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source: palm/trunk/SCRIPTS/palmrun @ 3312

Last change on this file since 3312 was 3312, checked in by knoop, 6 years ago
Added proper exit code to PALM and fixed exit code handling by palmbuild and palmrun
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 100.0 KB

Rev	Line
[2380]	1	#!/bin/bash
	2
	3	# palmrun - script for running PALM jobs
	4
	5	#--------------------------------------------------------------------------------#
[2696]	6	# This file is part of the PALM model system.
[2380]	7	#
	8	# PALM is free software: you can redistribute it and/or modify it under the terms
	9	# of the GNU General Public License as published by the Free Software Foundation,
	10	# either version 3 of the License, or (at your option) any later version.
	11	#
	12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
	13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	15	#
	16	# You should have received a copy of the GNU General Public License along with
	17	# PALM. If not, see <http://www.gnu.org/licenses/>.
	18	#
[2718]	19	# Copyright 2017-2018 Leibniz Universitaet Hannover
[2380]	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
	23	# ------------------
	24	#
[2410]	25	#
[2380]	26	# Former revisions:
	27	# -----------------
[3032]	28	# $Id: palmrun 3312 2018-10-06 14:15:46Z knoop $
[3294]	29	# more detailed error message for outdated fileconnection file
	30	#
	31	# 3236 2018-09-10 09:07:06Z raasch
[3236]	32	# warning issued in case of file connection file version mismatch,
	33	# host_configuration renamed configuration_identifier,
	34	# "host identifier" in header output renamed "config. identifier",
	35	# jobname renamed run_identifier,
	36	# run_id renamed run_id_number
	37	# job_id renamed run_id
	38	# option -r renamed -i
	39	#
	40	# 3151 2018-07-19 08:45:38Z raasch
[3151]	41	# removed additional listing of files to be compiled, print PALM code revision
	42	# in header
	43	#
	44	# 3132 2018-07-16 11:44:58Z raasch
[3132]	45	# create consistent error messages in case of failed restarts,
	46	# check existence of remote job catalog
	47	#
	48	# 3043 2018-05-25 10:47:54Z raasch
[3043]	49	# check for setting of fast_io_catalog
	50	#
	51	# 3033 2018-05-23 15:26:19Z raasch
[3025]	52	# -T option not required for interactive runs (tasks per node =
	53	# total number of cores is assumed as default, if option is not given),
	54	# reformatting of a few messages,
	55	# bugfix: destination output directory is created if attribute "pe" is set in
	56	# .palm.iofiles
	57	#
	58	# 2718 2018-01-02 08:49:38Z maronga
[2993]	59	# bugfix of r2990
	60	#
	61	# 2718 2018-01-02 08:49:38Z maronga
[2990]	62	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	63	# not in the working directory from where palmrun is called
	64	#
	65	# 2718 2018-01-02 08:49:38Z maronga
[2957]	66	# svfout in the activation string will be replaced now by svfin in case of
	67	# automatic restarts
	68	#
	69	# 2718 2018-01-02 08:49:38Z maronga
[2906]	70	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	71	# the possible output or input of sky view factors
	72	#
	73	# 2718 2018-01-02 08:49:38Z maronga
[2834]	74	# "fname" renamed to "jobname"
	75	#
	76	# 2718 2018-01-02 08:49:38Z maronga
[2799]	77	# parameters are allowed in output commands (OC:)
	78	#
	79	# 2718 2018-01-02 08:49:38Z maronga
[2789]	80	# bugfix: exit if no queue has been given neither with option -q nor in the
	81	# configuration file
	82	#
	83	# 2718 2018-01-02 08:49:38Z maronga
[2762]	84	# file connection file from trunk/SCRIPTS is taken by default
	85	#
	86	# 2718 2018-01-02 08:49:38Z maronga
[2716]	87	# Corrected "Former revisions" section
	88	#
	89	# 2696 2017-12-14 17:12:51Z kanani
	90	# Change in file header (GPL part)
	91	#
	92	# 2693 2017-12-13 12:33:49Z raasch
[2693]	93	# replacement of variables given by {{<variable>}} in configuration file is now
	94	# done in a more general way, variable names are written in small letters
	95	#
	96	# 2670 2017-12-06 16:32:19Z raasch
[2670]	97	# test printouts removed
	98	#
	99	# 2669 2017-12-06 16:03:27Z raasch
[2669]	100	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	101	# removed,
	102	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	103	# files,
	104	# informative messages in case of missing optional input files shortened
	105	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	106	#
	107	# 2638 2017-11-23 12:44:23Z raasch
[2610]	108	# use of wildcards in file connection statements enabled
	109	#
	110	# 2605 2017-11-09 15:31:46Z raasch
[2605]	111	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	112	# will not be sent with the job file any more, but copied into the
[2610]	113	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	114	#
	115	# 2600 2017-11-01 14:11:20Z raasch
[2600]	116	# cycle numbers are made three digits wide
	117	#
	118	# 2566 2017-10-20 08:50:47Z raasch
[2566]	119	# execute command for combine_plot_fields added
	120	# "TEMPDIR" renamed "tempdir"
	121	# temporary working directory for local batch jobs is created immediately within
	122	# the user's palmrun call, due to a requirement of the "grid engine" batch
	123	# system, where the working directory is given with batch directive -wd and must
	124	# already exist when the job is submitted,
	125	# informative messages in non-trace mode reduced and partly reformatted
	126	#
	127	# 2551 2017-10-18 07:25:11Z raasch
[2551]	128	# TEMPDIR added as replacement string to be used in batch directives
	129	#
	130	# 2512 2017-10-04 08:26:59Z raasch
[2507]	131	# bugfix for determining cycle numbers of NetCDF input files
	132	#
	133	# 2506 2017-09-29 08:30:37Z raasch
[2506]	134	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	135	# host configuration added to SOURCES_FOR_RUN_... folder name
	136	# host_identifier renamed host_configuration
	137	# option -W added to allow for job dependencies
	138	#
	139	# 2501 2017-09-26 11:41:55Z raasch
[2501]	140	# default value for number of cores (option -X) set to 1
	141	# bugfix for mechanism which overwrites configuration file settings with values
	142	# provided by palmrun options
	143	#
	144	# 2499 2017-09-22 16:47:58Z kanani
[2499]	145	# option -h named configuration identifier
	146	#
	147	# 2480 2017-09-19 06:24:14Z maronga
[2480]	148	# bugfix for last revision
	149	#
	150	# 2479 2017-09-19 06:12:16Z raasch
[2479]	151	# option -A (project account number) added
	152	#
	153	# 2422 2017-09-08 08:25:41Z raasch
[2410]	154	# initial revision
[2380]	155	#
	156	#--------------------------------------------------------------------------------#
	157	# palmrun - script for running PALM jobs on local and remote hosts
	158	#--------------------------------------------------------------------------------#
	159
	160
	161
	162	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	163
	164	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	165	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	166	# (TOO MANY ARGUMENTS - PROBLEM)
	167	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	168
[2610]	169	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	170	typeset -i nr_of_output_files=0
[2380]	171	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	172	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	173	# SCRIPT-OPTION ARGUMENTS
	174	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	175	typeset -i icycle inode ival maxcycle mpi_tasks
	176	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	177
	178	activation_string_list=""
	179	AddFilenames=""
	180	combine_plot_fields=true
	181	compiler_name=""
	182	compiler_name_ser=""
	183	compiler_options=""
[3236]	184	configuration_identifier="default"
[2501]	185	cores=1
[2380]	186	cores_atmos=0
	187	cores_ocean=0
	188	coupled_dist=""
	189	cpp_options=""
	190	cpumax=0
[2506]	191	create_batch_job=false
[2380]	192	create_jobfile_only=false
	193	create_remote_batch_job=false
	194	dashes=" ----------------------------------------------------------------------------"
	195	defaultqueue=""
[2506]	196	delete_temporary_catalog=true
[2380]	197	do_compile=true
	198	do_trace=false
	199	executable=""
	200	execute_command=""
	201	execution_error=false
[2762]	202	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	203	global_revision=""
	204	hostfile=""
	205	hp=""
	206	keep_data_from_previous_run=false
	207	link_local_input=false
	208	link_local_output=false
[2388]	209	linker_options=""
[2385]	210	local_jobcatalog=""
[2380]	211	locat=normal
	212	makefile=""
	213	max_par_io_str=""
	214	prc=$0
	215	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	216	do
	217	prc=`echo $prc \| cut -f2- -d"/"`
	218	done
	219	module_calls=""
[2506]	220	palmrun_memory=""
[2380]	221	palmrun_script_name=$prc
	222	openmp=false
[2506]	223	previous_job=""
[2479]	224	project_account=""
[2380]	225	queue=none
[2906]	226	read_svf=""
[2380]	227	restart_run=false
	228	return_address=""
[2385]	229	remote_jobcatalog=""
[2380]	230	remote_username=""
	231	running_in_batch_mode=false
	232	run_coupled_model=false
	233	run_id=""
[3236]	234	run_id_number=""
	235	run_identifier=test
[2380]	236	silent=false
	237	source_list=""
	238	source_path=""
[2501]	239	tasks_per_node=0
[2380]	240	threads_per_task=1
	241	transfer_problems=false
[2384]	242	user_source_path=""
[2506]	243	use_existing_sources_folder=""
[2380]	244	use_openmp=false
[3033]	245	version="palmrun 1.0 Rev$Rev: 3312 $"
[2380]	246	working_directory=`pwd`
	247	write_binary=""
[2906]	248	write_svf=""
[2380]	249
	250
	251	# ERROR HANDLING IN CASE OF EXIT
[2404]	252	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	253	then
	254
	255	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	256	(( i = 0 ))
	257	while (( i < iec ))
	258	do
	259	(( i = i + 1 ))
	260	printf "\n *** Execution of ERROR-command:\n"
	261	printf " >>> ${err_command[$i]}\n"
	262	eval ${err_command[$i]}
	263	done
[2566]	264	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	265	printf "\n\n+++ palmrun crashed \n\n"
	266	exit 1
	267	elif [[ $locat != normal ]]
[2380]	268	then
[3312]	269	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	270	printf "\n+++ palmrun killed by \"^C\" \n\n"
	271	exit 2
	272	else
[2566]	273	printf "\n --> palmrun finished\n\n"
[3312]	274	exit 0
[2380]	275	fi' exit
	276
	277
	278	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	279	trap 'locat=control_c
	280	exit 1
[2380]	281	' 2
	282
	283
	284	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	285	# WHICH WILL BE USED TO START RESTART-JOBS
[3236]	286	while getopts :a:A:bBCd:FG:h:i:jkm:M:O:q:R:s:t:T:u:U:vVw:W:xX:yY:Z option
[2380]	287	do
	288	case $option in
	289	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	290	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	291	(b) create_batch_job=true; prc="$prc -b";;
	292	(B) delete_temporary_catalog=false; prc="$prc -B";;
	293	(C) restart_run=true; prc="$prc -C";;
[3236]	294	(d) run_identifier=$OPTARG; prc="$prc -d$OPTARG";;
[2380]	295	(F) create_jobfile_only=true;;
	296	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	297	(h) configuration_identifier=$OPTARG; prc="$prc -h$OPTARG";;
	298	(i) run_id_number=$OPTARG;;
[2380]	299	(j) running_in_batch_mode=true;;
	300	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	301	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	302	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	303	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	304	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	305	(R) return_address=$OPTARG;;
	306	(s) source_list=$OPTARG;;
[2501]	307	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	308	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	309	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	310	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	311	(v) silent=true; prc="$prc -v";;
[2506]	312	(V) use_existing_sources_folder="-V";;
[2380]	313	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	314	(W) previous_job=$OPTARG;;
[2380]	315	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	316	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	317	(y) ocean_file_appendix=true; prc="$prc -y";;
	318	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	319	(Z) combine_plot_fields=false; prc="$prc -Z";;
	320	(\?) printf "\n +++ unknown option $OPTARG \n"
	321	printf "\n --> type \"$0 ?\" for available options \n"
	322	locat=parameter;exit;;
	323	esac
	324	done
	325
	326
	327	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	328	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	329	(( to_shift = $OPTIND - 1 ))
	330	shift $to_shift
	331
	332	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	333	if [[ "$1" = "?" ]]
	334	then
	335	(printf "\n *** Description of available palmrun options:\n"
	336	printf "\n Option Description Default-Value"
	337	printf "\n -a activation string list \"\" "
[2479]	338	printf "\n -A project account number ---"
[2380]	339	printf "\n -b batch-job on local machine ---"
	340	printf "\n -B do not delete temporary directory at end ---"
[3025]	341	printf "\n -d run identifier test"
[2380]	342	printf "\n -F create batch job file only ---"
[2506]	343	printf "\n -h host configuration \"default\" "
[2380]	344	printf "\n -k keep data from previous run"
	345	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	346	printf "\n -M Makefile name Makefile"
	347	printf "\n -O threads per openMP task ---"
	348	printf "\n -q queue \"$queue\" "
	349	printf "\n -s filenames of routines to be compiled \"\" "
	350	printf "\n must end with .f, .f90, .F, or .c !"
	351	printf "\n use \"..\" for more than one file and wildcards"
	352	printf "\n -s LM compiles all locally modified files"
	353	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	354	printf "\n -T tasks per node ---"
[2380]	355	printf "\n -u username on remote machine \"\" "
	356	printf "\n -v no prompt for confirmation ---"
[2506]	357	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	358	printf "\n -w maximum parallel io streams as given by -X"
[2506]	359	printf "\n -W name of job to wait for ---"
[2380]	360	printf "\n -x tracing of palmrun for debug purposes ---"
	361	printf "\n -X # of processors (on parallel machines) 1"
	362	printf "\n -y add appendix \"_O\" to all local output"
	363	printf "\n files (ocean precursor runs followed by"
	364	printf "\n coupled atmosphere-ocean runs) ---"
	365	printf "\n -Y run coupled model, \"#1 #2\" with"
	366	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	367	printf "\n -Z skip combine_plot_fields at the end of "
	368	printf "\n the simulation ---"
	369	printf "\n "
	370	printf "\n Possible values of positional parameter <modus>:"
	371	printf "\n \"?\" - this outline \n\n") \| more
	372	exit
	373	elif [[ "$1" != "" ]]
	374	then
	375	printf "\n +++ positional parameter $1 unknown \n"
	376	locat=parameter; exit
	377	fi
	378
	379
	380
	381	# SHORT STARTING MESSAGE
	382	printf "\n*** $version "
	383	printf "\n will be executed. Please wait ..."
	384
	385
[3236]	386	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLES
	387	export fname=$run_identifier
	388	export jobname=$run_identifier
[2834]	389
	390
[2506]	391	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	392	config_file=.palm.config.$configuration_identifier
	393	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	394
	395
	396	# CHECK, IF CONFIGURATION FILE EXISTS
	397	if [[ ! -f $config_file ]]
	398	then
	399	printf "\n\n +++ configuration file: "
	400	printf "\n $config_file"
	401	printf "\n does not exist"
	402	locat=connect; exit
	403	fi
	404
	405
[2762]	406	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	407	if [[ -f .palm.iofiles ]]
	408	then
[3236]	409
	410	# CHECK VERSION MISMATCH
	411	if [[ $running_in_batch_mode != true ]]
	412	then
	413	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	414	then
	415	printf "\n\n +++ WARNING: A file connection file has been found in your"
	416	printf "\n working directory, but its revision does not match"
	417	printf "\n the revision of the default (trunk) version."
[3294]	418	printf "\n You may need to update your connection file"
	419	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	420	fi
	421	fi
	422
[2762]	423	fileconnection_file=.palm.iofiles
[3236]	424
[2762]	425	fi
	426
	427
[2380]	428	# CHECK, IF FILE CONNECTION FILE EXISTS
	429	if [[ ! -f $fileconnection_file ]]
	430	then
	431	printf "\n\n +++ file connection file: "
	432	printf "\n $fileconnection_file"
	433	printf "\n does not exist"
	434	locat=connect; exit
	435	fi
	436
	437
[2404]	438	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	439	if [[ "$activation_string_list" = "" ]]
	440	then
	441	printf "\n\n +++ no activation string list given: "
	442	printf "\n please set palmrun option \"-a\" "
	443	locat=palmrun_option; exit
	444	fi
	445
	446
	447	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	448	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	449	then
	450	write_binary=true
	451	else
	452	write_binary=false
	453	fi
	454
[2906]	455	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	456	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	457	then
	458	write_svf=true
	459	else
	460	write_svf=false
	461	fi
[2404]	462
[2906]	463	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	464	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	465	then
	466	read_svf=true
	467	else
	468	read_svf=false
	469	fi
	470
	471
[2380]	472	# READ AND EVALUATE THE CONFIGURATION-FILE
	473	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	474
	475	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	476	while read line
	477	do
	478
	479	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	480	eval line=\"$line\"
	481
	482
	483	# INTERPRET THE LINE
	484	if [[ "$(echo $line)" = "" ]]
	485	then
	486
	487	# EMPTY LINE, NO ACTION
	488	continue
	489
	490	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	491	then
	492
	493	# LINE IS A COMMENT LINE
	494	continue
	495
	496	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	497	then
	498
	499	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	500	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	501	value=`echo $line \| cut -d" " -s -f2-`
	502
	503
	504	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	505	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	506	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	507	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	508	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	509	# CONFIGURATION-FILE.
	510	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	511	then
	512	eval export $var="\$value"
	513
	514	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	515	if [[ $do_trace = true ]]
	516	then
	517	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	518	fi
	519	fi
	520
	521	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	522	then
	523
	524	# LINE DEFINES BATCH-DIRECTIVE
	525	(( ibd = ibd + 1 ))
	526	line=$(echo $line \| cut -c4-)
	527	batch_directive[$ibd]="$line"
	528
	529	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	530	then
	531
	532	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	533	# REMOTE TO A LOCAL HOST
	534	(( ibdt = ibdt + 1 ))
	535	line=$(echo $line \| cut -c5-)
	536	batch_directive_transfer[$ibdt]="$line"
	537
	538	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	539	then
	540
	541	# LINE DEFINES ERROR-COMMAND
	542	(( iec = iec + 1 ))
	543	line=$(echo $line \| cut -c4-)
	544	err_command[$iec]="$line"
	545
	546	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	547	then
	548
	549	# LINE DEFINES INPUT-COMMAND
	550	(( iic = iic + 1 ))
	551	line=$(echo $line \| cut -c4-)
	552	in_command[$iic]="$line"
	553
	554	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	555	then
	556
	557	# LINE DEFINES OUTPUT-COMMAND
	558	(( ioc = ioc + 1 ))
	559	line=$(echo $line \| cut -c4-)
	560	out_command[$ioc]="$line"
	561
	562	else
	563
	564	# SKIP ALL OTHER LINES
	565	continue
	566
	567	fi
	568
	569	done < $config_file
	570
	571
	572	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	573	if [[ "$fast_io_catalog" = "" ]]
	574	then
	575	printf "\n +++ no fast_io_catalog found in $config_file"
	576	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	577	locat=config_file; exit
	578	fi
[2380]	579	if [[ "$compiler_name" = "" ]]
	580	then
	581	printf "\n +++ no compiler name found in $config_file"
	582	printf "\n Please add line \"compiler_name ...\" to that file."
	583	locat=config_file; exit
	584	fi
	585	if [[ "$compiler_name_ser" = "" ]]
	586	then
	587	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	588	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	589	locat=config_file; exit
	590	fi
	591	if [[ "$compiler_options" = "" ]]
	592	then
	593	printf "\n +++ no compiler options found in $config_file"
	594	printf "\n Please add line \"compiler_options ...\" to that file."
	595	locat=config_file; exit
	596	fi
[2388]	597	if [[ "$linker_options" = "" ]]
[2380]	598	then
[2388]	599	printf "\n +++ no linker options found in $config_file"
	600	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	601	locat=config_file; exit
	602	fi
	603	if [[ "$execute_command" = "" ]]
	604	then
	605	printf "\n +++ no execute command found in $config_file"
	606	printf "\n Please add line \"execute_command ...\" to that file."
	607	locat=config_file; exit
	608	fi
	609
	610	if [[ "$hostfile" != "" ]]
	611	then
	612	if [[ $hostfile != auto && ! -f $hostfile ]]
	613	then
	614	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	615	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	616	locat=config_file; exit
	617	fi
	618	fi
	619
	620
	621	# DETERMINE THE CALL STATUS
	622	if [[ "$return_address" != "" ]]
	623	then
	624
	625	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	626	# BATCH MODE AND ...
	627	running_on_remote=true
	628
	629	else
	630
	631	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	632	if [[ "$remote_ip" != "" ]]
	633	then
	634
	635	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	636	create_remote_batch_job=true
	637
[3132]	638	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	639	if [[ "$remote_jobcatalog" = "" ]]
	640	then
	641	printf "\n +++ no remote jobcatalog found in $config_file"
	642	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	643	locat=config_file; exit
	644	fi
	645
	646
[2380]	647	fi
	648	running_on_remote=false
	649	fi
	650
	651
	652
	653	# READ AND EVALUATE THE I/O-FILE LIST
	654	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	655
	656	# READ THE FILE CONNECTION FILE LINE BY LINE
	657	while read line
	658	do
	659
[2669]	660	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	661	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	662
	663	# INTERPRET THE LINE
	664	if [[ "$(echo $line)" = "" ]]
	665	then
	666	# EMPTY LINE, NO ACTION
	667	continue
	668
	669	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	670	then
	671
	672	# LINE IS A COMMENT LINE
	673	true
	674
	675	else
	676
	677	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	678	# s2a: in/out - field
[2669]	679	# s2b: action - field (optional)
	680	s1=`echo "$line" \| cut -d" " -f1`
	681	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	682	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	683	then
[2669]	684	s2a=$s2
[2380]	685	s2b=""
	686	else
[2669]	687	s2a=`echo $s2 \| cut -d":" -f1`
	688	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	689	fi
[2669]	690	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	691	s4=`echo "$line" \| cut -d" " -s -f4`
	692	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	693	s5=`echo "$line" \| cut -d" " -s -f5`
	694	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	695
	696
	697	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	698	# INPUT- OR OUTPUT-LIST.
	699	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	700	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	701	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	702	# IS NOT CHECKED AND STORED.
[2610]	703	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	704	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	705	then
	706	found=false
	707	for actual in $activation_string_list
	708	do
	709	for formal in $s3
	710	do
	711	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	712	done
	713	done
	714	if [[ $found = true ]]
	715	then
	716	(( iin = iin + 1 ))
[2669]	717	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	718	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	719	if [[ "$s2a" = inopt ]]
	720	then
	721	optin_pre[$iin]=yes
	722	else
	723	optin_pre[$iin]=no
	724	fi
[2605]	725
	726	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	727	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	728	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	729	then
[2610]	730	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	731	fi
	732
[2610]	733	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	734	# THE WILDCARD FROM THE ENDING
	735	if [[ "${s5: -1}" = "*" ]]
	736	then
[2669]	737	if [[ "$s2b" = "di" ]]
[2610]	738	then
	739	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	740	printf "\n see file \"$fileconnection_file\", line"
	741	printf "\n$line"
	742	locat=iofiles_file; exit
	743	fi
	744	multin[$iin]=true
	745	string=${endin_pre[$iin]}
	746	endin_pre[$iin]="${string%?}"
	747	else
	748	multin[$iin]=false
	749	fi
[2380]	750	fi
[2669]	751	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	752	then
	753	found=false
	754	for actual in $activation_string_list
	755	do
	756	for formal in $s3
	757	do
[2670]	758	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	759	done
	760	done
	761	if [[ $found = true ]]
	762	then
	763	(( iout = iout + 1 ))
[2669]	764	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	765	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	766
[2669]	767	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	768	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	769	if [[ $formal = wildcard ]]
	770	then
	771	warnout_pre[$iout]=false
	772	else
	773	warnout_pre[$iout]=true
	774	fi
	775
[2610]	776	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	777	# THE WILDCARD FROM THE LOCAL FILENAME
	778	if [[ "${s1: -1}" = "*" ]]
	779	then
[2669]	780	if [[ "$s2b" = "di" ]]
[2610]	781	then
	782	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	783	printf "\n see file \"$fileconnection_file\", line"
	784	printf "\n$line"
	785	locat=iofiles_file; exit
	786	fi
	787	multout[$iout]=true
	788	string=${localout_pre[$iout]}
	789	localout_pre[$iout]="${string%?}"
	790	else
	791	multout[$iout]=false
	792	fi
[2380]	793	fi
[2669]	794	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	795	then
[2669]	796	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	797	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	798	locat=connect; exit
	799	fi
	800	IFS="$IFSALT"
	801	fi
	802
	803	done < $fileconnection_file
	804
	805
	806
[2501]	807	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	808	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	809	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	810	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	811	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	812	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	813
	814
	815
[2380]	816	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	817	if [[ $run_coupled_model = true ]]
	818	then
	819
	820	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	821	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	822
	823	if (( $cores_ocean + $cores_atmos != $cores ))
	824	then
	825
	826	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	827	printf "\n PEs (total) : $cores"
	828	printf "\n PEs (atmosphere): $cores_atmos"
	829	printf "\n PEs (ocean) : $cores_ocean"
	830	locat=coupling; exit
	831
	832	fi
	833
	834	fi
	835
	836
	837	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	838	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	839	# FOLDER
	840	if [[ $running_in_batch_mode = true ]]
	841	then
	842
[2506]	843	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	844	then
[2506]	845	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	846	printf "\n Please check the output of the palmrun-call"
	847	printf "\n that you did on your local host."
	848	locat=SOURCES_FOR_RUN; exit
	849	fi
	850
	851	else
	852
	853	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	854	# AUTOMATIC RESTART RUN
	855	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	856	if [[ $restart_run = false ]]
	857	then
	858
	859	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	860	# THE LOCAL HOST
	861	if [[ ! -d $source_path ]]
	862	then
	863	printf "\n\n +++ source path \"$source_path\" on local host"
	864	printf "\n \"$(hostname)\" does not exist"
	865	locat=source_path; exit
	866	fi
	867
[2990]	868	rm -rf ${base_directory}/${sources_for_run_catalog}
	869	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	870
	871	if [[ "$source_list" = LM ]]
	872	then
	873
	874	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	875	source_list=""
	876	cd $source_path
	877
	878
[2512]	879	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	880	if [[ ! -d ../.svn ]]
[2380]	881	then
	882	printf "\n\n +++ source directory"
	883	printf "\n \"$source_path\" "
	884	printf "\n is not under control of \"subversion\"."
[2512]	885	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	886	fi
	887
	888
	889	# LIST ALL MODIFIED SOURCE CODE FILES
	890	Filenames=""
[2404]	891	svn status > tmp_svnstatus
[2380]	892	while read line
	893	do
	894	firstc=`echo $line \| cut -c1`
	895	if [[ $firstc = M \|\| $firstc = "?" ]]
	896	then
	897	Name=`echo "$line" \| cut -c8-`
	898	extension=`echo $Name \| cut -d. -f2`
	899	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	900	then
	901	Filenames="$Filenames "$Name
	902	fi
	903	fi
[2404]	904	done < tmp_svnstatus
	905	rm -rf tmp_svnstatus
[2380]	906
	907
	908	# COPY FILES TO SOURCES_FOR_RUN_...
	909	for filename in $Filenames
	910	do
[2990]	911	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	912	source_list=$source_list"$filename "
	913	done
	914
	915	cd - > /dev/null
	916
	917
	918	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	919	elif [[ "$source_list" != "" ]]
	920	then
	921
	922	cd $source_path
	923
	924	for filename in $source_list
	925	do
	926
	927	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	928	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	929	then
	930	printf "\n +++ source code file: $filename"
	931	printf "\n must not contain (\"/\") "
	932	locat=source; exit
	933	fi
	934
	935	if [[ ! -f $filename ]]
	936	then
	937	printf "\n +++ source code file: $filename"
	938	printf "\n does not exist"
	939	locat=source; exit
	940	else
[2990]	941	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	942	fi
	943
	944	done
	945
	946	cd - > /dev/null
	947
	948	fi
	949
	950	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	951	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	952	if [[ ! -f $makefile ]]
	953	then
	954	printf "\n +++ file \"$makefile\" does not exist"
	955	locat=make; exit
	956	else
[2990]	957	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	958	fi
	959
	960
	961	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	962	if [[ "$user_source_path" != "" ]]
[2380]	963	then
	964
	965	# DOES THE DIRECTORY EXIST?
[2384]	966	if [[ ! -d $user_source_path ]]
[2380]	967	then
	968
	969	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	970	printf "\n \"$user_source_path\" "
[2380]	971	printf "\n does not exist or is not a directory."
	972	printf "\n No source code will be used from this directory!\n"
[2384]	973	user_source_path=""
[2380]	974	if [[ $silent == false ]]
	975	then
	976	sleep 2
	977	fi
	978
	979	else
	980
[2384]	981	cd $user_source_path
[2380]	982
	983	Names=$(ls -1 *.f90 2>&1)
	984	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	985	Names=$(ls -1 *.F90 2>&1)
	986	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	987	Names=$(ls -1 *.F 2>&1)
	988	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	989	Names=$(ls -1 *.f 2>&1)
	990	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	991	Names=$(ls -1 *.c 2>&1)
	992	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	993
	994	cd - > /dev/null
[2990]	995	cd ${base_directory}/${sources_for_run_catalog}
[2380]	996
	997	# COPY MAKEFILE IF EXISTING
[2384]	998	if [[ -f $user_source_path/Makefile ]]
[2380]	999	then
	1000	printf "\n\n *** user Makefile from directory"
[2384]	1001	printf "\n \"$user_source_path\" is used \n"
[2380]	1002	if [[ $silent == false ]]
	1003	then
	1004	sleep 1
	1005	fi
[2384]	1006	cp $user_source_path/Makefile .
[2380]	1007	fi
	1008
	1009	for filename in $AddFilenames
	1010	do
	1011	if [[ -f $filename ]]
	1012	then
	1013	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1014	printf "\n source code directory \"$user_source_path\" "
[2380]	1015	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1016	printf "\n from directory \"$source_path\"."
	1017	locat=source; exit
	1018	fi
	1019
[2384]	1020	cp $user_source_path/$filename .
[2380]	1021	source_list="$source_list $filename"
	1022
	1023	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1024	if [[ $(grep -c $filename Makefile) = 0 ]]
	1025	then
	1026	printf "\n\n +++ user file \"$filename\" "
	1027	printf "\n is not listed in Makefile \n"
	1028	locat=source; exit
	1029	fi
	1030	done
	1031	cd - > /dev/null
	1032	fi
	1033	fi
	1034
	1035	# COPY CONFIGURATION FILES
[2990]	1036	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1037	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1038
	1039	# COPY SHELLSCRIPTS
[2990]	1040	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1041	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1042
	1043	fi
	1044
	1045	fi
	1046
[2605]	1047
[2380]	1048	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1049	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1050	if [[ "$global_revision" = "" ]]
	1051	then
	1052	global_revision=`svnversion $source_path 2>/dev/null`
	1053	global_revision="Rev: $global_revision"
	1054	fi
	1055
	1056
	1057	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1058	if [[ -n $cores ]]
	1059	then
	1060
	1061	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1062	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1063	if [[ $tasks_per_node = 0 ]]
[2380]	1064	then
[3025]	1065	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1066	then
	1067	printf "\n"
	1068	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1069	printf "\n set -T option or define tasks_per_node in the config file"
	1070	locat=tasks_per_node; (( iec = 0 )); exit
	1071	else
	1072	# DEFAULT FOR INTERACTIVE RUN
	1073	tasks_per_node=$cores
	1074	fi
[2380]	1075	fi
	1076
	1077	if (( cores < tasks_per_node ))
	1078	then
	1079	printf "\n"
	1080	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1081	printf "\n given values: -T $tasks_per_node -X $cores"
	1082	locat=tasks_per_node; (( iec = 0 )); exit
	1083	fi
	1084
	1085	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1086	(( mpi_tasks = cores / threads_per_task ))
	1087	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1088	(( ii = cores / tasks_per_node ))
	1089	(( remaining_cores = cores - ii * tasks_per_node ))
	1090	if (( remaining_cores > 0 ))
	1091	then
	1092	printf "\n"
	1093	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1094	printf "\n divisor of the total number of cores (option \"-X\")"
	1095	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1096	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1097	(( nodes = nodes + 1 ))
	1098	fi
	1099
	1100	fi
	1101
	1102
	1103	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1104	if [[ "$maximum_parallel_io_streams" = "" ]]
	1105	then
	1106	maximum_parallel_io_streams=$cores
	1107	fi
	1108
	1109
	1110	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1111	if [[ "$scp_port" != "" ]]
	1112	then
	1113	PORTOPT="-P $scp_port"
	1114	SSH_PORTOPT="-p $scp_port"
	1115	fi
	1116
	1117
	1118	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1119	# CONFIG-FILE
	1120	if [[ "$ssh_key" != "" ]]
	1121	then
	1122	ssh_key="-i $HOME/.ssh/$ssh_key"
	1123	fi
	1124
	1125
	1126	# SET QUEUE, IF NOT GIVEN
	1127	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1128	then
	1129
	1130	if [[ $queue = none && "$defaultqueue" = "" ]]
	1131	then
	1132	printf "\n"
	1133	printf "\n +++ no default queue given in configuration file and no queue"
	1134	printf "\n given with option -q"
[2789]	1135	locat=queue; exit
[2380]	1136	fi
	1137	if [[ $queue = none ]]
	1138	then
	1139	queue=$defaultqueue
	1140	fi
	1141
	1142	fi
	1143
	1144
	1145	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1146	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1147	(( i = 0 ))
[2610]	1148	(( nr_of_input_files = 0 ))
[2380]	1149	while (( i < iin ))
	1150	do
	1151	(( i = i + 1 ))
	1152
	1153	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1154	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1155	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1156	then
[2610]	1157	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1158	else
[3236]	1159	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1160	fi
	1161
[2610]	1162
[2380]	1163	# CHECK IF FILE EXISTS
	1164	if ! ls $filename* 1>/dev/null 2>&1
	1165	then
	1166
[2669]	1167	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1168	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1169	then
	1170	printf "\n\n +++ INPUT-file: "
[2610]	1171	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1172	then
	1173	printf "\n $filename"
	1174	else
[2610]	1175	printf "\n $filename.${extin_pre[$i]}"
[2380]	1176	fi
	1177	printf "\n does not exist\n"
	1178	locat=input; exit
	1179	else
[2610]	1180	(( nr_of_input_files = nr_of_input_files + 1 ))
	1181	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1182	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1183	actionin[$nr_of_input_files]="unavailable"
[2610]	1184	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1185	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1186	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1187	fi
[2605]	1188
[2380]	1189	else
	1190
[3236]	1191	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1192	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1193	# ENDINGS
[2610]	1194	if [[ "${multin[$i]}" = true ]]
	1195	then
	1196	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1197	ls -1 -d ${filename} > filelist 2>/dev/null
	1198	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1199	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1200
[2610]	1201	endings=""
	1202	while read line
	1203	do
	1204	# filename without path (i.e. after the last "/")
	1205	basefilename=$(basename ${line})
[2380]	1206
[2610]	1207	# check if there is an extension and remove it
	1208	ext=${basefilename##*.}
	1209	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1210	then
	1211	basefilename=${basefilename%.*}
	1212	fi
[2380]	1213
[2610]	1214	# check for an existing cycle number and remove it
	1215	cycle=${basefilename##*.}
	1216	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1217	then
	1218	basefilename=${basefilename%.*}
	1219	fi
[2600]	1220
[3236]	1221	# remove the run_identifier from the beginning
	1222	length_run_identifier=${#run_identifier}
	1223	ending=${basefilename:${length_run_identifier}}
[2610]	1224
	1225	# remove the ending given in the .iofiles from the beginning
	1226	endingstring="${endin_pre[$i]}"
	1227	length_ending=${#endingstring}
	1228	ending=${ending:${length_ending}}
	1229
	1230	if [[ "$ending" = "" ]]
[2600]	1231	then
[2610]	1232	# standard ending as given in the .iofiles
	1233	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1234	then
	1235	endings="$endings DEFAULT"
	1236	fi
[2600]	1237	else
[2610]	1238	# ending must start with "_", otherwise its a different file
	1239	if [[ "${ending:0:1}" = "_" ]]
	1240	then
	1241	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1242	then
	1243	endings="$endings $ending"
	1244	fi
	1245	fi
[2600]	1246	fi
[2610]	1247
	1248	done <filelist
[2380]	1249
[2610]	1250	rm filelist
[2380]	1251
[2600]	1252	else
[2610]	1253
	1254	# SINGLE NAME
	1255	endings=DEFAULT
	1256
[2600]	1257	fi
	1258
[2610]	1259	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1260	for ending in $endings
	1261	do
	1262
	1263	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1264	if [[ $ending = DEFAULT ]]
[2380]	1265	then
[2610]	1266	ending=""
	1267	fi
	1268
	1269	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1270	(( nr_of_input_files = nr_of_input_files + 1 ))
	1271	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1272	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1273	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1274	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1275	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1276	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1277
	1278
	1279	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1280	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1281	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1282	then
	1283	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1284	else
[3236]	1285	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1286	fi
[2610]	1287
	1288	# DETERMINE THE FILE'S CYCLE NUMBER
	1289	(( maxcycle = 0 ))
	1290	ls -1 -d $filename > filelist 2>/dev/null
	1291	ls -1 -d $filename.* >> filelist 2>/dev/null
	1292	while read line
	1293	do
	1294	# filename without path (i.e. after the last "/")
	1295	basefilename=$(basename ${line})
	1296
	1297	# check if there is an extension
	1298	extension=${basefilename##*.}
	1299	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1300	then
	1301	basefilename=${basefilename%.*}
	1302	fi
	1303
	1304	# check for an existing cycle number
	1305	cycle=${basefilename##*.}
	1306	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1307	then
[2669]	1308	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1309	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1310	(( icycle = $((10#$cycle)) ))
[2610]	1311	else
	1312	(( icycle = 0 ))
	1313	fi
	1314
	1315	if (( icycle > maxcycle ))
	1316	then
	1317	(( maxcycle = icycle ))
	1318
	1319	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1320	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1321	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1322	then
	1323	leading_zero=true
	1324	else
	1325	leading_zero=false
	1326	fi
	1327	fi
	1328
	1329	done <filelist
	1330	rm filelist
	1331
	1332	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1333	if [[ $leading_zero = true ]]
[2380]	1334	then
[2610]	1335	cyclestring=`printf "%03d" $maxcycle`
	1336	else
	1337	cyclestring=$maxcycle
[2380]	1338	fi
[2610]	1339
	1340	# APPEND CYCLE NUMBER TO FILENAME
	1341	if (( maxcycle > 0 ))
[2380]	1342	then
[2610]	1343	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1344	then
	1345	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1346	else
	1347	filename=${filename}.$cyclestring
	1348	fi
[2380]	1349	else
[2610]	1350	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1351	then
	1352	filename=${filename}.${extin[$nr_of_input_files]}
	1353	fi
[2380]	1354	fi
[2610]	1355
	1356	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1357	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1358	absnamein[$nr_of_input_files]=$filename
	1359	if (( maxcycle > 0 ))
[2380]	1360	then
[2610]	1361	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1362	then
	1363	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1364	else
[3236]	1365	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1366	fi
[2380]	1367	else
[2610]	1368	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1369	then
	1370	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1371	else
[3236]	1372	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1373	fi
[2380]	1374	fi
	1375
[2610]	1376	done
	1377
[2380]	1378	fi
[2610]	1379
[2380]	1380	done
	1381
[2610]	1382
[2380]	1383	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1384	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1385	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1386	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1387	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1388	# REMOTE HOST)
	1389	(( i = 0 ))
	1390	while (( i < iout ))
	1391	do
	1392	(( i = i + 1 ))
[2610]	1393	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1394	then
[2610]	1395	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1396	then
[2610]	1397	actionout_pre[$i]=""
	1398	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1399	then
[2610]	1400	actionout_pre[$i]=pe
	1401	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1402	then
[2610]	1403	actionout_pre[$i]=a
[2380]	1404	fi
	1405	(( maxcycle = 0 ))
[3236]	1406	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1407	eval catalogname=${pathout_pre[$i]}
[2380]	1408	if ! ls $filename* 1>/dev/null 2>&1
	1409	then
	1410
	1411	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1412	if cat /dev/null > $filename
	1413	then
	1414	rm $filename
	1415	else
	1416
	1417	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1418	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1419	if [[ ! -d $catalogname ]]
	1420	then
	1421	if mkdir -p $catalogname
	1422	then
	1423	printf "\n\n *** directory:"
	1424	printf "\n $catalogname"
	1425	printf "\n was created\n"
	1426	else
	1427	printf "\n\n +++ OUTPUT-file:"
	1428	printf "\n $filename"
	1429	printf "\n cannot be created, because directory does not exist"
	1430	printf "\n and cannot be created either"
	1431	printf "\n"
	1432	locat=output ; exit
	1433	fi 2>/dev/null
	1434	else
	1435	printf "\n\n +++ OUTPUT-file:"
	1436	printf "\n $filename"
	1437	printf "\n cannot be created, although directory exists"
	1438	printf "\n"
	1439	locat=output ; exit
	1440	fi
	1441	fi 2>/dev/null
	1442
	1443	fi
	1444
	1445	fi
	1446	done
	1447
	1448
	1449	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1450	if [[ $running_in_batch_mode = false ]]
	1451	then
[3236]	1452	run_id_number=$RANDOM
	1453	run_id=${run_identifier}.$run_id_number
[2380]	1454
[3236]	1455	tempdir=$fast_io_catalog/$run_id
[2380]	1456	fi
	1457
	1458
	1459	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1460	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1461	then
	1462
	1463	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1464	if [[ $ibd = 0 ]]
	1465	then
	1466	printf "\n"
	1467	printf "\n +++ no batch directives found in configuration file"
	1468	locat=config_file_batch_directives; (( iec = 0 )); exit
	1469	fi
	1470
	1471	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1472	done=false
[2384]	1473	cputime=$cpumax
[2380]	1474	while [[ $done = false ]]
	1475	do
[2384]	1476	if (( cputime == 0 ))
[2380]	1477	then
	1478	printf "\n +++ cpu-time is undefined"
	1479	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1480	printf "\n >>> "
[2384]	1481	read cputime 1>/dev/null 2>&1
[2380]	1482	else
	1483	done=true
	1484	fi
	1485	done
[2420]	1486	cpumax=$cputime
[2380]	1487
	1488	# CHECK THE MEMORY DEMAND
	1489	done=false
	1490	while [[ $done = false ]]
	1491	do
	1492	if (( memory == 0 ))
	1493	then
	1494	printf "\n +++ memory demand is undefined"
	1495	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1496	printf "\n >>> "
	1497	read memory 1>/dev/null 2>&1
	1498	else
	1499	done=true
	1500	fi
	1501	done
	1502
	1503	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1504	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1505	then
	1506	while [[ -z $remote_username ]]
	1507	do
[2420]	1508	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1509	printf "\n >>> Please type username:"
	1510	printf "\n >>> "
	1511	read remote_username
	1512	done
	1513	fi
	1514
	1515	else
	1516
[2420]	1517	if [[ $running_in_batch_mode = false ]]
	1518	then
	1519	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1520	cpumax=$cputime
	1521	else
	1522	cputime=$cpumax
	1523	fi
[2380]	1524
	1525	fi
	1526
	1527
	1528	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1529	(( cpu_hours = cputime / 3600 ))
	1530	(( resttime = cputime - cpu_hours * 3600 ))
	1531	(( cpu_minutes = resttime / 60 ))
	1532	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1533	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1534
	1535
	1536	# OUTPUT OF THE PALMRUN-HEADER
	1537	calltime=$(date)
	1538	printf "\n"
	1539	printf "#------------------------------------------------------------------------# \n"
	1540	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1541	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1542	printf "\| \| \n"
	1543	column1="called on:"; column2=$(hostname)
	1544	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1545	if [[ $create_remote_batch_job = true ]]
	1546	then
[3236]	1547	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1548	else
	1549	if [[ $running_on_remote = true ]]
	1550	then
[3236]	1551	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1552	else
[3236]	1553	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1554	fi
	1555	fi
	1556	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1557
	1558	column1="running in:"
	1559	if [[ $running_in_batch_mode = true ]]
	1560	then
	1561	column2="batch job mode"
	1562	else
	1563	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1564	then
	1565	column2="job creation mode"
	1566	else
	1567	column2="interactive run mode"
	1568	fi
	1569	fi
	1570	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1571
[2479]	1572	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1573	then
[2480]	1574	if [[ "$project_account" != "" ]]
[2479]	1575	then
	1576	column1="project account number:"
	1577	column2="$project_account"
	1578	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1579	fi
	1580	fi
	1581
[2380]	1582	if [[ -n $cores ]]
	1583	then
	1584	if [[ $run_coupled_model = false ]]
	1585	then
	1586	column1="number of cores:"; column2=$cores
	1587	else
	1588	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1589	fi
	1590	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1591	fi
	1592	if [[ -n $tasks_per_node ]]
	1593	then
	1594	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1595	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1596	if (( remaining_cores > 0 ))
	1597	then
	1598	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1599	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1600	fi
	1601	fi
	1602	if [[ $maximum_parallel_io_streams != $cores ]]
	1603	then
	1604	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1605	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1606	fi
	1607	if [[ $use_openmp = true ]]
	1608	then
	1609	column1="threads per task:"; column2="$threads_per_task"
	1610	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1611	fi
[2384]	1612	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1613	then
[2506]	1614	column1="memory demand / PE":; column2="$memory MB"
	1615	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1616	column1="job cpu time (h:m:s):"; column2="$timestring"
	1617	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1618	fi
[2380]	1619	printf "\| \| \n"
	1620	if [[ "$source_list" != "" ]]
	1621	then
	1622	if [[ "$make_options" != "" ]]
	1623	then
	1624	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1625	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1626	line=$(echo "$make_options" \| cut -c46-)
	1627	while [[ "$line" != "" ]]
	1628	do
	1629	column1=""
	1630	column2=$(echo "$line" \| cut -c-45)
	1631	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1632	line=$(echo "$line" \| cut -c46-)
	1633	done
	1634	fi
	1635	fi
	1636
	1637	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1638	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1639	line=$(echo "$cpp_options" \| cut -c46-)
	1640	while [[ "$line" != "" ]]
	1641	do
	1642	column1=""
	1643	column2=$(echo "$line" \| cut -c-45)
	1644	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1645	line=$(echo "$line" \| cut -c46-)
	1646	done
	1647
	1648	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1649	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1650	line=$(echo "$compiler_options" \| cut -c46-)
	1651	while [[ "$line" != "" ]]
	1652	do
	1653	column1=""
	1654	column2=$(echo "$line" \| cut -c-45)
	1655	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1656	line=$(echo "$line" \| cut -c46-)
	1657	done
	1658
[2388]	1659	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1660	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1661	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1662	while [[ "$line" != "" ]]
	1663	do
	1664	column1=""
	1665	column2=$(echo "$line" \| cut -c-45)
	1666	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1667	line=$(echo "$line" \| cut -c46-)
	1668	done
	1669
	1670	if [[ "$login_init_cmd" != "" ]]
	1671	then
	1672	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1673	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1674	line=$(echo "$login_init_cmd" \| cut -c46-)
	1675	while [[ "$line" != "" ]]
	1676	do
	1677	column1=""
	1678	column2=$(echo "$line" \| cut -c-45)
	1679	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1680	line=$(echo "$line" \| cut -c46-)
	1681	done
	1682	fi
	1683
	1684	if [[ "$module_commands" != "" ]]
	1685	then
	1686	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1687	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1688	line=$(echo "$module_commands" \| cut -c46-)
	1689	while [[ "$line" != "" ]]
	1690	do
	1691	column1=""
	1692	column2=$(echo "$line" \| cut -c-45)
	1693	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1694	line=$(echo "$line" \| cut -c46-)
	1695	done
	1696	fi
	1697	printf "\| \| \n"
[3236]	1698	column1="run identifier:"; column2=$run_identifier
[2380]	1699	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1700	column1="activation string list:"; column2=$(echo $activation_string_list)
	1701	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1702
	1703	if [[ "$ocean_file_appendix" = true ]]
	1704	then
	1705	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1706	fi
	1707
	1708	if [[ "$source_list" != "" ]]
	1709	then
	1710	printf "\| \| \n"
	1711	printf "\| Files to be compiled: \| \n"
	1712	line=$source_list
	1713	while [[ "$line" != "" ]]
	1714	do
	1715	linestart=$(echo $line \| cut -c-70)
	1716	printf "\| %-70s \| \n" "$linestart"
	1717	line=$(echo "$line" \| cut -c71-)
	1718	done
	1719	fi
	1720	printf "#------------------------------------------------------------------------#"
	1721
	1722
	1723
	1724	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1725	if [[ $do_trace = true ]]
	1726	then
	1727	(( i = 0 ))
[2610]	1728	while (( i < nr_of_input_files ))
[2380]	1729	do
	1730	(( i = i + 1 ))
	1731	if (( i == 1 ))
	1732	then
	1733	printf "\n\n >>> INPUT-file assignments:\n"
	1734	fi
	1735	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1736	done
	1737	(( i = 0 ))
	1738	while (( i < iout ))
	1739	do
	1740	(( i = i + 1 ))
	1741	if (( i == 1 ))
	1742	then
	1743	printf "\n\n >>> OUTPUT-file assignments:\n"
	1744	fi
	1745	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1746	done
	1747	(( i = 0 ))
	1748	while (( i < iic ))
	1749	do
	1750	(( i = i + 1 ))
	1751	if (( i == 1 ))
	1752	then
	1753	printf "\n\n >>> INPUT-commands:\n"
	1754	fi
	1755	printf "\n ${in_command[$i]}"
	1756	done
	1757	(( i = 0 ))
	1758	while (( i < ioc ))
	1759	do
	1760	(( i = i + 1 ))
	1761	if (( i == 1 ))
	1762	then
	1763	printf "\n\n >>> OUTPUT-commands:\n"
	1764	fi
	1765	printf "\n ${out_command[$i]}"
	1766	done
	1767	fi
	1768
	1769	# QUERY FOR CONTINUE
	1770	if [[ $silent = false && $running_in_batch_mode = false ]]
	1771	then
	1772	antwort=dummy
	1773	printf "\n\n"
	1774	printf " >>> everything o.k. (y/n) ? "
	1775	while read antwort
	1776	do
	1777	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1778	then
	1779	printf " >>> everything o.k. (y/n) ? "
	1780	else
	1781	break
	1782	fi
	1783	done
	1784	if [[ $antwort = n \|\| $antwort = N ]]
	1785	then
	1786	locat=user_abort; (( iec = 0 )); exit
	1787	fi
	1788	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1789	then
[2566]	1790	printf "\n *** batch-job will be created and submitted"
[2380]	1791	else
[2566]	1792	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1793	fi
	1794	fi
	1795
	1796
	1797
	1798	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1799	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1800	then
	1801
	1802	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1803	then
[2566]	1804	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1805	else
[2566]	1806	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1807	fi
	1808
[2422]	1809	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1810	# IT SHALL BE CREATED
	1811	ask_for_make_depository=false
	1812	if [[ $create_remote_batch_job = true ]]
	1813	then
	1814
	1815	line=`grep %base_directory $config_file`
[3236]	1816	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
	1817	echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1818
[3236]	1819	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1820	then
	1821	printf "\n\n +++ make depository \"${make_depository}\""
	1822	printf "\n on remote host not found!"
	1823	ask_for_make_depository=true
	1824	fi
[3236]	1825	rm ${configuration_identifier}_last_make_protokoll
[2422]	1826
	1827	else
	1828
	1829	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1830	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1831	if [[ ! -d ${make_depository} ]]
	1832	then
	1833	printf "\n\n +++ make depository \"${make_depository}\""
	1834	printf "\n on local host not found!"
	1835	ask_for_make_depository=true
	1836	fi
	1837
	1838	fi
	1839
	1840	if [[ $ask_for_make_depository = true ]]
	1841	then
	1842
	1843	antwort=dummy
	1844	printf "\n\n"
	1845	printf " >>> Create a new one (y/n) ? "
	1846	while read antwort
	1847	do
	1848	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1849	then
	1850	printf " >>> Create a new one (y/n) ? "
	1851	else
	1852	break
	1853	fi
	1854	done
	1855	if [[ $antwort = n \|\| $antwort = N ]]
	1856	then
	1857	locat=user_abort; (( iec = 0 )); exit
	1858	fi
	1859
[2566]	1860	if [[ $do_trace = true ]]
	1861	then
[3236]	1862	palmbuild -h $configuration_identifier
[2566]	1863	else
[3236]	1864	palmbuild -v -h $configuration_identifier
[2566]	1865	fi
[2422]	1866
[3312]	1867	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1868	then
	1869
	1870	# ABORT IN CASE OF COMPILATION PROBLEMS
	1871	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1872	locat=make_depository
	1873	exit
	1874	else
	1875	echo " *** now continue with creating executable and other sources"
	1876	fi
	1877
	1878	fi
	1879
[2566]	1880	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3236]	1881	palmbuild -v $use_existing_sources_folder -h $configuration_identifier -d $run_identifier
[2380]	1882
[3312]	1883	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1884	then
	1885
	1886	# ABORT IN CASE OF COMPILATION PROBLEMS
	1887	printf "\n +++ error while creating executable and/or other sources"
	1888	locat=execution
[2990]	1889	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1890	exit
	1891
	1892	else
	1893
[2566]	1894	printf " *** executable and other sources created\n"
[2990]	1895	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1896
	1897	fi
	1898
	1899	fi
	1900
	1901
[2669]	1902	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1903	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1904	if [[ $create_remote_batch_job = true ]]
	1905	then
	1906	(( i = 0 ))
[2610]	1907	while (( i < nr_of_input_files ))
[2605]	1908	do
	1909	(( i = i + 1 ))
[2669]	1910	if [[ "${actionin[$i]}" = tr ]]
[2605]	1911	then
	1912	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1913	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1914	fi
	1915	done
	1916	if (( i > 0 ))
	1917	then
[3025]	1918	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1919	fi
	1920	fi
	1921
	1922
[2380]	1923	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1924	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1925	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1926	then
	1927
	1928	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1929	if [[ $running_in_batch_mode = false ]]
	1930	then
	1931	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1932	# FOLDER
[2566]	1933	mkdir -p $tempdir
	1934	chmod go+rx $tempdir
	1935	cd $tempdir
	1936	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1937	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1938
	1939	else
	1940
	1941	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1942	printf "\n *** running in temporary directory: $tempdir"
[2380]	1943
	1944	fi
	1945
	1946
	1947	# PROVIDE THE INPUT FILES
	1948	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1949	optional_files_missing=false
[2380]	1950	(( i = 0 ))
[2610]	1951	while (( i < nr_of_input_files ))
[2380]	1952	do
	1953	(( i = i + 1 ))
	1954	if (( i == 1 ))
	1955	then
	1956	printf "\n\n *** providing INPUT-files:\n$dashes"
	1957	fi
	1958
	1959
	1960	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1961	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1962	then
[2669]	1963	optional_files_missing=true
[2380]	1964	continue
	1965	fi
	1966
	1967	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1968	files_for_cores=false; filetype=file
	1969	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1970	then
	1971	files_for_cores=true; filetype=files
	1972	actionin[$i]=""
	1973	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1974	then
	1975	actionin[$i]=""
	1976	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1977	then
	1978	files_for_cores=true; filetype=files
	1979	actionin[$i]="ln"
	1980	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1981	then
	1982	actionin[$i]="ln"
	1983	fi
	1984
	1985	if [[ $files_for_cores = true ]]
	1986	then
	1987	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1988	else
	1989	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1990	fi
	1991
	1992	# INPUT-FILES TO BE LINKED
	1993	if [[ "${actionin[$i]}" = ln ]]
	1994	then
	1995
	1996	printf "\n $filetype will be linked"
	1997	if [[ $files_for_cores = false ]]
	1998	then
	1999	if [[ -f "${absnamein[$i]}" ]]
	2000	then
	2001	ln ${absnamein[$i]} ${localin[$i]}
	2002	got_tmp[$i]=true
	2003	fi
	2004	else
	2005	if [[ -d "${absnamein[$i]}" ]]
	2006	then
[2396]	2007	mkdir -p ${localin[$i]}
[2380]	2008	cd ${absnamein[$i]}
	2009	for file in $(ls *)
	2010	do
[2566]	2011	ln $file $tempdir/${localin[$i]}
[2380]	2012	done >\|/dev/null 2>&1
[2566]	2013	cd $tempdir
[2380]	2014	fi
	2015
	2016	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2017	if [[ ! -f "${localin[$i]}/_000000" ]]
	2018	then
	2019	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2020	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2021	fi
	2022
	2023	got_tmp[$i]=true
	2024	fi
	2025	fi
	2026
	2027	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2028	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2029	then
	2030
	2031	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2032	then
	2033
	2034	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2035	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2036	printf "\n file will be provided for $cores processors"
[2396]	2037	mkdir -p ${localin[$i]}
[2380]	2038	ival=$cores
	2039	(( ii = 0 ))
	2040	while (( ii <= ival-1 ))
	2041	do
	2042	if (( ii < 10 ))
	2043	then
	2044	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2045	elif (( ii < 100 ))
	2046	then
	2047	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2048	elif (( ii < 1000 ))
	2049	then
	2050	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2051	else
	2052	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2053	fi
	2054	(( ii = ii + 1 ))
	2055	done
	2056
	2057	else
	2058
	2059	if [[ $files_for_cores = true ]]
	2060	then
	2061
	2062	# PROVIDE FILES FOR EACH CORE
	2063	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2064	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2065	printf "\n providing $cores files for the respective cores"
[2396]	2066	mkdir -p ${localin[$i]}
[2380]	2067	if [[ $link_local_input = true ]]
	2068	then
	2069	printf " files will be linked\n"
	2070	cd ${absnamein[$i]}
	2071	for file in $(ls *)
	2072	do
	2073	ln -f $file ${localin[$i]}
	2074	done
[2566]	2075	cd $tempdir
[2380]	2076	fi
	2077
	2078	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2079	if [[ ! -f "${localin[$i]}/_000000" ]]
	2080	then
	2081	if [[ $link_local_input = true ]]
	2082	then
	2083	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2084	fi
	2085	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2086	fi
	2087
	2088	else
	2089
	2090	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2091	if [[ $link_local_input = true ]]
	2092	then
	2093	printf " file will be linked\n"
	2094	ln -f ${absnamein[$i]} ${localin[$i]}
	2095	fi
[2605]	2096	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2097	if [[ ! -f "${localin[$i]}" ]]
	2098	then
	2099	if [[ $link_local_input = true ]]
	2100	then
	2101	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2102	fi
[2669]	2103	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2104	then
	2105	mv ${absnamein[$i]} ${localin[$i]}
	2106	else
	2107	cp ${absnamein[$i]} ${localin[$i]}
	2108	fi
[2380]	2109	fi
	2110	fi
	2111	fi
	2112	fi
	2113
	2114	done
	2115	if (( i != 0 ))
	2116	then
[2669]	2117	if [[ $optional_files_missing = true ]]
	2118	then
	2119	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2120	fi
[2380]	2121	printf "\n$dashes\n *** all INPUT-files provided \n"
	2122	fi
	2123
	2124
	2125	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2126	(( i = 0 ))
	2127	while (( i < iic ))
	2128	do
	2129	(( i = i + 1 ))
	2130	if (( i == 1 ))
	2131	then
	2132	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2133	fi
	2134	printf "\n >>> ${in_command[$i]}"
	2135	eval ${in_command[$i]}
	2136	if (( i == iic ))
	2137	then
	2138	printf "\n$dashes\n"
	2139	fi
	2140	done
	2141
	2142
	2143	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2144	# (FILE ENVPAR WILL BE READ BY PALM)
	2145	cat > ENVPAR << EOF
[3236]	2146	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2147	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2148	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2149	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2150	maximum_cpu_time_allowed = ${cpumax}.,
	2151	revision = '$global_revision',
	2152	batch_job = .${running_in_batch_mode}. /
	2153
	2154	EOF
	2155
	2156
	2157	# STARTING THE EXECUTABLE
	2158	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2159	PATH=$PATH:$tempdir
[2380]	2160
	2161
	2162	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2163	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2164	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2165	eval line=\"$line\"
	2166	execute_command="$line"
	2167
	2168
	2169	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2170	if [[ "$execute_command_for_combine" = "" ]]
	2171	then
	2172	eval line2=\"$line2\"
	2173	execute_command_for_combine="$line2"
	2174	fi
	2175
[2380]	2176
	2177
	2178	# PROVIDE A HOSTFILE, IF REQUIRED
	2179	if [[ "$hostfile" != "" ]]
	2180	then
	2181
	2182	if [[ $hostfile = auto ]]
	2183	then
	2184	# CREATE A NEW HOSTFILE
	2185	(( ii = 1 ))
	2186	while (( ii <= cores / threads_per_task ))
	2187	do
	2188	echo $(hostname) >> hostfile
	2189	(( ii = ii + 1 ))
	2190	done
	2191	if (( cores / threads_per_task == 0 ))
	2192	then
	2193	echo $(hostname) >> hostfile
	2194	fi
	2195
	2196	else
	2197	cp $hostfile hostfile
	2198	fi
	2199	eval line=\"`head -n $ii hostfile`\"
	2200	printf "\n *** running on: $line"
	2201	fi
	2202
	2203
	2204
	2205	# SET THE NUMBER OF OPENMP-THREADS
	2206	if [[ $use_openmp = true ]]
	2207	then
	2208	export OMP_NUM_THREADS=$threads_per_task
	2209	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2210	else
	2211	export OMP_NUM_THREADS=1
	2212	fi
	2213
	2214
[2610]	2215	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2216	if [[ $run_coupled_model = false ]]
	2217	then
	2218	if [[ "$ocean_file_appendix" = true ]]
	2219	then
	2220	echo "precursor_ocean" > coupling_steering
	2221	else
	2222	echo "precursor_atmos" > coupling_steering
	2223	fi
	2224	else
	2225	(( iia = $cores_atmos / $threads_per_task ))
	2226	(( iio = $cores_ocean / $threads_per_task ))
	2227	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2228	printf "\n\n"
	2229	echo "coupled_run $iia $iio" > coupling_steering
	2230	fi
	2231
	2232	printf "\n *** execute command:"
	2233	printf "\n \"$execute_command\" \n\n"
	2234
	2235	$execute_command < coupling_steering
	2236
[3312]	2237	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	2238	then
	2239
	2240	# ABORT IN CASE OF RUNTIME ERRORS
	2241	printf "\n +++ runtime error occured"
	2242	locat=execution
	2243	exit
	2244
	2245	else
	2246
	2247	printf "\n$dashes\n *** execution finished \n"
	2248
	2249	fi
	2250
	2251
	2252	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2253	# BY EACH CORE INTO ONE FILE
	2254	if [[ ! -f combine_plot_fields.x ]]
	2255	then
	2256
	2257	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2258	printf "\n 2d- and/or 3d-data may be incomplete!"
	2259	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2260
	2261	elif [[ "$combine_plot_fields" == true ]]
	2262	then
	2263
	2264	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2265	$execute_command_for_combine
	2266
	2267	else
	2268
	2269	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2270	# DATA OUTPUT
[2380]	2271	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2272	fi
	2273
	2274
	2275
	2276	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2277	(( i = 0 ))
	2278	while (( i < ioc ))
	2279	do
	2280	(( i = i + 1 ))
	2281	if (( i == 1 ))
	2282	then
	2283	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2284	fi
[2799]	2285
	2286	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2287	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2288
[2380]	2289	printf "\n >>> ${out_command[$i]}"
	2290	eval ${out_command[$i]}
	2291	if (( i == ioc ))
	2292	then
	2293	printf "\n$dashes\n"
	2294	fi
	2295	done
	2296
	2297
[2610]	2298	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2299	# WILDCARDS
[2380]	2300	(( i = 0 ))
[2610]	2301	(( nr_of_output_files = 0 ))
	2302
[2380]	2303	while (( i < iout ))
	2304	do
[2610]	2305
[2380]	2306	(( i = i + 1 ))
[2610]	2307
	2308	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2309	# CREATE A LIST FOR THE DETECTED ENDINGS
	2310	if [[ "${multout[$i]}" = true ]]
	2311	then
	2312	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2313	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2314	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2315
	2316	endings="DEFAULT"
	2317	while read line
	2318	do
	2319	# remove the local name from the beginning
	2320	localnamestring="${localout_pre[$i]}"
	2321	length_localname=${#localnamestring}
	2322	ending=${line:${length_localname}}
	2323
	2324	if [[ "$ending" != "" ]]
	2325	then
	2326	endings="$endings $ending"
	2327	fi
	2328
	2329	done <filelist
	2330
	2331	rm filelist
	2332
	2333	else
	2334
	2335	# SINGLE NAME
	2336	endings=DEFAULT
	2337
	2338	fi
	2339
	2340	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2341	for ending in $endings
	2342	do
	2343
	2344	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2345	if [[ $ending = DEFAULT ]]
	2346	then
	2347	ending=""
	2348	fi
	2349
	2350	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2351	(( nr_of_output_files = nr_of_output_files + 1 ))
	2352	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2353	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2354	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2355	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2356	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2357	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2358	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2359
	2360	done
	2361
	2362	done
	2363
	2364
	2365
	2366
	2367	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2368	(( i = 0 ))
	2369	while (( i < nr_of_output_files ))
	2370	do
	2371	(( i = i + 1 ))
[2380]	2372	if (( i == 1 ))
	2373	then
	2374	printf "\n\n *** saving OUTPUT-files:"
	2375
	2376	# GET RUN NUMBER ASSIGNED BY PALM
	2377	if [[ -f RUN_NUMBER ]]
	2378	then
	2379	read run_number < RUN_NUMBER
	2380	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2381	usecycle_option="-U $run_number"
	2382	else
	2383	run_number=0
	2384	usecycle_option=""
	2385	fi
	2386	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2387	then
[2404]	2388	printf "\n *** in case of SCP transfers to local host"
	2389	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2390	fi
	2391	printf "\n$dashes"
	2392	fi
	2393
	2394	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2395	then
	2396
[3236]	2397	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2398
	2399	# DETERMINE THE CYCLE NUMBER
	2400	ls -1 -d $filename > filelist 2>/dev/null
	2401	ls -1 -d $filename.* >> filelist 2>/dev/null
	2402	while read line
	2403	do
	2404
	2405	# filename without path (i.e. after the last "/")
	2406	basefilename=$(basename ${line})
	2407
	2408	# check if there is an extension
	2409	extension=${basefilename##*.}
	2410	if [[ "$extension" = "${extout[$i]}" ]]
	2411	then
	2412	basefilename=${basefilename%.*}
	2413	fi
	2414
	2415	# check for an existing cycle number
	2416	cycle=${basefilename##*.}
	2417	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2418	then
[2669]	2419	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2420	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2421	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2422	else
	2423	(( icycle = 1 ))
	2424	fi
	2425
	2426	if (( icycle > maxcycle ))
	2427	then
	2428	(( maxcycle = icycle ))
	2429	fi
	2430
	2431	done <filelist
	2432	rm filelist
	2433
	2434
	2435	# SET THE CYCLE NUMBER
	2436	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2437	if [[ "${actionout[$i]}" = a ]]
	2438	then
	2439	(( maxcycle = maxcycle - 1 ))
	2440	fi
	2441
	2442	(( cycnum[$i] = maxcycle ))
	2443	pathout[$i]=$filename
	2444
	2445
	2446	# ADD CYCLE NUMBER TO FILENAME
	2447	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2448	if [[ "${actionout[$i]}" != "a" ]]
	2449	then
	2450	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2451	# WITH AN EXISTING CYCLE NUMBER
	2452	if (( run_number >= cycnum[$i] ))
	2453	then
	2454	(( cycnum[$i] = run_number ))
	2455	else
	2456	if (( run_number > 0 ))
	2457	then
	2458	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2459	fi
	2460	fi
	2461	fi
	2462	if (( cycnum[$i] > 0 ))
	2463	then
[2600]	2464	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2465	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2466	fi
	2467	fi
	2468
	2469	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2470	files_for_cores=false; filetype=file
	2471	link_local_output=false
	2472	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2473	then
	2474	files_for_cores=true; filetype=directory
	2475	actionout[$i]=""
	2476	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2477	then
	2478	actionout[$i]=""
	2479	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2480	then
	2481	files_for_cores=true; filetype=directory
	2482	link_local_output=true
	2483	actionout[$i]=""
	2484	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2485	then
	2486	link_local_output
	2487	actionout[$i]=""
	2488	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2489	then
	2490	files_for_cores=true; filetype=directory
	2491	actionout[$i]="tr"
	2492	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2493	then
	2494	actionout[$i]="tr"
	2495	fi
	2496
	2497	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2498	then
[2669]	2499	if [[ ${warnout[$i]} = true ]]
	2500	then
	2501	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2502	fi
[2380]	2503	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2504	then
[2669]	2505	if [[ ${warnout[$i]} = true ]]
	2506	then
	2507	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2508	fi
[2380]	2509	else
	2510
	2511
	2512	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2513	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2514	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2515	then
	2516	if [[ $running_on_remote = true ]]
	2517	then
	2518
	2519	# SET OPTIONS FOR TRANSFER
	2520	if [[ "${actionout[$i]}" = tr ]]
	2521	then
	2522	if [[ $files_for_cores = false ]]
	2523	then
	2524	catalog_option=""
	2525	catalog_string=""
	2526	else
	2527	catalog_option="-c"
	2528	catalog_string="/"
	2529	fi
	2530	append_option=""
	2531	append_string=""
	2532	else
	2533	append_option="-A"
	2534	append_string="append"
	2535	fi
	2536
	2537	transfer_failed=false
	2538	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2539	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2540
	2541	# TRANSFER VIA SCP
	2542	if [[ "$remote_loginnode" != "" ]]
	2543	then
[3236]	2544	echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
[2380]	2545	else
[3236]	2546	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}
[2380]	2547	fi
[3312]	2548	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2549
	2550
	2551	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2552	if [[ $transfer_failed = true ]]
	2553	then
	2554	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2555	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2556
	2557	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2558	eval local_catalog=${pathout[$i]}
	2559	if [[ ! -d $local_catalog ]]
	2560	then
	2561	printf " *** local directory does not exist. Trying to create:\n"
	2562	printf " $local_catalog \n"
	2563	mkdir -p $local_catalog
	2564	fi
[3236]	2565	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2566	transfer_problems=true
	2567	fi
	2568
	2569	else
	2570
	2571	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2572	# BE COPIED OR APPENDED ON THIS MACHINE
	2573	if [[ "${actionout[$i]}" = tr ]]
	2574	then
	2575	actionout[$i]=""
	2576	else
	2577	actionout[$i]="a"
	2578	fi
	2579	fi
	2580	fi
	2581
	2582
	2583	# APPEND ON THIS MACHINE
	2584	if [[ "${actionout[$i]}" = "a" ]]
	2585	then
	2586	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2587	then
	2588	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2589	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2590	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2591	else
	2592	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2593	printf "\n ${pathout[$i]}\n"
	2594	cat ${localout[$i]} >> ${pathout[$i]}
	2595	fi
	2596	fi
	2597
	2598	# COPY ON THIS MACHINE
	2599	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2600	# ON DIFFERENT FILE-SYSTEMS
	2601	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2602	then
	2603
	2604	# COPY IN CASE OF RUNS ON SINGLE CORES
	2605	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2606	then
	2607	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2608	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2609	if [[ $link_local_output = true ]]
	2610	then
	2611	printf " file will be linked\n"
	2612	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2613	fi
	2614	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2615	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2616	then
	2617	if [[ $link_local_output = true ]]
	2618	then
	2619	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2620	fi
	2621	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2622	else
	2623	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2624	fi
	2625	else
	2626	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2627	printf "\n ${pathout[$i]}\n"
	2628	if [[ $link_local_output = true ]]
	2629	then
	2630	printf " file will be linked\n"
	2631	ln -f ${localout[$i]} ${pathout[$i]}
	2632	fi
	2633	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2634	if [[ ! -f "${pathout[$i]}" ]]
	2635	then
	2636	if [[ $link_local_output = true ]]
	2637	then
	2638	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2639	fi
	2640	cp ${localout[$i]} ${pathout[$i]}
	2641	else
	2642	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2643	fi
	2644	fi
	2645
	2646	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2647	then
	2648
	2649	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2650	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2651	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2652	printf "\n ${pathout[$i]}\n"
	2653	if [[ $link_local_output = true ]]
	2654	then
	2655	printf " files will be linked\n"
[2396]	2656	mkdir -p ${pathout[$i]}
[2380]	2657	cd ${localout[$i]}
	2658	for file in $(ls *)
	2659	do
	2660	ln -f $file ${pathout[$i]}
	2661	done >\|/dev/null 2>&1
[2566]	2662	cd $tempdir
[2380]	2663	fi
	2664
	2665	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2666	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2667	then
	2668	if [[ $link_local_output = true ]]
	2669	then
	2670	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2671	fi
[3025]	2672	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2673	cp -r ${localout[$i]}/* ${pathout[$i]}
	2674	fi
	2675
	2676	fi
	2677	fi
	2678	done
	2679
	2680	if (( i != 0 ))
	2681	then
	2682	if [[ $transfer_problems = true ]]
	2683	then
	2684	printf "\n$dashes\n *** OUTPUT-files saved"
	2685	printf "\n +++ WARNING: some data transfers failed! \n"
	2686	else
	2687	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2688	fi
	2689	fi
	2690
	2691
	2692	# IF REQUIRED, START A RESTART-JOB
	2693	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2694	if [[ -f CONTINUE_RUN ]]
	2695	then
	2696
	2697	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2698	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2699	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2700	# -b START A BATCH JOB
	2701	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2702	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2703	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2704
[2957]	2705	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2706	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2707	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2708	then
	2709	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2710	fi
[2380]	2711
	2712	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2713	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2714	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2715	then
[2381]	2716	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2717	fi
	2718
	2719
	2720	# START THE RESTART-JOB
	2721	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2722	echo " $prc"
	2723	printf "\n$dashes\n"
	2724	if [[ $running_on_remote = true ]]
	2725	then
	2726
	2727	echo "*** ssh will be used to initiate restart-runs!"
	2728	echo " return_address=\"$return_address\" "
	2729	echo " return_username=\"$local_username\" "
	2730
	2731	if [[ "$remote_loginnode" != "" ]]
	2732	then
[3132]	2733	echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address " \| ssh -q $remote_username@$remote_loginnode \| tee palmrun_restart.log
[2380]	2734	else
[3132]	2735	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
[2380]	2736	fi
	2737
	2738	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2739	sleep 30
	2740
	2741	else
	2742
	2743	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2744	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2745	cd - > /dev/null
	2746
	2747	fi
	2748
[3132]	2749	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2750	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2751	then
	2752	printf "\n$dashes\n +++ creating restart run failed \n"
	2753	locat=create_restart
	2754	exit
	2755	rm palmrun_restart.log
	2756	else
	2757	printf "\n$dashes\n *** restart run initiated \n"
	2758	rm palmrun_restart.log
	2759	fi
[2380]	2760
[3132]	2761
[2380]	2762	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2763	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2764	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2765	# MAY BE VERY HUGE)
	2766	(( i = 0 ))
[2610]	2767	while (( i < nr_of_input_files ))
[2380]	2768	do
	2769	(( i = i + 1 ))
	2770	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2771	then
	2772	rm -r ${absnamein[$i]}
	2773	fi
	2774	done
	2775
	2776	fi
	2777
	2778
	2779	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2780	cd $HOME
[2566]	2781	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2782
	2783
	2784	else
	2785
	2786
	2787	# PREPARING ACTIONS,
	2788	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2789
	2790	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3236]	2791	palmrun_com="$palmrun_script_name -d $run_identifier -h $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2792	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2793	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2794	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2795	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2796	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2797	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2798	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2799	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2800	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2801	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2802	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2803	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2804	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2805	if [[ $create_remote_batch_job = true ]]
	2806	then
	2807	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2808	if [[ $do_trace = true ]]
	2809	then
	2810	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2811	fi
[2380]	2812	elif [[ $create_batch_job = true ]]
	2813	then
	2814	palmrun_com=${palmrun_com}" -j"
[2420]	2815	if [[ $do_trace = true ]]
	2816	then
	2817	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2818	fi
[2380]	2819	fi
	2820
	2821
	2822	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2823	# REMOTE HOST
[3236]	2824	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2825	job_protocol_file=$job_protocol_file_local
	2826	if [[ $create_remote_batch_job = true ]]
	2827	then
[3236]	2828	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2829	job_protocol_file=$job_protocol_file_remote
	2830	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2831	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2832	fi
	2833
	2834
	2835	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2836	jobfile=jobfile.$run_id_number
[2380]	2837
	2838
	2839	# FIRST CREATE THE BATCH DIRECTIVES
	2840	(( i = 0 ))
	2841	while (( i < ibd ))
	2842	do
	2843	(( i = i + 1 ))
[2693]	2844	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2845	eval line=\"$line\"
	2846	echo "$line" >> $jobfile
	2847	done
	2848	echo " " >> $jobfile
	2849
	2850
	2851	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2852	# PROTOCOL
	2853	if [[ $create_remote_batch_job = true ]]
	2854	then
[3236]	2855	echo "set +vx" >> $jobfile
	2856	echo "trap '" >> $jobfile
	2857	echo "set +vx" >> $jobfile
	2858	echo "cd ${remote_jobcatalog}" >> $jobfile
	2859	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2860
	2861	# ADD THE BATCH DIRECTIVES
	2862	(( i = 0 ))
	2863	while (( i < ibdt ))
	2864	do
	2865	(( i = i + 1 ))
[2693]	2866	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2867	eval line=\"$line\"
	2868	echo "$line" >> $jobfile
	2869	done
	2870	echo " " >> $jobfile
	2871
	2872	echo "set -x" >> $jobfile
[3236]	2873	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${configuration_identifier}_${run_identifier}" >> $jobfile
[2380]	2874	echo "%%END%%" >> $jobfile
	2875	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2876	echo "$submit_command $scpjob_file" >> $jobfile
	2877	echo "rm $scpjob_file" >> $jobfile
[2404]	2878	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2879	echo "set -x" >> $jobfile
	2880	echo " ' exit" >> $jobfile
	2881	fi
	2882
	2883
	2884	# ACTIVATE ERROR-TRACEBACK
	2885	if [[ $do_trace = true ]]
	2886	then
	2887	echo "set -x" >> $jobfile
	2888	else
	2889	echo "set +vx" >> $jobfile
	2890	fi
	2891
	2892
	2893	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2894	if [[ "$login_init_cmd" != "" ]]
	2895	then
	2896	echo "$login_init_cmd" >> $jobfile
	2897	fi
	2898	if [[ "$module_commands" != "" ]]
	2899	then
	2900	echo "$module_commands" >> $jobfile
	2901	fi
	2902
	2903
	2904	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2905	if [[ $create_remote_batch_job = true ]]
	2906	then
	2907	echo "mkdir $tempdir" >> $jobfile
	2908	echo "chmod go+rx $tempdir" >> $jobfile
	2909	else
	2910	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2911	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2912	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2913	mkdir $tempdir
	2914	chmod go+rx $tempdir
	2915	fi
	2916	echo "cd $tempdir" >> $jobfile
	2917	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2918	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2919	echo "export PATH=.:\$PATH" >> $jobfile
	2920	echo "export execute_palmrun=true" >> $jobfile
	2921
	2922
	2923	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2924	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2925	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2926	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2927	echo "export LOCAL_PWD" >> $jobfile
	2928
	2929
	2930	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2931	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2932	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2933
	2934
	2935	# CALL PALMRUN WITHIN THE JOB
	2936	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2937	echo "set -x" >> $jobfile
	2938	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2939
	2940
	2941	# TRANSFER JOBFILE TO THE TARGET HOST
	2942	if [[ $create_jobfile_only = false ]]
	2943	then
	2944
	2945	if [[ $create_remote_batch_job = true ]]
	2946	then
	2947
[2420]	2948	echo " "
[2566]	2949	echo " *** transfer of job to remote host via scp"
[2420]	2950	if [[ $do_trace = true ]]
	2951	then
[3236]	2952	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	2953	fi
[3236]	2954	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	2955
[2566]	2956	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2957	if [[ $do_trace = true ]]
	2958	then
[3236]	2959	echo " cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id} \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1"
[2420]	2960	fi
[3236]	2961	echo "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
[2380]	2962
	2963	elif [[ $create_batch_job = true ]]
	2964	then
	2965
[2385]	2966	eval local_jobcatalog=$local_jobcatalog
[3236]	2967	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	2968	cd $local_jobcatalog
[2380]	2969	echo " "
[2420]	2970	echo " *** submit the job"
	2971	if [[ $do_trace = true ]]
	2972	then
[3236]	2973	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	2974	fi
[3236]	2975	$submit_command ${configuration_identifier}_${run_id}
	2976	rm ${configuration_identifier}_${run_id}
[2380]	2977	cd - > /dev/null
	2978
	2979	fi
	2980
	2981	rm -rf $jobfile
	2982
	2983	else
	2984
	2985	printf "\n *** jobfile created under name \"$jobfile\" "
	2986	printf "\n no batch-job has been sent!"
	2987
	2988	fi
	2989
	2990	fi # END OF REMOTE-PART

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