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source: palm/trunk/SCRIPTS/palmrun @ 3189

Last change on this file since 3189 was 3151, checked in by raasch, 6 years ago
output of PALM code revision number in palmrun header, some preprocessor define strings removed, small revisions in configuration files
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 98.3 KB

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

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