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source: palm/trunk/SCRIPTS/palmrun @ 2699

Last change on this file since 2699 was 2696, checked in by kanani, 7 years ago
Merge of branch palm4u into trunk
Property svn:executable set to ``* Property svn:keywords set to `Id`
File size: 94.7 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	#
[2696]	19	# Copyright 2017-2017 Leibniz Universitaet Hannover
[2380]	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
	23	# ------------------
	24	#
[2410]	25	#
[2380]	26	# Former revisions:
	27	# -----------------
	28	# $Id: palmrun 2696 2017-12-14 17:12:51Z kanani $
[2693]	29	# replacement of variables given by {{<variable>}} in configuration file is now
	30	# done in a more general way, variable names are written in small letters
	31	#
	32	# 2670 2017-12-06 16:32:19Z raasch
[2670]	33	# test printouts removed
	34	#
	35	# 2669 2017-12-06 16:03:27Z raasch
[2669]	36	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	37	# removed,
	38	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	39	# files,
	40	# informative messages in case of missing optional input files shortened
	41	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	42	#
	43	# 2638 2017-11-23 12:44:23Z raasch
[2610]	44	# use of wildcards in file connection statements enabled
	45	#
	46	# 2605 2017-11-09 15:31:46Z raasch
[2605]	47	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	48	# will not be sent with the job file any more, but copied into the
[2610]	49	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	50	#
	51	# 2600 2017-11-01 14:11:20Z raasch
[2600]	52	# cycle numbers are made three digits wide
	53	#
	54	# 2566 2017-10-20 08:50:47Z raasch
[2566]	55	# execute command for combine_plot_fields added
	56	# "TEMPDIR" renamed "tempdir"
	57	# temporary working directory for local batch jobs is created immediately within
	58	# the user's palmrun call, due to a requirement of the "grid engine" batch
	59	# system, where the working directory is given with batch directive -wd and must
	60	# already exist when the job is submitted,
	61	# informative messages in non-trace mode reduced and partly reformatted
	62	#
	63	# 2551 2017-10-18 07:25:11Z raasch
[2551]	64	# TEMPDIR added as replacement string to be used in batch directives
	65	#
	66	# 2512 2017-10-04 08:26:59Z raasch
[2507]	67	# bugfix for determining cycle numbers of NetCDF input files
	68	#
	69	# 2506 2017-09-29 08:30:37Z raasch
[2506]	70	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	71	# host configuration added to SOURCES_FOR_RUN_... folder name
	72	# host_identifier renamed host_configuration
	73	# option -W added to allow for job dependencies
	74	#
	75	# 2501 2017-09-26 11:41:55Z raasch
[2501]	76	# default value for number of cores (option -X) set to 1
	77	# bugfix for mechanism which overwrites configuration file settings with values
	78	# provided by palmrun options
	79	#
	80	# 2499 2017-09-22 16:47:58Z kanani
[2499]	81	# option -h named configuration identifier
	82	#
	83	# 2480 2017-09-19 06:24:14Z maronga
[2480]	84	# bugfix for last revision
	85	#
	86	# 2479 2017-09-19 06:12:16Z raasch
[2479]	87	# option -A (project account number) added
	88	#
	89	# 2422 2017-09-08 08:25:41Z raasch
[2410]	90	# initial revision
[2380]	91	#
	92	#--------------------------------------------------------------------------------#
	93	# palmrun - script for running PALM jobs on local and remote hosts
	94	#--------------------------------------------------------------------------------#
	95
	96
	97
	98	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	99
	100	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	101	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	102	# (TOO MANY ARGUMENTS - PROBLEM)
	103	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	104
[2610]	105	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	106	typeset -i nr_of_output_files=0
[2380]	107	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	108	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	109	# SCRIPT-OPTION ARGUMENTS
	110	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	111	typeset -i icycle inode ival maxcycle mpi_tasks
	112	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	113
	114	activation_string_list=""
	115	AddFilenames=""
	116	combine_plot_fields=true
	117	compiler_name=""
	118	compiler_name_ser=""
	119	compiler_options=""
[2501]	120	cores=1
[2380]	121	cores_atmos=0
	122	cores_ocean=0
	123	coupled_dist=""
	124	cpp_options=""
	125	cpumax=0
[2506]	126	create_batch_job=false
[2380]	127	create_jobfile_only=false
	128	create_remote_batch_job=false
	129	dashes=" ----------------------------------------------------------------------------"
	130	defaultqueue=""
[2506]	131	delete_temporary_catalog=true
[2380]	132	do_compile=true
	133	do_trace=false
	134	executable=""
	135	execute_command=""
	136	execution_error=false
	137	fileconnection_file=.palm.iofiles
	138	fname=test
	139	global_revision=""
[2506]	140	host_configuration="default"
[2380]	141	hostfile=""
	142	hp=""
	143	keep_data_from_previous_run=false
	144	link_local_input=false
	145	link_local_output=false
[2388]	146	linker_options=""
[2385]	147	local_jobcatalog=""
[2380]	148	locat=normal
	149	makefile=""
	150	max_par_io_str=""
	151	prc=$0
	152	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	153	do
	154	prc=`echo $prc \| cut -f2- -d"/"`
	155	done
	156	module_calls=""
[2506]	157	palmrun_memory=""
[2380]	158	palmrun_script_name=$prc
	159	openmp=false
[2506]	160	previous_job=""
[2479]	161	project_account=""
[2380]	162	queue=none
	163	restart_run=false
	164	return_address=""
[2385]	165	remote_jobcatalog=""
[2380]	166	remote_username=""
	167	running_in_batch_mode=false
	168	run_coupled_model=false
	169	run_id=""
	170	silent=false
	171	source_list=""
	172	source_path=""
[2501]	173	tasks_per_node=0
[2380]	174	threads_per_task=1
	175	transfer_problems=false
[2384]	176	user_source_path=""
[2506]	177	use_existing_sources_folder=""
[2380]	178	use_openmp=false
[2422]	179	version="palmrun 1.0 Rev$Rev: 2303 $"
[2380]	180	working_directory=`pwd`
	181	write_binary=""
	182	TOPT=""
	183
	184
	185	# ERROR HANDLING IN CASE OF EXIT
[2404]	186	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	187	then
	188
	189	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	190	(( i = 0 ))
	191	while (( i < iec ))
	192	do
	193	(( i = i + 1 ))
	194	printf "\n *** Execution of ERROR-command:\n"
	195	printf " >>> ${err_command[$i]}\n"
	196	eval ${err_command[$i]}
	197	done
[2566]	198	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	199	printf "\n\n+++ palmrun killed \n\n"
	200	elif [[ $locat != control_c ]]
	201	then
[2566]	202	printf "\n --> palmrun finished\n\n"
[2380]	203	fi' exit
	204
	205
	206	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	207	trap 'cd; rm -rf $tempdir
[2380]	208	printf "\n+++ palmrun killed by \"^C\" \n\n"
	209	locat=control_c
	210	exit
	211	' 2
	212
	213
	214	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	215	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	216	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]	217	do
	218	case $option in
	219	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	220	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	221	(b) create_batch_job=true; prc="$prc -b";;
	222	(B) delete_temporary_catalog=false; prc="$prc -B";;
	223	(C) restart_run=true; prc="$prc -C";;
	224	(d) fname=$OPTARG; prc="$prc -d$OPTARG";;
	225	(F) create_jobfile_only=true;;
	226	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	227	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	228	(j) running_in_batch_mode=true;;
	229	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	230	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	231	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	232	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	233	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	234	(r) run_id=$OPTARG;;
	235	(R) return_address=$OPTARG;;
	236	(s) source_list=$OPTARG;;
[2501]	237	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	238	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	239	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	240	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	241	(v) silent=true; prc="$prc -v";;
[2506]	242	(V) use_existing_sources_folder="-V";;
[2380]	243	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	244	(W) previous_job=$OPTARG;;
[2380]	245	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	246	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	247	(y) ocean_file_appendix=true; prc="$prc -y";;
	248	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	249	(Z) combine_plot_fields=false; prc="$prc -Z";;
	250	(\?) printf "\n +++ unknown option $OPTARG \n"
	251	printf "\n --> type \"$0 ?\" for available options \n"
	252	locat=parameter;exit;;
	253	esac
	254	done
	255
	256
	257	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	258	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	259	(( to_shift = $OPTIND - 1 ))
	260	shift $to_shift
	261
	262	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	263	if [[ "$1" = "?" ]]
	264	then
	265	(printf "\n *** Description of available palmrun options:\n"
	266	printf "\n Option Description Default-Value"
	267	printf "\n -a activation string list \"\" "
[2479]	268	printf "\n -A project account number ---"
[2380]	269	printf "\n -b batch-job on local machine ---"
	270	printf "\n -B do not delete temporary directory at end ---"
	271	printf "\n -d base name of files attached to program test"
	272	printf "\n -F create batch job file only ---"
[2506]	273	printf "\n -h host configuration \"default\" "
[2380]	274	printf "\n -k keep data from previous run"
	275	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	276	printf "\n -M Makefile name Makefile"
	277	printf "\n -O threads per openMP task ---"
	278	printf "\n -q queue \"$queue\" "
	279	printf "\n -s filenames of routines to be compiled \"\" "
	280	printf "\n must end with .f, .f90, .F, or .c !"
	281	printf "\n use \"..\" for more than one file and wildcards"
	282	printf "\n -s LM compiles all locally modified files"
	283	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	284	printf "\n -T tasks per node ---"
[2380]	285	printf "\n -u username on remote machine \"\" "
	286	printf "\n -v no prompt for confirmation ---"
[2506]	287	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	288	printf "\n -w maximum parallel io streams as given by -X"
[2506]	289	printf "\n -W name of job to wait for ---"
[2380]	290	printf "\n -x tracing of palmrun for debug purposes ---"
	291	printf "\n -X # of processors (on parallel machines) 1"
	292	printf "\n -y add appendix \"_O\" to all local output"
	293	printf "\n files (ocean precursor runs followed by"
	294	printf "\n coupled atmosphere-ocean runs) ---"
	295	printf "\n -Y run coupled model, \"#1 #2\" with"
	296	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	297	printf "\n -Z skip combine_plot_fields at the end of "
	298	printf "\n the simulation ---"
	299	printf "\n "
	300	printf "\n Possible values of positional parameter <modus>:"
	301	printf "\n \"?\" - this outline \n\n") \| more
	302	exit
	303	elif [[ "$1" != "" ]]
	304	then
	305	printf "\n +++ positional parameter $1 unknown \n"
	306	locat=parameter; exit
	307	fi
	308
	309
	310
	311	# SHORT STARTING MESSAGE
	312	printf "\n*** $version "
	313	printf "\n will be executed. Please wait ..."
	314
	315
[2506]	316	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	317	config_file=.palm.config.$host_configuration
	318	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$fname
[2380]	319
	320
	321	# CHECK, IF CONFIGURATION FILE EXISTS
	322	if [[ ! -f $config_file ]]
	323	then
	324	printf "\n\n +++ configuration file: "
	325	printf "\n $config_file"
	326	printf "\n does not exist"
	327	locat=connect; exit
	328	fi
	329
	330
	331	# CHECK, IF FILE CONNECTION FILE EXISTS
	332	if [[ ! -f $fileconnection_file ]]
	333	then
	334	printf "\n\n +++ file connection file: "
	335	printf "\n $fileconnection_file"
	336	printf "\n does not exist"
	337	locat=connect; exit
	338	fi
	339
	340
[2404]	341	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	342	if [[ "$activation_string_list" = "" ]]
	343	then
	344	printf "\n\n +++ no activation string list given: "
	345	printf "\n please set palmrun option \"-a\" "
	346	locat=palmrun_option; exit
	347	fi
	348
	349
	350	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	351	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	352	then
	353	write_binary=true
	354	else
	355	write_binary=false
	356	fi
	357
	358
[2380]	359	# READ AND EVALUATE THE CONFIGURATION-FILE
	360	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	361
	362	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	363	while read line
	364	do
	365
	366	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	367	eval line=\"$line\"
	368
	369
	370	# INTERPRET THE LINE
	371	if [[ "$(echo $line)" = "" ]]
	372	then
	373
	374	# EMPTY LINE, NO ACTION
	375	continue
	376
	377	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	378	then
	379
	380	# LINE IS A COMMENT LINE
	381	continue
	382
	383	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	384	then
	385
	386	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	387	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	388	value=`echo $line \| cut -d" " -s -f2-`
	389
	390
	391	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	392	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	393	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	394	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	395	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	396	# CONFIGURATION-FILE.
	397	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	398	then
	399	eval export $var="\$value"
	400
	401	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	402	if [[ $do_trace = true ]]
	403	then
	404	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	405	fi
	406	fi
	407
	408	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	409	then
	410
	411	# LINE DEFINES BATCH-DIRECTIVE
	412	(( ibd = ibd + 1 ))
	413	line=$(echo $line \| cut -c4-)
	414	batch_directive[$ibd]="$line"
	415
	416	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	417	then
	418
	419	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	420	# REMOTE TO A LOCAL HOST
	421	(( ibdt = ibdt + 1 ))
	422	line=$(echo $line \| cut -c5-)
	423	batch_directive_transfer[$ibdt]="$line"
	424
	425	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	426	then
	427
	428	# LINE DEFINES ERROR-COMMAND
	429	(( iec = iec + 1 ))
	430	line=$(echo $line \| cut -c4-)
	431	err_command[$iec]="$line"
	432
	433	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	434	then
	435
	436	# LINE DEFINES INPUT-COMMAND
	437	(( iic = iic + 1 ))
	438	line=$(echo $line \| cut -c4-)
	439	in_command[$iic]="$line"
	440
	441	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	442	then
	443
	444	# LINE DEFINES OUTPUT-COMMAND
	445	(( ioc = ioc + 1 ))
	446	line=$(echo $line \| cut -c4-)
	447	out_command[$ioc]="$line"
	448
	449	else
	450
	451	# SKIP ALL OTHER LINES
	452	continue
	453
	454	fi
	455
	456	done < $config_file
	457
	458
	459	# CHECK SETTING OF REQUIRED PARAMETERS
	460	if [[ "$compiler_name" = "" ]]
	461	then
	462	printf "\n +++ no compiler name found in $config_file"
	463	printf "\n Please add line \"compiler_name ...\" to that file."
	464	locat=config_file; exit
	465	fi
	466	if [[ "$compiler_name_ser" = "" ]]
	467	then
	468	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	469	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	470	locat=config_file; exit
	471	fi
	472	if [[ "$compiler_options" = "" ]]
	473	then
	474	printf "\n +++ no compiler options found in $config_file"
	475	printf "\n Please add line \"compiler_options ...\" to that file."
	476	locat=config_file; exit
	477	fi
[2388]	478	if [[ "$linker_options" = "" ]]
[2380]	479	then
[2388]	480	printf "\n +++ no linker options found in $config_file"
	481	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	482	locat=config_file; exit
	483	fi
	484	if [[ "$execute_command" = "" ]]
	485	then
	486	printf "\n +++ no execute command found in $config_file"
	487	printf "\n Please add line \"execute_command ...\" to that file."
	488	locat=config_file; exit
	489	fi
	490
	491	if [[ "$hostfile" != "" ]]
	492	then
	493	if [[ $hostfile != auto && ! -f $hostfile ]]
	494	then
	495	printf "\n +++ no hostfile \"$hostfile\" found"
	496	printf "\n Please check line \"hostfile ...\" in $config_file"
	497	locat=config_file; exit
	498	fi
	499	fi
	500
	501
	502	# DETERMINE THE CALL STATUS
	503	if [[ "$return_address" != "" ]]
	504	then
	505
	506	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	507	# BATCH MODE AND ...
	508	running_on_remote=true
	509
	510	else
	511
	512	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	513	if [[ "$remote_ip" != "" ]]
	514	then
	515
	516	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	517	create_remote_batch_job=true
	518
	519	fi
	520	running_on_remote=false
	521	fi
	522
	523
	524
	525	# READ AND EVALUATE THE I/O-FILE LIST
	526	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	527
	528	# READ THE FILE CONNECTION FILE LINE BY LINE
	529	while read line
	530	do
	531
[2669]	532	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	533	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	534
	535	# INTERPRET THE LINE
	536	if [[ "$(echo $line)" = "" ]]
	537	then
	538	# EMPTY LINE, NO ACTION
	539	continue
	540
	541	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	542	then
	543
	544	# LINE IS A COMMENT LINE
	545	true
	546
	547	else
	548
	549	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	550	# s2a: in/out - field
[2669]	551	# s2b: action - field (optional)
	552	s1=`echo "$line" \| cut -d" " -f1`
	553	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	554	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	555	then
[2669]	556	s2a=$s2
[2380]	557	s2b=""
	558	else
[2669]	559	s2a=`echo $s2 \| cut -d":" -f1`
	560	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	561	fi
[2669]	562	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	563	s4=`echo "$line" \| cut -d" " -s -f4`
	564	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	565	s5=`echo "$line" \| cut -d" " -s -f5`
	566	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	567
	568
	569	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	570	# INPUT- OR OUTPUT-LIST.
	571	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	572	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	573	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	574	# IS NOT CHECKED AND STORED.
[2610]	575	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	576	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	577	then
	578	found=false
	579	for actual in $activation_string_list
	580	do
	581	for formal in $s3
	582	do
	583	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	584	done
	585	done
	586	if [[ $found = true ]]
	587	then
	588	(( iin = iin + 1 ))
[2669]	589	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	590	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	591	if [[ "$s2a" = inopt ]]
	592	then
	593	optin_pre[$iin]=yes
	594	else
	595	optin_pre[$iin]=no
	596	fi
[2605]	597
	598	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	599	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	600	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	601	then
[2610]	602	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	603	fi
	604
[2610]	605	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	606	# THE WILDCARD FROM THE ENDING
	607	if [[ "${s5: -1}" = "*" ]]
	608	then
[2669]	609	if [[ "$s2b" = "di" ]]
[2610]	610	then
	611	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	612	printf "\n see file \"$fileconnection_file\", line"
	613	printf "\n$line"
	614	locat=iofiles_file; exit
	615	fi
	616	multin[$iin]=true
	617	string=${endin_pre[$iin]}
	618	endin_pre[$iin]="${string%?}"
	619	else
	620	multin[$iin]=false
	621	fi
[2380]	622	fi
[2669]	623	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	624	then
	625	found=false
	626	for actual in $activation_string_list
	627	do
	628	for formal in $s3
	629	do
[2670]	630	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	631	done
	632	done
	633	if [[ $found = true ]]
	634	then
	635	(( iout = iout + 1 ))
[2669]	636	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	637	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	638
[2669]	639	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	640	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	641	if [[ $formal = wildcard ]]
	642	then
	643	warnout_pre[$iout]=false
	644	else
	645	warnout_pre[$iout]=true
	646	fi
	647
[2610]	648	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	649	# THE WILDCARD FROM THE LOCAL FILENAME
	650	if [[ "${s1: -1}" = "*" ]]
	651	then
[2669]	652	if [[ "$s2b" = "di" ]]
[2610]	653	then
	654	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	655	printf "\n see file \"$fileconnection_file\", line"
	656	printf "\n$line"
	657	locat=iofiles_file; exit
	658	fi
	659	multout[$iout]=true
	660	string=${localout_pre[$iout]}
	661	localout_pre[$iout]="${string%?}"
	662	else
	663	multout[$iout]=false
	664	fi
[2380]	665	fi
[2669]	666	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	667	then
[2669]	668	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	669	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	670	locat=connect; exit
	671	fi
	672	IFS="$IFSALT"
	673	fi
	674
	675	done < $fileconnection_file
	676
	677
	678
[2501]	679	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[2506]	680	[[ $palmrun_memory != "" ]] && memory=$palmrun_memory
[2501]	681	[[ $palmrun_cpumax != "" ]] && cpumax=$palmrun_cpumax
	682	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
	683	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	684	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	685
	686
	687
[2380]	688	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	689	if [[ $run_coupled_model = true ]]
	690	then
	691
	692	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	693	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	694
	695	if (( $cores_ocean + $cores_atmos != $cores ))
	696	then
	697
	698	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	699	printf "\n PEs (total) : $cores"
	700	printf "\n PEs (atmosphere): $cores_atmos"
	701	printf "\n PEs (ocean) : $cores_ocean"
	702	locat=coupling; exit
	703
	704	fi
	705
	706	fi
	707
	708
	709	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	710	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	711	# FOLDER
	712	if [[ $running_in_batch_mode = true ]]
	713	then
	714
[2506]	715	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	716	then
[2506]	717	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	718	printf "\n Please check the output of the palmrun-call"
	719	printf "\n that you did on your local host."
	720	locat=SOURCES_FOR_RUN; exit
	721	fi
	722
	723	else
	724
	725	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	726	# AUTOMATIC RESTART RUN
	727	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	728	if [[ $restart_run = false ]]
	729	then
	730
	731	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	732	# THE LOCAL HOST
	733	if [[ ! -d $source_path ]]
	734	then
	735	printf "\n\n +++ source path \"$source_path\" on local host"
	736	printf "\n \"$(hostname)\" does not exist"
	737	locat=source_path; exit
	738	fi
	739
[2506]	740	rm -rf $sources_for_run_catalog
	741	mkdir -p $sources_for_run_catalog
[2380]	742
	743	if [[ "$source_list" = LM ]]
	744	then
	745
	746	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	747	source_list=""
	748	cd $source_path
	749
	750
[2512]	751	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	752	if [[ ! -d ../.svn ]]
[2380]	753	then
	754	printf "\n\n +++ source directory"
	755	printf "\n \"$source_path\" "
	756	printf "\n is not under control of \"subversion\"."
[2512]	757	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	758	fi
	759
	760
	761	# LIST ALL MODIFIED SOURCE CODE FILES
	762	Filenames=""
[2404]	763	svn status > tmp_svnstatus
[2380]	764	while read line
	765	do
	766	firstc=`echo $line \| cut -c1`
	767	if [[ $firstc = M \|\| $firstc = "?" ]]
	768	then
	769	Name=`echo "$line" \| cut -c8-`
	770	extension=`echo $Name \| cut -d. -f2`
	771	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	772	then
	773	Filenames="$Filenames "$Name
	774	fi
	775	fi
[2404]	776	done < tmp_svnstatus
	777	rm -rf tmp_svnstatus
[2380]	778
	779
	780	# COPY FILES TO SOURCES_FOR_RUN_...
	781	for filename in $Filenames
	782	do
[2506]	783	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	784	source_list=$source_list"$filename "
	785	done
	786
	787	cd - > /dev/null
	788
	789
	790	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	791	elif [[ "$source_list" != "" ]]
	792	then
	793
	794	cd $source_path
	795
	796	for filename in $source_list
	797	do
	798
	799	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	800	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	801	then
	802	printf "\n +++ source code file: $filename"
	803	printf "\n must not contain (\"/\") "
	804	locat=source; exit
	805	fi
	806
	807	if [[ ! -f $filename ]]
	808	then
	809	printf "\n +++ source code file: $filename"
	810	printf "\n does not exist"
	811	locat=source; exit
	812	else
[2506]	813	cp $filename ${working_directory}/${sources_for_run_catalog}
[2380]	814	fi
	815
	816	done
	817
	818	cd - > /dev/null
	819
	820	fi
	821
	822	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	823	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	824	if [[ ! -f $makefile ]]
	825	then
	826	printf "\n +++ file \"$makefile\" does not exist"
	827	locat=make; exit
	828	else
[2506]	829	cp $makefile ${sources_for_run_catalog}/Makefile
[2380]	830	fi
	831
	832
	833	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	834	if [[ "$user_source_path" != "" ]]
[2380]	835	then
	836
	837	# DOES THE DIRECTORY EXIST?
[2384]	838	if [[ ! -d $user_source_path ]]
[2380]	839	then
	840
	841	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	842	printf "\n \"$user_source_path\" "
[2380]	843	printf "\n does not exist or is not a directory."
	844	printf "\n No source code will be used from this directory!\n"
[2384]	845	user_source_path=""
[2380]	846	if [[ $silent == false ]]
	847	then
	848	sleep 2
	849	fi
	850
	851	else
	852
[2384]	853	cd $user_source_path
[2380]	854	found=false
	855
	856	Names=$(ls -1 *.f90 2>&1)
	857	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	858	Names=$(ls -1 *.F90 2>&1)
	859	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	860	Names=$(ls -1 *.F 2>&1)
	861	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	862	Names=$(ls -1 *.f 2>&1)
	863	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	864	Names=$(ls -1 *.c 2>&1)
	865	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	866
	867	cd - > /dev/null
[2506]	868	cd $sources_for_run_catalog
[2380]	869
	870	# COPY MAKEFILE IF EXISTING
[2384]	871	if [[ -f $user_source_path/Makefile ]]
[2380]	872	then
	873	printf "\n\n *** user Makefile from directory"
[2384]	874	printf "\n \"$user_source_path\" is used \n"
[2380]	875	if [[ $silent == false ]]
	876	then
	877	sleep 1
	878	fi
[2384]	879	cp $user_source_path/Makefile .
[2380]	880	fi
	881
	882	for filename in $AddFilenames
	883	do
	884	if [[ -f $filename ]]
	885	then
	886	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	887	printf "\n source code directory \"$user_source_path\" "
[2380]	888	printf "\n but was also given with option \"-s\" which means that it should be taken"
	889	printf "\n from directory \"$source_path\"."
	890	locat=source; exit
	891	fi
	892
[2384]	893	cp $user_source_path/$filename .
[2380]	894	source_list="$source_list $filename"
	895
	896	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	897	if [[ $(grep -c $filename Makefile) = 0 ]]
	898	then
	899	printf "\n\n +++ user file \"$filename\" "
	900	printf "\n is not listed in Makefile \n"
	901	locat=source; exit
	902	else
	903
	904	if [[ $found = false ]]
	905	then
	906	found=true
	907	printf "\n\n *** following user file(s) added to the"
	908	printf " files to be translated:\n "
	909	fi
	910	printf "$filename "
	911	if [[ $silent == false ]]
	912	then
	913	sleep 0.5
	914	fi
	915
	916	fi
	917	done
	918	[[ $found = true ]] && printf "\n"
	919	cd - > /dev/null
	920	fi
	921	fi
	922
	923	# COPY CONFIGURATION FILES
[2506]	924	cp $config_file $sources_for_run_catalog
	925	cp $fileconnection_file $sources_for_run_catalog
[2380]	926
	927	# COPY SHELLSCRIPTS
[2506]	928	cp ${source_path}/../SCRIPTS/palmrun $sources_for_run_catalog
	929	cp ${source_path}/../SCRIPTS/batch_scp $sources_for_run_catalog
[2380]	930
	931	fi
	932
	933	fi
	934
[2605]	935
[2380]	936	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	937	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	938	if [[ "$global_revision" = "" ]]
	939	then
	940	global_revision=`svnversion $source_path 2>/dev/null`
	941	global_revision="Rev: $global_revision"
	942	fi
	943
	944
	945	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	946	if [[ -n $cores ]]
	947	then
	948
	949	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	950	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	951	if [[ $tasks_per_node = 0 ]]
[2380]	952	then
	953	printf "\n"
	954	printf "\n +++ option \"-T\" (tasks per node) is missing"
	955	printf "\n set -T option or define tasks_per_node in the config file"
	956	locat=tasks_per_node; (( iec = 0 )); exit
	957	fi
	958
	959	if (( cores < tasks_per_node ))
	960	then
	961	printf "\n"
	962	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	963	printf "\n given values: -T $tasks_per_node -X $cores"
	964	locat=tasks_per_node; (( iec = 0 )); exit
	965	fi
	966
	967	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	968	(( mpi_tasks = cores / threads_per_task ))
	969	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	970	(( ii = cores / tasks_per_node ))
	971	(( remaining_cores = cores - ii * tasks_per_node ))
	972	if (( remaining_cores > 0 ))
	973	then
	974	printf "\n"
	975	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	976	printf "\n divisor of the total number of cores (option \"-X\")"
	977	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	978	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	979	(( nodes = nodes + 1 ))
	980	fi
	981
	982	# SET THE TOTAL NUMBER OF NODES, REQUIRED FOR THE SUBJOB-COMMAND (SEE FURTHER BELOW)
	983	if [[ "$tasks_per_node" != "" ]]
	984	then
	985	TOPT="-T $tasks_per_node"
	986	fi
	987
	988	fi
	989
	990
	991	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	992	if [[ "$maximum_parallel_io_streams" = "" ]]
	993	then
	994	maximum_parallel_io_streams=$cores
	995	fi
	996
	997
	998	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	999	if [[ "$scp_port" != "" ]]
	1000	then
	1001	PORTOPT="-P $scp_port"
	1002	SSH_PORTOPT="-p $scp_port"
	1003	fi
	1004
	1005
	1006	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1007	# CONFIG-FILE
	1008	if [[ "$ssh_key" != "" ]]
	1009	then
	1010	ssh_key="-i $HOME/.ssh/$ssh_key"
	1011	fi
	1012
	1013
	1014	# SET QUEUE, IF NOT GIVEN
	1015	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1016	then
	1017
	1018	if [[ $queue = none && "$defaultqueue" = "" ]]
	1019	then
	1020	printf "\n"
	1021	printf "\n +++ no default queue given in configuration file and no queue"
	1022	printf "\n given with option -q"
	1023	fi
	1024	if [[ $queue = none ]]
	1025	then
	1026	queue=$defaultqueue
	1027	fi
	1028
	1029	fi
	1030
	1031
	1032	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1033	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1034	(( i = 0 ))
[2610]	1035	(( nr_of_input_files = 0 ))
[2380]	1036	while (( i < iin ))
	1037	do
	1038	(( i = i + 1 ))
	1039
	1040	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1041	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1042	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1043	then
[2610]	1044	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1045	else
[2610]	1046	eval filename=${pathin_pre[$i]}/${fname}${endin_pre[$i]}
[2380]	1047	fi
	1048
[2610]	1049
[2380]	1050	# CHECK IF FILE EXISTS
	1051	if ! ls $filename* 1>/dev/null 2>&1
	1052	then
	1053
[2669]	1054	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1055	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1056	then
	1057	printf "\n\n +++ INPUT-file: "
[2610]	1058	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1059	then
	1060	printf "\n $filename"
	1061	else
[2610]	1062	printf "\n $filename.${extin_pre[$i]}"
[2380]	1063	fi
	1064	printf "\n does not exist\n"
	1065	locat=input; exit
	1066	else
[2610]	1067	(( nr_of_input_files = nr_of_input_files + 1 ))
	1068	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1069	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1070	actionin[$nr_of_input_files]="unavailable"
[2610]	1071	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1072	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1073	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1074	fi
[2605]	1075
[2380]	1076	else
	1077
[2610]	1078	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($fname) AND
	1079	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
	1080	if [[ "${multin[$i]}" = true ]]
	1081	then
	1082	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1083	ls -1 -d ${filename} > filelist 2>/dev/null
	1084	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1085	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1086
[2610]	1087	endings=""
	1088	while read line
	1089	do
	1090	# filename without path (i.e. after the last "/")
	1091	basefilename=$(basename ${line})
[2380]	1092
[2610]	1093	# check if there is an extension and remove it
	1094	ext=${basefilename##*.}
	1095	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1096	then
	1097	basefilename=${basefilename%.*}
	1098	fi
[2380]	1099
[2610]	1100	# check for an existing cycle number and remove it
	1101	cycle=${basefilename##*.}
	1102	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1103	then
	1104	basefilename=${basefilename%.*}
	1105	fi
[2600]	1106
[2610]	1107	# remove the fname from the beginning
	1108	length_fname=${#fname}
	1109	ending=${basefilename:${length_fname}}
	1110
	1111	# remove the ending given in the .iofiles from the beginning
	1112	endingstring="${endin_pre[$i]}"
	1113	length_ending=${#endingstring}
	1114	ending=${ending:${length_ending}}
	1115
	1116	if [[ "$ending" = "" ]]
[2600]	1117	then
[2610]	1118	# standard ending as given in the .iofiles
	1119	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1120	then
	1121	endings="$endings DEFAULT"
	1122	fi
[2600]	1123	else
[2610]	1124	# ending must start with "_", otherwise its a different file
	1125	if [[ "${ending:0:1}" = "_" ]]
	1126	then
	1127	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1128	then
	1129	endings="$endings $ending"
	1130	fi
	1131	fi
[2600]	1132	fi
[2610]	1133
	1134	done <filelist
[2380]	1135
[2610]	1136	rm filelist
[2380]	1137
[2600]	1138	else
[2610]	1139
	1140	# SINGLE NAME
	1141	endings=DEFAULT
	1142
[2600]	1143	fi
	1144
[2610]	1145	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1146	for ending in $endings
	1147	do
	1148
	1149	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1150	if [[ $ending = DEFAULT ]]
[2380]	1151	then
[2610]	1152	ending=""
	1153	fi
	1154
	1155	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1156	(( nr_of_input_files = nr_of_input_files + 1 ))
	1157	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1158	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1159	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1160	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1161	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1162	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1163
	1164
	1165	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1166	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1167	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1168	then
	1169	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1170	else
[2610]	1171	eval filename=${pathin[$nr_of_input_files]}/${fname}${endin[$nr_of_input_files]}
[2380]	1172	fi
[2610]	1173
	1174	# DETERMINE THE FILE'S CYCLE NUMBER
	1175	(( maxcycle = 0 ))
	1176	ls -1 -d $filename > filelist 2>/dev/null
	1177	ls -1 -d $filename.* >> filelist 2>/dev/null
	1178	while read line
	1179	do
	1180	# filename without path (i.e. after the last "/")
	1181	basefilename=$(basename ${line})
	1182
	1183	# check if there is an extension
	1184	extension=${basefilename##*.}
	1185	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1186	then
	1187	basefilename=${basefilename%.*}
	1188	fi
	1189
	1190	# check for an existing cycle number
	1191	cycle=${basefilename##*.}
	1192	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1193	then
[2669]	1194	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1195	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1196	(( icycle = $((10#$cycle)) ))
[2610]	1197	else
	1198	(( icycle = 0 ))
	1199	fi
	1200
	1201	if (( icycle > maxcycle ))
	1202	then
	1203	(( maxcycle = icycle ))
	1204
	1205	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1206	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1207	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1208	then
	1209	leading_zero=true
	1210	else
	1211	leading_zero=false
	1212	fi
	1213	fi
	1214
	1215	done <filelist
	1216	rm filelist
	1217
	1218	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1219	if [[ $leading_zero = true ]]
[2380]	1220	then
[2610]	1221	cyclestring=`printf "%03d" $maxcycle`
	1222	else
	1223	cyclestring=$maxcycle
[2380]	1224	fi
[2610]	1225
	1226	# APPEND CYCLE NUMBER TO FILENAME
	1227	if (( maxcycle > 0 ))
[2380]	1228	then
[2610]	1229	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1230	then
	1231	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1232	else
	1233	filename=${filename}.$cyclestring
	1234	fi
[2380]	1235	else
[2610]	1236	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1237	then
	1238	filename=${filename}.${extin[$nr_of_input_files]}
	1239	fi
[2380]	1240	fi
[2610]	1241
	1242	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1243	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1244	absnamein[$nr_of_input_files]=$filename
	1245	if (( maxcycle > 0 ))
[2380]	1246	then
[2610]	1247	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1248	then
	1249	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1250	else
	1251	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}.$cyclestring
	1252	fi
[2380]	1253	else
[2610]	1254	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1255	then
	1256	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1257	else
	1258	frelin[$nr_of_input_files]=${fname}${endin[$nr_of_input_files]}
	1259	fi
[2380]	1260	fi
	1261
[2610]	1262	done
	1263
[2380]	1264	fi
[2610]	1265
[2380]	1266	done
	1267
[2610]	1268
[2380]	1269	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1270	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1271	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1272	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1273	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1274	# REMOTE HOST)
	1275	(( i = 0 ))
	1276	while (( i < iout ))
	1277	do
	1278	(( i = i + 1 ))
[2610]	1279	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1280	then
[2610]	1281	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1282	then
[2610]	1283	actionout_pre[$i]=""
	1284	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1285	then
[2610]	1286	actionout_pre[$i]=pe
	1287	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1288	then
[2610]	1289	actionout_pre[$i]=a
[2380]	1290	fi
	1291	(( maxcycle = 0 ))
[2610]	1292	eval filename=${pathout_pre[$i]}/${fname}${endout_pre[$i]}
	1293	eval catalogname=${pathout_pre[$i]}
[2380]	1294	if ! ls $filename* 1>/dev/null 2>&1
	1295	then
	1296
	1297	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1298	if cat /dev/null > $filename
	1299	then
	1300	rm $filename
	1301	else
	1302
	1303	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1304	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1305	if [[ ! -d $catalogname ]]
	1306	then
	1307	if mkdir -p $catalogname
	1308	then
	1309	printf "\n\n *** directory:"
	1310	printf "\n $catalogname"
	1311	printf "\n was created\n"
	1312	else
	1313	printf "\n\n +++ OUTPUT-file:"
	1314	printf "\n $filename"
	1315	printf "\n cannot be created, because directory does not exist"
	1316	printf "\n and cannot be created either"
	1317	printf "\n"
	1318	locat=output ; exit
	1319	fi 2>/dev/null
	1320	else
	1321	printf "\n\n +++ OUTPUT-file:"
	1322	printf "\n $filename"
	1323	printf "\n cannot be created, although directory exists"
	1324	printf "\n"
	1325	locat=output ; exit
	1326	fi
	1327	fi 2>/dev/null
	1328
	1329	fi
	1330
	1331	fi
	1332	done
	1333
	1334
	1335	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1336	if [[ $running_in_batch_mode = false ]]
	1337	then
	1338	run_id=$RANDOM
	1339	job_id=${fname}.$run_id
	1340
[2566]	1341	tempdir=$fast_io_catalog/$job_id
[2380]	1342	fi
	1343
	1344
	1345	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1346	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1347	then
	1348
	1349	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1350	if [[ $ibd = 0 ]]
	1351	then
	1352	printf "\n"
	1353	printf "\n +++ no batch directives found in configuration file"
	1354	locat=config_file_batch_directives; (( iec = 0 )); exit
	1355	fi
	1356
	1357	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1358	done=false
[2384]	1359	cputime=$cpumax
[2380]	1360	while [[ $done = false ]]
	1361	do
[2384]	1362	if (( cputime == 0 ))
[2380]	1363	then
	1364	printf "\n +++ cpu-time is undefined"
	1365	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1366	printf "\n >>> "
[2384]	1367	read cputime 1>/dev/null 2>&1
[2380]	1368	else
	1369	done=true
	1370	fi
	1371	done
[2420]	1372	cpumax=$cputime
[2380]	1373
	1374	# CHECK THE MEMORY DEMAND
	1375	done=false
	1376	while [[ $done = false ]]
	1377	do
	1378	if (( memory == 0 ))
	1379	then
	1380	printf "\n +++ memory demand is undefined"
	1381	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1382	printf "\n >>> "
	1383	read memory 1>/dev/null 2>&1
	1384	else
	1385	done=true
	1386	fi
	1387	done
	1388
	1389	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1390	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1391	then
	1392	while [[ -z $remote_username ]]
	1393	do
[2420]	1394	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1395	printf "\n >>> Please type username:"
	1396	printf "\n >>> "
	1397	read remote_username
	1398	done
	1399	fi
	1400
	1401	else
	1402
[2420]	1403	if [[ $running_in_batch_mode = false ]]
	1404	then
	1405	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1406	cpumax=$cputime
	1407	else
	1408	cputime=$cpumax
	1409	fi
[2380]	1410
	1411	fi
	1412
	1413
	1414	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1415	(( cpu_hours = cputime / 3600 ))
	1416	(( resttime = cputime - cpu_hours * 3600 ))
	1417	(( cpu_minutes = resttime / 60 ))
	1418	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1419	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1420
	1421
	1422	# OUTPUT OF THE PALMRUN-HEADER
	1423	calltime=$(date)
	1424	printf "\n"
	1425	printf "#------------------------------------------------------------------------# \n"
	1426	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1427	printf "\| \| \n"
	1428	column1="called on:"; column2=$(hostname)
	1429	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1430	if [[ $create_remote_batch_job = true ]]
	1431	then
[2506]	1432	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1433	else
	1434	if [[ $running_on_remote = true ]]
	1435	then
[2506]	1436	column1="execution on:"; column2="$host_configuration (IP:$remote_ip)"
[2380]	1437	else
[2506]	1438	column1="execution on:"; column2="$host_configuration (IP:$local_ip)"
[2380]	1439	fi
	1440	fi
	1441	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1442
	1443	column1="running in:"
	1444	if [[ $running_in_batch_mode = true ]]
	1445	then
	1446	column2="batch job mode"
	1447	else
	1448	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1449	then
	1450	column2="job creation mode"
	1451	else
	1452	column2="interactive run mode"
	1453	fi
	1454	fi
	1455	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1456
[2479]	1457	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1458	then
[2480]	1459	if [[ "$project_account" != "" ]]
[2479]	1460	then
	1461	column1="project account number:"
	1462	column2="$project_account"
	1463	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1464	fi
	1465	fi
	1466
[2380]	1467	if [[ -n $cores ]]
	1468	then
	1469	if [[ $run_coupled_model = false ]]
	1470	then
	1471	column1="number of cores:"; column2=$cores
	1472	else
	1473	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1474	fi
	1475	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1476	fi
	1477	if [[ -n $tasks_per_node ]]
	1478	then
	1479	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1480	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1481	if (( remaining_cores > 0 ))
	1482	then
	1483	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1484	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1485	fi
	1486	fi
	1487	if [[ $maximum_parallel_io_streams != $cores ]]
	1488	then
	1489	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1490	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1491	fi
	1492	if [[ $use_openmp = true ]]
	1493	then
	1494	column1="threads per task:"; column2="$threads_per_task"
	1495	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1496	fi
[2384]	1497	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1498	then
[2506]	1499	column1="memory demand / PE":; column2="$memory MB"
	1500	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1501	column1="job cpu time (h:m:s):"; column2="$timestring"
	1502	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1503	fi
[2380]	1504	printf "\| \| \n"
	1505	if [[ "$source_list" != "" ]]
	1506	then
	1507	if [[ "$make_options" != "" ]]
	1508	then
	1509	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1510	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1511	line=$(echo "$make_options" \| cut -c46-)
	1512	while [[ "$line" != "" ]]
	1513	do
	1514	column1=""
	1515	column2=$(echo "$line" \| cut -c-45)
	1516	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1517	line=$(echo "$line" \| cut -c46-)
	1518	done
	1519	fi
	1520	fi
	1521
	1522	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1523	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1524	line=$(echo "$cpp_options" \| cut -c46-)
	1525	while [[ "$line" != "" ]]
	1526	do
	1527	column1=""
	1528	column2=$(echo "$line" \| cut -c-45)
	1529	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1530	line=$(echo "$line" \| cut -c46-)
	1531	done
	1532
	1533	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1534	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1535	line=$(echo "$compiler_options" \| cut -c46-)
	1536	while [[ "$line" != "" ]]
	1537	do
	1538	column1=""
	1539	column2=$(echo "$line" \| cut -c-45)
	1540	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1541	line=$(echo "$line" \| cut -c46-)
	1542	done
	1543
[2388]	1544	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1545	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1546	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1547	while [[ "$line" != "" ]]
	1548	do
	1549	column1=""
	1550	column2=$(echo "$line" \| cut -c-45)
	1551	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1552	line=$(echo "$line" \| cut -c46-)
	1553	done
	1554
	1555	if [[ "$login_init_cmd" != "" ]]
	1556	then
	1557	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1558	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1559	line=$(echo "$login_init_cmd" \| cut -c46-)
	1560	while [[ "$line" != "" ]]
	1561	do
	1562	column1=""
	1563	column2=$(echo "$line" \| cut -c-45)
	1564	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1565	line=$(echo "$line" \| cut -c46-)
	1566	done
	1567	fi
	1568
	1569	if [[ "$module_commands" != "" ]]
	1570	then
	1571	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1572	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1573	line=$(echo "$module_commands" \| cut -c46-)
	1574	while [[ "$line" != "" ]]
	1575	do
	1576	column1=""
	1577	column2=$(echo "$line" \| cut -c-45)
	1578	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1579	line=$(echo "$line" \| cut -c46-)
	1580	done
	1581	fi
	1582	printf "\| \| \n"
	1583	column1="base name of files:"; column2=$fname
	1584	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1585	column1="activation string list:"; column2=$(echo $activation_string_list)
	1586	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1587
	1588	if [[ "$ocean_file_appendix" = true ]]
	1589	then
	1590	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1591	fi
	1592
	1593	if [[ "$source_list" != "" ]]
	1594	then
	1595	printf "\| \| \n"
	1596	printf "\| Files to be compiled: \| \n"
	1597	line=$source_list
	1598	while [[ "$line" != "" ]]
	1599	do
	1600	linestart=$(echo $line \| cut -c-70)
	1601	printf "\| %-70s \| \n" "$linestart"
	1602	line=$(echo "$line" \| cut -c71-)
	1603	done
	1604	fi
	1605	printf "#------------------------------------------------------------------------#"
	1606
	1607
	1608
	1609	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1610	if [[ $do_trace = true ]]
	1611	then
	1612	(( i = 0 ))
[2610]	1613	while (( i < nr_of_input_files ))
[2380]	1614	do
	1615	(( i = i + 1 ))
	1616	if (( i == 1 ))
	1617	then
	1618	printf "\n\n >>> INPUT-file assignments:\n"
	1619	fi
	1620	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1621	done
	1622	(( i = 0 ))
	1623	while (( i < iout ))
	1624	do
	1625	(( i = i + 1 ))
	1626	if (( i == 1 ))
	1627	then
	1628	printf "\n\n >>> OUTPUT-file assignments:\n"
	1629	fi
	1630	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1631	done
	1632	(( i = 0 ))
	1633	while (( i < iic ))
	1634	do
	1635	(( i = i + 1 ))
	1636	if (( i == 1 ))
	1637	then
	1638	printf "\n\n >>> INPUT-commands:\n"
	1639	fi
	1640	printf "\n ${in_command[$i]}"
	1641	done
	1642	(( i = 0 ))
	1643	while (( i < ioc ))
	1644	do
	1645	(( i = i + 1 ))
	1646	if (( i == 1 ))
	1647	then
	1648	printf "\n\n >>> OUTPUT-commands:\n"
	1649	fi
	1650	printf "\n ${out_command[$i]}"
	1651	done
	1652	fi
	1653
	1654	# QUERY FOR CONTINUE
	1655	if [[ $silent = false && $running_in_batch_mode = false ]]
	1656	then
	1657	antwort=dummy
	1658	printf "\n\n"
	1659	printf " >>> everything o.k. (y/n) ? "
	1660	while read antwort
	1661	do
	1662	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1663	then
	1664	printf " >>> everything o.k. (y/n) ? "
	1665	else
	1666	break
	1667	fi
	1668	done
	1669	if [[ $antwort = n \|\| $antwort = N ]]
	1670	then
	1671	locat=user_abort; (( iec = 0 )); exit
	1672	fi
	1673	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1674	then
[2566]	1675	printf "\n *** batch-job will be created and submitted"
[2380]	1676	else
[2566]	1677	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1678	fi
	1679	fi
	1680
	1681
	1682
	1683	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1684	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1685	then
	1686
	1687	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1688	then
[2566]	1689	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1690	else
[2566]	1691	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1692	fi
	1693
[2422]	1694	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1695	# IT SHALL BE CREATED
	1696	ask_for_make_depository=false
	1697	if [[ $create_remote_batch_job = true ]]
	1698	then
	1699
	1700	line=`grep %base_directory $config_file`
[2506]	1701	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1702	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]	1703
[2506]	1704	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1705	then
	1706	printf "\n\n +++ make depository \"${make_depository}\""
	1707	printf "\n on remote host not found!"
	1708	ask_for_make_depository=true
	1709	fi
[2506]	1710	rm ${host_configuration}_last_make_protokoll
[2422]	1711
	1712	else
	1713
	1714	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1715	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1716	if [[ ! -d ${make_depository} ]]
	1717	then
	1718	printf "\n\n +++ make depository \"${make_depository}\""
	1719	printf "\n on local host not found!"
	1720	ask_for_make_depository=true
	1721	fi
	1722
	1723	fi
	1724
	1725	if [[ $ask_for_make_depository = true ]]
	1726	then
	1727
	1728	antwort=dummy
	1729	printf "\n\n"
	1730	printf " >>> Create a new one (y/n) ? "
	1731	while read antwort
	1732	do
	1733	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1734	then
	1735	printf " >>> Create a new one (y/n) ? "
	1736	else
	1737	break
	1738	fi
	1739	done
	1740	if [[ $antwort = n \|\| $antwort = N ]]
	1741	then
	1742	locat=user_abort; (( iec = 0 )); exit
	1743	fi
	1744
[2566]	1745	if [[ $do_trace = true ]]
	1746	then
	1747	palmbuild -h $host_configuration
	1748	else
	1749	palmbuild -v -h $host_configuration
	1750	fi
[2422]	1751
	1752	if [[ $? != 0 ]]
	1753	then
	1754
	1755	# ABORT IN CASE OF COMPILATION PROBLEMS
	1756	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1757	locat=make_depository
	1758	exit
	1759	else
	1760	echo " *** now continue with creating executable and other sources"
	1761	fi
	1762
	1763	fi
	1764
[2566]	1765	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2506]	1766	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $fname
[2380]	1767
	1768	if [[ $? != 0 ]]
	1769	then
	1770
	1771	# ABORT IN CASE OF COMPILATION PROBLEMS
	1772	printf "\n +++ error while creating executable and/or other sources"
	1773	locat=execution
[2506]	1774	rm -rf $sources_for_run_catalog
[2380]	1775	exit
	1776
	1777	else
	1778
[2566]	1779	printf " *** executable and other sources created\n"
[2506]	1780	rm -rf $sources_for_run_catalog
[2380]	1781
	1782	fi
	1783
	1784	fi
	1785
	1786
[2669]	1787	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1788	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1789	if [[ $create_remote_batch_job = true ]]
	1790	then
	1791	(( i = 0 ))
[2610]	1792	while (( i < nr_of_input_files ))
[2605]	1793	do
	1794	(( i = i + 1 ))
[2669]	1795	if [[ "${actionin[$i]}" = tr ]]
[2605]	1796	then
	1797	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1798	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1799	fi
	1800	done
	1801	if (( i > 0 ))
	1802	then
	1803	printf " *** input files have been copied to the remote host\n"
	1804	fi
	1805	fi
	1806
	1807
[2380]	1808	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1809	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1810	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1811	then
	1812
	1813	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1814	if [[ $running_in_batch_mode = false ]]
	1815	then
	1816	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1817	# FOLDER
[2566]	1818	mkdir -p $tempdir
	1819	chmod go+rx $tempdir
	1820	cd $tempdir
	1821	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1822	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1823
	1824	else
	1825
	1826	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1827	printf "\n *** running in temporary directory: $tempdir"
[2380]	1828
	1829	fi
	1830
	1831
	1832	# PROVIDE THE INPUT FILES
	1833	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1834	optional_files_missing=false
[2380]	1835	(( i = 0 ))
[2610]	1836	while (( i < nr_of_input_files ))
[2380]	1837	do
	1838	(( i = i + 1 ))
	1839	if (( i == 1 ))
	1840	then
	1841	printf "\n\n *** providing INPUT-files:\n$dashes"
	1842	fi
	1843
	1844
	1845	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1846	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1847	then
[2669]	1848	optional_files_missing=true
[2380]	1849	continue
	1850	fi
	1851
	1852	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1853	files_for_cores=false; filetype=file
	1854	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1855	then
	1856	files_for_cores=true; filetype=files
	1857	actionin[$i]=""
	1858	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1859	then
	1860	actionin[$i]=""
	1861	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1862	then
	1863	files_for_cores=true; filetype=files
	1864	actionin[$i]="ln"
	1865	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1866	then
	1867	actionin[$i]="ln"
	1868	fi
	1869
	1870	if [[ $files_for_cores = true ]]
	1871	then
	1872	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1873	else
	1874	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1875	fi
	1876
	1877	# INPUT-FILES TO BE LINKED
	1878	if [[ "${actionin[$i]}" = ln ]]
	1879	then
	1880
	1881	printf "\n $filetype will be linked"
	1882	if [[ $files_for_cores = false ]]
	1883	then
	1884	if [[ -f "${absnamein[$i]}" ]]
	1885	then
	1886	ln ${absnamein[$i]} ${localin[$i]}
	1887	got_tmp[$i]=true
	1888	fi
	1889	else
	1890	if [[ -d "${absnamein[$i]}" ]]
	1891	then
[2396]	1892	mkdir -p ${localin[$i]}
[2380]	1893	cd ${absnamein[$i]}
	1894	for file in $(ls *)
	1895	do
[2566]	1896	ln $file $tempdir/${localin[$i]}
[2380]	1897	done >\|/dev/null 2>&1
[2566]	1898	cd $tempdir
[2380]	1899	fi
	1900
	1901	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1902	if [[ ! -f "${localin[$i]}/_000000" ]]
	1903	then
	1904	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1905	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1906	fi
	1907
	1908	got_tmp[$i]=true
	1909	fi
	1910	fi
	1911
	1912	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	1913	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	1914	then
	1915
	1916	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1917	then
	1918
	1919	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1920	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	1921	printf "\n file will be provided for $cores processors"
[2396]	1922	mkdir -p ${localin[$i]}
[2380]	1923	ival=$cores
	1924	(( ii = 0 ))
	1925	while (( ii <= ival-1 ))
	1926	do
	1927	if (( ii < 10 ))
	1928	then
	1929	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	1930	elif (( ii < 100 ))
	1931	then
	1932	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	1933	elif (( ii < 1000 ))
	1934	then
	1935	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	1936	else
	1937	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	1938	fi
	1939	(( ii = ii + 1 ))
	1940	done
	1941
	1942	else
	1943
	1944	if [[ $files_for_cores = true ]]
	1945	then
	1946
	1947	# PROVIDE FILES FOR EACH CORE
	1948	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	1949	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	1950	printf "\n providing $cores files for the respective cores"
[2396]	1951	mkdir -p ${localin[$i]}
[2380]	1952	if [[ $link_local_input = true ]]
	1953	then
	1954	printf " files will be linked\n"
	1955	cd ${absnamein[$i]}
	1956	for file in $(ls *)
	1957	do
	1958	ln -f $file ${localin[$i]}
	1959	done
[2566]	1960	cd $tempdir
[2380]	1961	fi
	1962
	1963	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	1964	if [[ ! -f "${localin[$i]}/_000000" ]]
	1965	then
	1966	if [[ $link_local_input = true ]]
	1967	then
	1968	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1969	fi
	1970	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1971	fi
	1972
	1973	else
	1974
	1975	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	1976	if [[ $link_local_input = true ]]
	1977	then
	1978	printf " file will be linked\n"
	1979	ln -f ${absnamein[$i]} ${localin[$i]}
	1980	fi
[2605]	1981	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	1982	if [[ ! -f "${localin[$i]}" ]]
	1983	then
	1984	if [[ $link_local_input = true ]]
	1985	then
	1986	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1987	fi
[2669]	1988	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	1989	then
	1990	mv ${absnamein[$i]} ${localin[$i]}
	1991	else
	1992	cp ${absnamein[$i]} ${localin[$i]}
	1993	fi
[2380]	1994	fi
	1995	fi
	1996	fi
	1997	fi
	1998
	1999	done
	2000	if (( i != 0 ))
	2001	then
[2669]	2002	if [[ $optional_files_missing = true ]]
	2003	then
	2004	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2005	fi
[2380]	2006	printf "\n$dashes\n *** all INPUT-files provided \n"
	2007	fi
	2008
	2009
	2010	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2011	(( i = 0 ))
	2012	while (( i < iic ))
	2013	do
	2014	(( i = i + 1 ))
	2015	if (( i == 1 ))
	2016	then
	2017	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2018	fi
	2019	printf "\n >>> ${in_command[$i]}"
	2020	eval ${in_command[$i]}
	2021	if (( i == iic ))
	2022	then
	2023	printf "\n$dashes\n"
	2024	fi
	2025	done
	2026
	2027
	2028	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2029	# (FILE ENVPAR WILL BE READ BY PALM)
	2030	cat > ENVPAR << EOF
[2506]	2031	&envpar run_identifier = '$fname', host = '$host_configuration',
[2380]	2032	write_binary = .${write_binary}., tasks_per_node = $tasks_per_node,
	2033	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2034	maximum_cpu_time_allowed = ${cpumax}.,
	2035	revision = '$global_revision',
	2036	batch_job = .${running_in_batch_mode}. /
	2037
	2038	EOF
	2039
	2040
	2041	# STARTING THE EXECUTABLE
	2042	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2043	PATH=$PATH:$tempdir
[2380]	2044
	2045
	2046	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2047	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2048	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2049	eval line=\"$line\"
	2050	execute_command="$line"
	2051
	2052
	2053	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2054	if [[ "$execute_command_for_combine" = "" ]]
	2055	then
	2056	eval line2=\"$line2\"
	2057	execute_command_for_combine="$line2"
	2058	fi
	2059
[2380]	2060
	2061
	2062	# PROVIDE A HOSTFILE, IF REQUIRED
	2063	if [[ "$hostfile" != "" ]]
	2064	then
	2065
	2066	if [[ $hostfile = auto ]]
	2067	then
	2068	# CREATE A NEW HOSTFILE
	2069	(( ii = 1 ))
	2070	while (( ii <= cores / threads_per_task ))
	2071	do
	2072	echo $(hostname) >> hostfile
	2073	(( ii = ii + 1 ))
	2074	done
	2075	if (( cores / threads_per_task == 0 ))
	2076	then
	2077	echo $(hostname) >> hostfile
	2078	fi
	2079
	2080	else
	2081	cp $hostfile hostfile
	2082	fi
	2083	eval line=\"`head -n $ii hostfile`\"
	2084	printf "\n *** running on: $line"
	2085	fi
	2086
	2087
	2088
	2089	# SET THE NUMBER OF OPENMP-THREADS
	2090	if [[ $use_openmp = true ]]
	2091	then
	2092	export OMP_NUM_THREADS=$threads_per_task
	2093	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2094	else
	2095	export OMP_NUM_THREADS=1
	2096	fi
	2097
	2098
[2610]	2099	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2100	if [[ $run_coupled_model = false ]]
	2101	then
	2102	if [[ "$ocean_file_appendix" = true ]]
	2103	then
	2104	echo "precursor_ocean" > coupling_steering
	2105	else
	2106	echo "precursor_atmos" > coupling_steering
	2107	fi
	2108	else
	2109	(( iia = $cores_atmos / $threads_per_task ))
	2110	(( iio = $cores_ocean / $threads_per_task ))
	2111	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2112	printf "\n\n"
	2113	echo "coupled_run $iia $iio" > coupling_steering
	2114	fi
	2115
	2116	printf "\n *** execute command:"
	2117	printf "\n \"$execute_command\" \n\n"
	2118
	2119	$execute_command < coupling_steering
	2120
	2121	if [[ $? != 0 ]]
	2122	then
	2123
	2124	# ABORT IN CASE OF RUNTIME ERRORS
	2125	printf "\n +++ runtime error occured"
	2126	locat=execution
	2127	exit
	2128
	2129	else
	2130
	2131	printf "\n$dashes\n *** execution finished \n"
	2132
	2133	fi
	2134
	2135
	2136	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2137	# BY EACH CORE INTO ONE FILE
	2138	if [[ ! -f combine_plot_fields.x ]]
	2139	then
	2140
	2141	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2142	printf "\n 2d- and/or 3d-data may be incomplete!"
	2143	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2144
	2145	elif [[ "$combine_plot_fields" == true ]]
	2146	then
	2147
	2148	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2149	$execute_command_for_combine
	2150
	2151	else
	2152
	2153	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2154	# DATA OUTPUT
[2380]	2155	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2156	fi
	2157
	2158
	2159
	2160	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2161	(( i = 0 ))
	2162	while (( i < ioc ))
	2163	do
	2164	(( i = i + 1 ))
	2165	if (( i == 1 ))
	2166	then
	2167	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2168	fi
	2169	printf "\n >>> ${out_command[$i]}"
	2170	eval ${out_command[$i]}
	2171	if (( i == ioc ))
	2172	then
	2173	printf "\n$dashes\n"
	2174	fi
	2175	done
	2176
	2177
[2610]	2178	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2179	# WILDCARDS
[2380]	2180	(( i = 0 ))
[2610]	2181	(( nr_of_output_files = 0 ))
	2182
[2380]	2183	while (( i < iout ))
	2184	do
[2610]	2185
[2380]	2186	(( i = i + 1 ))
[2610]	2187
	2188	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2189	# CREATE A LIST FOR THE DETECTED ENDINGS
	2190	if [[ "${multout[$i]}" = true ]]
	2191	then
	2192	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2193	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2194	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2195
	2196	endings="DEFAULT"
	2197	while read line
	2198	do
	2199	# remove the local name from the beginning
	2200	localnamestring="${localout_pre[$i]}"
	2201	length_localname=${#localnamestring}
	2202	ending=${line:${length_localname}}
	2203
	2204	if [[ "$ending" != "" ]]
	2205	then
	2206	endings="$endings $ending"
	2207	fi
	2208
	2209	done <filelist
	2210
	2211	rm filelist
	2212
	2213	else
	2214
	2215	# SINGLE NAME
	2216	endings=DEFAULT
	2217
	2218	fi
	2219
	2220	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2221	for ending in $endings
	2222	do
	2223
	2224	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2225	if [[ $ending = DEFAULT ]]
	2226	then
	2227	ending=""
	2228	fi
	2229
	2230	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2231	(( nr_of_output_files = nr_of_output_files + 1 ))
	2232	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2233	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2234	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2235	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2236	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2237	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2238	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2239
	2240	done
	2241
	2242	done
	2243
	2244
	2245
	2246
	2247	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2248	(( i = 0 ))
	2249	while (( i < nr_of_output_files ))
	2250	do
	2251	(( i = i + 1 ))
[2380]	2252	if (( i == 1 ))
	2253	then
	2254	printf "\n\n *** saving OUTPUT-files:"
	2255
	2256	# GET RUN NUMBER ASSIGNED BY PALM
	2257	if [[ -f RUN_NUMBER ]]
	2258	then
	2259	read run_number < RUN_NUMBER
	2260	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2261	usecycle_option="-U $run_number"
	2262	else
	2263	run_number=0
	2264	usecycle_option=""
	2265	fi
	2266	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2267	then
[2404]	2268	printf "\n *** in case of SCP transfers to local host"
	2269	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2270	fi
	2271	printf "\n$dashes"
	2272	fi
	2273
	2274	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2275	then
	2276
[2610]	2277	eval filename=${pathout[$i]}/${fname}${endout[$i]}
	2278
	2279	# DETERMINE THE CYCLE NUMBER
	2280	ls -1 -d $filename > filelist 2>/dev/null
	2281	ls -1 -d $filename.* >> filelist 2>/dev/null
	2282	while read line
	2283	do
	2284
	2285	# filename without path (i.e. after the last "/")
	2286	basefilename=$(basename ${line})
	2287
	2288	# check if there is an extension
	2289	extension=${basefilename##*.}
	2290	if [[ "$extension" = "${extout[$i]}" ]]
	2291	then
	2292	basefilename=${basefilename%.*}
	2293	fi
	2294
	2295	# check for an existing cycle number
	2296	cycle=${basefilename##*.}
	2297	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2298	then
[2669]	2299	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2300	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2301	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2302	else
	2303	(( icycle = 1 ))
	2304	fi
	2305
	2306	if (( icycle > maxcycle ))
	2307	then
	2308	(( maxcycle = icycle ))
	2309	fi
	2310
	2311	done <filelist
	2312	rm filelist
	2313
	2314
	2315	# SET THE CYCLE NUMBER
	2316	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2317	if [[ "${actionout[$i]}" = a ]]
	2318	then
	2319	(( maxcycle = maxcycle - 1 ))
	2320	fi
	2321
	2322	(( cycnum[$i] = maxcycle ))
	2323	pathout[$i]=$filename
	2324
	2325
	2326	# ADD CYCLE NUMBER TO FILENAME
	2327	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2328	if [[ "${actionout[$i]}" != "a" ]]
	2329	then
	2330	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2331	# WITH AN EXISTING CYCLE NUMBER
	2332	if (( run_number >= cycnum[$i] ))
	2333	then
	2334	(( cycnum[$i] = run_number ))
	2335	else
	2336	if (( run_number > 0 ))
	2337	then
	2338	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2339	fi
	2340	fi
	2341	fi
	2342	if (( cycnum[$i] > 0 ))
	2343	then
[2600]	2344	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2345	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2346	fi
	2347	fi
	2348
	2349	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2350	files_for_cores=false; filetype=file
	2351	link_local_output=false
	2352	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2353	then
	2354	files_for_cores=true; filetype=directory
	2355	actionout[$i]=""
	2356	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2357	then
	2358	actionout[$i]=""
	2359	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2360	then
	2361	files_for_cores=true; filetype=directory
	2362	link_local_output=true
	2363	actionout[$i]=""
	2364	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2365	then
	2366	link_local_output
	2367	actionout[$i]=""
	2368	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2369	then
	2370	files_for_cores=true; filetype=directory
	2371	actionout[$i]="tr"
	2372	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2373	then
	2374	actionout[$i]="tr"
	2375	fi
	2376
	2377	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2378	then
[2669]	2379	if [[ ${warnout[$i]} = true ]]
	2380	then
	2381	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2382	fi
[2380]	2383	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2384	then
[2669]	2385	if [[ ${warnout[$i]} = true ]]
	2386	then
	2387	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2388	fi
[2380]	2389	else
	2390
	2391
	2392	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2393	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2394	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2395	then
	2396	if [[ $running_on_remote = true ]]
	2397	then
	2398
	2399	# SET OPTIONS FOR TRANSFER
	2400	if [[ "${actionout[$i]}" = tr ]]
	2401	then
	2402	if [[ $files_for_cores = false ]]
	2403	then
	2404	catalog_option=""
	2405	catalog_string=""
	2406	else
	2407	catalog_option="-c"
	2408	catalog_string="/"
	2409	fi
	2410	append_option=""
	2411	append_string=""
	2412	else
	2413	append_option="-A"
	2414	append_string="append"
	2415	fi
	2416
	2417	transfer_failed=false
	2418	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2506]	2419	printf "\n ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}$catalog_string\n"
[2380]	2420
	2421	# TRANSFER VIA SCP
	2422	if [[ "$remote_loginnode" != "" ]]
	2423	then
[2566]	2424	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]}\" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
[2380]	2425	else
[2506]	2426	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${host_configuration}_${fname}${endout[$i]} ${extout[$i]}
[2380]	2427	fi
	2428	[[ $? != 0 ]] && transfer_failed=true
	2429
	2430
	2431	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2432	if [[ $transfer_failed = true ]]
	2433	then
	2434	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2506]	2435	printf " ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id\n"
[2380]	2436
	2437	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2438	eval local_catalog=${pathout[$i]}
	2439	if [[ ! -d $local_catalog ]]
	2440	then
	2441	printf " *** local directory does not exist. Trying to create:\n"
	2442	printf " $local_catalog \n"
	2443	mkdir -p $local_catalog
	2444	fi
[2506]	2445	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${fname}${endout[$i]}_$run_id
[2380]	2446	transfer_problems=true
	2447	fi
	2448
	2449	else
	2450
	2451	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2452	# BE COPIED OR APPENDED ON THIS MACHINE
	2453	if [[ "${actionout[$i]}" = tr ]]
	2454	then
	2455	actionout[$i]=""
	2456	else
	2457	actionout[$i]="a"
	2458	fi
	2459	fi
	2460	fi
	2461
	2462
	2463	# APPEND ON THIS MACHINE
	2464	if [[ "${actionout[$i]}" = "a" ]]
	2465	then
	2466	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2467	then
	2468	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2469	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2470	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2471	else
	2472	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2473	printf "\n ${pathout[$i]}\n"
	2474	cat ${localout[$i]} >> ${pathout[$i]}
	2475	fi
	2476	fi
	2477
	2478	# COPY ON THIS MACHINE
	2479	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2480	# ON DIFFERENT FILE-SYSTEMS
	2481	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2482	then
	2483
	2484	# COPY IN CASE OF RUNS ON SINGLE CORES
	2485	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2486	then
	2487	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2488	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2489	if [[ $link_local_output = true ]]
	2490	then
	2491	printf " file will be linked\n"
	2492	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2493	fi
	2494	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2495	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2496	then
	2497	if [[ $link_local_output = true ]]
	2498	then
	2499	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2500	fi
	2501	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2502	else
	2503	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2504	fi
	2505	else
	2506	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2507	printf "\n ${pathout[$i]}\n"
	2508	if [[ $link_local_output = true ]]
	2509	then
	2510	printf " file will be linked\n"
	2511	ln -f ${localout[$i]} ${pathout[$i]}
	2512	fi
	2513	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2514	if [[ ! -f "${pathout[$i]}" ]]
	2515	then
	2516	if [[ $link_local_output = true ]]
	2517	then
	2518	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2519	fi
	2520	cp ${localout[$i]} ${pathout[$i]}
	2521	else
	2522	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2523	fi
	2524	fi
	2525
	2526	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2527	then
	2528
	2529	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2530	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2531	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2532	printf "\n ${pathout[$i]}\n"
	2533	if [[ $link_local_output = true ]]
	2534	then
	2535	printf " files will be linked\n"
[2396]	2536	mkdir -p ${pathout[$i]}
[2380]	2537	cd ${localout[$i]}
	2538	for file in $(ls *)
	2539	do
	2540	ln -f $file ${pathout[$i]}
	2541	done >\|/dev/null 2>&1
[2566]	2542	cd $tempdir
[2380]	2543	fi
	2544
	2545	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2546	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2547	then
	2548	if [[ $link_local_output = true ]]
	2549	then
	2550	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2551	fi
	2552	cp -r ${localout[$i]}/* ${pathout[$i]}
	2553	fi
	2554
	2555	fi
	2556	fi
	2557	done
	2558
	2559	if (( i != 0 ))
	2560	then
	2561	if [[ $transfer_problems = true ]]
	2562	then
	2563	printf "\n$dashes\n *** OUTPUT-files saved"
	2564	printf "\n +++ WARNING: some data transfers failed! \n"
	2565	else
	2566	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2567	fi
	2568	fi
	2569
	2570
	2571	# IF REQUIRED, START A RESTART-JOB
	2572	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2573	if [[ -f CONTINUE_RUN ]]
	2574	then
	2575
	2576	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2577	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2578	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2579	# -b START A BATCH JOB
	2580	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2581	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2582	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2583
	2584
	2585	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2586	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2587	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2588	then
[2381]	2589	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2590	fi
	2591
	2592
	2593	# START THE RESTART-JOB
	2594	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2595	echo " $prc"
	2596	printf "\n$dashes\n"
	2597	if [[ $running_on_remote = true ]]
	2598	then
	2599
	2600	echo "*** ssh will be used to initiate restart-runs!"
	2601	echo " return_address=\"$return_address\" "
	2602	echo " return_username=\"$local_username\" "
	2603
	2604	if [[ "$remote_loginnode" != "" ]]
	2605	then
[2420]	2606	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]	2607	else
[2420]	2608	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2609	fi
	2610
	2611	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2612	sleep 30
	2613
	2614	else
	2615
	2616	# START THE RESTART JOB ON THE LOCAL HOST
	2617	eval $prc # THE ' MUST BE EVALUATED
	2618	cd - > /dev/null
	2619
	2620	fi
	2621	printf "\n$dashes\n *** restart-run initiated \n"
	2622
	2623
	2624	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2625	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2626	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2627	# MAY BE VERY HUGE)
	2628	(( i = 0 ))
[2610]	2629	while (( i < nr_of_input_files ))
[2380]	2630	do
	2631	(( i = i + 1 ))
	2632	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2633	then
	2634	rm -r ${absnamein[$i]}
	2635	fi
	2636	done
	2637
	2638	fi
	2639
	2640
	2641	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2642	cd $HOME
[2566]	2643	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2644
	2645
	2646	else
	2647
	2648
	2649	# PREPARING ACTIONS,
	2650	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2651
	2652	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2506]	2653	palmrun_com="$palmrun_script_name -d $fname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2654	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2655	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2656	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2657	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2658	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2659	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2660	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2661	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2662	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2663	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2664	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2665	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2666	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2667	if [[ $create_remote_batch_job = true ]]
	2668	then
	2669	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2670	if [[ $do_trace = true ]]
	2671	then
	2672	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2673	fi
[2380]	2674	elif [[ $create_batch_job = true ]]
	2675	then
	2676	palmrun_com=${palmrun_com}" -j"
[2420]	2677	if [[ $do_trace = true ]]
	2678	then
	2679	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2680	fi
[2380]	2681	fi
	2682
	2683
	2684	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2685	# REMOTE HOST
[2506]	2686	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2687	job_protocol_file=$job_protocol_file_local
	2688	if [[ $create_remote_batch_job = true ]]
	2689	then
[2506]	2690	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2691	job_protocol_file=$job_protocol_file_remote
	2692	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2693	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2694	fi
	2695
	2696
	2697	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2698	jobfile=jobfile.$run_id
	2699
	2700
	2701	# FIRST CREATE THE BATCH DIRECTIVES
	2702	(( i = 0 ))
	2703	while (( i < ibd ))
	2704	do
	2705	(( i = i + 1 ))
[2693]	2706	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2707	eval line=\"$line\"
	2708	echo "$line" >> $jobfile
	2709	done
	2710	echo " " >> $jobfile
	2711
	2712
	2713	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2714	# PROTOCOL
	2715	if [[ $create_remote_batch_job = true ]]
	2716	then
	2717	echo "set +vx" >> $jobfile
	2718	echo "trap '" >> $jobfile
	2719	echo "set +vx" >> $jobfile
	2720	echo "cd ${remote_jobcatalog}" >> $jobfile
	2721	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2722
	2723	# ADD THE BATCH DIRECTIVES
	2724	(( i = 0 ))
	2725	while (( i < ibdt ))
	2726	do
	2727	(( i = i + 1 ))
[2693]	2728	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2729	eval line=\"$line\"
	2730	echo "$line" >> $jobfile
	2731	done
	2732	echo " " >> $jobfile
	2733
	2734	echo "set -x" >> $jobfile
[2506]	2735	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${host_configuration}_${fname}" >> $jobfile
[2380]	2736	echo "%%END%%" >> $jobfile
	2737	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2738	echo "$submit_command $scpjob_file" >> $jobfile
	2739	echo "rm $scpjob_file" >> $jobfile
[2404]	2740	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2741	echo "set -x" >> $jobfile
	2742	echo " ' exit" >> $jobfile
	2743	fi
	2744
	2745
	2746	# ACTIVATE ERROR-TRACEBACK
	2747	if [[ $do_trace = true ]]
	2748	then
	2749	echo "set -x" >> $jobfile
	2750	else
	2751	echo "set +vx" >> $jobfile
	2752	fi
	2753
	2754
	2755	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2756	if [[ "$login_init_cmd" != "" ]]
	2757	then
	2758	echo "$login_init_cmd" >> $jobfile
	2759	fi
	2760	if [[ "$module_commands" != "" ]]
	2761	then
	2762	echo "$module_commands" >> $jobfile
	2763	fi
	2764
	2765
	2766	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2767	if [[ $create_remote_batch_job = true ]]
	2768	then
	2769	echo "mkdir $tempdir" >> $jobfile
	2770	echo "chmod go+rx $tempdir" >> $jobfile
	2771	else
	2772	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2773	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2774	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2775	mkdir $tempdir
	2776	chmod go+rx $tempdir
	2777	fi
	2778	echo "cd $tempdir" >> $jobfile
	2779	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2780	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2781	echo "export PATH=.:\$PATH" >> $jobfile
	2782	echo "export execute_palmrun=true" >> $jobfile
	2783
	2784
	2785	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2786	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2787	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2788	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2789	echo "export LOCAL_PWD" >> $jobfile
	2790
	2791
	2792	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2793	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2794	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2795
	2796
	2797	# CALL PALMRUN WITHIN THE JOB
	2798	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2799	echo "set -x" >> $jobfile
	2800	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2801
	2802
	2803	# TRANSFER JOBFILE TO THE TARGET HOST
	2804	if [[ $create_jobfile_only = false ]]
	2805	then
	2806
	2807	if [[ $create_remote_batch_job = true ]]
	2808	then
	2809
[2420]	2810	echo " "
[2566]	2811	echo " *** transfer of job to remote host via scp"
[2420]	2812	if [[ $do_trace = true ]]
	2813	then
[2506]	2814	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2815	fi
[2566]	2816	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2817
[2566]	2818	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2819	if [[ $do_trace = true ]]
	2820	then
[2506]	2821	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]	2822	fi
[2506]	2823	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]	2824
	2825	elif [[ $create_batch_job = true ]]
	2826	then
	2827
[2385]	2828	eval local_jobcatalog=$local_jobcatalog
[2506]	2829	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2830	cd $local_jobcatalog
[2380]	2831	echo " "
[2420]	2832	echo " *** submit the job"
	2833	if [[ $do_trace = true ]]
	2834	then
[2506]	2835	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2836	fi
[2506]	2837	$submit_command ${host_configuration}_${job_id}
	2838	rm ${host_configuration}_${job_id}
[2380]	2839	cd - > /dev/null
	2840
	2841	fi
	2842
	2843	rm -rf $jobfile
	2844
	2845	else
	2846
	2847	printf "\n *** jobfile created under name \"$jobfile\" "
	2848	printf "\n no batch-job has been sent!"
	2849
	2850	fi
	2851
	2852	fi # END OF REMOTE-PART

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