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source: palm/trunk/SCRIPTS/palmrun @ 2846

Last change on this file since 2846 was 2834, checked in by raasch, 7 years ago
fname renamed jobname
Property svn:executable set to ``* Property svn:keywords set to `Rev`
File size: 95.7 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	# -----------------
[2732]	28	# $Id: palmrun 2718 2018-01-02 08:49:38Z maronga $
[2834]	29	# "fname" renamed to "jobname"
	30	#
	31	# 2718 2018-01-02 08:49:38Z maronga
[2799]	32	# parameters are allowed in output commands (OC:)
	33	#
	34	# 2718 2018-01-02 08:49:38Z maronga
[2789]	35	# bugfix: exit if no queue has been given neither with option -q nor in the
	36	# configuration file
	37	#
	38	# 2718 2018-01-02 08:49:38Z maronga
[2762]	39	# file connection file from trunk/SCRIPTS is taken by default
	40	#
	41	# 2718 2018-01-02 08:49:38Z maronga
[2716]	42	# Corrected "Former revisions" section
	43	#
	44	# 2696 2017-12-14 17:12:51Z kanani
	45	# Change in file header (GPL part)
	46	#
	47	# 2693 2017-12-13 12:33:49Z raasch
[2693]	48	# replacement of variables given by {{<variable>}} in configuration file is now
	49	# done in a more general way, variable names are written in small letters
	50	#
	51	# 2670 2017-12-06 16:32:19Z raasch
[2670]	52	# test printouts removed
	53	#
	54	# 2669 2017-12-06 16:03:27Z raasch
[2669]	55	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	56	# removed,
	57	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	58	# files,
	59	# informative messages in case of missing optional input files shortened
	60	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	61	#
	62	# 2638 2017-11-23 12:44:23Z raasch
[2610]	63	# use of wildcards in file connection statements enabled
	64	#
	65	# 2605 2017-11-09 15:31:46Z raasch
[2605]	66	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	67	# will not be sent with the job file any more, but copied into the
[2610]	68	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	69	#
	70	# 2600 2017-11-01 14:11:20Z raasch
[2600]	71	# cycle numbers are made three digits wide
	72	#
	73	# 2566 2017-10-20 08:50:47Z raasch
[2566]	74	# execute command for combine_plot_fields added
	75	# "TEMPDIR" renamed "tempdir"
	76	# temporary working directory for local batch jobs is created immediately within
	77	# the user's palmrun call, due to a requirement of the "grid engine" batch
	78	# system, where the working directory is given with batch directive -wd and must
	79	# already exist when the job is submitted,
	80	# informative messages in non-trace mode reduced and partly reformatted
	81	#
	82	# 2551 2017-10-18 07:25:11Z raasch
[2551]	83	# TEMPDIR added as replacement string to be used in batch directives
	84	#
	85	# 2512 2017-10-04 08:26:59Z raasch
[2507]	86	# bugfix for determining cycle numbers of NetCDF input files
	87	#
	88	# 2506 2017-09-29 08:30:37Z raasch
[2506]	89	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	90	# host configuration added to SOURCES_FOR_RUN_... folder name
	91	# host_identifier renamed host_configuration
	92	# option -W added to allow for job dependencies
	93	#
	94	# 2501 2017-09-26 11:41:55Z raasch
[2501]	95	# default value for number of cores (option -X) set to 1
	96	# bugfix for mechanism which overwrites configuration file settings with values
	97	# provided by palmrun options
	98	#
	99	# 2499 2017-09-22 16:47:58Z kanani
[2499]	100	# option -h named configuration identifier
	101	#
	102	# 2480 2017-09-19 06:24:14Z maronga
[2480]	103	# bugfix for last revision
	104	#
	105	# 2479 2017-09-19 06:12:16Z raasch
[2479]	106	# option -A (project account number) added
	107	#
	108	# 2422 2017-09-08 08:25:41Z raasch
[2410]	109	# initial revision
[2380]	110	#
	111	#--------------------------------------------------------------------------------#
	112	# palmrun - script for running PALM jobs on local and remote hosts
	113	#--------------------------------------------------------------------------------#
	114
	115
	116
	117	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	118
	119	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	120	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	121	# (TOO MANY ARGUMENTS - PROBLEM)
	122	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	123
[2610]	124	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	125	typeset -i nr_of_output_files=0
[2380]	126	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	127	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	128	# SCRIPT-OPTION ARGUMENTS
	129	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	130	typeset -i icycle inode ival maxcycle mpi_tasks
	131	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	132
	133	activation_string_list=""
	134	AddFilenames=""
	135	combine_plot_fields=true
	136	compiler_name=""
	137	compiler_name_ser=""
	138	compiler_options=""
[2501]	139	cores=1
[2380]	140	cores_atmos=0
	141	cores_ocean=0
	142	coupled_dist=""
	143	cpp_options=""
	144	cpumax=0
[2506]	145	create_batch_job=false
[2380]	146	create_jobfile_only=false
	147	create_remote_batch_job=false
	148	dashes=" ----------------------------------------------------------------------------"
	149	defaultqueue=""
[2506]	150	delete_temporary_catalog=true
[2380]	151	do_compile=true
	152	do_trace=false
	153	executable=""
	154	execute_command=""
	155	execution_error=false
[2762]	156	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2834]	157	jobname=test
[2380]	158	global_revision=""
[2506]	159	host_configuration="default"
[2380]	160	hostfile=""
	161	hp=""
	162	keep_data_from_previous_run=false
	163	link_local_input=false
	164	link_local_output=false
[2388]	165	linker_options=""
[2385]	166	local_jobcatalog=""
[2380]	167	locat=normal
	168	makefile=""
	169	max_par_io_str=""
	170	prc=$0
	171	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	172	do
	173	prc=`echo $prc \| cut -f2- -d"/"`
	174	done
	175	module_calls=""
[2506]	176	palmrun_memory=""
[2380]	177	palmrun_script_name=$prc
	178	openmp=false
[2506]	179	previous_job=""
[2479]	180	project_account=""
[2380]	181	queue=none
	182	restart_run=false
	183	return_address=""
[2385]	184	remote_jobcatalog=""
[2380]	185	remote_username=""
	186	running_in_batch_mode=false
	187	run_coupled_model=false
	188	run_id=""
	189	silent=false
	190	source_list=""
	191	source_path=""
[2501]	192	tasks_per_node=0
[2380]	193	threads_per_task=1
	194	transfer_problems=false
[2384]	195	user_source_path=""
[2506]	196	use_existing_sources_folder=""
[2380]	197	use_openmp=false
[2732]	198	version="palmrun 1.0 Rev$Rev: 2834 $"
[2380]	199	working_directory=`pwd`
	200	write_binary=""
	201	TOPT=""
	202
	203
	204	# ERROR HANDLING IN CASE OF EXIT
[2404]	205	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	206	then
	207
	208	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	209	(( i = 0 ))
	210	while (( i < iec ))
	211	do
	212	(( i = i + 1 ))
	213	printf "\n *** Execution of ERROR-command:\n"
	214	printf " >>> ${err_command[$i]}\n"
	215	eval ${err_command[$i]}
	216	done
[2566]	217	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	218	printf "\n\n+++ palmrun killed \n\n"
	219	elif [[ $locat != control_c ]]
	220	then
[2566]	221	printf "\n --> palmrun finished\n\n"
[2380]	222	fi' exit
	223
	224
	225	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	226	trap 'cd; rm -rf $tempdir
[2380]	227	printf "\n+++ palmrun killed by \"^C\" \n\n"
	228	locat=control_c
	229	exit
	230	' 2
	231
	232
	233	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	234	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	235	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]	236	do
	237	case $option in
	238	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	239	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	240	(b) create_batch_job=true; prc="$prc -b";;
	241	(B) delete_temporary_catalog=false; prc="$prc -B";;
	242	(C) restart_run=true; prc="$prc -C";;
[2834]	243	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
[2380]	244	(F) create_jobfile_only=true;;
	245	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	246	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	247	(j) running_in_batch_mode=true;;
	248	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	249	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	250	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	251	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	252	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	253	(r) run_id=$OPTARG;;
	254	(R) return_address=$OPTARG;;
	255	(s) source_list=$OPTARG;;
[2501]	256	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	257	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	258	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	259	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	260	(v) silent=true; prc="$prc -v";;
[2506]	261	(V) use_existing_sources_folder="-V";;
[2380]	262	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	263	(W) previous_job=$OPTARG;;
[2380]	264	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	265	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	266	(y) ocean_file_appendix=true; prc="$prc -y";;
	267	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	268	(Z) combine_plot_fields=false; prc="$prc -Z";;
	269	(\?) printf "\n +++ unknown option $OPTARG \n"
	270	printf "\n --> type \"$0 ?\" for available options \n"
	271	locat=parameter;exit;;
	272	esac
	273	done
	274
	275
	276	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	277	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	278	(( to_shift = $OPTIND - 1 ))
	279	shift $to_shift
	280
	281	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	282	if [[ "$1" = "?" ]]
	283	then
	284	(printf "\n *** Description of available palmrun options:\n"
	285	printf "\n Option Description Default-Value"
	286	printf "\n -a activation string list \"\" "
[2479]	287	printf "\n -A project account number ---"
[2380]	288	printf "\n -b batch-job on local machine ---"
	289	printf "\n -B do not delete temporary directory at end ---"
	290	printf "\n -d base name of files attached to program test"
	291	printf "\n -F create batch job file only ---"
[2506]	292	printf "\n -h host configuration \"default\" "
[2380]	293	printf "\n -k keep data from previous run"
	294	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	295	printf "\n -M Makefile name Makefile"
	296	printf "\n -O threads per openMP task ---"
	297	printf "\n -q queue \"$queue\" "
	298	printf "\n -s filenames of routines to be compiled \"\" "
	299	printf "\n must end with .f, .f90, .F, or .c !"
	300	printf "\n use \"..\" for more than one file and wildcards"
	301	printf "\n -s LM compiles all locally modified files"
	302	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	303	printf "\n -T tasks per node ---"
[2380]	304	printf "\n -u username on remote machine \"\" "
	305	printf "\n -v no prompt for confirmation ---"
[2506]	306	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	307	printf "\n -w maximum parallel io streams as given by -X"
[2506]	308	printf "\n -W name of job to wait for ---"
[2380]	309	printf "\n -x tracing of palmrun for debug purposes ---"
	310	printf "\n -X # of processors (on parallel machines) 1"
	311	printf "\n -y add appendix \"_O\" to all local output"
	312	printf "\n files (ocean precursor runs followed by"
	313	printf "\n coupled atmosphere-ocean runs) ---"
	314	printf "\n -Y run coupled model, \"#1 #2\" with"
	315	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	316	printf "\n -Z skip combine_plot_fields at the end of "
	317	printf "\n the simulation ---"
	318	printf "\n "
	319	printf "\n Possible values of positional parameter <modus>:"
	320	printf "\n \"?\" - this outline \n\n") \| more
	321	exit
	322	elif [[ "$1" != "" ]]
	323	then
	324	printf "\n +++ positional parameter $1 unknown \n"
	325	locat=parameter; exit
	326	fi
	327
	328
	329
	330	# SHORT STARTING MESSAGE
	331	printf "\n*** $version "
	332	printf "\n will be executed. Please wait ..."
	333
	334
[2834]	335	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
	336	export fname=$jobname
	337
	338
[2506]	339	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	340	config_file=.palm.config.$host_configuration
[2834]	341	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
[2380]	342
	343
	344	# CHECK, IF CONFIGURATION FILE EXISTS
	345	if [[ ! -f $config_file ]]
	346	then
	347	printf "\n\n +++ configuration file: "
	348	printf "\n $config_file"
	349	printf "\n does not exist"
	350	locat=connect; exit
	351	fi
	352
	353
[2762]	354	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	355	if [[ -f .palm.iofiles ]]
	356	then
	357	fileconnection_file=.palm.iofiles
	358	fi
	359
	360
[2380]	361	# CHECK, IF FILE CONNECTION FILE EXISTS
	362	if [[ ! -f $fileconnection_file ]]
	363	then
	364	printf "\n\n +++ file connection file: "
	365	printf "\n $fileconnection_file"
	366	printf "\n does not exist"
	367	locat=connect; exit
	368	fi
	369
	370
[2404]	371	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	372	if [[ "$activation_string_list" = "" ]]
	373	then
	374	printf "\n\n +++ no activation string list given: "
	375	printf "\n please set palmrun option \"-a\" "
	376	locat=palmrun_option; exit
	377	fi
	378
	379
	380	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	381	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	382	then
	383	write_binary=true
	384	else
	385	write_binary=false
	386	fi
	387
	388
[2380]	389	# READ AND EVALUATE THE CONFIGURATION-FILE
	390	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	391
	392	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	393	while read line
	394	do
	395
	396	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	397	eval line=\"$line\"
	398
	399
	400	# INTERPRET THE LINE
	401	if [[ "$(echo $line)" = "" ]]
	402	then
	403
	404	# EMPTY LINE, NO ACTION
	405	continue
	406
	407	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	408	then
	409
	410	# LINE IS A COMMENT LINE
	411	continue
	412
	413	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	414	then
	415
	416	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	417	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	418	value=`echo $line \| cut -d" " -s -f2-`
	419
	420
	421	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	422	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	423	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	424	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	425	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	426	# CONFIGURATION-FILE.
	427	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	428	then
	429	eval export $var="\$value"
	430
	431	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	432	if [[ $do_trace = true ]]
	433	then
	434	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	435	fi
	436	fi
	437
	438	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	439	then
	440
	441	# LINE DEFINES BATCH-DIRECTIVE
	442	(( ibd = ibd + 1 ))
	443	line=$(echo $line \| cut -c4-)
	444	batch_directive[$ibd]="$line"
	445
	446	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	447	then
	448
	449	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	450	# REMOTE TO A LOCAL HOST
	451	(( ibdt = ibdt + 1 ))
	452	line=$(echo $line \| cut -c5-)
	453	batch_directive_transfer[$ibdt]="$line"
	454
	455	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	456	then
	457
	458	# LINE DEFINES ERROR-COMMAND
	459	(( iec = iec + 1 ))
	460	line=$(echo $line \| cut -c4-)
	461	err_command[$iec]="$line"
	462
	463	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	464	then
	465
	466	# LINE DEFINES INPUT-COMMAND
	467	(( iic = iic + 1 ))
	468	line=$(echo $line \| cut -c4-)
	469	in_command[$iic]="$line"
	470
	471	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	472	then
	473
	474	# LINE DEFINES OUTPUT-COMMAND
	475	(( ioc = ioc + 1 ))
	476	line=$(echo $line \| cut -c4-)
	477	out_command[$ioc]="$line"
	478
	479	else
	480
	481	# SKIP ALL OTHER LINES
	482	continue
	483
	484	fi
	485
	486	done < $config_file
	487
	488
	489	# CHECK SETTING OF REQUIRED PARAMETERS
	490	if [[ "$compiler_name" = "" ]]
	491	then
	492	printf "\n +++ no compiler name found in $config_file"
	493	printf "\n Please add line \"compiler_name ...\" to that file."
	494	locat=config_file; exit
	495	fi
	496	if [[ "$compiler_name_ser" = "" ]]
	497	then
	498	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	499	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	500	locat=config_file; exit
	501	fi
	502	if [[ "$compiler_options" = "" ]]
	503	then
	504	printf "\n +++ no compiler options found in $config_file"
	505	printf "\n Please add line \"compiler_options ...\" to that file."
	506	locat=config_file; exit
	507	fi
[2388]	508	if [[ "$linker_options" = "" ]]
[2380]	509	then
[2388]	510	printf "\n +++ no linker options found in $config_file"
	511	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	512	locat=config_file; exit
	513	fi
	514	if [[ "$execute_command" = "" ]]
	515	then
	516	printf "\n +++ no execute command found in $config_file"
	517	printf "\n Please add line \"execute_command ...\" to that file."
	518	locat=config_file; exit
	519	fi
	520
	521	if [[ "$hostfile" != "" ]]
	522	then
	523	if [[ $hostfile != auto && ! -f $hostfile ]]
	524	then
	525	printf "\n +++ no hostfile \"$hostfile\" found"
	526	printf "\n Please check line \"hostfile ...\" in $config_file"
	527	locat=config_file; exit
	528	fi
	529	fi
	530
	531
	532	# DETERMINE THE CALL STATUS
	533	if [[ "$return_address" != "" ]]
	534	then
	535
	536	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	537	# BATCH MODE AND ...
	538	running_on_remote=true
	539
	540	else
	541
	542	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	543	if [[ "$remote_ip" != "" ]]
	544	then
	545
	546	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	547	create_remote_batch_job=true
	548
	549	fi
	550	running_on_remote=false
	551	fi
	552
	553
	554
	555	# READ AND EVALUATE THE I/O-FILE LIST
	556	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	557
	558	# READ THE FILE CONNECTION FILE LINE BY LINE
	559	while read line
	560	do
	561
[2669]	562	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	563	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	564
	565	# INTERPRET THE LINE
	566	if [[ "$(echo $line)" = "" ]]
	567	then
	568	# EMPTY LINE, NO ACTION
	569	continue
	570
	571	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	572	then
	573
	574	# LINE IS A COMMENT LINE
	575	true
	576
	577	else
	578
	579	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	580	# s2a: in/out - field
[2669]	581	# s2b: action - field (optional)
	582	s1=`echo "$line" \| cut -d" " -f1`
	583	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	584	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	585	then
[2669]	586	s2a=$s2
[2380]	587	s2b=""
	588	else
[2669]	589	s2a=`echo $s2 \| cut -d":" -f1`
	590	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	591	fi
[2669]	592	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	593	s4=`echo "$line" \| cut -d" " -s -f4`
	594	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	595	s5=`echo "$line" \| cut -d" " -s -f5`
	596	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	597
	598
	599	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	600	# INPUT- OR OUTPUT-LIST.
	601	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	602	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	603	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	604	# IS NOT CHECKED AND STORED.
[2610]	605	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	606	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	607	then
	608	found=false
	609	for actual in $activation_string_list
	610	do
	611	for formal in $s3
	612	do
	613	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	614	done
	615	done
	616	if [[ $found = true ]]
	617	then
	618	(( iin = iin + 1 ))
[2669]	619	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	620	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	621	if [[ "$s2a" = inopt ]]
	622	then
	623	optin_pre[$iin]=yes
	624	else
	625	optin_pre[$iin]=no
	626	fi
[2605]	627
	628	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	629	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	630	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	631	then
[2610]	632	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	633	fi
	634
[2610]	635	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	636	# THE WILDCARD FROM THE ENDING
	637	if [[ "${s5: -1}" = "*" ]]
	638	then
[2669]	639	if [[ "$s2b" = "di" ]]
[2610]	640	then
	641	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	642	printf "\n see file \"$fileconnection_file\", line"
	643	printf "\n$line"
	644	locat=iofiles_file; exit
	645	fi
	646	multin[$iin]=true
	647	string=${endin_pre[$iin]}
	648	endin_pre[$iin]="${string%?}"
	649	else
	650	multin[$iin]=false
	651	fi
[2380]	652	fi
[2669]	653	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	654	then
	655	found=false
	656	for actual in $activation_string_list
	657	do
	658	for formal in $s3
	659	do
[2670]	660	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	661	done
	662	done
	663	if [[ $found = true ]]
	664	then
	665	(( iout = iout + 1 ))
[2669]	666	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	667	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	668
[2669]	669	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	670	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	671	if [[ $formal = wildcard ]]
	672	then
	673	warnout_pre[$iout]=false
	674	else
	675	warnout_pre[$iout]=true
	676	fi
	677
[2610]	678	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	679	# THE WILDCARD FROM THE LOCAL FILENAME
	680	if [[ "${s1: -1}" = "*" ]]
	681	then
[2669]	682	if [[ "$s2b" = "di" ]]
[2610]	683	then
	684	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	685	printf "\n see file \"$fileconnection_file\", line"
	686	printf "\n$line"
	687	locat=iofiles_file; exit
	688	fi
	689	multout[$iout]=true
	690	string=${localout_pre[$iout]}
	691	localout_pre[$iout]="${string%?}"
	692	else
	693	multout[$iout]=false
	694	fi
[2380]	695	fi
[2669]	696	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	697	then
[2669]	698	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	699	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	700	locat=connect; exit
	701	fi
	702	IFS="$IFSALT"
	703	fi
	704
	705	done < $fileconnection_file
	706
	707
	708
[2501]	709	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	710	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	711	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	712	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	713	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	714	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	715
	716
	717
[2380]	718	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	719	if [[ $run_coupled_model = true ]]
	720	then
	721
	722	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	723	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	724
	725	if (( $cores_ocean + $cores_atmos != $cores ))
	726	then
	727
	728	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	729	printf "\n PEs (total) : $cores"
	730	printf "\n PEs (atmosphere): $cores_atmos"
	731	printf "\n PEs (ocean) : $cores_ocean"
	732	locat=coupling; exit
	733
	734	fi
	735
	736	fi
	737
	738
	739	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	740	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	741	# FOLDER
	742	if [[ $running_in_batch_mode = true ]]
	743	then
	744
[2506]	745	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	746	then
[2506]	747	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	748	printf "\n Please check the output of the palmrun-call"
	749	printf "\n that you did on your local host."
	750	locat=SOURCES_FOR_RUN; exit
	751	fi
	752
	753	else
	754
	755	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	756	# AUTOMATIC RESTART RUN
	757	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	758	if [[ $restart_run = false ]]
	759	then
	760
	761	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	762	# THE LOCAL HOST
	763	if [[ ! -d $source_path ]]
	764	then
	765	printf "\n\n +++ source path \"$source_path\" on local host"
	766	printf "\n \"$(hostname)\" does not exist"
	767	locat=source_path; exit
	768	fi
	769
[2506]	770	rm -rf $sources_for_run_catalog
	771	mkdir -p $sources_for_run_catalog
[2380]	772
	773	if [[ "$source_list" = LM ]]
	774	then
	775
	776	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	777	source_list=""
	778	cd $source_path
	779
	780
[2512]	781	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	782	if [[ ! -d ../.svn ]]
[2380]	783	then
	784	printf "\n\n +++ source directory"
	785	printf "\n \"$source_path\" "
	786	printf "\n is not under control of \"subversion\"."
[2512]	787	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	788	fi
	789
	790
	791	# LIST ALL MODIFIED SOURCE CODE FILES
	792	Filenames=""
[2404]	793	svn status > tmp_svnstatus
[2380]	794	while read line
	795	do
	796	firstc=`echo $line \| cut -c1`
	797	if [[ $firstc = M \|\| $firstc = "?" ]]
	798	then
	799	Name=`echo "$line" \| cut -c8-`
	800	extension=`echo $Name \| cut -d. -f2`
	801	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	802	then
	803	Filenames="$Filenames "$Name
	804	fi
	805	fi
[2404]	806	done < tmp_svnstatus
	807	rm -rf tmp_svnstatus
[2380]	808
	809
	810	# COPY FILES TO SOURCES_FOR_RUN_...
	811	for filename in $Filenames
	812	do
[2506]	813	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	814	source_list=$source_list"$filename "
	815	done
	816
	817	cd - > /dev/null
	818
	819
	820	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	821	elif [[ "$source_list" != "" ]]
	822	then
	823
	824	cd $source_path
	825
	826	for filename in $source_list
	827	do
	828
	829	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	830	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	831	then
	832	printf "\n +++ source code file: $filename"
	833	printf "\n must not contain (\"/\") "
	834	locat=source; exit
	835	fi
	836
	837	if [[ ! -f $filename ]]
	838	then
	839	printf "\n +++ source code file: $filename"
	840	printf "\n does not exist"
	841	locat=source; exit
	842	else
[2506]	843	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	844	fi
	845
	846	done
	847
	848	cd - > /dev/null
	849
	850	fi
	851
	852	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	853	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	854	if [[ ! -f $makefile ]]
	855	then
	856	printf "\n +++ file \"$makefile\" does not exist"
	857	locat=make; exit
	858	else
[2506]	859	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	860	fi
	861
	862
	863	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	864	if [[ "$user_source_path" != "" ]]
[2380]	865	then
	866
	867	# DOES THE DIRECTORY EXIST?
[2384]	868	if [[ ! -d $user_source_path ]]
[2380]	869	then
	870
	871	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	872	printf "\n \"$user_source_path\" "
[2380]	873	printf "\n does not exist or is not a directory."
	874	printf "\n No source code will be used from this directory!\n"
[2384]	875	user_source_path=""
[2380]	876	if [[ $silent == false ]]
	877	then
	878	sleep 2
	879	fi
	880
	881	else
	882
[2384]	883	cd $user_source_path
[2380]	884	found=false
	885
	886	Names=$(ls -1 *.f90 2>&1)
	887	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	888	Names=$(ls -1 *.F90 2>&1)
	889	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	890	Names=$(ls -1 *.F 2>&1)
	891	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	892	Names=$(ls -1 *.f 2>&1)
	893	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	894	Names=$(ls -1 *.c 2>&1)
	895	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	896
	897	cd - > /dev/null
[2506]	898	cd $sources_for_run_catalog
[2380]	899
	900	# COPY MAKEFILE IF EXISTING
[2384]	901	if [[ -f $user_source_path/Makefile ]]
[2380]	902	then
	903	printf "\n\n *** user Makefile from directory"
[2384]	904	printf "\n \"$user_source_path\" is used \n"
[2380]	905	if [[ $silent == false ]]
	906	then
	907	sleep 1
	908	fi
[2384]	909	cp $user_source_path/Makefile .
[2380]	910	fi
	911
	912	for filename in $AddFilenames
	913	do
	914	if [[ -f $filename ]]
	915	then
	916	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	917	printf "\n source code directory \"$user_source_path\" "
[2380]	918	printf "\n but was also given with option \"-s\" which means that it should be taken"
	919	printf "\n from directory \"$source_path\"."
	920	locat=source; exit
	921	fi
	922
[2384]	923	cp $user_source_path/$filename .
[2380]	924	source_list="$source_list $filename"
	925
	926	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	927	if [[ $(grep -c $filename Makefile) = 0 ]]
	928	then
	929	printf "\n\n +++ user file \"$filename\" "
	930	printf "\n is not listed in Makefile \n"
	931	locat=source; exit
	932	else
	933
	934	if [[ $found = false ]]
	935	then
	936	found=true
	937	printf "\n\n *** following user file(s) added to the"
	938	printf " files to be translated:\n "
	939	fi
	940	printf "$filename "
	941	if [[ $silent == false ]]
	942	then
	943	sleep 0.5
	944	fi
	945
	946	fi
	947	done
	948	[[ $found = true ]] && printf "\n"
	949	cd - > /dev/null
	950	fi
	951	fi
	952
	953	# COPY CONFIGURATION FILES
[2506]	954	cp $config_file $sources_for_run_catalog
	955	cp $fileconnection_file $sources_for_run_catalog
[2380]	956
	957	# COPY SHELLSCRIPTS
[2506]	958	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	959	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	960
	961	fi
	962
	963	fi
	964
[2605]	965
[2380]	966	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	967	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	968	if [[ "$global_revision" = "" ]]
	969	then
	970	global_revision=`svnversion $source_path 2>/dev/null`
	971	global_revision="Rev: $global_revision"
	972	fi
	973
	974
	975	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	976	if [[ -n $cores ]]
	977	then
	978
	979	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	980	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	981	if [[ $tasks_per_node = 0 ]]
[2380]	982	then
	983	printf "\n"
	984	printf "\n +++ option \"-T\" (tasks per node) is missing"
	985	printf "\n set -T option or define tasks_per_node in the config file"
	986	locat=tasks_per_node; (( iec = 0 )); exit
	987	fi
	988
	989	if (( cores < tasks_per_node ))
	990	then
	991	printf "\n"
	992	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	993	printf "\n given values: -T $tasks_per_node -X $cores"
	994	locat=tasks_per_node; (( iec = 0 )); exit
	995	fi
	996
	997	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	998	(( mpi_tasks = cores / threads_per_task ))
	999	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1000	(( ii = cores / tasks_per_node ))
	1001	(( remaining_cores = cores - ii * tasks_per_node ))
	1002	if (( remaining_cores > 0 ))
	1003	then
	1004	printf "\n"
	1005	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1006	printf "\n divisor of the total number of cores (option \"-X\")"
	1007	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1008	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1009	(( nodes = nodes + 1 ))
	1010	fi
	1011
	1012	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	1013	if [[ "$tasks_per_node" != "" ]]
	1014	then
	1015	TOPT="-T $tasks_per_node"
	1016	fi
	1017
	1018	fi
	1019
	1020
	1021	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1022	if [[ "$maximum_parallel_io_streams" = "" ]]
	1023	then
	1024	maximum_parallel_io_streams=$cores
	1025	fi
	1026
	1027
	1028	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1029	if [[ "$scp_port" != "" ]]
	1030	then
	1031	PORTOPT="-P $scp_port"
	1032	SSH_PORTOPT="-p $scp_port"
	1033	fi
	1034
	1035
	1036	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1037	# CONFIG-FILE
	1038	if [[ "$ssh_key" != "" ]]
	1039	then
	1040	ssh_key="-i $HOME/.ssh/$ssh_key"
	1041	fi
	1042
	1043
	1044	# SET QUEUE, IF NOT GIVEN
	1045	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1046	then
	1047
	1048	if [[ $queue = none && "$defaultqueue" = "" ]]
	1049	then
	1050	printf "\n"
	1051	printf "\n +++ no default queue given in configuration file and no queue"
	1052	printf "\n given with option -q"
[2789]	1053	locat=queue; exit
[2380]	1054	fi
	1055	if [[ $queue = none ]]
	1056	then
	1057	queue=$defaultqueue
	1058	fi
	1059
	1060	fi
	1061
	1062
	1063	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1064	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1065	(( i = 0 ))
[2610]	1066	(( nr_of_input_files = 0 ))
[2380]	1067	while (( i < iin ))
	1068	do
	1069	(( i = i + 1 ))
	1070
	1071	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1072	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1073	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1074	then
[2610]	1075	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1076	else
[2834]	1077	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
[2380]	1078	fi
	1079
[2610]	1080
[2380]	1081	# CHECK IF FILE EXISTS
	1082	if ! ls $filename* 1>/dev/null 2>&1
	1083	then
	1084
[2669]	1085	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1086	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1087	then
	1088	printf "\n\n +++ INPUT-file: "
[2610]	1089	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1090	then
	1091	printf "\n $filename"
	1092	else
[2610]	1093	printf "\n $filename.${extin_pre[$i]}"
[2380]	1094	fi
	1095	printf "\n does not exist\n"
	1096	locat=input; exit
	1097	else
[2610]	1098	(( nr_of_input_files = nr_of_input_files + 1 ))
	1099	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1100	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1101	actionin[$nr_of_input_files]="unavailable"
[2610]	1102	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1103	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1104	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1105	fi
[2605]	1106
[2380]	1107	else
	1108
[2834]	1109	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
[2610]	1110	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
	1111	if [[ "${multin[$i]}" = true ]]
	1112	then
	1113	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1114	ls -1 -d ${filename} > filelist 2>/dev/null
	1115	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1116	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1117
[2610]	1118	endings=""
	1119	while read line
	1120	do
	1121	# filename without path (i.e. after the last "/")
	1122	basefilename=$(basename ${line})
[2380]	1123
[2610]	1124	# check if there is an extension and remove it
	1125	ext=${basefilename##*.}
	1126	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1127	then
	1128	basefilename=${basefilename%.*}
	1129	fi
[2380]	1130
[2610]	1131	# check for an existing cycle number and remove it
	1132	cycle=${basefilename##*.}
	1133	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1134	then
	1135	basefilename=${basefilename%.*}
	1136	fi
[2600]	1137
[2834]	1138	# remove the jobname from the beginning
	1139	length_jobname=${#jobname}
	1140	ending=${basefilename:${length_jobname}}
[2610]	1141
	1142	# remove the ending given in the .iofiles from the beginning
	1143	endingstring="${endin_pre[$i]}"
	1144	length_ending=${#endingstring}
	1145	ending=${ending:${length_ending}}
	1146
	1147	if [[ "$ending" = "" ]]
[2600]	1148	then
[2610]	1149	# standard ending as given in the .iofiles
	1150	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1151	then
	1152	endings="$endings DEFAULT"
	1153	fi
[2600]	1154	else
[2610]	1155	# ending must start with "_", otherwise its a different file
	1156	if [[ "${ending:0:1}" = "_" ]]
	1157	then
	1158	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1159	then
	1160	endings="$endings $ending"
	1161	fi
	1162	fi
[2600]	1163	fi
[2610]	1164
	1165	done <filelist
[2380]	1166
[2610]	1167	rm filelist
[2380]	1168
[2600]	1169	else
[2610]	1170
	1171	# SINGLE NAME
	1172	endings=DEFAULT
	1173
[2600]	1174	fi
	1175
[2610]	1176	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1177	for ending in $endings
	1178	do
	1179
	1180	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1181	if [[ $ending = DEFAULT ]]
[2380]	1182	then
[2610]	1183	ending=""
	1184	fi
	1185
	1186	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1187	(( nr_of_input_files = nr_of_input_files + 1 ))
	1188	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1189	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1190	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1191	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1192	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1193	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1194
	1195
	1196	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1197	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1198	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1199	then
	1200	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1201	else
[2834]	1202	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
[2380]	1203	fi
[2610]	1204
	1205	# DETERMINE THE FILE'S CYCLE NUMBER
	1206	(( maxcycle = 0 ))
	1207	ls -1 -d $filename > filelist 2>/dev/null
	1208	ls -1 -d $filename.* >> filelist 2>/dev/null
	1209	while read line
	1210	do
	1211	# filename without path (i.e. after the last "/")
	1212	basefilename=$(basename ${line})
	1213
	1214	# check if there is an extension
	1215	extension=${basefilename##*.}
	1216	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1217	then
	1218	basefilename=${basefilename%.*}
	1219	fi
	1220
	1221	# check for an existing cycle number
	1222	cycle=${basefilename##*.}
	1223	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1224	then
[2669]	1225	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1226	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1227	(( icycle = $((10#$cycle)) ))
[2610]	1228	else
	1229	(( icycle = 0 ))
	1230	fi
	1231
	1232	if (( icycle > maxcycle ))
	1233	then
	1234	(( maxcycle = icycle ))
	1235
	1236	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1237	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1238	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1239	then
	1240	leading_zero=true
	1241	else
	1242	leading_zero=false
	1243	fi
	1244	fi
	1245
	1246	done <filelist
	1247	rm filelist
	1248
	1249	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1250	if [[ $leading_zero = true ]]
[2380]	1251	then
[2610]	1252	cyclestring=`printf "%03d" $maxcycle`
	1253	else
	1254	cyclestring=$maxcycle
[2380]	1255	fi
[2610]	1256
	1257	# APPEND CYCLE NUMBER TO FILENAME
	1258	if (( maxcycle > 0 ))
[2380]	1259	then
[2610]	1260	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1261	then
	1262	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1263	else
	1264	filename=${filename}.$cyclestring
	1265	fi
[2380]	1266	else
[2610]	1267	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1268	then
	1269	filename=${filename}.${extin[$nr_of_input_files]}
	1270	fi
[2380]	1271	fi
[2610]	1272
	1273	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1274	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1275	absnamein[$nr_of_input_files]=$filename
	1276	if (( maxcycle > 0 ))
[2380]	1277	then
[2610]	1278	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1279	then
	1280	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1281	else
[2834]	1282	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1283	fi
[2380]	1284	else
[2610]	1285	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1286	then
	1287	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1288	else
[2834]	1289	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
[2610]	1290	fi
[2380]	1291	fi
	1292
[2610]	1293	done
	1294
[2380]	1295	fi
[2610]	1296
[2380]	1297	done
	1298
[2610]	1299
[2380]	1300	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1301	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1302	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1303	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1304	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1305	# REMOTE HOST)
	1306	(( i = 0 ))
	1307	while (( i < iout ))
	1308	do
	1309	(( i = i + 1 ))
[2610]	1310	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1311	then
[2610]	1312	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1313	then
[2610]	1314	actionout_pre[$i]=""
	1315	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1316	then
[2610]	1317	actionout_pre[$i]=pe
	1318	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1319	then
[2610]	1320	actionout_pre[$i]=a
[2380]	1321	fi
	1322	(( maxcycle = 0 ))
[2834]	1323	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
[2610]	1324	eval catalogname=${pathout_pre[$i]}
[2380]	1325	if ! ls $filename* 1>/dev/null 2>&1
	1326	then
	1327
	1328	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1329	if cat /dev/null > $filename
	1330	then
	1331	rm $filename
	1332	else
	1333
	1334	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1335	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1336	if [[ ! -d $catalogname ]]
	1337	then
	1338	if mkdir -p $catalogname
	1339	then
	1340	printf "\n\n *** directory:"
	1341	printf "\n $catalogname"
	1342	printf "\n was created\n"
	1343	else
	1344	printf "\n\n +++ OUTPUT-file:"
	1345	printf "\n $filename"
	1346	printf "\n cannot be created, because directory does not exist"
	1347	printf "\n and cannot be created either"
	1348	printf "\n"
	1349	locat=output ; exit
	1350	fi 2>/dev/null
	1351	else
	1352	printf "\n\n +++ OUTPUT-file:"
	1353	printf "\n $filename"
	1354	printf "\n cannot be created, although directory exists"
	1355	printf "\n"
	1356	locat=output ; exit
	1357	fi
	1358	fi 2>/dev/null
	1359
	1360	fi
	1361
	1362	fi
	1363	done
	1364
	1365
	1366	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1367	if [[ $running_in_batch_mode = false ]]
	1368	then
	1369	run_id=$RANDOM
[2834]	1370	job_id=${jobname}.$run_id
[2380]	1371
[2566]	1372	tempdir=$fast_io_catalog/$job_id
[2380]	1373	fi
	1374
	1375
	1376	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1377	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1378	then
	1379
	1380	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1381	if [[ $ibd = 0 ]]
	1382	then
	1383	printf "\n"
	1384	printf "\n +++ no batch directives found in configuration file"
	1385	locat=config_file_batch_directives; (( iec = 0 )); exit
	1386	fi
	1387
	1388	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1389	done=false
[2384]	1390	cputime=$cpumax
[2380]	1391	while [[ $done = false ]]
	1392	do
[2384]	1393	if (( cputime == 0 ))
[2380]	1394	then
	1395	printf "\n +++ cpu-time is undefined"
	1396	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1397	printf "\n >>> "
[2384]	1398	read cputime 1>/dev/null 2>&1
[2380]	1399	else
	1400	done=true
	1401	fi
	1402	done
[2420]	1403	cpumax=$cputime
[2380]	1404
	1405	# CHECK THE MEMORY DEMAND
	1406	done=false
	1407	while [[ $done = false ]]
	1408	do
	1409	if (( memory == 0 ))
	1410	then
	1411	printf "\n +++ memory demand is undefined"
	1412	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1413	printf "\n >>> "
	1414	read memory 1>/dev/null 2>&1
	1415	else
	1416	done=true
	1417	fi
	1418	done
	1419
	1420	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1421	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1422	then
	1423	while [[ -z $remote_username ]]
	1424	do
[2420]	1425	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1426	printf "\n >>> Please type username:"
	1427	printf "\n >>> "
	1428	read remote_username
	1429	done
	1430	fi
	1431
	1432	else
	1433
[2420]	1434	if [[ $running_in_batch_mode = false ]]
	1435	then
	1436	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1437	cpumax=$cputime
	1438	else
	1439	cputime=$cpumax
	1440	fi
[2380]	1441
	1442	fi
	1443
	1444
	1445	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1446	(( cpu_hours = cputime / 3600 ))
	1447	(( resttime = cputime - cpu_hours * 3600 ))
	1448	(( cpu_minutes = resttime / 60 ))
	1449	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1450	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1451
	1452
	1453	# OUTPUT OF THE PALMRUN-HEADER
	1454	calltime=$(date)
	1455	printf "\n"
	1456	printf "#------------------------------------------------------------------------# \n"
	1457	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1458	printf "\| \| \n"
	1459	column1="called on:"; column2=$(hostname)
	1460	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1461	if [[ $create_remote_batch_job = true ]]
	1462	then
[2506]	1463	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1464	else
	1465	if [[ $running_on_remote = true ]]
	1466	then
[2506]	1467	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1468	else
[2506]	1469	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1470	fi
	1471	fi
	1472	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1473
	1474	column1="running in:"
	1475	if [[ $running_in_batch_mode = true ]]
	1476	then
	1477	column2="batch job mode"
	1478	else
	1479	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1480	then
	1481	column2="job creation mode"
	1482	else
	1483	column2="interactive run mode"
	1484	fi
	1485	fi
	1486	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1487
[2479]	1488	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1489	then
[2480]	1490	if [[ "$project_account" != "" ]]
[2479]	1491	then
	1492	column1="project account number:"
	1493	column2="$project_account"
	1494	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1495	fi
	1496	fi
	1497
[2380]	1498	if [[ -n $cores ]]
	1499	then
	1500	if [[ $run_coupled_model = false ]]
	1501	then
	1502	column1="number of cores:"; column2=$cores
	1503	else
	1504	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1505	fi
	1506	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1507	fi
	1508	if [[ -n $tasks_per_node ]]
	1509	then
	1510	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1511	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1512	if (( remaining_cores > 0 ))
	1513	then
	1514	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1515	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1516	fi
	1517	fi
	1518	if [[ $maximum_parallel_io_streams != $cores ]]
	1519	then
	1520	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1521	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1522	fi
	1523	if [[ $use_openmp = true ]]
	1524	then
	1525	column1="threads per task:"; column2="$threads_per_task"
	1526	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1527	fi
[2384]	1528	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1529	then
[2506]	1530	column1="memory demand / PE":; column2="$memory MB"
	1531	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1532	column1="job cpu time (h:m:s):"; column2="$timestring"
	1533	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1534	fi
[2380]	1535	printf "\| \| \n"
	1536	if [[ "$source_list" != "" ]]
	1537	then
	1538	if [[ "$make_options" != "" ]]
	1539	then
	1540	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1541	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1542	line=$(echo "$make_options" \| cut -c46-)
	1543	while [[ "$line" != "" ]]
	1544	do
	1545	column1=""
	1546	column2=$(echo "$line" \| cut -c-45)
	1547	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1548	line=$(echo "$line" \| cut -c46-)
	1549	done
	1550	fi
	1551	fi
	1552
	1553	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1554	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1555	line=$(echo "$cpp_options" \| cut -c46-)
	1556	while [[ "$line" != "" ]]
	1557	do
	1558	column1=""
	1559	column2=$(echo "$line" \| cut -c-45)
	1560	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1561	line=$(echo "$line" \| cut -c46-)
	1562	done
	1563
	1564	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1565	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1566	line=$(echo "$compiler_options" \| cut -c46-)
	1567	while [[ "$line" != "" ]]
	1568	do
	1569	column1=""
	1570	column2=$(echo "$line" \| cut -c-45)
	1571	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1572	line=$(echo "$line" \| cut -c46-)
	1573	done
	1574
[2388]	1575	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1576	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1577	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1578	while [[ "$line" != "" ]]
	1579	do
	1580	column1=""
	1581	column2=$(echo "$line" \| cut -c-45)
	1582	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1583	line=$(echo "$line" \| cut -c46-)
	1584	done
	1585
	1586	if [[ "$login_init_cmd" != "" ]]
	1587	then
	1588	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1589	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1590	line=$(echo "$login_init_cmd" \| cut -c46-)
	1591	while [[ "$line" != "" ]]
	1592	do
	1593	column1=""
	1594	column2=$(echo "$line" \| cut -c-45)
	1595	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1596	line=$(echo "$line" \| cut -c46-)
	1597	done
	1598	fi
	1599
	1600	if [[ "$module_commands" != "" ]]
	1601	then
	1602	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1603	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1604	line=$(echo "$module_commands" \| cut -c46-)
	1605	while [[ "$line" != "" ]]
	1606	do
	1607	column1=""
	1608	column2=$(echo "$line" \| cut -c-45)
	1609	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1610	line=$(echo "$line" \| cut -c46-)
	1611	done
	1612	fi
	1613	printf "\| \| \n"
[2834]	1614	column1="base name of files:"; column2=$jobname
[2380]	1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1616	column1="activation string list:"; column2=$(echo $activation_string_list)
	1617	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1618
	1619	if [[ "$ocean_file_appendix" = true ]]
	1620	then
	1621	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1622	fi
	1623
	1624	if [[ "$source_list" != "" ]]
	1625	then
	1626	printf "\| \| \n"
	1627	printf "\| Files to be compiled: \| \n"
	1628	line=$source_list
	1629	while [[ "$line" != "" ]]
	1630	do
	1631	linestart=$(echo $line \| cut -c-70)
	1632	printf "\| %-70s \| \n" "$linestart"
	1633	line=$(echo "$line" \| cut -c71-)
	1634	done
	1635	fi
	1636	printf "#------------------------------------------------------------------------#"
	1637
	1638
	1639
	1640	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1641	if [[ $do_trace = true ]]
	1642	then
	1643	(( i = 0 ))
[2610]	1644	while (( i < nr_of_input_files ))
[2380]	1645	do
	1646	(( i = i + 1 ))
	1647	if (( i == 1 ))
	1648	then
	1649	printf "\n\n >>> INPUT-file assignments:\n"
	1650	fi
	1651	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1652	done
	1653	(( i = 0 ))
	1654	while (( i < iout ))
	1655	do
	1656	(( i = i + 1 ))
	1657	if (( i == 1 ))
	1658	then
	1659	printf "\n\n >>> OUTPUT-file assignments:\n"
	1660	fi
	1661	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1662	done
	1663	(( i = 0 ))
	1664	while (( i < iic ))
	1665	do
	1666	(( i = i + 1 ))
	1667	if (( i == 1 ))
	1668	then
	1669	printf "\n\n >>> INPUT-commands:\n"
	1670	fi
	1671	printf "\n ${in_command[$i]}"
	1672	done
	1673	(( i = 0 ))
	1674	while (( i < ioc ))
	1675	do
	1676	(( i = i + 1 ))
	1677	if (( i == 1 ))
	1678	then
	1679	printf "\n\n >>> OUTPUT-commands:\n"
	1680	fi
	1681	printf "\n ${out_command[$i]}"
	1682	done
	1683	fi
	1684
	1685	# QUERY FOR CONTINUE
	1686	if [[ $silent = false && $running_in_batch_mode = false ]]
	1687	then
	1688	antwort=dummy
	1689	printf "\n\n"
	1690	printf " >>> everything o.k. (y/n) ? "
	1691	while read antwort
	1692	do
	1693	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1694	then
	1695	printf " >>> everything o.k. (y/n) ? "
	1696	else
	1697	break
	1698	fi
	1699	done
	1700	if [[ $antwort = n \|\| $antwort = N ]]
	1701	then
	1702	locat=user_abort; (( iec = 0 )); exit
	1703	fi
	1704	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1705	then
[2566]	1706	printf "\n *** batch-job will be created and submitted"
[2380]	1707	else
[2566]	1708	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1709	fi
	1710	fi
	1711
	1712
	1713
	1714	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1715	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1716	then
	1717
	1718	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1719	then
[2566]	1720	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1721	else
[2566]	1722	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1723	fi
	1724
[2422]	1725	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1726	# IT SHALL BE CREATED
	1727	ask_for_make_depository=false
	1728	if [[ $create_remote_batch_job = true ]]
	1729	then
	1730
	1731	line=`grep %base_directory $config_file`
[2506]	1732	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1733	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]	1734
[2506]	1735	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1736	then
	1737	printf "\n\n +++ make depository \"${make_depository}\""
	1738	printf "\n on remote host not found!"
	1739	ask_for_make_depository=true
	1740	fi
[2506]	1741	rm ${host_configuration}_last_make_protokoll
[2422]	1742
	1743	else
	1744
	1745	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1746	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1747	if [[ ! -d ${make_depository} ]]
	1748	then
	1749	printf "\n\n +++ make depository \"${make_depository}\""
	1750	printf "\n on local host not found!"
	1751	ask_for_make_depository=true
	1752	fi
	1753
	1754	fi
	1755
	1756	if [[ $ask_for_make_depository = true ]]
	1757	then
	1758
	1759	antwort=dummy
	1760	printf "\n\n"
	1761	printf " >>> Create a new one (y/n) ? "
	1762	while read antwort
	1763	do
	1764	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1765	then
	1766	printf " >>> Create a new one (y/n) ? "
	1767	else
	1768	break
	1769	fi
	1770	done
	1771	if [[ $antwort = n \|\| $antwort = N ]]
	1772	then
	1773	locat=user_abort; (( iec = 0 )); exit
	1774	fi
	1775
[2566]	1776	if [[ $do_trace = true ]]
	1777	then
	1778	palmbuild -h $host_configuration
	1779	else
	1780	palmbuild -v -h $host_configuration
	1781	fi
[2422]	1782
	1783	if [[ $? != 0 ]]
	1784	then
	1785
	1786	# ABORT IN CASE OF COMPILATION PROBLEMS
	1787	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1788	locat=make_depository
	1789	exit
	1790	else
	1791	echo " *** now continue with creating executable and other sources"
	1792	fi
	1793
	1794	fi
	1795
[2566]	1796	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2834]	1797	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
[2380]	1798
	1799	if [[ $? != 0 ]]
	1800	then
	1801
	1802	# ABORT IN CASE OF COMPILATION PROBLEMS
	1803	printf "\n +++ error while creating executable and/or other sources"
	1804	locat=execution
[2506]	1805	rm -rf $sources_for_run_catalog
[2380]	1806	exit
	1807
	1808	else
	1809
[2566]	1810	printf " *** executable and other sources created\n"
[2506]	1811	rm -rf $sources_for_run_catalog
[2380]	1812
	1813	fi
	1814
	1815	fi
	1816
	1817
[2669]	1818	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1819	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1820	if [[ $create_remote_batch_job = true ]]
	1821	then
	1822	(( i = 0 ))
[2610]	1823	while (( i < nr_of_input_files ))
[2605]	1824	do
	1825	(( i = i + 1 ))
[2669]	1826	if [[ "${actionin[$i]}" = tr ]]
[2605]	1827	then
	1828	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1829	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1830	fi
	1831	done
	1832	if (( i > 0 ))
	1833	then
	1834	printf " *** input files have been copied to the remote host\n"
	1835	fi
	1836	fi
	1837
	1838
[2380]	1839	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1840	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1841	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1842	then
	1843
	1844	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1845	if [[ $running_in_batch_mode = false ]]
	1846	then
	1847	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1848	# FOLDER
[2566]	1849	mkdir -p $tempdir
	1850	chmod go+rx $tempdir
	1851	cd $tempdir
	1852	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1853	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1854
	1855	else
	1856
	1857	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1858	printf "\n *** running in temporary directory: $tempdir"
[2380]	1859
	1860	fi
	1861
	1862
	1863	# PROVIDE THE INPUT FILES
	1864	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1865	optional_files_missing=false
[2380]	1866	(( i = 0 ))
[2610]	1867	while (( i < nr_of_input_files ))
[2380]	1868	do
	1869	(( i = i + 1 ))
	1870	if (( i == 1 ))
	1871	then
	1872	printf "\n\n *** providing INPUT-files:\n$dashes"
	1873	fi
	1874
	1875
	1876	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1877	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1878	then
[2669]	1879	optional_files_missing=true
[2380]	1880	continue
	1881	fi
	1882
	1883	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1884	files_for_cores=false; filetype=file
	1885	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1886	then
	1887	files_for_cores=true; filetype=files
	1888	actionin[$i]=""
	1889	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1890	then
	1891	actionin[$i]=""
	1892	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1893	then
	1894	files_for_cores=true; filetype=files
	1895	actionin[$i]="ln"
	1896	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1897	then
	1898	actionin[$i]="ln"
	1899	fi
	1900
	1901	if [[ $files_for_cores = true ]]
	1902	then
	1903	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1904	else
	1905	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1906	fi
	1907
	1908	# INPUT-FILES TO BE LINKED
	1909	if [[ "${actionin[$i]}" = ln ]]
	1910	then
	1911
	1912	printf "\n $filetype will be linked"
	1913	if [[ $files_for_cores = false ]]
	1914	then
	1915	if [[ -f "${absnamein[$i]}" ]]
	1916	then
	1917	ln ${absnamein[$i]} ${localin[$i]}
	1918	got_tmp[$i]=true
	1919	fi
	1920	else
	1921	if [[ -d "${absnamein[$i]}" ]]
	1922	then
[2396]	1923	mkdir -p ${localin[$i]}
[2380]	1924	cd ${absnamein[$i]}
	1925	for file in $(ls *)
	1926	do
[2566]	1927	ln $file $tempdir/${localin[$i]}
[2380]	1928	done >\|/dev/null 2>&1
[2566]	1929	cd $tempdir
[2380]	1930	fi
	1931
	1932	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1933	if [[ ! -f "${localin[$i]}/_000000" ]]
	1934	then
	1935	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1936	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1937	fi
	1938
	1939	got_tmp[$i]=true
	1940	fi
	1941	fi
	1942
	1943	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	1944	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	1945	then
	1946
	1947	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1948	then
	1949
	1950	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1951	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1952	printf "\n file will be provided for $cores processors"
[2396]	1953	mkdir -p ${localin[$i]}
[2380]	1954	ival=$cores
	1955	(( ii = 0 ))
	1956	while (( ii <= ival-1 ))
	1957	do
	1958	if (( ii < 10 ))
	1959	then
	1960	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1961	elif (( ii < 100 ))
	1962	then
	1963	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1964	elif (( ii < 1000 ))
	1965	then
	1966	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1967	else
	1968	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1969	fi
	1970	(( ii = ii + 1 ))
	1971	done
	1972
	1973	else
	1974
	1975	if [[ $files_for_cores = true ]]
	1976	then
	1977
	1978	# PROVIDE FILES FOR EACH CORE
	1979	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1980	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1981	printf "\n providing $cores files for the respective cores"
[2396]	1982	mkdir -p ${localin[$i]}
[2380]	1983	if [[ $link_local_input = true ]]
	1984	then
	1985	printf " files will be linked\n"
	1986	cd ${absnamein[$i]}
	1987	for file in $(ls *)
	1988	do
	1989	ln -f $file ${localin[$i]}
	1990	done
[2566]	1991	cd $tempdir
[2380]	1992	fi
	1993
	1994	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1995	if [[ ! -f "${localin[$i]}/_000000" ]]
	1996	then
	1997	if [[ $link_local_input = true ]]
	1998	then
	1999	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2000	fi
	2001	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2002	fi
	2003
	2004	else
	2005
	2006	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2007	if [[ $link_local_input = true ]]
	2008	then
	2009	printf " file will be linked\n"
	2010	ln -f ${absnamein[$i]} ${localin[$i]}
	2011	fi
[2605]	2012	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2013	if [[ ! -f "${localin[$i]}" ]]
	2014	then
	2015	if [[ $link_local_input = true ]]
	2016	then
	2017	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2018	fi
[2669]	2019	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2020	then
	2021	mv ${absnamein[$i]} ${localin[$i]}
	2022	else
	2023	cp ${absnamein[$i]} ${localin[$i]}
	2024	fi
[2380]	2025	fi
	2026	fi
	2027	fi
	2028	fi
	2029
	2030	done
	2031	if (( i != 0 ))
	2032	then
[2669]	2033	if [[ $optional_files_missing = true ]]
	2034	then
	2035	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2036	fi
[2380]	2037	printf "\n$dashes\n *** all INPUT-files provided \n"
	2038	fi
	2039
	2040
	2041	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2042	(( i = 0 ))
	2043	while (( i < iic ))
	2044	do
	2045	(( i = i + 1 ))
	2046	if (( i == 1 ))
	2047	then
	2048	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2049	fi
	2050	printf "\n >>> ${in_command[$i]}"
	2051	eval ${in_command[$i]}
	2052	if (( i == iic ))
	2053	then
	2054	printf "\n$dashes\n"
	2055	fi
	2056	done
	2057
	2058
	2059	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2060	# (FILE ENVPAR WILL BE READ BY PALM)
	2061	cat > ENVPAR << EOF
[2834]	2062	&envpar run_identifier = '$jobname', host = '$host_configuration',
[2380]	2063	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	2064	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2065	maximum_cpu_time_allowed = ${cpumax}.,
	2066	revision = '$global_revision',
	2067	batch_job = .${running_in_batch_mode}. /
	2068
	2069	EOF
	2070
	2071
	2072	# STARTING THE EXECUTABLE
	2073	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2074	PATH=$PATH:$tempdir
[2380]	2075
	2076
	2077	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2078	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2079	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2080	eval line=\"$line\"
	2081	execute_command="$line"
	2082
	2083
	2084	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2085	if [[ "$execute_command_for_combine" = "" ]]
	2086	then
	2087	eval line2=\"$line2\"
	2088	execute_command_for_combine="$line2"
	2089	fi
	2090
[2380]	2091
	2092
	2093	# PROVIDE A HOSTFILE, IF REQUIRED
	2094	if [[ "$hostfile" != "" ]]
	2095	then
	2096
	2097	if [[ $hostfile = auto ]]
	2098	then
	2099	# CREATE A NEW HOSTFILE
	2100	(( ii = 1 ))
	2101	while (( ii <= cores / threads_per_task ))
	2102	do
	2103	echo $(hostname) >> hostfile
	2104	(( ii = ii + 1 ))
	2105	done
	2106	if (( cores / threads_per_task == 0 ))
	2107	then
	2108	echo $(hostname) >> hostfile
	2109	fi
	2110
	2111	else
	2112	cp $hostfile hostfile
	2113	fi
	2114	eval line=\"`head -n $ii hostfile`\"
	2115	printf "\n *** running on: $line"
	2116	fi
	2117
	2118
	2119
	2120	# SET THE NUMBER OF OPENMP-THREADS
	2121	if [[ $use_openmp = true ]]
	2122	then
	2123	export OMP_NUM_THREADS=$threads_per_task
	2124	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2125	else
	2126	export OMP_NUM_THREADS=1
	2127	fi
	2128
	2129
[2610]	2130	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2131	if [[ $run_coupled_model = false ]]
	2132	then
	2133	if [[ "$ocean_file_appendix" = true ]]
	2134	then
	2135	echo "precursor_ocean" > coupling_steering
	2136	else
	2137	echo "precursor_atmos" > coupling_steering
	2138	fi
	2139	else
	2140	(( iia = $cores_atmos / $threads_per_task ))
	2141	(( iio = $cores_ocean / $threads_per_task ))
	2142	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2143	printf "\n\n"
	2144	echo "coupled_run $iia $iio" > coupling_steering
	2145	fi
	2146
	2147	printf "\n *** execute command:"
	2148	printf "\n \"$execute_command\" \n\n"
	2149
	2150	$execute_command < coupling_steering
	2151
	2152	if [[ $? != 0 ]]
	2153	then
	2154
	2155	# ABORT IN CASE OF RUNTIME ERRORS
	2156	printf "\n +++ runtime error occured"
	2157	locat=execution
	2158	exit
	2159
	2160	else
	2161
	2162	printf "\n$dashes\n *** execution finished \n"
	2163
	2164	fi
	2165
	2166
	2167	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2168	# BY EACH CORE INTO ONE FILE
	2169	if [[ ! -f combine_plot_fields.x ]]
	2170	then
	2171
	2172	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2173	printf "\n 2d- and/or 3d-data may be incomplete!"
	2174	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2175
	2176	elif [[ "$combine_plot_fields" == true ]]
	2177	then
	2178
	2179	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2180	$execute_command_for_combine
	2181
	2182	else
	2183
	2184	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2185	# DATA OUTPUT
[2380]	2186	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2187	fi
	2188
	2189
	2190
	2191	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2192	(( i = 0 ))
	2193	while (( i < ioc ))
	2194	do
	2195	(( i = i + 1 ))
	2196	if (( i == 1 ))
	2197	then
	2198	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2199	fi
[2799]	2200
	2201	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2202	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2203
[2380]	2204	printf "\n >>> ${out_command[$i]}"
	2205	eval ${out_command[$i]}
	2206	if (( i == ioc ))
	2207	then
	2208	printf "\n$dashes\n"
	2209	fi
	2210	done
	2211
	2212
[2610]	2213	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2214	# WILDCARDS
[2380]	2215	(( i = 0 ))
[2610]	2216	(( nr_of_output_files = 0 ))
	2217
[2380]	2218	while (( i < iout ))
	2219	do
[2610]	2220
[2380]	2221	(( i = i + 1 ))
[2610]	2222
	2223	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2224	# CREATE A LIST FOR THE DETECTED ENDINGS
	2225	if [[ "${multout[$i]}" = true ]]
	2226	then
	2227	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2228	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2229	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2230
	2231	endings="DEFAULT"
	2232	while read line
	2233	do
	2234	# remove the local name from the beginning
	2235	localnamestring="${localout_pre[$i]}"
	2236	length_localname=${#localnamestring}
	2237	ending=${line:${length_localname}}
	2238
	2239	if [[ "$ending" != "" ]]
	2240	then
	2241	endings="$endings $ending"
	2242	fi
	2243
	2244	done <filelist
	2245
	2246	rm filelist
	2247
	2248	else
	2249
	2250	# SINGLE NAME
	2251	endings=DEFAULT
	2252
	2253	fi
	2254
	2255	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2256	for ending in $endings
	2257	do
	2258
	2259	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2260	if [[ $ending = DEFAULT ]]
	2261	then
	2262	ending=""
	2263	fi
	2264
	2265	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2266	(( nr_of_output_files = nr_of_output_files + 1 ))
	2267	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2268	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2269	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2270	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2271	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2272	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2273	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2274
	2275	done
	2276
	2277	done
	2278
	2279
	2280
	2281
	2282	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2283	(( i = 0 ))
	2284	while (( i < nr_of_output_files ))
	2285	do
	2286	(( i = i + 1 ))
[2380]	2287	if (( i == 1 ))
	2288	then
	2289	printf "\n\n *** saving OUTPUT-files:"
	2290
	2291	# GET RUN NUMBER ASSIGNED BY PALM
	2292	if [[ -f RUN_NUMBER ]]
	2293	then
	2294	read run_number < RUN_NUMBER
	2295	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2296	usecycle_option="-U $run_number"
	2297	else
	2298	run_number=0
	2299	usecycle_option=""
	2300	fi
	2301	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2302	then
[2404]	2303	printf "\n *** in case of SCP transfers to local host"
	2304	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2305	fi
	2306	printf "\n$dashes"
	2307	fi
	2308
	2309	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2310	then
	2311
[2834]	2312	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
[2610]	2313
	2314	# DETERMINE THE CYCLE NUMBER
	2315	ls -1 -d $filename > filelist 2>/dev/null
	2316	ls -1 -d $filename.* >> filelist 2>/dev/null
	2317	while read line
	2318	do
	2319
	2320	# filename without path (i.e. after the last "/")
	2321	basefilename=$(basename ${line})
	2322
	2323	# check if there is an extension
	2324	extension=${basefilename##*.}
	2325	if [[ "$extension" = "${extout[$i]}" ]]
	2326	then
	2327	basefilename=${basefilename%.*}
	2328	fi
	2329
	2330	# check for an existing cycle number
	2331	cycle=${basefilename##*.}
	2332	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2333	then
[2669]	2334	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2335	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2336	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2337	else
	2338	(( icycle = 1 ))
	2339	fi
	2340
	2341	if (( icycle > maxcycle ))
	2342	then
	2343	(( maxcycle = icycle ))
	2344	fi
	2345
	2346	done <filelist
	2347	rm filelist
	2348
	2349
	2350	# SET THE CYCLE NUMBER
	2351	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2352	if [[ "${actionout[$i]}" = a ]]
	2353	then
	2354	(( maxcycle = maxcycle - 1 ))
	2355	fi
	2356
	2357	(( cycnum[$i] = maxcycle ))
	2358	pathout[$i]=$filename
	2359
	2360
	2361	# ADD CYCLE NUMBER TO FILENAME
	2362	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2363	if [[ "${actionout[$i]}" != "a" ]]
	2364	then
	2365	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2366	# WITH AN EXISTING CYCLE NUMBER
	2367	if (( run_number >= cycnum[$i] ))
	2368	then
	2369	(( cycnum[$i] = run_number ))
	2370	else
	2371	if (( run_number > 0 ))
	2372	then
	2373	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2374	fi
	2375	fi
	2376	fi
	2377	if (( cycnum[$i] > 0 ))
	2378	then
[2600]	2379	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2380	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2381	fi
	2382	fi
	2383
	2384	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2385	files_for_cores=false; filetype=file
	2386	link_local_output=false
	2387	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2388	then
	2389	files_for_cores=true; filetype=directory
	2390	actionout[$i]=""
	2391	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2392	then
	2393	actionout[$i]=""
	2394	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2395	then
	2396	files_for_cores=true; filetype=directory
	2397	link_local_output=true
	2398	actionout[$i]=""
	2399	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2400	then
	2401	link_local_output
	2402	actionout[$i]=""
	2403	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2404	then
	2405	files_for_cores=true; filetype=directory
	2406	actionout[$i]="tr"
	2407	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2408	then
	2409	actionout[$i]="tr"
	2410	fi
	2411
	2412	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2413	then
[2669]	2414	if [[ ${warnout[$i]} = true ]]
	2415	then
	2416	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2417	fi
[2380]	2418	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2419	then
[2669]	2420	if [[ ${warnout[$i]} = true ]]
	2421	then
	2422	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2423	fi
[2380]	2424	else
	2425
	2426
	2427	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2428	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2429	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2430	then
	2431	if [[ $running_on_remote = true ]]
	2432	then
	2433
	2434	# SET OPTIONS FOR TRANSFER
	2435	if [[ "${actionout[$i]}" = tr ]]
	2436	then
	2437	if [[ $files_for_cores = false ]]
	2438	then
	2439	catalog_option=""
	2440	catalog_string=""
	2441	else
	2442	catalog_option="-c"
	2443	catalog_string="/"
	2444	fi
	2445	append_option=""
	2446	append_string=""
	2447	else
	2448	append_option="-A"
	2449	append_string="append"
	2450	fi
	2451
	2452	transfer_failed=false
	2453	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2834]	2454	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
[2380]	2455
	2456	# TRANSFER VIA SCP
	2457	if [[ "$remote_loginnode" != "" ]]
	2458	then
[2834]	2459	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]	2460	else
[2834]	2461	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]	2462	fi
	2463	[[ $? != 0 ]] && transfer_failed=true
	2464
	2465
	2466	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2467	if [[ $transfer_failed = true ]]
	2468	then
	2469	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2834]	2470	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
[2380]	2471
	2472	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2473	eval local_catalog=${pathout[$i]}
	2474	if [[ ! -d $local_catalog ]]
	2475	then
	2476	printf " *** local directory does not exist. Trying to create:\n"
	2477	printf " $local_catalog \n"
	2478	mkdir -p $local_catalog
	2479	fi
[2834]	2480	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
[2380]	2481	transfer_problems=true
	2482	fi
	2483
	2484	else
	2485
	2486	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2487	# BE COPIED OR APPENDED ON THIS MACHINE
	2488	if [[ "${actionout[$i]}" = tr ]]
	2489	then
	2490	actionout[$i]=""
	2491	else
	2492	actionout[$i]="a"
	2493	fi
	2494	fi
	2495	fi
	2496
	2497
	2498	# APPEND ON THIS MACHINE
	2499	if [[ "${actionout[$i]}" = "a" ]]
	2500	then
	2501	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2502	then
	2503	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2504	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2505	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2506	else
	2507	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2508	printf "\n ${pathout[$i]}\n"
	2509	cat ${localout[$i]} >> ${pathout[$i]}
	2510	fi
	2511	fi
	2512
	2513	# COPY ON THIS MACHINE
	2514	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2515	# ON DIFFERENT FILE-SYSTEMS
	2516	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2517	then
	2518
	2519	# COPY IN CASE OF RUNS ON SINGLE CORES
	2520	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2521	then
	2522	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2523	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2524	if [[ $link_local_output = true ]]
	2525	then
	2526	printf " file will be linked\n"
	2527	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2528	fi
	2529	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2530	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2531	then
	2532	if [[ $link_local_output = true ]]
	2533	then
	2534	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2535	fi
	2536	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2537	else
	2538	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2539	fi
	2540	else
	2541	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2542	printf "\n ${pathout[$i]}\n"
	2543	if [[ $link_local_output = true ]]
	2544	then
	2545	printf " file will be linked\n"
	2546	ln -f ${localout[$i]} ${pathout[$i]}
	2547	fi
	2548	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2549	if [[ ! -f "${pathout[$i]}" ]]
	2550	then
	2551	if [[ $link_local_output = true ]]
	2552	then
	2553	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2554	fi
	2555	cp ${localout[$i]} ${pathout[$i]}
	2556	else
	2557	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2558	fi
	2559	fi
	2560
	2561	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2562	then
	2563
	2564	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2565	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2566	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2567	printf "\n ${pathout[$i]}\n"
	2568	if [[ $link_local_output = true ]]
	2569	then
	2570	printf " files will be linked\n"
[2396]	2571	mkdir -p ${pathout[$i]}
[2380]	2572	cd ${localout[$i]}
	2573	for file in $(ls *)
	2574	do
	2575	ln -f $file ${pathout[$i]}
	2576	done >\|/dev/null 2>&1
[2566]	2577	cd $tempdir
[2380]	2578	fi
	2579
	2580	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2581	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2582	then
	2583	if [[ $link_local_output = true ]]
	2584	then
	2585	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2586	fi
	2587	cp -r ${localout[$i]}/* ${pathout[$i]}
	2588	fi
	2589
	2590	fi
	2591	fi
	2592	done
	2593
	2594	if (( i != 0 ))
	2595	then
	2596	if [[ $transfer_problems = true ]]
	2597	then
	2598	printf "\n$dashes\n *** OUTPUT-files saved"
	2599	printf "\n +++ WARNING: some data transfers failed! \n"
	2600	else
	2601	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2602	fi
	2603	fi
	2604
	2605
	2606	# IF REQUIRED, START A RESTART-JOB
	2607	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2608	if [[ -f CONTINUE_RUN ]]
	2609	then
	2610
	2611	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2612	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2613	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2614	# -b START A BATCH JOB
	2615	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2616	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2617	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2618
	2619
	2620	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2621	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2622	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2623	then
[2381]	2624	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2625	fi
	2626
	2627
	2628	# START THE RESTART-JOB
	2629	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2630	echo " $prc"
	2631	printf "\n$dashes\n"
	2632	if [[ $running_on_remote = true ]]
	2633	then
	2634
	2635	echo "*** ssh will be used to initiate restart-runs!"
	2636	echo " return_address=\"$return_address\" "
	2637	echo " return_username=\"$local_username\" "
	2638
	2639	if [[ "$remote_loginnode" != "" ]]
	2640	then
[2420]	2641	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]	2642	else
[2420]	2643	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2644	fi
	2645
	2646	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2647	sleep 30
	2648
	2649	else
	2650
	2651	# START THE RESTART JOB ON THE LOCAL HOST
	2652	eval $prc # THE ' MUST BE EVALUATED
	2653	cd - > /dev/null
	2654
	2655	fi
	2656	printf "\n$dashes\n *** restart-run initiated \n"
	2657
	2658
	2659	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2660	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2661	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2662	# MAY BE VERY HUGE)
	2663	(( i = 0 ))
[2610]	2664	while (( i < nr_of_input_files ))
[2380]	2665	do
	2666	(( i = i + 1 ))
	2667	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2668	then
	2669	rm -r ${absnamein[$i]}
	2670	fi
	2671	done
	2672
	2673	fi
	2674
	2675
	2676	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2677	cd $HOME
[2566]	2678	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2679
	2680
	2681	else
	2682
	2683
	2684	# PREPARING ACTIONS,
	2685	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2686
	2687	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2834]	2688	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2689	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2690	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2691	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2692	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2693	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2694	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2695	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2696	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2697	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2698	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2699	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2700	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2701	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2702	if [[ $create_remote_batch_job = true ]]
	2703	then
	2704	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2705	if [[ $do_trace = true ]]
	2706	then
	2707	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2708	fi
[2380]	2709	elif [[ $create_batch_job = true ]]
	2710	then
	2711	palmrun_com=${palmrun_com}" -j"
[2420]	2712	if [[ $do_trace = true ]]
	2713	then
	2714	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2715	fi
[2380]	2716	fi
	2717
	2718
	2719	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2720	# REMOTE HOST
[2506]	2721	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2722	job_protocol_file=$job_protocol_file_local
	2723	if [[ $create_remote_batch_job = true ]]
	2724	then
[2506]	2725	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2726	job_protocol_file=$job_protocol_file_remote
	2727	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2728	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2729	fi
	2730
	2731
	2732	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2733	jobfile=jobfile.$run_id
	2734
	2735
	2736	# FIRST CREATE THE BATCH DIRECTIVES
	2737	(( i = 0 ))
	2738	while (( i < ibd ))
	2739	do
	2740	(( i = i + 1 ))
[2693]	2741	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2742	eval line=\"$line\"
	2743	echo "$line" >> $jobfile
	2744	done
	2745	echo " " >> $jobfile
	2746
	2747
	2748	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2749	# PROTOCOL
	2750	if [[ $create_remote_batch_job = true ]]
	2751	then
	2752	echo "set +vx" >> $jobfile
	2753	echo "trap '" >> $jobfile
	2754	echo "set +vx" >> $jobfile
	2755	echo "cd ${remote_jobcatalog}" >> $jobfile
	2756	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2757
	2758	# ADD THE BATCH DIRECTIVES
	2759	(( i = 0 ))
	2760	while (( i < ibdt ))
	2761	do
	2762	(( i = i + 1 ))
[2693]	2763	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2764	eval line=\"$line\"
	2765	echo "$line" >> $jobfile
	2766	done
	2767	echo " " >> $jobfile
	2768
	2769	echo "set -x" >> $jobfile
[2834]	2770	echo "${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]	2771	echo "%%END%%" >> $jobfile
	2772	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2773	echo "$submit_command $scpjob_file" >> $jobfile
	2774	echo "rm $scpjob_file" >> $jobfile
[2404]	2775	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2776	echo "set -x" >> $jobfile
	2777	echo " ' exit" >> $jobfile
	2778	fi
	2779
	2780
	2781	# ACTIVATE ERROR-TRACEBACK
	2782	if [[ $do_trace = true ]]
	2783	then
	2784	echo "set -x" >> $jobfile
	2785	else
	2786	echo "set +vx" >> $jobfile
	2787	fi
	2788
	2789
	2790	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2791	if [[ "$login_init_cmd" != "" ]]
	2792	then
	2793	echo "$login_init_cmd" >> $jobfile
	2794	fi
	2795	if [[ "$module_commands" != "" ]]
	2796	then
	2797	echo "$module_commands" >> $jobfile
	2798	fi
	2799
	2800
	2801	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2802	if [[ $create_remote_batch_job = true ]]
	2803	then
	2804	echo "mkdir $tempdir" >> $jobfile
	2805	echo "chmod go+rx $tempdir" >> $jobfile
	2806	else
	2807	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2808	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2809	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2810	mkdir $tempdir
	2811	chmod go+rx $tempdir
	2812	fi
	2813	echo "cd $tempdir" >> $jobfile
	2814	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2815	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2816	echo "export PATH=.:\$PATH" >> $jobfile
	2817	echo "export execute_palmrun=true" >> $jobfile
	2818
	2819
	2820	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2821	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2822	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2823	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2824	echo "export LOCAL_PWD" >> $jobfile
	2825
	2826
	2827	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2828	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2829	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2830
	2831
	2832	# CALL PALMRUN WITHIN THE JOB
	2833	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2834	echo "set -x" >> $jobfile
	2835	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2836
	2837
	2838	# TRANSFER JOBFILE TO THE TARGET HOST
	2839	if [[ $create_jobfile_only = false ]]
	2840	then
	2841
	2842	if [[ $create_remote_batch_job = true ]]
	2843	then
	2844
[2420]	2845	echo " "
[2566]	2846	echo " *** transfer of job to remote host via scp"
[2420]	2847	if [[ $do_trace = true ]]
	2848	then
[2506]	2849	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2850	fi
[2566]	2851	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2852
[2566]	2853	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2854	if [[ $do_trace = true ]]
	2855	then
[2506]	2856	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]	2857	fi
[2506]	2858	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]	2859
	2860	elif [[ $create_batch_job = true ]]
	2861	then
	2862
[2385]	2863	eval local_jobcatalog=$local_jobcatalog
[2506]	2864	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2865	cd $local_jobcatalog
[2380]	2866	echo " "
[2420]	2867	echo " *** submit the job"
	2868	if [[ $do_trace = true ]]
	2869	then
[2506]	2870	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2871	fi
[2506]	2872	$submit_command ${host_configuration}_${job_id}
	2873	rm ${host_configuration}_${job_id}
[2380]	2874	cd - > /dev/null
	2875
	2876	fi
	2877
	2878	rm -rf $jobfile
	2879
	2880	else
	2881
	2882	printf "\n *** jobfile created under name \"$jobfile\" "
	2883	printf "\n no batch-job has been sent!"
	2884
	2885	fi
	2886
	2887	fi # END OF REMOTE-PART

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