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source: palm/trunk/SCRIPTS/palmrun @ 3032

Last change on this file since 3032 was 3032, checked in by raasch, 7 years ago
keyword correction
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 97.5 KB

Rev	Line
[2380]	1	#!/bin/bash
	2
	3	# palmrun - script for running PALM jobs
	4
	5	#--------------------------------------------------------------------------------#
[2696]	6	# This file is part of the PALM model system.
[2380]	7	#
	8	# PALM is free software: you can redistribute it and/or modify it under the terms
	9	# of the GNU General Public License as published by the Free Software Foundation,
	10	# either version 3 of the License, or (at your option) any later version.
	11	#
	12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
	13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	15	#
	16	# You should have received a copy of the GNU General Public License along with
	17	# PALM. If not, see <http://www.gnu.org/licenses/>.
	18	#
[2718]	19	# Copyright 2017-2018 Leibniz Universitaet Hannover
[2380]	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
	23	# ------------------
	24	#
[2410]	25	#
[2380]	26	# Former revisions:
	27	# -----------------
[3032]	28	# $Id: palmrun 3032 2018-05-23 15:22:52Z raasch $
[3025]	29	# -T option not required for interactive runs (tasks per node =
	30	# total number of cores is assumed as default, if option is not given),
	31	# reformatting of a few messages,
	32	# bugfix: destination output directory is created if attribute "pe" is set in
	33	# .palm.iofiles
	34	#
	35	# 2718 2018-01-02 08:49:38Z maronga
[2993]	36	# bugfix of r2990
	37	#
	38	# 2718 2018-01-02 08:49:38Z maronga
[2990]	39	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	40	# not in the working directory from where palmrun is called
	41	#
	42	# 2718 2018-01-02 08:49:38Z maronga
[2957]	43	# svfout in the activation string will be replaced now by svfin in case of
	44	# automatic restarts
	45	#
	46	# 2718 2018-01-02 08:49:38Z maronga
[2906]	47	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	48	# the possible output or input of sky view factors
	49	#
	50	# 2718 2018-01-02 08:49:38Z maronga
[2834]	51	# "fname" renamed to "jobname"
	52	#
	53	# 2718 2018-01-02 08:49:38Z maronga
[2799]	54	# parameters are allowed in output commands (OC:)
	55	#
	56	# 2718 2018-01-02 08:49:38Z maronga
[2789]	57	# bugfix: exit if no queue has been given neither with option -q nor in the
	58	# configuration file
	59	#
	60	# 2718 2018-01-02 08:49:38Z maronga
[2762]	61	# file connection file from trunk/SCRIPTS is taken by default
	62	#
	63	# 2718 2018-01-02 08:49:38Z maronga
[2716]	64	# Corrected "Former revisions" section
	65	#
	66	# 2696 2017-12-14 17:12:51Z kanani
	67	# Change in file header (GPL part)
	68	#
	69	# 2693 2017-12-13 12:33:49Z raasch
[2693]	70	# replacement of variables given by {{<variable>}} in configuration file is now
	71	# done in a more general way, variable names are written in small letters
	72	#
	73	# 2670 2017-12-06 16:32:19Z raasch
[2670]	74	# test printouts removed
	75	#
	76	# 2669 2017-12-06 16:03:27Z raasch
[2669]	77	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	78	# removed,
	79	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	80	# files,
	81	# informative messages in case of missing optional input files shortened
	82	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	83	#
	84	# 2638 2017-11-23 12:44:23Z raasch
[2610]	85	# use of wildcards in file connection statements enabled
	86	#
	87	# 2605 2017-11-09 15:31:46Z raasch
[2605]	88	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	89	# will not be sent with the job file any more, but copied into the
[2610]	90	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	91	#
	92	# 2600 2017-11-01 14:11:20Z raasch
[2600]	93	# cycle numbers are made three digits wide
	94	#
	95	# 2566 2017-10-20 08:50:47Z raasch
[2566]	96	# execute command for combine_plot_fields added
	97	# "TEMPDIR" renamed "tempdir"
	98	# temporary working directory for local batch jobs is created immediately within
	99	# the user's palmrun call, due to a requirement of the "grid engine" batch
	100	# system, where the working directory is given with batch directive -wd and must
	101	# already exist when the job is submitted,
	102	# informative messages in non-trace mode reduced and partly reformatted
	103	#
	104	# 2551 2017-10-18 07:25:11Z raasch
[2551]	105	# TEMPDIR added as replacement string to be used in batch directives
	106	#
	107	# 2512 2017-10-04 08:26:59Z raasch
[2507]	108	# bugfix for determining cycle numbers of NetCDF input files
	109	#
	110	# 2506 2017-09-29 08:30:37Z raasch
[2506]	111	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	112	# host configuration added to SOURCES_FOR_RUN_... folder name
	113	# host_identifier renamed host_configuration
	114	# option -W added to allow for job dependencies
	115	#
	116	# 2501 2017-09-26 11:41:55Z raasch
[2501]	117	# default value for number of cores (option -X) set to 1
	118	# bugfix for mechanism which overwrites configuration file settings with values
	119	# provided by palmrun options
	120	#
	121	# 2499 2017-09-22 16:47:58Z kanani
[2499]	122	# option -h named configuration identifier
	123	#
	124	# 2480 2017-09-19 06:24:14Z maronga
[2480]	125	# bugfix for last revision
	126	#
	127	# 2479 2017-09-19 06:12:16Z raasch
[2479]	128	# option -A (project account number) added
	129	#
	130	# 2422 2017-09-08 08:25:41Z raasch
[2410]	131	# initial revision
[2380]	132	#
	133	#--------------------------------------------------------------------------------#
	134	# palmrun - script for running PALM jobs on local and remote hosts
	135	#--------------------------------------------------------------------------------#
	136
	137
	138
	139	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	140
	141	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	142	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	143	# (TOO MANY ARGUMENTS - PROBLEM)
	144	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	145
[2610]	146	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	147	typeset -i nr_of_output_files=0
[2380]	148	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	149	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	150	# SCRIPT-OPTION ARGUMENTS
	151	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	152	typeset -i icycle inode ival maxcycle mpi_tasks
	153	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	154
	155	activation_string_list=""
	156	AddFilenames=""
	157	combine_plot_fields=true
	158	compiler_name=""
	159	compiler_name_ser=""
	160	compiler_options=""
[2501]	161	cores=1
[2380]	162	cores_atmos=0
	163	cores_ocean=0
	164	coupled_dist=""
	165	cpp_options=""
	166	cpumax=0
[2506]	167	create_batch_job=false
[2380]	168	create_jobfile_only=false
	169	create_remote_batch_job=false
	170	dashes=" ----------------------------------------------------------------------------"
	171	defaultqueue=""
[2506]	172	delete_temporary_catalog=true
[2380]	173	do_compile=true
	174	do_trace=false
	175	executable=""
	176	execute_command=""
	177	execution_error=false
[2762]	178	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2834]	179	jobname=test
[2380]	180	global_revision=""
[2506]	181	host_configuration="default"
[2380]	182	hostfile=""
	183	hp=""
	184	keep_data_from_previous_run=false
	185	link_local_input=false
	186	link_local_output=false
[2388]	187	linker_options=""
[2385]	188	local_jobcatalog=""
[2380]	189	locat=normal
	190	makefile=""
	191	max_par_io_str=""
	192	prc=$0
	193	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	194	do
	195	prc=`echo $prc \| cut -f2- -d"/"`
	196	done
	197	module_calls=""
[2506]	198	palmrun_memory=""
[2380]	199	palmrun_script_name=$prc
	200	openmp=false
[2506]	201	previous_job=""
[2479]	202	project_account=""
[2380]	203	queue=none
[2906]	204	read_svf=""
[2380]	205	restart_run=false
	206	return_address=""
[2385]	207	remote_jobcatalog=""
[2380]	208	remote_username=""
	209	running_in_batch_mode=false
	210	run_coupled_model=false
	211	run_id=""
	212	silent=false
	213	source_list=""
	214	source_path=""
[2501]	215	tasks_per_node=0
[2380]	216	threads_per_task=1
	217	transfer_problems=false
[2384]	218	user_source_path=""
[2506]	219	use_existing_sources_folder=""
[2380]	220	use_openmp=false
[3032]	221	version="palmrun 1.0 $Rev: 3032 $"
[2380]	222	working_directory=`pwd`
	223	write_binary=""
[2906]	224	write_svf=""
[2380]	225
	226
	227	# ERROR HANDLING IN CASE OF EXIT
[2404]	228	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	229	then
	230
	231	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	232	(( i = 0 ))
	233	while (( i < iec ))
	234	do
	235	(( i = i + 1 ))
	236	printf "\n *** Execution of ERROR-command:\n"
	237	printf " >>> ${err_command[$i]}\n"
	238	eval ${err_command[$i]}
	239	done
[2566]	240	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	241	printf "\n\n+++ palmrun killed \n\n"
	242	elif [[ $locat != control_c ]]
	243	then
[2566]	244	printf "\n --> palmrun finished\n\n"
[2380]	245	fi' exit
	246
	247
	248	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	249	trap 'cd; rm -rf $tempdir
[2380]	250	printf "\n+++ palmrun killed by \"^C\" \n\n"
	251	locat=control_c
	252	exit
	253	' 2
	254
	255
	256	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	257	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	258	while getopts :a:A:bBCd:FG:h:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:Z option
[2380]	259	do
	260	case $option in
	261	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	262	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	263	(b) create_batch_job=true; prc="$prc -b";;
	264	(B) delete_temporary_catalog=false; prc="$prc -B";;
	265	(C) restart_run=true; prc="$prc -C";;
[2834]	266	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
[2380]	267	(F) create_jobfile_only=true;;
	268	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	269	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	270	(j) running_in_batch_mode=true;;
	271	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	272	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	273	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	274	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	275	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	276	(r) run_id=$OPTARG;;
	277	(R) return_address=$OPTARG;;
	278	(s) source_list=$OPTARG;;
[2501]	279	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	280	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	281	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	282	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	283	(v) silent=true; prc="$prc -v";;
[2506]	284	(V) use_existing_sources_folder="-V";;
[2380]	285	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	286	(W) previous_job=$OPTARG;;
[2380]	287	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	288	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	289	(y) ocean_file_appendix=true; prc="$prc -y";;
	290	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	291	(Z) combine_plot_fields=false; prc="$prc -Z";;
	292	(\?) printf "\n +++ unknown option $OPTARG \n"
	293	printf "\n --> type \"$0 ?\" for available options \n"
	294	locat=parameter;exit;;
	295	esac
	296	done
	297
	298
	299	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	300	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	301	(( to_shift = $OPTIND - 1 ))
	302	shift $to_shift
	303
	304	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	305	if [[ "$1" = "?" ]]
	306	then
	307	(printf "\n *** Description of available palmrun options:\n"
	308	printf "\n Option Description Default-Value"
	309	printf "\n -a activation string list \"\" "
[2479]	310	printf "\n -A project account number ---"
[2380]	311	printf "\n -b batch-job on local machine ---"
	312	printf "\n -B do not delete temporary directory at end ---"
[3025]	313	printf "\n -d run identifier test"
[2380]	314	printf "\n -F create batch job file only ---"
[2506]	315	printf "\n -h host configuration \"default\" "
[2380]	316	printf "\n -k keep data from previous run"
	317	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	318	printf "\n -M Makefile name Makefile"
	319	printf "\n -O threads per openMP task ---"
	320	printf "\n -q queue \"$queue\" "
	321	printf "\n -s filenames of routines to be compiled \"\" "
	322	printf "\n must end with .f, .f90, .F, or .c !"
	323	printf "\n use \"..\" for more than one file and wildcards"
	324	printf "\n -s LM compiles all locally modified files"
	325	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	326	printf "\n -T tasks per node ---"
[2380]	327	printf "\n -u username on remote machine \"\" "
	328	printf "\n -v no prompt for confirmation ---"
[2506]	329	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	330	printf "\n -w maximum parallel io streams as given by -X"
[2506]	331	printf "\n -W name of job to wait for ---"
[2380]	332	printf "\n -x tracing of palmrun for debug purposes ---"
	333	printf "\n -X # of processors (on parallel machines) 1"
	334	printf "\n -y add appendix \"_O\" to all local output"
	335	printf "\n files (ocean precursor runs followed by"
	336	printf "\n coupled atmosphere-ocean runs) ---"
	337	printf "\n -Y run coupled model, \"#1 #2\" with"
	338	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	339	printf "\n -Z skip combine_plot_fields at the end of "
	340	printf "\n the simulation ---"
	341	printf "\n "
	342	printf "\n Possible values of positional parameter <modus>:"
	343	printf "\n \"?\" - this outline \n\n") \| more
	344	exit
	345	elif [[ "$1" != "" ]]
	346	then
	347	printf "\n +++ positional parameter $1 unknown \n"
	348	locat=parameter; exit
	349	fi
	350
	351
	352
	353	# SHORT STARTING MESSAGE
	354	printf "\n*** $version "
	355	printf "\n will be executed. Please wait ..."
	356
	357
[2834]	358	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
	359	export fname=$jobname
	360
	361
[2506]	362	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	363	config_file=.palm.config.$host_configuration
[2834]	364	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
[2380]	365
	366
	367	# CHECK, IF CONFIGURATION FILE EXISTS
	368	if [[ ! -f $config_file ]]
	369	then
	370	printf "\n\n +++ configuration file: "
	371	printf "\n $config_file"
	372	printf "\n does not exist"
	373	locat=connect; exit
	374	fi
	375
	376
[2762]	377	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	378	if [[ -f .palm.iofiles ]]
	379	then
	380	fileconnection_file=.palm.iofiles
	381	fi
	382
	383
[2380]	384	# CHECK, IF FILE CONNECTION FILE EXISTS
	385	if [[ ! -f $fileconnection_file ]]
	386	then
	387	printf "\n\n +++ file connection file: "
	388	printf "\n $fileconnection_file"
	389	printf "\n does not exist"
	390	locat=connect; exit
	391	fi
	392
	393
[2404]	394	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	395	if [[ "$activation_string_list" = "" ]]
	396	then
	397	printf "\n\n +++ no activation string list given: "
	398	printf "\n please set palmrun option \"-a\" "
	399	locat=palmrun_option; exit
	400	fi
	401
	402
	403	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	404	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	405	then
	406	write_binary=true
	407	else
	408	write_binary=false
	409	fi
	410
[2906]	411	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	412	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	413	then
	414	write_svf=true
	415	else
	416	write_svf=false
	417	fi
[2404]	418
[2906]	419	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	420	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	421	then
	422	read_svf=true
	423	else
	424	read_svf=false
	425	fi
	426
	427
[2380]	428	# READ AND EVALUATE THE CONFIGURATION-FILE
	429	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	430
	431	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	432	while read line
	433	do
	434
	435	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	436	eval line=\"$line\"
	437
	438
	439	# INTERPRET THE LINE
	440	if [[ "$(echo $line)" = "" ]]
	441	then
	442
	443	# EMPTY LINE, NO ACTION
	444	continue
	445
	446	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	447	then
	448
	449	# LINE IS A COMMENT LINE
	450	continue
	451
	452	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	453	then
	454
	455	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	456	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	457	value=`echo $line \| cut -d" " -s -f2-`
	458
	459
	460	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	461	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	462	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	463	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	464	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	465	# CONFIGURATION-FILE.
	466	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	467	then
	468	eval export $var="\$value"
	469
	470	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	471	if [[ $do_trace = true ]]
	472	then
	473	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	474	fi
	475	fi
	476
	477	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	478	then
	479
	480	# LINE DEFINES BATCH-DIRECTIVE
	481	(( ibd = ibd + 1 ))
	482	line=$(echo $line \| cut -c4-)
	483	batch_directive[$ibd]="$line"
	484
	485	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	486	then
	487
	488	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	489	# REMOTE TO A LOCAL HOST
	490	(( ibdt = ibdt + 1 ))
	491	line=$(echo $line \| cut -c5-)
	492	batch_directive_transfer[$ibdt]="$line"
	493
	494	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	495	then
	496
	497	# LINE DEFINES ERROR-COMMAND
	498	(( iec = iec + 1 ))
	499	line=$(echo $line \| cut -c4-)
	500	err_command[$iec]="$line"
	501
	502	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	503	then
	504
	505	# LINE DEFINES INPUT-COMMAND
	506	(( iic = iic + 1 ))
	507	line=$(echo $line \| cut -c4-)
	508	in_command[$iic]="$line"
	509
	510	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	511	then
	512
	513	# LINE DEFINES OUTPUT-COMMAND
	514	(( ioc = ioc + 1 ))
	515	line=$(echo $line \| cut -c4-)
	516	out_command[$ioc]="$line"
	517
	518	else
	519
	520	# SKIP ALL OTHER LINES
	521	continue
	522
	523	fi
	524
	525	done < $config_file
	526
	527
	528	# CHECK SETTING OF REQUIRED PARAMETERS
	529	if [[ "$compiler_name" = "" ]]
	530	then
	531	printf "\n +++ no compiler name found in $config_file"
	532	printf "\n Please add line \"compiler_name ...\" to that file."
	533	locat=config_file; exit
	534	fi
	535	if [[ "$compiler_name_ser" = "" ]]
	536	then
	537	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	538	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	539	locat=config_file; exit
	540	fi
	541	if [[ "$compiler_options" = "" ]]
	542	then
	543	printf "\n +++ no compiler options found in $config_file"
	544	printf "\n Please add line \"compiler_options ...\" to that file."
	545	locat=config_file; exit
	546	fi
[2388]	547	if [[ "$linker_options" = "" ]]
[2380]	548	then
[2388]	549	printf "\n +++ no linker options found in $config_file"
	550	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	551	locat=config_file; exit
	552	fi
	553	if [[ "$execute_command" = "" ]]
	554	then
	555	printf "\n +++ no execute command found in $config_file"
	556	printf "\n Please add line \"execute_command ...\" to that file."
	557	locat=config_file; exit
	558	fi
	559
	560	if [[ "$hostfile" != "" ]]
	561	then
	562	if [[ $hostfile != auto && ! -f $hostfile ]]
	563	then
	564	printf "\n +++ no hostfile \"$hostfile\" found"
	565	printf "\n Please check line \"hostfile ...\" in $config_file"
	566	locat=config_file; exit
	567	fi
	568	fi
	569
	570
	571	# DETERMINE THE CALL STATUS
	572	if [[ "$return_address" != "" ]]
	573	then
	574
	575	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	576	# BATCH MODE AND ...
	577	running_on_remote=true
	578
	579	else
	580
	581	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	582	if [[ "$remote_ip" != "" ]]
	583	then
	584
	585	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	586	create_remote_batch_job=true
	587
	588	fi
	589	running_on_remote=false
	590	fi
	591
	592
	593
	594	# READ AND EVALUATE THE I/O-FILE LIST
	595	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	596
	597	# READ THE FILE CONNECTION FILE LINE BY LINE
	598	while read line
	599	do
	600
[2669]	601	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	602	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	603
	604	# INTERPRET THE LINE
	605	if [[ "$(echo $line)" = "" ]]
	606	then
	607	# EMPTY LINE, NO ACTION
	608	continue
	609
	610	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	611	then
	612
	613	# LINE IS A COMMENT LINE
	614	true
	615
	616	else
	617
	618	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	619	# s2a: in/out - field
[2669]	620	# s2b: action - field (optional)
	621	s1=`echo "$line" \| cut -d" " -f1`
	622	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	623	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	624	then
[2669]	625	s2a=$s2
[2380]	626	s2b=""
	627	else
[2669]	628	s2a=`echo $s2 \| cut -d":" -f1`
	629	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	630	fi
[2669]	631	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	632	s4=`echo "$line" \| cut -d" " -s -f4`
	633	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	634	s5=`echo "$line" \| cut -d" " -s -f5`
	635	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	636
	637
	638	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	639	# INPUT- OR OUTPUT-LIST.
	640	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	641	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	642	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	643	# IS NOT CHECKED AND STORED.
[2610]	644	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	645	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	646	then
	647	found=false
	648	for actual in $activation_string_list
	649	do
	650	for formal in $s3
	651	do
	652	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	653	done
	654	done
	655	if [[ $found = true ]]
	656	then
	657	(( iin = iin + 1 ))
[2669]	658	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	659	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	660	if [[ "$s2a" = inopt ]]
	661	then
	662	optin_pre[$iin]=yes
	663	else
	664	optin_pre[$iin]=no
	665	fi
[2605]	666
	667	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	668	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	669	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	670	then
[2610]	671	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	672	fi
	673
[2610]	674	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	675	# THE WILDCARD FROM THE ENDING
	676	if [[ "${s5: -1}" = "*" ]]
	677	then
[2669]	678	if [[ "$s2b" = "di" ]]
[2610]	679	then
	680	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	681	printf "\n see file \"$fileconnection_file\", line"
	682	printf "\n$line"
	683	locat=iofiles_file; exit
	684	fi
	685	multin[$iin]=true
	686	string=${endin_pre[$iin]}
	687	endin_pre[$iin]="${string%?}"
	688	else
	689	multin[$iin]=false
	690	fi
[2380]	691	fi
[2669]	692	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	693	then
	694	found=false
	695	for actual in $activation_string_list
	696	do
	697	for formal in $s3
	698	do
[2670]	699	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	700	done
	701	done
	702	if [[ $found = true ]]
	703	then
	704	(( iout = iout + 1 ))
[2669]	705	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	706	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	707
[2669]	708	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	709	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	710	if [[ $formal = wildcard ]]
	711	then
	712	warnout_pre[$iout]=false
	713	else
	714	warnout_pre[$iout]=true
	715	fi
	716
[2610]	717	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	718	# THE WILDCARD FROM THE LOCAL FILENAME
	719	if [[ "${s1: -1}" = "*" ]]
	720	then
[2669]	721	if [[ "$s2b" = "di" ]]
[2610]	722	then
	723	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	724	printf "\n see file \"$fileconnection_file\", line"
	725	printf "\n$line"
	726	locat=iofiles_file; exit
	727	fi
	728	multout[$iout]=true
	729	string=${localout_pre[$iout]}
	730	localout_pre[$iout]="${string%?}"
	731	else
	732	multout[$iout]=false
	733	fi
[2380]	734	fi
[2669]	735	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	736	then
[2669]	737	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	738	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	739	locat=connect; exit
	740	fi
	741	IFS="$IFSALT"
	742	fi
	743
	744	done < $fileconnection_file
	745
	746
	747
[2501]	748	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	749	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	750	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	751	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	752	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	753	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	754
	755
	756
[2380]	757	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	758	if [[ $run_coupled_model = true ]]
	759	then
	760
	761	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	762	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	763
	764	if (( $cores_ocean + $cores_atmos != $cores ))
	765	then
	766
	767	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	768	printf "\n PEs (total) : $cores"
	769	printf "\n PEs (atmosphere): $cores_atmos"
	770	printf "\n PEs (ocean) : $cores_ocean"
	771	locat=coupling; exit
	772
	773	fi
	774
	775	fi
	776
	777
	778	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	779	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	780	# FOLDER
	781	if [[ $running_in_batch_mode = true ]]
	782	then
	783
[2506]	784	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	785	then
[2506]	786	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	787	printf "\n Please check the output of the palmrun-call"
	788	printf "\n that you did on your local host."
	789	locat=SOURCES_FOR_RUN; exit
	790	fi
	791
	792	else
	793
	794	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	795	# AUTOMATIC RESTART RUN
	796	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	797	if [[ $restart_run = false ]]
	798	then
	799
	800	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	801	# THE LOCAL HOST
	802	if [[ ! -d $source_path ]]
	803	then
	804	printf "\n\n +++ source path \"$source_path\" on local host"
	805	printf "\n \"$(hostname)\" does not exist"
	806	locat=source_path; exit
	807	fi
	808
[2990]	809	rm -rf ${base_directory}/${sources_for_run_catalog}
	810	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	811
	812	if [[ "$source_list" = LM ]]
	813	then
	814
	815	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	816	source_list=""
	817	cd $source_path
	818
	819
[2512]	820	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	821	if [[ ! -d ../.svn ]]
[2380]	822	then
	823	printf "\n\n +++ source directory"
	824	printf "\n \"$source_path\" "
	825	printf "\n is not under control of \"subversion\"."
[2512]	826	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	827	fi
	828
	829
	830	# LIST ALL MODIFIED SOURCE CODE FILES
	831	Filenames=""
[2404]	832	svn status > tmp_svnstatus
[2380]	833	while read line
	834	do
	835	firstc=`echo $line \| cut -c1`
	836	if [[ $firstc = M \|\| $firstc = "?" ]]
	837	then
	838	Name=`echo "$line" \| cut -c8-`
	839	extension=`echo $Name \| cut -d. -f2`
	840	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	841	then
	842	Filenames="$Filenames "$Name
	843	fi
	844	fi
[2404]	845	done < tmp_svnstatus
	846	rm -rf tmp_svnstatus
[2380]	847
	848
	849	# COPY FILES TO SOURCES_FOR_RUN_...
	850	for filename in $Filenames
	851	do
[2990]	852	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	853	source_list=$source_list"$filename "
	854	done
	855
	856	cd - > /dev/null
	857
	858
	859	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	860	elif [[ "$source_list" != "" ]]
	861	then
	862
	863	cd $source_path
	864
	865	for filename in $source_list
	866	do
	867
	868	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	869	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	870	then
	871	printf "\n +++ source code file: $filename"
	872	printf "\n must not contain (\"/\") "
	873	locat=source; exit
	874	fi
	875
	876	if [[ ! -f $filename ]]
	877	then
	878	printf "\n +++ source code file: $filename"
	879	printf "\n does not exist"
	880	locat=source; exit
	881	else
[2990]	882	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	883	fi
	884
	885	done
	886
	887	cd - > /dev/null
	888
	889	fi
	890
	891	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	892	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	893	if [[ ! -f $makefile ]]
	894	then
	895	printf "\n +++ file \"$makefile\" does not exist"
	896	locat=make; exit
	897	else
[2990]	898	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	899	fi
	900
	901
	902	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	903	if [[ "$user_source_path" != "" ]]
[2380]	904	then
	905
	906	# DOES THE DIRECTORY EXIST?
[2384]	907	if [[ ! -d $user_source_path ]]
[2380]	908	then
	909
	910	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	911	printf "\n \"$user_source_path\" "
[2380]	912	printf "\n does not exist or is not a directory."
	913	printf "\n No source code will be used from this directory!\n"
[2384]	914	user_source_path=""
[2380]	915	if [[ $silent == false ]]
	916	then
	917	sleep 2
	918	fi
	919
	920	else
	921
[2384]	922	cd $user_source_path
[2380]	923	found=false
	924
	925	Names=$(ls -1 *.f90 2>&1)
	926	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	927	Names=$(ls -1 *.F90 2>&1)
	928	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	929	Names=$(ls -1 *.F 2>&1)
	930	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	931	Names=$(ls -1 *.f 2>&1)
	932	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	933	Names=$(ls -1 *.c 2>&1)
	934	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	935
	936	cd - > /dev/null
[2990]	937	cd ${base_directory}/${sources_for_run_catalog}
[2380]	938
	939	# COPY MAKEFILE IF EXISTING
[2384]	940	if [[ -f $user_source_path/Makefile ]]
[2380]	941	then
	942	printf "\n\n *** user Makefile from directory"
[2384]	943	printf "\n \"$user_source_path\" is used \n"
[2380]	944	if [[ $silent == false ]]
	945	then
	946	sleep 1
	947	fi
[2384]	948	cp $user_source_path/Makefile .
[2380]	949	fi
	950
	951	for filename in $AddFilenames
	952	do
	953	if [[ -f $filename ]]
	954	then
	955	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	956	printf "\n source code directory \"$user_source_path\" "
[2380]	957	printf "\n but was also given with option \"-s\" which means that it should be taken"
	958	printf "\n from directory \"$source_path\"."
	959	locat=source; exit
	960	fi
	961
[2384]	962	cp $user_source_path/$filename .
[2380]	963	source_list="$source_list $filename"
	964
	965	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	966	if [[ $(grep -c $filename Makefile) = 0 ]]
	967	then
	968	printf "\n\n +++ user file \"$filename\" "
	969	printf "\n is not listed in Makefile \n"
	970	locat=source; exit
	971	else
	972
	973	if [[ $found = false ]]
	974	then
	975	found=true
	976	printf "\n\n *** following user file(s) added to the"
	977	printf " files to be translated:\n "
	978	fi
	979	printf "$filename "
	980	if [[ $silent == false ]]
	981	then
	982	sleep 0.5
	983	fi
	984
	985	fi
	986	done
	987	[[ $found = true ]] && printf "\n"
	988	cd - > /dev/null
	989	fi
	990	fi
	991
	992	# COPY CONFIGURATION FILES
[2990]	993	cp $config_file ${base_directory}/${sources_for_run_catalog}
	994	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	995
	996	# COPY SHELLSCRIPTS
[2990]	997	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	998	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	999
	1000	fi
	1001
	1002	fi
	1003
[2605]	1004
[2380]	1005	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1006	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1007	if [[ "$global_revision" = "" ]]
	1008	then
	1009	global_revision=`svnversion $source_path 2>/dev/null`
	1010	global_revision="Rev: $global_revision"
	1011	fi
	1012
	1013
	1014	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1015	if [[ -n $cores ]]
	1016	then
	1017
	1018	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1019	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1020	if [[ $tasks_per_node = 0 ]]
[2380]	1021	then
[3025]	1022	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1023	then
	1024	printf "\n"
	1025	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1026	printf "\n set -T option or define tasks_per_node in the config file"
	1027	locat=tasks_per_node; (( iec = 0 )); exit
	1028	else
	1029	# DEFAULT FOR INTERACTIVE RUN
	1030	tasks_per_node=$cores
	1031	fi
[2380]	1032	fi
	1033
	1034	if (( cores < tasks_per_node ))
	1035	then
	1036	printf "\n"
	1037	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1038	printf "\n given values: -T $tasks_per_node -X $cores"
	1039	locat=tasks_per_node; (( iec = 0 )); exit
	1040	fi
	1041
	1042	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1043	(( mpi_tasks = cores / threads_per_task ))
	1044	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1045	(( ii = cores / tasks_per_node ))
	1046	(( remaining_cores = cores - ii * tasks_per_node ))
	1047	if (( remaining_cores > 0 ))
	1048	then
	1049	printf "\n"
	1050	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1051	printf "\n divisor of the total number of cores (option \"-X\")"
	1052	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1053	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1054	(( nodes = nodes + 1 ))
	1055	fi
	1056
	1057	fi
	1058
	1059
	1060	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1061	if [[ "$maximum_parallel_io_streams" = "" ]]
	1062	then
	1063	maximum_parallel_io_streams=$cores
	1064	fi
	1065
	1066
	1067	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1068	if [[ "$scp_port" != "" ]]
	1069	then
	1070	PORTOPT="-P $scp_port"
	1071	SSH_PORTOPT="-p $scp_port"
	1072	fi
	1073
	1074
	1075	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1076	# CONFIG-FILE
	1077	if [[ "$ssh_key" != "" ]]
	1078	then
	1079	ssh_key="-i $HOME/.ssh/$ssh_key"
	1080	fi
	1081
	1082
	1083	# SET QUEUE, IF NOT GIVEN
	1084	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1085	then
	1086
	1087	if [[ $queue = none && "$defaultqueue" = "" ]]
	1088	then
	1089	printf "\n"
	1090	printf "\n +++ no default queue given in configuration file and no queue"
	1091	printf "\n given with option -q"
[2789]	1092	locat=queue; exit
[2380]	1093	fi
	1094	if [[ $queue = none ]]
	1095	then
	1096	queue=$defaultqueue
	1097	fi
	1098
	1099	fi
	1100
	1101
	1102	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1103	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1104	(( i = 0 ))
[2610]	1105	(( nr_of_input_files = 0 ))
[2380]	1106	while (( i < iin ))
	1107	do
	1108	(( i = i + 1 ))
	1109
	1110	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1111	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1112	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1113	then
[2610]	1114	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1115	else
[2834]	1116	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
[2380]	1117	fi
	1118
[2610]	1119
[2380]	1120	# CHECK IF FILE EXISTS
	1121	if ! ls $filename* 1>/dev/null 2>&1
	1122	then
	1123
[2669]	1124	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1125	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1126	then
	1127	printf "\n\n +++ INPUT-file: "
[2610]	1128	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1129	then
	1130	printf "\n $filename"
	1131	else
[2610]	1132	printf "\n $filename.${extin_pre[$i]}"
[2380]	1133	fi
	1134	printf "\n does not exist\n"
	1135	locat=input; exit
	1136	else
[2610]	1137	(( nr_of_input_files = nr_of_input_files + 1 ))
	1138	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1139	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1140	actionin[$nr_of_input_files]="unavailable"
[2610]	1141	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1142	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1143	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1144	fi
[2605]	1145
[2380]	1146	else
	1147
[2834]	1148	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
[2610]	1149	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
	1150	if [[ "${multin[$i]}" = true ]]
	1151	then
	1152	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1153	ls -1 -d ${filename} > filelist 2>/dev/null
	1154	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1155	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1156
[2610]	1157	endings=""
	1158	while read line
	1159	do
	1160	# filename without path (i.e. after the last "/")
	1161	basefilename=$(basename ${line})
[2380]	1162
[2610]	1163	# check if there is an extension and remove it
	1164	ext=${basefilename##*.}
	1165	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1166	then
	1167	basefilename=${basefilename%.*}
	1168	fi
[2380]	1169
[2610]	1170	# check for an existing cycle number and remove it
	1171	cycle=${basefilename##*.}
	1172	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1173	then
	1174	basefilename=${basefilename%.*}
	1175	fi
[2600]	1176
[2834]	1177	# remove the jobname from the beginning
	1178	length_jobname=${#jobname}
	1179	ending=${basefilename:${length_jobname}}
[2610]	1180
	1181	# remove the ending given in the .iofiles from the beginning
	1182	endingstring="${endin_pre[$i]}"
	1183	length_ending=${#endingstring}
	1184	ending=${ending:${length_ending}}
	1185
	1186	if [[ "$ending" = "" ]]
[2600]	1187	then
[2610]	1188	# standard ending as given in the .iofiles
	1189	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1190	then
	1191	endings="$endings DEFAULT"
	1192	fi
[2600]	1193	else
[2610]	1194	# ending must start with "_", otherwise its a different file
	1195	if [[ "${ending:0:1}" = "_" ]]
	1196	then
	1197	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1198	then
	1199	endings="$endings $ending"
	1200	fi
	1201	fi
[2600]	1202	fi
[2610]	1203
	1204	done <filelist
[2380]	1205
[2610]	1206	rm filelist
[2380]	1207
[2600]	1208	else
[2610]	1209
	1210	# SINGLE NAME
	1211	endings=DEFAULT
	1212
[2600]	1213	fi
	1214
[2610]	1215	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1216	for ending in $endings
	1217	do
	1218
	1219	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1220	if [[ $ending = DEFAULT ]]
[2380]	1221	then
[2610]	1222	ending=""
	1223	fi
	1224
	1225	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1226	(( nr_of_input_files = nr_of_input_files + 1 ))
	1227	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1228	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1229	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1230	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1231	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1232	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1233
	1234
	1235	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1236	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1237	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1238	then
	1239	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1240	else
[2834]	1241	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
[2380]	1242	fi
[2610]	1243
	1244	# DETERMINE THE FILE'S CYCLE NUMBER
	1245	(( maxcycle = 0 ))
	1246	ls -1 -d $filename > filelist 2>/dev/null
	1247	ls -1 -d $filename.* >> filelist 2>/dev/null
	1248	while read line
	1249	do
	1250	# filename without path (i.e. after the last "/")
	1251	basefilename=$(basename ${line})
	1252
	1253	# check if there is an extension
	1254	extension=${basefilename##*.}
	1255	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1256	then
	1257	basefilename=${basefilename%.*}
	1258	fi
	1259
	1260	# check for an existing cycle number
	1261	cycle=${basefilename##*.}
	1262	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1263	then
[2669]	1264	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1265	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1266	(( icycle = $((10#$cycle)) ))
[2610]	1267	else
	1268	(( icycle = 0 ))
	1269	fi
	1270
	1271	if (( icycle > maxcycle ))
	1272	then
	1273	(( maxcycle = icycle ))
	1274
	1275	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1276	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1277	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1278	then
	1279	leading_zero=true
	1280	else
	1281	leading_zero=false
	1282	fi
	1283	fi
	1284
	1285	done <filelist
	1286	rm filelist
	1287
	1288	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1289	if [[ $leading_zero = true ]]
[2380]	1290	then
[2610]	1291	cyclestring=`printf "%03d" $maxcycle`
	1292	else
	1293	cyclestring=$maxcycle
[2380]	1294	fi
[2610]	1295
	1296	# APPEND CYCLE NUMBER TO FILENAME
	1297	if (( maxcycle > 0 ))
[2380]	1298	then
[2610]	1299	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1300	then
	1301	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1302	else
	1303	filename=${filename}.$cyclestring
	1304	fi
[2380]	1305	else
[2610]	1306	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1307	then
	1308	filename=${filename}.${extin[$nr_of_input_files]}
	1309	fi
[2380]	1310	fi
[2610]	1311
	1312	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1313	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1314	absnamein[$nr_of_input_files]=$filename
	1315	if (( maxcycle > 0 ))
[2380]	1316	then
[2610]	1317	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1318	then
	1319	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1320	else
[2834]	1321	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1322	fi
[2380]	1323	else
[2610]	1324	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1325	then
	1326	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1327	else
[2834]	1328	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
[2610]	1329	fi
[2380]	1330	fi
	1331
[2610]	1332	done
	1333
[2380]	1334	fi
[2610]	1335
[2380]	1336	done
	1337
[2610]	1338
[2380]	1339	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1340	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1341	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1342	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1343	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1344	# REMOTE HOST)
	1345	(( i = 0 ))
	1346	while (( i < iout ))
	1347	do
	1348	(( i = i + 1 ))
[2610]	1349	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1350	then
[2610]	1351	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1352	then
[2610]	1353	actionout_pre[$i]=""
	1354	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1355	then
[2610]	1356	actionout_pre[$i]=pe
	1357	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1358	then
[2610]	1359	actionout_pre[$i]=a
[2380]	1360	fi
	1361	(( maxcycle = 0 ))
[2834]	1362	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
[2610]	1363	eval catalogname=${pathout_pre[$i]}
[2380]	1364	if ! ls $filename* 1>/dev/null 2>&1
	1365	then
	1366
	1367	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1368	if cat /dev/null > $filename
	1369	then
	1370	rm $filename
	1371	else
	1372
	1373	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1374	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1375	if [[ ! -d $catalogname ]]
	1376	then
	1377	if mkdir -p $catalogname
	1378	then
	1379	printf "\n\n *** directory:"
	1380	printf "\n $catalogname"
	1381	printf "\n was created\n"
	1382	else
	1383	printf "\n\n +++ OUTPUT-file:"
	1384	printf "\n $filename"
	1385	printf "\n cannot be created, because directory does not exist"
	1386	printf "\n and cannot be created either"
	1387	printf "\n"
	1388	locat=output ; exit
	1389	fi 2>/dev/null
	1390	else
	1391	printf "\n\n +++ OUTPUT-file:"
	1392	printf "\n $filename"
	1393	printf "\n cannot be created, although directory exists"
	1394	printf "\n"
	1395	locat=output ; exit
	1396	fi
	1397	fi 2>/dev/null
	1398
	1399	fi
	1400
	1401	fi
	1402	done
	1403
	1404
	1405	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1406	if [[ $running_in_batch_mode = false ]]
	1407	then
	1408	run_id=$RANDOM
[2834]	1409	job_id=${jobname}.$run_id
[2380]	1410
[2566]	1411	tempdir=$fast_io_catalog/$job_id
[2380]	1412	fi
	1413
	1414
	1415	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1416	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1417	then
	1418
	1419	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1420	if [[ $ibd = 0 ]]
	1421	then
	1422	printf "\n"
	1423	printf "\n +++ no batch directives found in configuration file"
	1424	locat=config_file_batch_directives; (( iec = 0 )); exit
	1425	fi
	1426
	1427	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1428	done=false
[2384]	1429	cputime=$cpumax
[2380]	1430	while [[ $done = false ]]
	1431	do
[2384]	1432	if (( cputime == 0 ))
[2380]	1433	then
	1434	printf "\n +++ cpu-time is undefined"
	1435	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1436	printf "\n >>> "
[2384]	1437	read cputime 1>/dev/null 2>&1
[2380]	1438	else
	1439	done=true
	1440	fi
	1441	done
[2420]	1442	cpumax=$cputime
[2380]	1443
	1444	# CHECK THE MEMORY DEMAND
	1445	done=false
	1446	while [[ $done = false ]]
	1447	do
	1448	if (( memory == 0 ))
	1449	then
	1450	printf "\n +++ memory demand is undefined"
	1451	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1452	printf "\n >>> "
	1453	read memory 1>/dev/null 2>&1
	1454	else
	1455	done=true
	1456	fi
	1457	done
	1458
	1459	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1460	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1461	then
	1462	while [[ -z $remote_username ]]
	1463	do
[2420]	1464	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1465	printf "\n >>> Please type username:"
	1466	printf "\n >>> "
	1467	read remote_username
	1468	done
	1469	fi
	1470
	1471	else
	1472
[2420]	1473	if [[ $running_in_batch_mode = false ]]
	1474	then
	1475	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1476	cpumax=$cputime
	1477	else
	1478	cputime=$cpumax
	1479	fi
[2380]	1480
	1481	fi
	1482
	1483
	1484	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1485	(( cpu_hours = cputime / 3600 ))
	1486	(( resttime = cputime - cpu_hours * 3600 ))
	1487	(( cpu_minutes = resttime / 60 ))
	1488	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1489	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1490
	1491
	1492	# OUTPUT OF THE PALMRUN-HEADER
	1493	calltime=$(date)
	1494	printf "\n"
	1495	printf "#------------------------------------------------------------------------# \n"
	1496	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1497	printf "\| \| \n"
	1498	column1="called on:"; column2=$(hostname)
	1499	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1500	if [[ $create_remote_batch_job = true ]]
	1501	then
[2506]	1502	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1503	else
	1504	if [[ $running_on_remote = true ]]
	1505	then
[3025]	1506	column1="host identifier:"; column2="$host_configuration (execute on IP: $remote_ip)"
[2380]	1507	else
[3025]	1508	column1="host identifier:"; column2="$host_configuration (execute on IP: $local_ip)"
[2380]	1509	fi
	1510	fi
	1511	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1512
	1513	column1="running in:"
	1514	if [[ $running_in_batch_mode = true ]]
	1515	then
	1516	column2="batch job mode"
	1517	else
	1518	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1519	then
	1520	column2="job creation mode"
	1521	else
	1522	column2="interactive run mode"
	1523	fi
	1524	fi
	1525	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1526
[2479]	1527	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1528	then
[2480]	1529	if [[ "$project_account" != "" ]]
[2479]	1530	then
	1531	column1="project account number:"
	1532	column2="$project_account"
	1533	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1534	fi
	1535	fi
	1536
[2380]	1537	if [[ -n $cores ]]
	1538	then
	1539	if [[ $run_coupled_model = false ]]
	1540	then
	1541	column1="number of cores:"; column2=$cores
	1542	else
	1543	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1544	fi
	1545	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1546	fi
	1547	if [[ -n $tasks_per_node ]]
	1548	then
	1549	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1550	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1551	if (( remaining_cores > 0 ))
	1552	then
	1553	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1554	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1555	fi
	1556	fi
	1557	if [[ $maximum_parallel_io_streams != $cores ]]
	1558	then
	1559	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1560	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1561	fi
	1562	if [[ $use_openmp = true ]]
	1563	then
	1564	column1="threads per task:"; column2="$threads_per_task"
	1565	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1566	fi
[2384]	1567	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1568	then
[2506]	1569	column1="memory demand / PE":; column2="$memory MB"
	1570	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1571	column1="job cpu time (h:m:s):"; column2="$timestring"
	1572	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1573	fi
[2380]	1574	printf "\| \| \n"
	1575	if [[ "$source_list" != "" ]]
	1576	then
	1577	if [[ "$make_options" != "" ]]
	1578	then
	1579	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1580	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1581	line=$(echo "$make_options" \| cut -c46-)
	1582	while [[ "$line" != "" ]]
	1583	do
	1584	column1=""
	1585	column2=$(echo "$line" \| cut -c-45)
	1586	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1587	line=$(echo "$line" \| cut -c46-)
	1588	done
	1589	fi
	1590	fi
	1591
	1592	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1593	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1594	line=$(echo "$cpp_options" \| cut -c46-)
	1595	while [[ "$line" != "" ]]
	1596	do
	1597	column1=""
	1598	column2=$(echo "$line" \| cut -c-45)
	1599	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1600	line=$(echo "$line" \| cut -c46-)
	1601	done
	1602
	1603	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1604	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1605	line=$(echo "$compiler_options" \| cut -c46-)
	1606	while [[ "$line" != "" ]]
	1607	do
	1608	column1=""
	1609	column2=$(echo "$line" \| cut -c-45)
	1610	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1611	line=$(echo "$line" \| cut -c46-)
	1612	done
	1613
[2388]	1614	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1616	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1617	while [[ "$line" != "" ]]
	1618	do
	1619	column1=""
	1620	column2=$(echo "$line" \| cut -c-45)
	1621	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1622	line=$(echo "$line" \| cut -c46-)
	1623	done
	1624
	1625	if [[ "$login_init_cmd" != "" ]]
	1626	then
	1627	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1628	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1629	line=$(echo "$login_init_cmd" \| cut -c46-)
	1630	while [[ "$line" != "" ]]
	1631	do
	1632	column1=""
	1633	column2=$(echo "$line" \| cut -c-45)
	1634	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1635	line=$(echo "$line" \| cut -c46-)
	1636	done
	1637	fi
	1638
	1639	if [[ "$module_commands" != "" ]]
	1640	then
	1641	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1642	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1643	line=$(echo "$module_commands" \| cut -c46-)
	1644	while [[ "$line" != "" ]]
	1645	do
	1646	column1=""
	1647	column2=$(echo "$line" \| cut -c-45)
	1648	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1649	line=$(echo "$line" \| cut -c46-)
	1650	done
	1651	fi
	1652	printf "\| \| \n"
[3025]	1653	column1="run identifier:"; column2=$jobname
[2380]	1654	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1655	column1="activation string list:"; column2=$(echo $activation_string_list)
	1656	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1657
	1658	if [[ "$ocean_file_appendix" = true ]]
	1659	then
	1660	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1661	fi
	1662
	1663	if [[ "$source_list" != "" ]]
	1664	then
	1665	printf "\| \| \n"
	1666	printf "\| Files to be compiled: \| \n"
	1667	line=$source_list
	1668	while [[ "$line" != "" ]]
	1669	do
	1670	linestart=$(echo $line \| cut -c-70)
	1671	printf "\| %-70s \| \n" "$linestart"
	1672	line=$(echo "$line" \| cut -c71-)
	1673	done
	1674	fi
	1675	printf "#------------------------------------------------------------------------#"
	1676
	1677
	1678
	1679	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1680	if [[ $do_trace = true ]]
	1681	then
	1682	(( i = 0 ))
[2610]	1683	while (( i < nr_of_input_files ))
[2380]	1684	do
	1685	(( i = i + 1 ))
	1686	if (( i == 1 ))
	1687	then
	1688	printf "\n\n >>> INPUT-file assignments:\n"
	1689	fi
	1690	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1691	done
	1692	(( i = 0 ))
	1693	while (( i < iout ))
	1694	do
	1695	(( i = i + 1 ))
	1696	if (( i == 1 ))
	1697	then
	1698	printf "\n\n >>> OUTPUT-file assignments:\n"
	1699	fi
	1700	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1701	done
	1702	(( i = 0 ))
	1703	while (( i < iic ))
	1704	do
	1705	(( i = i + 1 ))
	1706	if (( i == 1 ))
	1707	then
	1708	printf "\n\n >>> INPUT-commands:\n"
	1709	fi
	1710	printf "\n ${in_command[$i]}"
	1711	done
	1712	(( i = 0 ))
	1713	while (( i < ioc ))
	1714	do
	1715	(( i = i + 1 ))
	1716	if (( i == 1 ))
	1717	then
	1718	printf "\n\n >>> OUTPUT-commands:\n"
	1719	fi
	1720	printf "\n ${out_command[$i]}"
	1721	done
	1722	fi
	1723
	1724	# QUERY FOR CONTINUE
	1725	if [[ $silent = false && $running_in_batch_mode = false ]]
	1726	then
	1727	antwort=dummy
	1728	printf "\n\n"
	1729	printf " >>> everything o.k. (y/n) ? "
	1730	while read antwort
	1731	do
	1732	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1733	then
	1734	printf " >>> everything o.k. (y/n) ? "
	1735	else
	1736	break
	1737	fi
	1738	done
	1739	if [[ $antwort = n \|\| $antwort = N ]]
	1740	then
	1741	locat=user_abort; (( iec = 0 )); exit
	1742	fi
	1743	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1744	then
[2566]	1745	printf "\n *** batch-job will be created and submitted"
[2380]	1746	else
[2566]	1747	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1748	fi
	1749	fi
	1750
	1751
	1752
	1753	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1754	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1755	then
	1756
	1757	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1758	then
[2566]	1759	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1760	else
[2566]	1761	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1762	fi
	1763
[2422]	1764	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1765	# IT SHALL BE CREATED
	1766	ask_for_make_depository=false
	1767	if [[ $create_remote_batch_job = true ]]
	1768	then
	1769
	1770	line=`grep %base_directory $config_file`
[2506]	1771	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1772	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${host_configuration}_last_make_protokoll
[2422]	1773
[2506]	1774	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1775	then
	1776	printf "\n\n +++ make depository \"${make_depository}\""
	1777	printf "\n on remote host not found!"
	1778	ask_for_make_depository=true
	1779	fi
[2506]	1780	rm ${host_configuration}_last_make_protokoll
[2422]	1781
	1782	else
	1783
	1784	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1785	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1786	if [[ ! -d ${make_depository} ]]
	1787	then
	1788	printf "\n\n +++ make depository \"${make_depository}\""
	1789	printf "\n on local host not found!"
	1790	ask_for_make_depository=true
	1791	fi
	1792
	1793	fi
	1794
	1795	if [[ $ask_for_make_depository = true ]]
	1796	then
	1797
	1798	antwort=dummy
	1799	printf "\n\n"
	1800	printf " >>> Create a new one (y/n) ? "
	1801	while read antwort
	1802	do
	1803	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1804	then
	1805	printf " >>> Create a new one (y/n) ? "
	1806	else
	1807	break
	1808	fi
	1809	done
	1810	if [[ $antwort = n \|\| $antwort = N ]]
	1811	then
	1812	locat=user_abort; (( iec = 0 )); exit
	1813	fi
	1814
[2566]	1815	if [[ $do_trace = true ]]
	1816	then
	1817	palmbuild -h $host_configuration
	1818	else
	1819	palmbuild -v -h $host_configuration
	1820	fi
[2422]	1821
	1822	if [[ $? != 0 ]]
	1823	then
	1824
	1825	# ABORT IN CASE OF COMPILATION PROBLEMS
	1826	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1827	locat=make_depository
	1828	exit
	1829	else
	1830	echo " *** now continue with creating executable and other sources"
	1831	fi
	1832
	1833	fi
	1834
[2566]	1835	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2993]	1836	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
[2380]	1837
	1838	if [[ $? != 0 ]]
	1839	then
	1840
	1841	# ABORT IN CASE OF COMPILATION PROBLEMS
	1842	printf "\n +++ error while creating executable and/or other sources"
	1843	locat=execution
[2990]	1844	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1845	exit
	1846
	1847	else
	1848
[2566]	1849	printf " *** executable and other sources created\n"
[2990]	1850	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1851
	1852	fi
	1853
	1854	fi
	1855
	1856
[2669]	1857	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1858	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1859	if [[ $create_remote_batch_job = true ]]
	1860	then
	1861	(( i = 0 ))
[2610]	1862	while (( i < nr_of_input_files ))
[2605]	1863	do
	1864	(( i = i + 1 ))
[2669]	1865	if [[ "${actionin[$i]}" = tr ]]
[2605]	1866	then
	1867	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1868	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1869	fi
	1870	done
	1871	if (( i > 0 ))
	1872	then
[3025]	1873	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1874	fi
	1875	fi
	1876
	1877
[2380]	1878	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1879	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1880	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1881	then
	1882
	1883	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1884	if [[ $running_in_batch_mode = false ]]
	1885	then
	1886	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1887	# FOLDER
[2566]	1888	mkdir -p $tempdir
	1889	chmod go+rx $tempdir
	1890	cd $tempdir
	1891	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1892	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1893
	1894	else
	1895
	1896	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1897	printf "\n *** running in temporary directory: $tempdir"
[2380]	1898
	1899	fi
	1900
	1901
	1902	# PROVIDE THE INPUT FILES
	1903	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1904	optional_files_missing=false
[2380]	1905	(( i = 0 ))
[2610]	1906	while (( i < nr_of_input_files ))
[2380]	1907	do
	1908	(( i = i + 1 ))
	1909	if (( i == 1 ))
	1910	then
	1911	printf "\n\n *** providing INPUT-files:\n$dashes"
	1912	fi
	1913
	1914
	1915	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1916	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1917	then
[2669]	1918	optional_files_missing=true
[2380]	1919	continue
	1920	fi
	1921
	1922	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1923	files_for_cores=false; filetype=file
	1924	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1925	then
	1926	files_for_cores=true; filetype=files
	1927	actionin[$i]=""
	1928	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1929	then
	1930	actionin[$i]=""
	1931	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1932	then
	1933	files_for_cores=true; filetype=files
	1934	actionin[$i]="ln"
	1935	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1936	then
	1937	actionin[$i]="ln"
	1938	fi
	1939
	1940	if [[ $files_for_cores = true ]]
	1941	then
	1942	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1943	else
	1944	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1945	fi
	1946
	1947	# INPUT-FILES TO BE LINKED
	1948	if [[ "${actionin[$i]}" = ln ]]
	1949	then
	1950
	1951	printf "\n $filetype will be linked"
	1952	if [[ $files_for_cores = false ]]
	1953	then
	1954	if [[ -f "${absnamein[$i]}" ]]
	1955	then
	1956	ln ${absnamein[$i]} ${localin[$i]}
	1957	got_tmp[$i]=true
	1958	fi
	1959	else
	1960	if [[ -d "${absnamein[$i]}" ]]
	1961	then
[2396]	1962	mkdir -p ${localin[$i]}
[2380]	1963	cd ${absnamein[$i]}
	1964	for file in $(ls *)
	1965	do
[2566]	1966	ln $file $tempdir/${localin[$i]}
[2380]	1967	done >\|/dev/null 2>&1
[2566]	1968	cd $tempdir
[2380]	1969	fi
	1970
	1971	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1972	if [[ ! -f "${localin[$i]}/_000000" ]]
	1973	then
	1974	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1975	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1976	fi
	1977
	1978	got_tmp[$i]=true
	1979	fi
	1980	fi
	1981
	1982	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	1983	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	1984	then
	1985
	1986	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1987	then
	1988
	1989	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1990	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1991	printf "\n file will be provided for $cores processors"
[2396]	1992	mkdir -p ${localin[$i]}
[2380]	1993	ival=$cores
	1994	(( ii = 0 ))
	1995	while (( ii <= ival-1 ))
	1996	do
	1997	if (( ii < 10 ))
	1998	then
	1999	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2000	elif (( ii < 100 ))
	2001	then
	2002	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2003	elif (( ii < 1000 ))
	2004	then
	2005	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2006	else
	2007	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2008	fi
	2009	(( ii = ii + 1 ))
	2010	done
	2011
	2012	else
	2013
	2014	if [[ $files_for_cores = true ]]
	2015	then
	2016
	2017	# PROVIDE FILES FOR EACH CORE
	2018	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2019	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2020	printf "\n providing $cores files for the respective cores"
[2396]	2021	mkdir -p ${localin[$i]}
[2380]	2022	if [[ $link_local_input = true ]]
	2023	then
	2024	printf " files will be linked\n"
	2025	cd ${absnamein[$i]}
	2026	for file in $(ls *)
	2027	do
	2028	ln -f $file ${localin[$i]}
	2029	done
[2566]	2030	cd $tempdir
[2380]	2031	fi
	2032
	2033	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2034	if [[ ! -f "${localin[$i]}/_000000" ]]
	2035	then
	2036	if [[ $link_local_input = true ]]
	2037	then
	2038	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2039	fi
	2040	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2041	fi
	2042
	2043	else
	2044
	2045	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2046	if [[ $link_local_input = true ]]
	2047	then
	2048	printf " file will be linked\n"
	2049	ln -f ${absnamein[$i]} ${localin[$i]}
	2050	fi
[2605]	2051	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2052	if [[ ! -f "${localin[$i]}" ]]
	2053	then
	2054	if [[ $link_local_input = true ]]
	2055	then
	2056	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2057	fi
[2669]	2058	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2059	then
	2060	mv ${absnamein[$i]} ${localin[$i]}
	2061	else
	2062	cp ${absnamein[$i]} ${localin[$i]}
	2063	fi
[2380]	2064	fi
	2065	fi
	2066	fi
	2067	fi
	2068
	2069	done
	2070	if (( i != 0 ))
	2071	then
[2669]	2072	if [[ $optional_files_missing = true ]]
	2073	then
	2074	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2075	fi
[2380]	2076	printf "\n$dashes\n *** all INPUT-files provided \n"
	2077	fi
	2078
	2079
	2080	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2081	(( i = 0 ))
	2082	while (( i < iic ))
	2083	do
	2084	(( i = i + 1 ))
	2085	if (( i == 1 ))
	2086	then
	2087	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2088	fi
	2089	printf "\n >>> ${in_command[$i]}"
	2090	eval ${in_command[$i]}
	2091	if (( i == iic ))
	2092	then
	2093	printf "\n$dashes\n"
	2094	fi
	2095	done
	2096
	2097
	2098	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2099	# (FILE ENVPAR WILL BE READ BY PALM)
	2100	cat > ENVPAR << EOF
[2834]	2101	&envpar run_identifier = '$jobname', host = '$host_configuration',
[2906]	2102	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2103	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2104	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2105	maximum_cpu_time_allowed = ${cpumax}.,
	2106	revision = '$global_revision',
	2107	batch_job = .${running_in_batch_mode}. /
	2108
	2109	EOF
	2110
	2111
	2112	# STARTING THE EXECUTABLE
	2113	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2114	PATH=$PATH:$tempdir
[2380]	2115
	2116
	2117	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2118	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2119	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2120	eval line=\"$line\"
	2121	execute_command="$line"
	2122
	2123
	2124	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2125	if [[ "$execute_command_for_combine" = "" ]]
	2126	then
	2127	eval line2=\"$line2\"
	2128	execute_command_for_combine="$line2"
	2129	fi
	2130
[2380]	2131
	2132
	2133	# PROVIDE A HOSTFILE, IF REQUIRED
	2134	if [[ "$hostfile" != "" ]]
	2135	then
	2136
	2137	if [[ $hostfile = auto ]]
	2138	then
	2139	# CREATE A NEW HOSTFILE
	2140	(( ii = 1 ))
	2141	while (( ii <= cores / threads_per_task ))
	2142	do
	2143	echo $(hostname) >> hostfile
	2144	(( ii = ii + 1 ))
	2145	done
	2146	if (( cores / threads_per_task == 0 ))
	2147	then
	2148	echo $(hostname) >> hostfile
	2149	fi
	2150
	2151	else
	2152	cp $hostfile hostfile
	2153	fi
	2154	eval line=\"`head -n $ii hostfile`\"
	2155	printf "\n *** running on: $line"
	2156	fi
	2157
	2158
	2159
	2160	# SET THE NUMBER OF OPENMP-THREADS
	2161	if [[ $use_openmp = true ]]
	2162	then
	2163	export OMP_NUM_THREADS=$threads_per_task
	2164	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2165	else
	2166	export OMP_NUM_THREADS=1
	2167	fi
	2168
	2169
[2610]	2170	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2171	if [[ $run_coupled_model = false ]]
	2172	then
	2173	if [[ "$ocean_file_appendix" = true ]]
	2174	then
	2175	echo "precursor_ocean" > coupling_steering
	2176	else
	2177	echo "precursor_atmos" > coupling_steering
	2178	fi
	2179	else
	2180	(( iia = $cores_atmos / $threads_per_task ))
	2181	(( iio = $cores_ocean / $threads_per_task ))
	2182	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2183	printf "\n\n"
	2184	echo "coupled_run $iia $iio" > coupling_steering
	2185	fi
	2186
	2187	printf "\n *** execute command:"
	2188	printf "\n \"$execute_command\" \n\n"
	2189
	2190	$execute_command < coupling_steering
	2191
	2192	if [[ $? != 0 ]]
	2193	then
	2194
	2195	# ABORT IN CASE OF RUNTIME ERRORS
	2196	printf "\n +++ runtime error occured"
	2197	locat=execution
	2198	exit
	2199
	2200	else
	2201
	2202	printf "\n$dashes\n *** execution finished \n"
	2203
	2204	fi
	2205
	2206
	2207	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2208	# BY EACH CORE INTO ONE FILE
	2209	if [[ ! -f combine_plot_fields.x ]]
	2210	then
	2211
	2212	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2213	printf "\n 2d- and/or 3d-data may be incomplete!"
	2214	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2215
	2216	elif [[ "$combine_plot_fields" == true ]]
	2217	then
	2218
	2219	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2220	$execute_command_for_combine
	2221
	2222	else
	2223
	2224	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2225	# DATA OUTPUT
[2380]	2226	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2227	fi
	2228
	2229
	2230
	2231	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2232	(( i = 0 ))
	2233	while (( i < ioc ))
	2234	do
	2235	(( i = i + 1 ))
	2236	if (( i == 1 ))
	2237	then
	2238	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2239	fi
[2799]	2240
	2241	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2242	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2243
[2380]	2244	printf "\n >>> ${out_command[$i]}"
	2245	eval ${out_command[$i]}
	2246	if (( i == ioc ))
	2247	then
	2248	printf "\n$dashes\n"
	2249	fi
	2250	done
	2251
	2252
[2610]	2253	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2254	# WILDCARDS
[2380]	2255	(( i = 0 ))
[2610]	2256	(( nr_of_output_files = 0 ))
	2257
[2380]	2258	while (( i < iout ))
	2259	do
[2610]	2260
[2380]	2261	(( i = i + 1 ))
[2610]	2262
	2263	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2264	# CREATE A LIST FOR THE DETECTED ENDINGS
	2265	if [[ "${multout[$i]}" = true ]]
	2266	then
	2267	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2268	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2269	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2270
	2271	endings="DEFAULT"
	2272	while read line
	2273	do
	2274	# remove the local name from the beginning
	2275	localnamestring="${localout_pre[$i]}"
	2276	length_localname=${#localnamestring}
	2277	ending=${line:${length_localname}}
	2278
	2279	if [[ "$ending" != "" ]]
	2280	then
	2281	endings="$endings $ending"
	2282	fi
	2283
	2284	done <filelist
	2285
	2286	rm filelist
	2287
	2288	else
	2289
	2290	# SINGLE NAME
	2291	endings=DEFAULT
	2292
	2293	fi
	2294
	2295	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2296	for ending in $endings
	2297	do
	2298
	2299	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2300	if [[ $ending = DEFAULT ]]
	2301	then
	2302	ending=""
	2303	fi
	2304
	2305	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2306	(( nr_of_output_files = nr_of_output_files + 1 ))
	2307	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2308	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2309	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2310	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2311	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2312	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2313	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2314
	2315	done
	2316
	2317	done
	2318
	2319
	2320
	2321
	2322	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2323	(( i = 0 ))
	2324	while (( i < nr_of_output_files ))
	2325	do
	2326	(( i = i + 1 ))
[2380]	2327	if (( i == 1 ))
	2328	then
	2329	printf "\n\n *** saving OUTPUT-files:"
	2330
	2331	# GET RUN NUMBER ASSIGNED BY PALM
	2332	if [[ -f RUN_NUMBER ]]
	2333	then
	2334	read run_number < RUN_NUMBER
	2335	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2336	usecycle_option="-U $run_number"
	2337	else
	2338	run_number=0
	2339	usecycle_option=""
	2340	fi
	2341	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2342	then
[2404]	2343	printf "\n *** in case of SCP transfers to local host"
	2344	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2345	fi
	2346	printf "\n$dashes"
	2347	fi
	2348
	2349	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2350	then
	2351
[2834]	2352	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
[2610]	2353
	2354	# DETERMINE THE CYCLE NUMBER
	2355	ls -1 -d $filename > filelist 2>/dev/null
	2356	ls -1 -d $filename.* >> filelist 2>/dev/null
	2357	while read line
	2358	do
	2359
	2360	# filename without path (i.e. after the last "/")
	2361	basefilename=$(basename ${line})
	2362
	2363	# check if there is an extension
	2364	extension=${basefilename##*.}
	2365	if [[ "$extension" = "${extout[$i]}" ]]
	2366	then
	2367	basefilename=${basefilename%.*}
	2368	fi
	2369
	2370	# check for an existing cycle number
	2371	cycle=${basefilename##*.}
	2372	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2373	then
[2669]	2374	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2375	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2376	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2377	else
	2378	(( icycle = 1 ))
	2379	fi
	2380
	2381	if (( icycle > maxcycle ))
	2382	then
	2383	(( maxcycle = icycle ))
	2384	fi
	2385
	2386	done <filelist
	2387	rm filelist
	2388
	2389
	2390	# SET THE CYCLE NUMBER
	2391	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2392	if [[ "${actionout[$i]}" = a ]]
	2393	then
	2394	(( maxcycle = maxcycle - 1 ))
	2395	fi
	2396
	2397	(( cycnum[$i] = maxcycle ))
	2398	pathout[$i]=$filename
	2399
	2400
	2401	# ADD CYCLE NUMBER TO FILENAME
	2402	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2403	if [[ "${actionout[$i]}" != "a" ]]
	2404	then
	2405	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2406	# WITH AN EXISTING CYCLE NUMBER
	2407	if (( run_number >= cycnum[$i] ))
	2408	then
	2409	(( cycnum[$i] = run_number ))
	2410	else
	2411	if (( run_number > 0 ))
	2412	then
	2413	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2414	fi
	2415	fi
	2416	fi
	2417	if (( cycnum[$i] > 0 ))
	2418	then
[2600]	2419	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2420	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2421	fi
	2422	fi
	2423
	2424	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2425	files_for_cores=false; filetype=file
	2426	link_local_output=false
	2427	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2428	then
	2429	files_for_cores=true; filetype=directory
	2430	actionout[$i]=""
	2431	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2432	then
	2433	actionout[$i]=""
	2434	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2435	then
	2436	files_for_cores=true; filetype=directory
	2437	link_local_output=true
	2438	actionout[$i]=""
	2439	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2440	then
	2441	link_local_output
	2442	actionout[$i]=""
	2443	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2444	then
	2445	files_for_cores=true; filetype=directory
	2446	actionout[$i]="tr"
	2447	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2448	then
	2449	actionout[$i]="tr"
	2450	fi
	2451
	2452	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2453	then
[2669]	2454	if [[ ${warnout[$i]} = true ]]
	2455	then
	2456	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2457	fi
[2380]	2458	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2459	then
[2669]	2460	if [[ ${warnout[$i]} = true ]]
	2461	then
	2462	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2463	fi
[2380]	2464	else
	2465
	2466
	2467	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2468	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2469	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2470	then
	2471	if [[ $running_on_remote = true ]]
	2472	then
	2473
	2474	# SET OPTIONS FOR TRANSFER
	2475	if [[ "${actionout[$i]}" = tr ]]
	2476	then
	2477	if [[ $files_for_cores = false ]]
	2478	then
	2479	catalog_option=""
	2480	catalog_string=""
	2481	else
	2482	catalog_option="-c"
	2483	catalog_string="/"
	2484	fi
	2485	append_option=""
	2486	append_string=""
	2487	else
	2488	append_option="-A"
	2489	append_string="append"
	2490	fi
	2491
	2492	transfer_failed=false
	2493	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2834]	2494	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
[2380]	2495
	2496	# TRANSFER VIA SCP
	2497	if [[ "$remote_loginnode" != "" ]]
	2498	then
[2834]	2499	echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${host_configuration}_${jobname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
[2380]	2500	else
[2834]	2501	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${jobname}${endout[$i]} ${extout[$i]}
[2380]	2502	fi
	2503	[[ $? != 0 ]] && transfer_failed=true
	2504
	2505
	2506	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2507	if [[ $transfer_failed = true ]]
	2508	then
	2509	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2834]	2510	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
[2380]	2511
	2512	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2513	eval local_catalog=${pathout[$i]}
	2514	if [[ ! -d $local_catalog ]]
	2515	then
	2516	printf " *** local directory does not exist. Trying to create:\n"
	2517	printf " $local_catalog \n"
	2518	mkdir -p $local_catalog
	2519	fi
[2834]	2520	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
[2380]	2521	transfer_problems=true
	2522	fi
	2523
	2524	else
	2525
	2526	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2527	# BE COPIED OR APPENDED ON THIS MACHINE
	2528	if [[ "${actionout[$i]}" = tr ]]
	2529	then
	2530	actionout[$i]=""
	2531	else
	2532	actionout[$i]="a"
	2533	fi
	2534	fi
	2535	fi
	2536
	2537
	2538	# APPEND ON THIS MACHINE
	2539	if [[ "${actionout[$i]}" = "a" ]]
	2540	then
	2541	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2542	then
	2543	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2544	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2545	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2546	else
	2547	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2548	printf "\n ${pathout[$i]}\n"
	2549	cat ${localout[$i]} >> ${pathout[$i]}
	2550	fi
	2551	fi
	2552
	2553	# COPY ON THIS MACHINE
	2554	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2555	# ON DIFFERENT FILE-SYSTEMS
	2556	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2557	then
	2558
	2559	# COPY IN CASE OF RUNS ON SINGLE CORES
	2560	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2561	then
	2562	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2563	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2564	if [[ $link_local_output = true ]]
	2565	then
	2566	printf " file will be linked\n"
	2567	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2568	fi
	2569	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2570	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2571	then
	2572	if [[ $link_local_output = true ]]
	2573	then
	2574	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2575	fi
	2576	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2577	else
	2578	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2579	fi
	2580	else
	2581	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2582	printf "\n ${pathout[$i]}\n"
	2583	if [[ $link_local_output = true ]]
	2584	then
	2585	printf " file will be linked\n"
	2586	ln -f ${localout[$i]} ${pathout[$i]}
	2587	fi
	2588	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2589	if [[ ! -f "${pathout[$i]}" ]]
	2590	then
	2591	if [[ $link_local_output = true ]]
	2592	then
	2593	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2594	fi
	2595	cp ${localout[$i]} ${pathout[$i]}
	2596	else
	2597	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2598	fi
	2599	fi
	2600
	2601	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2602	then
	2603
	2604	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2605	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2606	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2607	printf "\n ${pathout[$i]}\n"
	2608	if [[ $link_local_output = true ]]
	2609	then
	2610	printf " files will be linked\n"
[2396]	2611	mkdir -p ${pathout[$i]}
[2380]	2612	cd ${localout[$i]}
	2613	for file in $(ls *)
	2614	do
	2615	ln -f $file ${pathout[$i]}
	2616	done >\|/dev/null 2>&1
[2566]	2617	cd $tempdir
[2380]	2618	fi
	2619
	2620	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2621	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2622	then
	2623	if [[ $link_local_output = true ]]
	2624	then
	2625	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2626	fi
[3025]	2627	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2628	cp -r ${localout[$i]}/* ${pathout[$i]}
	2629	fi
	2630
	2631	fi
	2632	fi
	2633	done
	2634
	2635	if (( i != 0 ))
	2636	then
	2637	if [[ $transfer_problems = true ]]
	2638	then
	2639	printf "\n$dashes\n *** OUTPUT-files saved"
	2640	printf "\n +++ WARNING: some data transfers failed! \n"
	2641	else
	2642	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2643	fi
	2644	fi
	2645
	2646
	2647	# IF REQUIRED, START A RESTART-JOB
	2648	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2649	if [[ -f CONTINUE_RUN ]]
	2650	then
	2651
	2652	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2653	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2654	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2655	# -b START A BATCH JOB
	2656	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2657	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2658	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2659
[2957]	2660	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2661	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2662	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2663	then
	2664	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2665	fi
[2380]	2666
	2667	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2668	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2669	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2670	then
[2381]	2671	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2672	fi
	2673
	2674
	2675	# START THE RESTART-JOB
	2676	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2677	echo " $prc"
	2678	printf "\n$dashes\n"
	2679	if [[ $running_on_remote = true ]]
	2680	then
	2681
	2682	echo "*** ssh will be used to initiate restart-runs!"
	2683	echo " return_address=\"$return_address\" "
	2684	echo " return_username=\"$local_username\" "
	2685
	2686	if [[ "$remote_loginnode" != "" ]]
	2687	then
[2420]	2688	echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address " \| ssh -q $remote_username@$remote_loginnode
[2380]	2689	else
[2420]	2690	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2691	fi
	2692
	2693	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2694	sleep 30
	2695
	2696	else
	2697
	2698	# START THE RESTART JOB ON THE LOCAL HOST
	2699	eval $prc # THE ' MUST BE EVALUATED
	2700	cd - > /dev/null
	2701
	2702	fi
	2703	printf "\n$dashes\n *** restart-run initiated \n"
	2704
	2705
	2706	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2707	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2708	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2709	# MAY BE VERY HUGE)
	2710	(( i = 0 ))
[2610]	2711	while (( i < nr_of_input_files ))
[2380]	2712	do
	2713	(( i = i + 1 ))
	2714	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2715	then
	2716	rm -r ${absnamein[$i]}
	2717	fi
	2718	done
	2719
	2720	fi
	2721
	2722
	2723	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2724	cd $HOME
[2566]	2725	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2726
	2727
	2728	else
	2729
	2730
	2731	# PREPARING ACTIONS,
	2732	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2733
	2734	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2834]	2735	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2736	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2737	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2738	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2739	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2740	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2741	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2742	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2743	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2744	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2745	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2746	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2747	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2748	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2749	if [[ $create_remote_batch_job = true ]]
	2750	then
	2751	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2752	if [[ $do_trace = true ]]
	2753	then
	2754	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2755	fi
[2380]	2756	elif [[ $create_batch_job = true ]]
	2757	then
	2758	palmrun_com=${palmrun_com}" -j"
[2420]	2759	if [[ $do_trace = true ]]
	2760	then
	2761	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2762	fi
[2380]	2763	fi
	2764
	2765
	2766	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2767	# REMOTE HOST
[2506]	2768	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2769	job_protocol_file=$job_protocol_file_local
	2770	if [[ $create_remote_batch_job = true ]]
	2771	then
[2506]	2772	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2773	job_protocol_file=$job_protocol_file_remote
	2774	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2775	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2776	fi
	2777
	2778
	2779	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2780	jobfile=jobfile.$run_id
	2781
	2782
	2783	# FIRST CREATE THE BATCH DIRECTIVES
	2784	(( i = 0 ))
	2785	while (( i < ibd ))
	2786	do
	2787	(( i = i + 1 ))
[2693]	2788	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2789	eval line=\"$line\"
	2790	echo "$line" >> $jobfile
	2791	done
	2792	echo " " >> $jobfile
	2793
	2794
	2795	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2796	# PROTOCOL
	2797	if [[ $create_remote_batch_job = true ]]
	2798	then
	2799	echo "set +vx" >> $jobfile
	2800	echo "trap '" >> $jobfile
	2801	echo "set +vx" >> $jobfile
	2802	echo "cd ${remote_jobcatalog}" >> $jobfile
	2803	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2804
	2805	# ADD THE BATCH DIRECTIVES
	2806	(( i = 0 ))
	2807	while (( i < ibdt ))
	2808	do
	2809	(( i = i + 1 ))
[2693]	2810	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2811	eval line=\"$line\"
	2812	echo "$line" >> $jobfile
	2813	done
	2814	echo " " >> $jobfile
	2815
	2816	echo "set -x" >> $jobfile
[2834]	2817	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${jobname}" >> $jobfile
[2380]	2818	echo "%%END%%" >> $jobfile
	2819	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2820	echo "$submit_command $scpjob_file" >> $jobfile
	2821	echo "rm $scpjob_file" >> $jobfile
[2404]	2822	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2823	echo "set -x" >> $jobfile
	2824	echo " ' exit" >> $jobfile
	2825	fi
	2826
	2827
	2828	# ACTIVATE ERROR-TRACEBACK
	2829	if [[ $do_trace = true ]]
	2830	then
	2831	echo "set -x" >> $jobfile
	2832	else
	2833	echo "set +vx" >> $jobfile
	2834	fi
	2835
	2836
	2837	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2838	if [[ "$login_init_cmd" != "" ]]
	2839	then
	2840	echo "$login_init_cmd" >> $jobfile
	2841	fi
	2842	if [[ "$module_commands" != "" ]]
	2843	then
	2844	echo "$module_commands" >> $jobfile
	2845	fi
	2846
	2847
	2848	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2849	if [[ $create_remote_batch_job = true ]]
	2850	then
	2851	echo "mkdir $tempdir" >> $jobfile
	2852	echo "chmod go+rx $tempdir" >> $jobfile
	2853	else
	2854	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2855	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2856	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2857	mkdir $tempdir
	2858	chmod go+rx $tempdir
	2859	fi
	2860	echo "cd $tempdir" >> $jobfile
	2861	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2862	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2863	echo "export PATH=.:\$PATH" >> $jobfile
	2864	echo "export execute_palmrun=true" >> $jobfile
	2865
	2866
	2867	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2868	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2869	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2870	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2871	echo "export LOCAL_PWD" >> $jobfile
	2872
	2873
	2874	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2875	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2876	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2877
	2878
	2879	# CALL PALMRUN WITHIN THE JOB
	2880	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2881	echo "set -x" >> $jobfile
	2882	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2883
	2884
	2885	# TRANSFER JOBFILE TO THE TARGET HOST
	2886	if [[ $create_jobfile_only = false ]]
	2887	then
	2888
	2889	if [[ $create_remote_batch_job = true ]]
	2890	then
	2891
[2420]	2892	echo " "
[2566]	2893	echo " *** transfer of job to remote host via scp"
[2420]	2894	if [[ $do_trace = true ]]
	2895	then
[2506]	2896	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2897	fi
[2566]	2898	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2899
[2566]	2900	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2901	if [[ $do_trace = true ]]
	2902	then
[2506]	2903	echo " cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
[2420]	2904	fi
[2506]	2905	echo "cd $remote_jobcatalog; $submit_command ${host_configuration}_${job_id}; rm ${host_configuration}_${job_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
[2380]	2906
	2907	elif [[ $create_batch_job = true ]]
	2908	then
	2909
[2385]	2910	eval local_jobcatalog=$local_jobcatalog
[2506]	2911	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2912	cd $local_jobcatalog
[2380]	2913	echo " "
[2420]	2914	echo " *** submit the job"
	2915	if [[ $do_trace = true ]]
	2916	then
[2506]	2917	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2918	fi
[2506]	2919	$submit_command ${host_configuration}_${job_id}
	2920	rm ${host_configuration}_${job_id}
[2380]	2921	cd - > /dev/null
	2922
	2923	fi
	2924
	2925	rm -rf $jobfile
	2926
	2927	else
	2928
	2929	printf "\n *** jobfile created under name \"$jobfile\" "
	2930	printf "\n no batch-job has been sent!"
	2931
	2932	fi
	2933
	2934	fi # END OF REMOTE-PART

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