862	if [[ $do_trace = true ]]
	1863	then
[3236]	1864	palmbuild -h $configuration_identifier
[2566]	1865	else
[3236]	1866	palmbuild -v -h $configuration_identifier
[2566]	1867	fi
[2422]	1868
[3312]	1869	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1870	then
	1871
	1872	# ABORT IN CASE OF COMPILATION PROBLEMS
	1873	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1874	locat=make_depository
	1875	exit
	1876	else
	1877	echo " *** now continue with creating executable and other sources"
	1878	fi
	1879
	1880	fi
	1881
[2566]	1882	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3236]	1883	palmbuild -v $use_existing_sources_folder -h $configuration_identifier -d $run_identifier
[2380]	1884
[3312]	1885	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1886	then
	1887
	1888	# ABORT IN CASE OF COMPILATION PROBLEMS
	1889	printf "\n +++ error while creating executable and/or other sources"
	1890	locat=execution
[2990]	1891	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1892	exit
	1893
	1894	else
	1895
[2566]	1896	printf " *** executable and other sources created\n"
[2990]	1897	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1898
	1899	fi
	1900
	1901	fi
	1902
	1903
[2669]	1904	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1905	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1906	if [[ $create_remote_batch_job = true ]]
	1907	then
	1908	(( i = 0 ))
[2610]	1909	while (( i < nr_of_input_files ))
[2605]	1910	do
	1911	(( i = i + 1 ))
[2669]	1912	if [[ "${actionin[$i]}" = tr ]]
[2605]	1913	then
	1914	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1915	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1916	fi
	1917	done
	1918	if (( i > 0 ))
	1919	then
[3025]	1920	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1921	fi
	1922	fi
	1923
	1924
[2380]	1925	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1926	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1927	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1928	then
	1929
	1930	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1931	if [[ $running_in_batch_mode = false ]]
	1932	then
	1933	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1934	# FOLDER
[2566]	1935	mkdir -p $tempdir
	1936	chmod go+rx $tempdir
	1937	cd $tempdir
	1938	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1939	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1940
	1941	else
	1942
	1943	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1944	printf "\n *** running in temporary directory: $tempdir"
[2380]	1945
	1946	fi
	1947
	1948
	1949	# PROVIDE THE INPUT FILES
	1950	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1951	optional_files_missing=false
[2380]	1952	(( i = 0 ))
[2610]	1953	while (( i < nr_of_input_files ))
[2380]	1954	do
	1955	(( i = i + 1 ))
	1956	if (( i == 1 ))
	1957	then
	1958	printf "\n\n *** providing INPUT-files:\n$dashes"
	1959	fi
	1960
	1961
	1962	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1963	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1964	then
[2669]	1965	optional_files_missing=true
[2380]	1966	continue
	1967	fi
	1968
	1969	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1970	files_for_cores=false; filetype=file
	1971	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1972	then
	1973	files_for_cores=true; filetype=files
	1974	actionin[$i]=""
	1975	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1976	then
	1977	actionin[$i]=""
	1978	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1979	then
	1980	files_for_cores=true; filetype=files
	1981	actionin[$i]="ln"
	1982	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1983	then
	1984	actionin[$i]="ln"
	1985	fi
	1986
	1987	if [[ $files_for_cores = true ]]
	1988	then
	1989	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1990	else
	1991	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1992	fi
	1993
	1994	# INPUT-FILES TO BE LINKED
	1995	if [[ "${actionin[$i]}" = ln ]]
	1996	then
	1997
	1998	printf "\n $filetype will be linked"
	1999	if [[ $files_for_cores = false ]]
	2000	then
	2001	if [[ -f "${absnamein[$i]}" ]]
	2002	then
	2003	ln ${absnamein[$i]} ${localin[$i]}
	2004	got_tmp[$i]=true
	2005	fi
	2006	else
	2007	if [[ -d "${absnamein[$i]}" ]]
	2008	then
[2396]	2009	mkdir -p ${localin[$i]}
[2380]	2010	cd ${absnamein[$i]}
	2011	for file in $(ls *)
	2012	do
[2566]	2013	ln $file $tempdir/${localin[$i]}
[2380]	2014	done >\|/dev/null 2>&1
[2566]	2015	cd $tempdir
[2380]	2016	fi
	2017
	2018	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2019	if [[ ! -f "${localin[$i]}/_000000" ]]
	2020	then
	2021	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2022	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2023	fi
	2024
	2025	got_tmp[$i]=true
	2026	fi
	2027	fi
	2028
	2029	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2030	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2031	then
	2032
	2033	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2034	then
	2035
	2036	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2037	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2038	printf "\n file will be provided for $cores processors"
[2396]	2039	mkdir -p ${localin[$i]}
[2380]	2040	ival=$cores
	2041	(( ii = 0 ))
	2042	while (( ii <= ival-1 ))
	2043	do
	2044	if (( ii < 10 ))
	2045	then
	2046	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2047	elif (( ii < 100 ))
	2048	then
	2049	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2050	elif (( ii < 1000 ))
	2051	then
	2052	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2053	else
	2054	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2055	fi
	2056	(( ii = ii + 1 ))
	2057	done
	2058
	2059	else
	2060
	2061	if [[ $files_for_cores = true ]]
	2062	then
	2063
	2064	# PROVIDE FILES FOR EACH CORE
	2065	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2066	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2067	printf "\n providing $cores files for the respective cores"
[2396]	2068	mkdir -p ${localin[$i]}
[2380]	2069	if [[ $link_local_input = true ]]
	2070	then
	2071	printf " files will be linked\n"
	2072	cd ${absnamein[$i]}
	2073	for file in $(ls *)
	2074	do
	2075	ln -f $file ${localin[$i]}
	2076	done
[2566]	2077	cd $tempdir
[2380]	2078	fi
	2079
	2080	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2081	if [[ ! -f "${localin[$i]}/_000000" ]]
	2082	then
	2083	if [[ $link_local_input = true ]]
	2084	then
	2085	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2086	fi
	2087	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2088	fi
	2089
	2090	else
	2091
	2092	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2093	if [[ $link_local_input = true ]]
	2094	then
	2095	printf " file will be linked\n"
	2096	ln -f ${absnamein[$i]} ${localin[$i]}
	2097	fi
[2605]	2098	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2099	if [[ ! -f "${localin[$i]}" ]]
	2100	then
	2101	if [[ $link_local_input = true ]]
	2102	then
	2103	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2104	fi
[2669]	2105	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2106	then
	2107	mv ${absnamein[$i]} ${localin[$i]}
	2108	else
	2109	cp ${absnamein[$i]} ${localin[$i]}
	2110	fi
[2380]	2111	fi
	2112	fi
	2113	fi
	2114	fi
	2115
	2116	done
	2117	if (( i != 0 ))
	2118	then
[2669]	2119	if [[ $optional_files_missing = true ]]
	2120	then
	2121	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2122	fi
[2380]	2123	printf "\n$dashes\n *** all INPUT-files provided \n"
	2124	fi
	2125
	2126
	2127	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2128	(( i = 0 ))
	2129	while (( i < iic ))
	2130	do
	2131	(( i = i + 1 ))
	2132	if (( i == 1 ))
	2133	then
	2134	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2135	fi
	2136	printf "\n >>> ${in_command[$i]}"
	2137	eval ${in_command[$i]}
	2138	if (( i == iic ))
	2139	then
	2140	printf "\n$dashes\n"
	2141	fi
	2142	done
	2143
	2144
[3313]	2145	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2146	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2147	then
	2148	progress_bar_disabled=true
	2149	else
	2150	progress_bar_disabled=false
	2151	fi
	2152
	2153
[2380]	2154	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2155	# (FILE ENVPAR WILL BE READ BY PALM)
	2156	cat > ENVPAR << EOF
[3236]	2157	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2158	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2159	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2160	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2161	maximum_cpu_time_allowed = ${cpumax}.,
	2162	revision = '$global_revision',
[3313]	2163	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2164
	2165	EOF
	2166
	2167
	2168	# STARTING THE EXECUTABLE
	2169	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2170	PATH=$PATH:$tempdir
[2380]	2171
	2172
	2173	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2174	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2175	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2176	eval line=\"$line\"
	2177	execute_command="$line"
	2178
	2179
	2180	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2181	if [[ "$execute_command_for_combine" = "" ]]
	2182	then
	2183	eval line2=\"$line2\"
	2184	execute_command_for_combine="$line2"
	2185	fi
	2186
[2380]	2187
	2188
	2189	# PROVIDE A HOSTFILE, IF REQUIRED
	2190	if [[ "$hostfile" != "" ]]
	2191	then
	2192
	2193	if [[ $hostfile = auto ]]
	2194	then
	2195	# CREATE A NEW HOSTFILE
	2196	(( ii = 1 ))
	2197	while (( ii <= cores / threads_per_task ))
	2198	do
	2199	echo $(hostname) >> hostfile
	2200	(( ii = ii + 1 ))
	2201	done
	2202	if (( cores / threads_per_task == 0 ))
	2203	then
	2204	echo $(hostname) >> hostfile
	2205	fi
	2206
	2207	else
	2208	cp $hostfile hostfile
	2209	fi
	2210	eval line=\"`head -n $ii hostfile`\"
	2211	printf "\n *** running on: $line"
	2212	fi
	2213
	2214
	2215
	2216	# SET THE NUMBER OF OPENMP-THREADS
	2217	if [[ $use_openmp = true ]]
	2218	then
	2219	export OMP_NUM_THREADS=$threads_per_task
	2220	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2221	else
	2222	export OMP_NUM_THREADS=1
	2223	fi
	2224
	2225
[2610]	2226	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2227	if [[ $run_coupled_model = false ]]
	2228	then
	2229	if [[ "$ocean_file_appendix" = true ]]
	2230	then
	2231	echo "precursor_ocean" > coupling_steering
	2232	else
	2233	echo "precursor_atmos" > coupling_steering
	2234	fi
	2235	else
	2236	(( iia = $cores_atmos / $threads_per_task ))
	2237	(( iio = $cores_ocean / $threads_per_task ))
	2238	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2239	printf "\n\n"
	2240	echo "coupled_run $iia $iio" > coupling_steering
	2241	fi
	2242
	2243	printf "\n *** execute command:"
	2244	printf "\n \"$execute_command\" \n\n"
	2245
	2246	$execute_command < coupling_steering
	2247
[3312]	2248	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	2249	then
	2250
	2251	# ABORT IN CASE OF RUNTIME ERRORS
	2252	printf "\n +++ runtime error occured"
	2253	locat=execution
	2254	exit
	2255
	2256	else
	2257
	2258	printf "\n$dashes\n *** execution finished \n"
	2259
	2260	fi
	2261
	2262
	2263	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2264	# BY EACH CORE INTO ONE FILE
	2265	if [[ ! -f combine_plot_fields.x ]]
	2266	then
	2267
	2268	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2269	printf "\n 2d- and/or 3d-data may be incomplete!"
	2270	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2271
	2272	elif [[ "$combine_plot_fields" == true ]]
	2273	then
	2274
	2275	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2276	$execute_command_for_combine
	2277
	2278	else
	2279
	2280	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2281	# DATA OUTPUT
[2380]	2282	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2283	fi
	2284
	2285
	2286
	2287	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2288	(( i = 0 ))
	2289	while (( i < ioc ))
	2290	do
	2291	(( i = i + 1 ))
	2292	if (( i == 1 ))
	2293	then
	2294	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2295	fi
[2799]	2296
	2297	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2298	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2299
[2380]	2300	printf "\n >>> ${out_command[$i]}"
	2301	eval ${out_command[$i]}
	2302	if (( i == ioc ))
	2303	then
	2304	printf "\n$dashes\n"
	2305	fi
	2306	done
	2307
	2308
[2610]	2309	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2310	# WILDCARDS
[2380]	2311	(( i = 0 ))
[2610]	2312	(( nr_of_output_files = 0 ))
	2313
[2380]	2314	while (( i < iout ))
	2315	do
[2610]	2316
[2380]	2317	(( i = i + 1 ))
[2610]	2318
	2319	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2320	# CREATE A LIST FOR THE DETECTED ENDINGS
	2321	if [[ "${multout[$i]}" = true ]]
	2322	then
	2323	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2324	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2325	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2326
	2327	endings="DEFAULT"
	2328	while read line
	2329	do
	2330	# remove the local name from the beginning
	2331	localnamestring="${localout_pre[$i]}"
	2332	length_localname=${#localnamestring}
	2333	ending=${line:${length_localname}}
	2334
	2335	if [[ "$ending" != "" ]]
	2336	then
	2337	endings="$endings $ending"
	2338	fi
	2339
	2340	done <filelist
	2341
	2342	rm filelist
	2343
	2344	else
	2345
	2346	# SINGLE NAME
	2347	endings=DEFAULT
	2348
	2349	fi
	2350
	2351	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2352	for ending in $endings
	2353	do
	2354
	2355	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2356	if [[ $ending = DEFAULT ]]
	2357	then
	2358	ending=""
	2359	fi
	2360
	2361	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2362	(( nr_of_output_files = nr_of_output_files + 1 ))
	2363	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2364	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2365	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2366	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2367	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2368	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2369	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2370
	2371	done
	2372
	2373	done
	2374
	2375
	2376
	2377
	2378	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2379	(( i = 0 ))
	2380	while (( i < nr_of_output_files ))
	2381	do
	2382	(( i = i + 1 ))
[2380]	2383	if (( i == 1 ))
	2384	then
	2385	printf "\n\n *** saving OUTPUT-files:"
	2386
	2387	# GET RUN NUMBER ASSIGNED BY PALM
	2388	if [[ -f RUN_NUMBER ]]
	2389	then
	2390	read run_number < RUN_NUMBER
	2391	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2392	usecycle_option="-U $run_number"
	2393	else
	2394	run_number=0
	2395	usecycle_option=""
	2396	fi
	2397	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2398	then
[2404]	2399	printf "\n *** in case of SCP transfers to local host"
	2400	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2401	fi
	2402	printf "\n$dashes"
	2403	fi
	2404
	2405	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2406	then
	2407
[3236]	2408	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2409
	2410	# DETERMINE THE CYCLE NUMBER
	2411	ls -1 -d $filename > filelist 2>/dev/null
	2412	ls -1 -d $filename.* >> filelist 2>/dev/null
	2413	while read line
	2414	do
	2415
	2416	# filename without path (i.e. after the last "/")
	2417	basefilename=$(basename ${line})
	2418
	2419	# check if there is an extension
	2420	extension=${basefilename##*.}
	2421	if [[ "$extension" = "${extout[$i]}" ]]
	2422	then
	2423	basefilename=${basefilename%.*}
	2424	fi
	2425
	2426	# check for an existing cycle number
	2427	cycle=${basefilename##*.}
	2428	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2429	then
[2669]	2430	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2431	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2432	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2433	else
	2434	(( icycle = 1 ))
	2435	fi
	2436
	2437	if (( icycle > maxcycle ))
	2438	then
	2439	(( maxcycle = icycle ))
	2440	fi
	2441
	2442	done <filelist
	2443	rm filelist
	2444
	2445
	2446	# SET THE CYCLE NUMBER
	2447	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2448	if [[ "${actionout[$i]}" = a ]]
	2449	then
	2450	(( maxcycle = maxcycle - 1 ))
	2451	fi
	2452
	2453	(( cycnum[$i] = maxcycle ))
	2454	pathout[$i]=$filename
	2455
	2456
	2457	# ADD CYCLE NUMBER TO FILENAME
	2458	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2459	if [[ "${actionout[$i]}" != "a" ]]
	2460	then
	2461	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2462	# WITH AN EXISTING CYCLE NUMBER
	2463	if (( run_number >= cycnum[$i] ))
	2464	then
	2465	(( cycnum[$i] = run_number ))
	2466	else
	2467	if (( run_number > 0 ))
	2468	then
	2469	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2470	fi
	2471	fi
	2472	fi
	2473	if (( cycnum[$i] > 0 ))
	2474	then
[2600]	2475	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2476	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2477	fi
	2478	fi
	2479
	2480	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2481	files_for_cores=false; filetype=file
	2482	link_local_output=false
	2483	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2484	then
	2485	files_for_cores=true; filetype=directory
	2486	actionout[$i]=""
	2487	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2488	then
	2489	actionout[$i]=""
	2490	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2491	then
	2492	files_for_cores=true; filetype=directory
	2493	link_local_output=true
	2494	actionout[$i]=""
	2495	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2496	then
	2497	link_local_output
	2498	actionout[$i]=""
	2499	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2500	then
	2501	files_for_cores=true; filetype=directory
	2502	actionout[$i]="tr"
	2503	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2504	then
	2505	actionout[$i]="tr"
	2506	fi
	2507
	2508	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2509	then
[2669]	2510	if [[ ${warnout[$i]} = true ]]
	2511	then
	2512	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2513	fi
[2380]	2514	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2515	then
[2669]	2516	if [[ ${warnout[$i]} = true ]]
	2517	then
	2518	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2519	fi
[2380]	2520	else
	2521
	2522
	2523	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2524	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2525	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2526	then
	2527	if [[ $running_on_remote = true ]]
	2528	then
	2529
	2530	# SET OPTIONS FOR TRANSFER
	2531	if [[ "${actionout[$i]}" = tr ]]
	2532	then
	2533	if [[ $files_for_cores = false ]]
	2534	then
	2535	catalog_option=""
	2536	catalog_string=""
	2537	else
	2538	catalog_option="-c"
	2539	catalog_string="/"
	2540	fi
	2541	append_option=""
	2542	append_string=""
	2543	else
	2544	append_option="-A"
	2545	append_string="append"
	2546	fi
	2547
	2548	transfer_failed=false
	2549	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2550	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2551
	2552	# TRANSFER VIA SCP
	2553	if [[ "$remote_loginnode" != "" ]]
	2554	then
[3236]	2555	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]	2556	else
[3236]	2557	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]	2558	fi
[3312]	2559	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2560
	2561
	2562	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2563	if [[ $transfer_failed = true ]]
	2564	then
	2565	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2566	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2567
	2568	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2569	eval local_catalog=${pathout[$i]}
	2570	if [[ ! -d $local_catalog ]]
	2571	then
	2572	printf " *** local directory does not exist. Trying to create:\n"
	2573	printf " $local_catalog \n"
	2574	mkdir -p $local_catalog
	2575	fi
[3236]	2576	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2577	transfer_problems=true
	2578	fi
	2579
	2580	else
	2581
	2582	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2583	# BE COPIED OR APPENDED ON THIS MACHINE
	2584	if [[ "${actionout[$i]}" = tr ]]
	2585	then
	2586	actionout[$i]=""
	2587	else
	2588	actionout[$i]="a"
	2589	fi
	2590	fi
	2591	fi
	2592
	2593
	2594	# APPEND ON THIS MACHINE
	2595	if [[ "${actionout[$i]}" = "a" ]]
	2596	then
	2597	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2598	then
	2599	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2600	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2601	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2602	else
	2603	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2604	printf "\n ${pathout[$i]}\n"
	2605	cat ${localout[$i]} >> ${pathout[$i]}
	2606	fi
	2607	fi
	2608
	2609	# COPY ON THIS MACHINE
	2610	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2611	# ON DIFFERENT FILE-SYSTEMS
	2612	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2613	then
	2614
	2615	# COPY IN CASE OF RUNS ON SINGLE CORES
	2616	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2617	then
	2618	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2619	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2620	if [[ $link_local_output = true ]]
	2621	then
	2622	printf " file will be linked\n"
	2623	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2624	fi
	2625	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2626	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2627	then
	2628	if [[ $link_local_output = true ]]
	2629	then
	2630	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2631	fi
	2632	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2633	else
	2634	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2635	fi
	2636	else
	2637	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2638	printf "\n ${pathout[$i]}\n"
	2639	if [[ $link_local_output = true ]]
	2640	then
	2641	printf " file will be linked\n"
	2642	ln -f ${localout[$i]} ${pathout[$i]}
	2643	fi
	2644	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2645	if [[ ! -f "${pathout[$i]}" ]]
	2646	then
	2647	if [[ $link_local_output = true ]]
	2648	then
	2649	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2650	fi
	2651	cp ${localout[$i]} ${pathout[$i]}
	2652	else
	2653	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2654	fi
	2655	fi
	2656
	2657	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2658	then
	2659
	2660	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2661	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2662	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2663	printf "\n ${pathout[$i]}\n"
	2664	if [[ $link_local_output = true ]]
	2665	then
	2666	printf " files will be linked\n"
[2396]	2667	mkdir -p ${pathout[$i]}
[2380]	2668	cd ${localout[$i]}
	2669	for file in $(ls *)
	2670	do
	2671	ln -f $file ${pathout[$i]}
	2672	done >\|/dev/null 2>&1
[2566]	2673	cd $tempdir
[2380]	2674	fi
	2675
	2676	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2677	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2678	then
	2679	if [[ $link_local_output = true ]]
	2680	then
	2681	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2682	fi
[3025]	2683	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2684	cp -r ${localout[$i]}/* ${pathout[$i]}
	2685	fi
	2686
	2687	fi
	2688	fi
	2689	done
	2690
	2691	if (( i != 0 ))
	2692	then
	2693	if [[ $transfer_problems = true ]]
	2694	then
	2695	printf "\n$dashes\n *** OUTPUT-files saved"
	2696	printf "\n +++ WARNING: some data transfers failed! \n"
	2697	else
	2698	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2699	fi
	2700	fi
	2701
	2702
	2703	# IF REQUIRED, START A RESTART-JOB
	2704	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2705	if [[ -f CONTINUE_RUN ]]
	2706	then
	2707
	2708	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2709	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2710	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2711	# -b START A BATCH JOB
	2712	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2713	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2714	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2715
[2957]	2716	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2717	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2718	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2719	then
	2720	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2721	fi
[2380]	2722
	2723	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2724	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2725	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2726	then
[2381]	2727	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2728	fi
	2729
	2730
	2731	# START THE RESTART-JOB
	2732	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2733	echo " $prc"
	2734	printf "\n$dashes\n"
	2735	if [[ $running_on_remote = true ]]
	2736	then
	2737
	2738	echo "*** ssh will be used to initiate restart-runs!"
	2739	echo " return_address=\"$return_address\" "
	2740	echo " return_username=\"$local_username\" "
	2741
	2742	if [[ "$remote_loginnode" != "" ]]
	2743	then
[3132]	2744	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]	2745	else
[3132]	2746	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
[2380]	2747	fi
	2748
	2749	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2750	sleep 30
	2751
	2752	else
	2753
	2754	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2755	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2756	cd - > /dev/null
	2757
	2758	fi
	2759
[3132]	2760	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2761	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2762	then
	2763	printf "\n$dashes\n +++ creating restart run failed \n"
	2764	locat=create_restart
	2765	exit
	2766	rm palmrun_restart.log
	2767	else
	2768	printf "\n$dashes\n *** restart run initiated \n"
	2769	rm palmrun_restart.log
	2770	fi
[2380]	2771
[3132]	2772
[2380]	2773	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2774	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2775	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2776	# MAY BE VERY HUGE)
	2777	(( i = 0 ))
[2610]	2778	while (( i < nr_of_input_files ))
[2380]	2779	do
	2780	(( i = i + 1 ))
	2781	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2782	then
	2783	rm -r ${absnamein[$i]}
	2784	fi
	2785	done
	2786
	2787	fi
	2788
	2789
	2790	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2791	cd $HOME
[2566]	2792	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2793
	2794
	2795	else
	2796
	2797
	2798	# PREPARING ACTIONS,
	2799	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2800
	2801	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3236]	2802	palmrun_com="$palmrun_script_name -d $run_identifier -h $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2803	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2804	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2805	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2806	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2807	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2808	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2809	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2810	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2811	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2812	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2813	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2814	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2815	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2816	if [[ $create_remote_batch_job = true ]]
	2817	then
	2818	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2819	if [[ $do_trace = true ]]
	2820	then
	2821	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2822	fi
[2380]	2823	elif [[ $create_batch_job = true ]]
	2824	then
	2825	palmrun_com=${palmrun_com}" -j"
[2420]	2826	if [[ $do_trace = true ]]
	2827	then
	2828	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2829	fi
[2380]	2830	fi
	2831
	2832
	2833	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2834	# REMOTE HOST
[3236]	2835	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2836	job_protocol_file=$job_protocol_file_local
	2837	if [[ $create_remote_batch_job = true ]]
	2838	then
[3236]	2839	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2840	job_protocol_file=$job_protocol_file_remote
	2841	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2842	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2843	fi
	2844
	2845
	2846	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2847	jobfile=jobfile.$run_id_number
[2380]	2848
	2849
	2850	# FIRST CREATE THE BATCH DIRECTIVES
	2851	(( i = 0 ))
	2852	while (( i < ibd ))
	2853	do
	2854	(( i = i + 1 ))
[2693]	2855	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2856	eval line=\"$line\"
	2857	echo "$line" >> $jobfile
	2858	done
	2859	echo " " >> $jobfile
	2860
	2861
	2862	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2863	# PROTOCOL
	2864	if [[ $create_remote_batch_job = true ]]
	2865	then
[3236]	2866	echo "set +vx" >> $jobfile
	2867	echo "trap '" >> $jobfile
	2868	echo "set +vx" >> $jobfile
	2869	echo "cd ${remote_jobcatalog}" >> $jobfile
	2870	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2871
	2872	# ADD THE BATCH DIRECTIVES
	2873	(( i = 0 ))
	2874	while (( i < ibdt ))
	2875	do
	2876	(( i = i + 1 ))
[2693]	2877	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2878	eval line=\"$line\"
	2879	echo "$line" >> $jobfile
	2880	done
	2881	echo " " >> $jobfile
	2882
	2883	echo "set -x" >> $jobfile
[3236]	2884	echo "${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]	2885	echo "%%END%%" >> $jobfile
	2886	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2887	echo "$submit_command $scpjob_file" >> $jobfile
	2888	echo "rm $scpjob_file" >> $jobfile
[2404]	2889	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2890	echo "set -x" >> $jobfile
	2891	echo " ' exit" >> $jobfile
	2892	fi
	2893
	2894
	2895	# ACTIVATE ERROR-TRACEBACK
	2896	if [[ $do_trace = true ]]
	2897	then
	2898	echo "set -x" >> $jobfile
	2899	else
	2900	echo "set +vx" >> $jobfile
	2901	fi
	2902
	2903
	2904	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2905	if [[ "$login_init_cmd" != "" ]]
	2906	then
	2907	echo "$login_init_cmd" >> $jobfile
	2908	fi
	2909	if [[ "$module_commands" != "" ]]
	2910	then
	2911	echo "$module_commands" >> $jobfile
	2912	fi
	2913
	2914
	2915	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2916	if [[ $create_remote_batch_job = true ]]
	2917	then
	2918	echo "mkdir $tempdir" >> $jobfile
	2919	echo "chmod go+rx $tempdir" >> $jobfile
	2920	else
	2921	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2922	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2923	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2924	mkdir $tempdir
	2925	chmod go+rx $tempdir
	2926	fi
	2927	echo "cd $tempdir" >> $jobfile
	2928	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2929	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2930	echo "export PATH=.:\$PATH" >> $jobfile
	2931	echo "export execute_palmrun=true" >> $jobfile
	2932
	2933
	2934	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2935	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2936	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2937	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2938	echo "export LOCAL_PWD" >> $jobfile
	2939
	2940
	2941	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2942	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2943	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2944
	2945
	2946	# CALL PALMRUN WITHIN THE JOB
	2947	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2948	echo "set -x" >> $jobfile
	2949	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2950
	2951
	2952	# TRANSFER JOBFILE TO THE TARGET HOST
	2953	if [[ $create_jobfile_only = false ]]
	2954	then
	2955
	2956	if [[ $create_remote_batch_job = true ]]
	2957	then
	2958
[2420]	2959	echo " "
[2566]	2960	echo " *** transfer of job to remote host via scp"
[2420]	2961	if [[ $do_trace = true ]]
	2962	then
[3236]	2963	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	2964	fi
[3236]	2965	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	2966
[2566]	2967	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2968	if [[ $do_trace = true ]]
	2969	then
[3236]	2970	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]	2971	fi
[3236]	2972	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]	2973
	2974	elif [[ $create_batch_job = true ]]
	2975	then
	2976
[2385]	2977	eval local_jobcatalog=$local_jobcatalog
[3236]	2978	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	2979	cd $local_jobcatalog
[2380]	2980	echo " "
[2420]	2981	echo " *** submit the job"
	2982	if [[ $do_trace = true ]]
	2983	then
[3236]	2984	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	2985	fi
[3236]	2986	$submit_command ${configuration_identifier}_${run_id}
	2987	rm ${configuration_identifier}_${run_id}
[2380]	2988	cd - > /dev/null
	2989
	2990	fi
	2991
	2992	rm -rf $jobfile
	2993
	2994	else
	2995
	2996	printf "\n *** jobfile created under name \"$jobfile\" "
	2997	printf "\n no batch-job has been sent!"
	2998
	2999	fi
	3000
	3001	fi # END OF REMOTE-PART

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