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source: palm/trunk/SCRIPTS/palmrun @ 3045

Last change on this file since 3045 was 3043, checked in by raasch, 7 years ago
check for setting of fast_io_catalog, update of default .palm.config.default
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 97.8 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 3043 2018-05-25 10:47:54Z Giersch $
[3043]	29	# check for setting of fast_io_catalog
	30	#
	31	# 3033 2018-05-23 15:26:19Z raasch
[3025]	32	# -T option not required for interactive runs (tasks per node =
	33	# total number of cores is assumed as default, if option is not given),
	34	# reformatting of a few messages,
	35	# bugfix: destination output directory is created if attribute "pe" is set in
	36	# .palm.iofiles
	37	#
	38	# 2718 2018-01-02 08:49:38Z maronga
[2993]	39	# bugfix of r2990
	40	#
	41	# 2718 2018-01-02 08:49:38Z maronga
[2990]	42	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	43	# not in the working directory from where palmrun is called
	44	#
	45	# 2718 2018-01-02 08:49:38Z maronga
[2957]	46	# svfout in the activation string will be replaced now by svfin in case of
	47	# automatic restarts
	48	#
	49	# 2718 2018-01-02 08:49:38Z maronga
[2906]	50	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	51	# the possible output or input of sky view factors
	52	#
	53	# 2718 2018-01-02 08:49:38Z maronga
[2834]	54	# "fname" renamed to "jobname"
	55	#
	56	# 2718 2018-01-02 08:49:38Z maronga
[2799]	57	# parameters are allowed in output commands (OC:)
	58	#
	59	# 2718 2018-01-02 08:49:38Z maronga
[2789]	60	# bugfix: exit if no queue has been given neither with option -q nor in the
	61	# configuration file
	62	#
	63	# 2718 2018-01-02 08:49:38Z maronga
[2762]	64	# file connection file from trunk/SCRIPTS is taken by default
	65	#
	66	# 2718 2018-01-02 08:49:38Z maronga
[2716]	67	# Corrected "Former revisions" section
	68	#
	69	# 2696 2017-12-14 17:12:51Z kanani
	70	# Change in file header (GPL part)
	71	#
	72	# 2693 2017-12-13 12:33:49Z raasch
[2693]	73	# replacement of variables given by {{<variable>}} in configuration file is now
	74	# done in a more general way, variable names are written in small letters
	75	#
	76	# 2670 2017-12-06 16:32:19Z raasch
[2670]	77	# test printouts removed
	78	#
	79	# 2669 2017-12-06 16:03:27Z raasch
[2669]	80	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	81	# removed,
	82	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	83	# files,
	84	# informative messages in case of missing optional input files shortened
	85	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	86	#
	87	# 2638 2017-11-23 12:44:23Z raasch
[2610]	88	# use of wildcards in file connection statements enabled
	89	#
	90	# 2605 2017-11-09 15:31:46Z raasch
[2605]	91	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	92	# will not be sent with the job file any more, but copied into the
[2610]	93	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	94	#
	95	# 2600 2017-11-01 14:11:20Z raasch
[2600]	96	# cycle numbers are made three digits wide
	97	#
	98	# 2566 2017-10-20 08:50:47Z raasch
[2566]	99	# execute command for combine_plot_fields added
	100	# "TEMPDIR" renamed "tempdir"
	101	# temporary working directory for local batch jobs is created immediately within
	102	# the user's palmrun call, due to a requirement of the "grid engine" batch
	103	# system, where the working directory is given with batch directive -wd and must
	104	# already exist when the job is submitted,
	105	# informative messages in non-trace mode reduced and partly reformatted
	106	#
	107	# 2551 2017-10-18 07:25:11Z raasch
[2551]	108	# TEMPDIR added as replacement string to be used in batch directives
	109	#
	110	# 2512 2017-10-04 08:26:59Z raasch
[2507]	111	# bugfix for determining cycle numbers of NetCDF input files
	112	#
	113	# 2506 2017-09-29 08:30:37Z raasch
[2506]	114	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	115	# host configuration added to SOURCES_FOR_RUN_... folder name
	116	# host_identifier renamed host_configuration
	117	# option -W added to allow for job dependencies
	118	#
	119	# 2501 2017-09-26 11:41:55Z raasch
[2501]	120	# default value for number of cores (option -X) set to 1
	121	# bugfix for mechanism which overwrites configuration file settings with values
	122	# provided by palmrun options
	123	#
	124	# 2499 2017-09-22 16:47:58Z kanani
[2499]	125	# option -h named configuration identifier
	126	#
	127	# 2480 2017-09-19 06:24:14Z maronga
[2480]	128	# bugfix for last revision
	129	#
	130	# 2479 2017-09-19 06:12:16Z raasch
[2479]	131	# option -A (project account number) added
	132	#
	133	# 2422 2017-09-08 08:25:41Z raasch
[2410]	134	# initial revision
[2380]	135	#
	136	#--------------------------------------------------------------------------------#
	137	# palmrun - script for running PALM jobs on local and remote hosts
	138	#--------------------------------------------------------------------------------#
	139
	140
	141
	142	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	143
	144	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	145	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	146	# (TOO MANY ARGUMENTS - PROBLEM)
	147	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	148
[2610]	149	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	150	typeset -i nr_of_output_files=0
[2380]	151	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	152	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	153	# SCRIPT-OPTION ARGUMENTS
	154	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	155	typeset -i icycle inode ival maxcycle mpi_tasks
	156	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	157
	158	activation_string_list=""
	159	AddFilenames=""
	160	combine_plot_fields=true
	161	compiler_name=""
	162	compiler_name_ser=""
	163	compiler_options=""
[2501]	164	cores=1
[2380]	165	cores_atmos=0
	166	cores_ocean=0
	167	coupled_dist=""
	168	cpp_options=""
	169	cpumax=0
[2506]	170	create_batch_job=false
[2380]	171	create_jobfile_only=false
	172	create_remote_batch_job=false
	173	dashes=" ----------------------------------------------------------------------------"
	174	defaultqueue=""
[2506]	175	delete_temporary_catalog=true
[2380]	176	do_compile=true
	177	do_trace=false
	178	executable=""
	179	execute_command=""
	180	execution_error=false
[2762]	181	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2834]	182	jobname=test
[2380]	183	global_revision=""
[2506]	184	host_configuration="default"
[2380]	185	hostfile=""
	186	hp=""
	187	keep_data_from_previous_run=false
	188	link_local_input=false
	189	link_local_output=false
[2388]	190	linker_options=""
[2385]	191	local_jobcatalog=""
[2380]	192	locat=normal
	193	makefile=""
	194	max_par_io_str=""
	195	prc=$0
	196	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	197	do
	198	prc=`echo $prc \| cut -f2- -d"/"`
	199	done
	200	module_calls=""
[2506]	201	palmrun_memory=""
[2380]	202	palmrun_script_name=$prc
	203	openmp=false
[2506]	204	previous_job=""
[2479]	205	project_account=""
[2380]	206	queue=none
[2906]	207	read_svf=""
[2380]	208	restart_run=false
	209	return_address=""
[2385]	210	remote_jobcatalog=""
[2380]	211	remote_username=""
	212	running_in_batch_mode=false
	213	run_coupled_model=false
	214	run_id=""
	215	silent=false
	216	source_list=""
	217	source_path=""
[2501]	218	tasks_per_node=0
[2380]	219	threads_per_task=1
	220	transfer_problems=false
[2384]	221	user_source_path=""
[2506]	222	use_existing_sources_folder=""
[2380]	223	use_openmp=false
[3033]	224	version="palmrun 1.0 Rev$Rev: 3043 $"
[2380]	225	working_directory=`pwd`
	226	write_binary=""
[2906]	227	write_svf=""
[2380]	228
	229
	230	# ERROR HANDLING IN CASE OF EXIT
[2404]	231	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	232	then
	233
	234	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	235	(( i = 0 ))
	236	while (( i < iec ))
	237	do
	238	(( i = i + 1 ))
	239	printf "\n *** Execution of ERROR-command:\n"
	240	printf " >>> ${err_command[$i]}\n"
	241	eval ${err_command[$i]}
	242	done
[2566]	243	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[2380]	244	printf "\n\n+++ palmrun killed \n\n"
	245	elif [[ $locat != control_c ]]
	246	then
[2566]	247	printf "\n --> palmrun finished\n\n"
[2380]	248	fi' exit
	249
	250
	251	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[2566]	252	trap 'cd; rm -rf $tempdir
[2380]	253	printf "\n+++ palmrun killed by \"^C\" \n\n"
	254	locat=control_c
	255	exit
	256	' 2
	257
	258
	259	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	260	# WHICH WILL BE USED TO START RESTART-JOBS
[2506]	261	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]	262	do
	263	case $option in
	264	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	265	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	266	(b) create_batch_job=true; prc="$prc -b";;
	267	(B) delete_temporary_catalog=false; prc="$prc -B";;
	268	(C) restart_run=true; prc="$prc -C";;
[2834]	269	(d) jobname=$OPTARG; prc="$prc -d$OPTARG";;
[2380]	270	(F) create_jobfile_only=true;;
	271	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[2506]	272	(h) host_configuration=$OPTARG; prc="$prc -h$OPTARG";;
[2380]	273	(j) running_in_batch_mode=true;;
	274	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	275	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	276	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	277	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	278	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
	279	(r) run_id=$OPTARG;;
	280	(R) return_address=$OPTARG;;
	281	(s) source_list=$OPTARG;;
[2501]	282	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	283	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	284	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	285	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	286	(v) silent=true; prc="$prc -v";;
[2506]	287	(V) use_existing_sources_folder="-V";;
[2380]	288	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	289	(W) previous_job=$OPTARG;;
[2380]	290	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	291	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	292	(y) ocean_file_appendix=true; prc="$prc -y";;
	293	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
	294	(Z) combine_plot_fields=false; prc="$prc -Z";;
	295	(\?) printf "\n +++ unknown option $OPTARG \n"
	296	printf "\n --> type \"$0 ?\" for available options \n"
	297	locat=parameter;exit;;
	298	esac
	299	done
	300
	301
	302	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	303	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	304	(( to_shift = $OPTIND - 1 ))
	305	shift $to_shift
	306
	307	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	308	if [[ "$1" = "?" ]]
	309	then
	310	(printf "\n *** Description of available palmrun options:\n"
	311	printf "\n Option Description Default-Value"
	312	printf "\n -a activation string list \"\" "
[2479]	313	printf "\n -A project account number ---"
[2380]	314	printf "\n -b batch-job on local machine ---"
	315	printf "\n -B do not delete temporary directory at end ---"
[3025]	316	printf "\n -d run identifier test"
[2380]	317	printf "\n -F create batch job file only ---"
[2506]	318	printf "\n -h host configuration \"default\" "
[2380]	319	printf "\n -k keep data from previous run"
	320	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	321	printf "\n -M Makefile name Makefile"
	322	printf "\n -O threads per openMP task ---"
	323	printf "\n -q queue \"$queue\" "
	324	printf "\n -s filenames of routines to be compiled \"\" "
	325	printf "\n must end with .f, .f90, .F, or .c !"
	326	printf "\n use \"..\" for more than one file and wildcards"
	327	printf "\n -s LM compiles all locally modified files"
	328	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	329	printf "\n -T tasks per node ---"
[2380]	330	printf "\n -u username on remote machine \"\" "
	331	printf "\n -v no prompt for confirmation ---"
[2506]	332	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	333	printf "\n -w maximum parallel io streams as given by -X"
[2506]	334	printf "\n -W name of job to wait for ---"
[2380]	335	printf "\n -x tracing of palmrun for debug purposes ---"
	336	printf "\n -X # of processors (on parallel machines) 1"
	337	printf "\n -y add appendix \"_O\" to all local output"
	338	printf "\n files (ocean precursor runs followed by"
	339	printf "\n coupled atmosphere-ocean runs) ---"
	340	printf "\n -Y run coupled model, \"#1 #2\" with"
	341	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	342	printf "\n -Z skip combine_plot_fields at the end of "
	343	printf "\n the simulation ---"
	344	printf "\n "
	345	printf "\n Possible values of positional parameter <modus>:"
	346	printf "\n \"?\" - this outline \n\n") \| more
	347	exit
	348	elif [[ "$1" != "" ]]
	349	then
	350	printf "\n +++ positional parameter $1 unknown \n"
	351	locat=parameter; exit
	352	fi
	353
	354
	355
	356	# SHORT STARTING MESSAGE
	357	printf "\n*** $version "
	358	printf "\n will be executed. Please wait ..."
	359
	360
[2834]	361	# FOR COMPATIBILITY REASONS SET OLD ENVIRONMENT VARIABLE
	362	export fname=$jobname
	363
	364
[2506]	365	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
	366	config_file=.palm.config.$host_configuration
[2834]	367	sources_for_run_catalog=SOURCES_FOR_RUN_${host_configuration}_$jobname
[2380]	368
	369
	370	# CHECK, IF CONFIGURATION FILE EXISTS
	371	if [[ ! -f $config_file ]]
	372	then
	373	printf "\n\n +++ configuration file: "
	374	printf "\n $config_file"
	375	printf "\n does not exist"
	376	locat=connect; exit
	377	fi
	378
	379
[2762]	380	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	381	if [[ -f .palm.iofiles ]]
	382	then
	383	fileconnection_file=.palm.iofiles
	384	fi
	385
	386
[2380]	387	# CHECK, IF FILE CONNECTION FILE EXISTS
	388	if [[ ! -f $fileconnection_file ]]
	389	then
	390	printf "\n\n +++ file connection file: "
	391	printf "\n $fileconnection_file"
	392	printf "\n does not exist"
	393	locat=connect; exit
	394	fi
	395
	396
[2404]	397	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	398	if [[ "$activation_string_list" = "" ]]
	399	then
	400	printf "\n\n +++ no activation string list given: "
	401	printf "\n please set palmrun option \"-a\" "
	402	locat=palmrun_option; exit
	403	fi
	404
	405
	406	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	407	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	408	then
	409	write_binary=true
	410	else
	411	write_binary=false
	412	fi
	413
[2906]	414	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	415	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	416	then
	417	write_svf=true
	418	else
	419	write_svf=false
	420	fi
[2404]	421
[2906]	422	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	423	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	424	then
	425	read_svf=true
	426	else
	427	read_svf=false
	428	fi
	429
	430
[2380]	431	# READ AND EVALUATE THE CONFIGURATION-FILE
	432	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	433
	434	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	435	while read line
	436	do
	437
	438	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	439	eval line=\"$line\"
	440
	441
	442	# INTERPRET THE LINE
	443	if [[ "$(echo $line)" = "" ]]
	444	then
	445
	446	# EMPTY LINE, NO ACTION
	447	continue
	448
	449	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	450	then
	451
	452	# LINE IS A COMMENT LINE
	453	continue
	454
	455	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	456	then
	457
	458	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	459	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	460	value=`echo $line \| cut -d" " -s -f2-`
	461
	462
	463	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	464	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	465	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	466	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	467	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	468	# CONFIGURATION-FILE.
	469	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	470	then
	471	eval export $var="\$value"
	472
	473	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	474	if [[ $do_trace = true ]]
	475	then
	476	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	477	fi
	478	fi
	479
	480	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	481	then
	482
	483	# LINE DEFINES BATCH-DIRECTIVE
	484	(( ibd = ibd + 1 ))
	485	line=$(echo $line \| cut -c4-)
	486	batch_directive[$ibd]="$line"
	487
	488	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	489	then
	490
	491	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	492	# REMOTE TO A LOCAL HOST
	493	(( ibdt = ibdt + 1 ))
	494	line=$(echo $line \| cut -c5-)
	495	batch_directive_transfer[$ibdt]="$line"
	496
	497	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	498	then
	499
	500	# LINE DEFINES ERROR-COMMAND
	501	(( iec = iec + 1 ))
	502	line=$(echo $line \| cut -c4-)
	503	err_command[$iec]="$line"
	504
	505	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	506	then
	507
	508	# LINE DEFINES INPUT-COMMAND
	509	(( iic = iic + 1 ))
	510	line=$(echo $line \| cut -c4-)
	511	in_command[$iic]="$line"
	512
	513	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	514	then
	515
	516	# LINE DEFINES OUTPUT-COMMAND
	517	(( ioc = ioc + 1 ))
	518	line=$(echo $line \| cut -c4-)
	519	out_command[$ioc]="$line"
	520
	521	else
	522
	523	# SKIP ALL OTHER LINES
	524	continue
	525
	526	fi
	527
	528	done < $config_file
	529
	530
	531	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	532	if [[ "$fast_io_catalog" = "" ]]
	533	then
	534	printf "\n +++ no fast_io_catalog found in $config_file"
	535	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	536	locat=config_file; exit
	537	fi
[2380]	538	if [[ "$compiler_name" = "" ]]
	539	then
	540	printf "\n +++ no compiler name found in $config_file"
	541	printf "\n Please add line \"compiler_name ...\" to that file."
	542	locat=config_file; exit
	543	fi
	544	if [[ "$compiler_name_ser" = "" ]]
	545	then
	546	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	547	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	548	locat=config_file; exit
	549	fi
	550	if [[ "$compiler_options" = "" ]]
	551	then
	552	printf "\n +++ no compiler options found in $config_file"
	553	printf "\n Please add line \"compiler_options ...\" to that file."
	554	locat=config_file; exit
	555	fi
[2388]	556	if [[ "$linker_options" = "" ]]
[2380]	557	then
[2388]	558	printf "\n +++ no linker options found in $config_file"
	559	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	560	locat=config_file; exit
	561	fi
	562	if [[ "$execute_command" = "" ]]
	563	then
	564	printf "\n +++ no execute command found in $config_file"
	565	printf "\n Please add line \"execute_command ...\" to that file."
	566	locat=config_file; exit
	567	fi
	568
	569	if [[ "$hostfile" != "" ]]
	570	then
	571	if [[ $hostfile != auto && ! -f $hostfile ]]
	572	then
	573	printf "\n +++ no hostfile \"$hostfile\" found"
[3043]	574	printf "\n Please check line \"%hostfile ...\" in $config_file"
[2380]	575	locat=config_file; exit
	576	fi
	577	fi
	578
	579
	580	# DETERMINE THE CALL STATUS
	581	if [[ "$return_address" != "" ]]
	582	then
	583
	584	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	585	# BATCH MODE AND ...
	586	running_on_remote=true
	587
	588	else
	589
	590	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	591	if [[ "$remote_ip" != "" ]]
	592	then
	593
	594	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	595	create_remote_batch_job=true
	596
	597	fi
	598	running_on_remote=false
	599	fi
	600
	601
	602
	603	# READ AND EVALUATE THE I/O-FILE LIST
	604	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	605
	606	# READ THE FILE CONNECTION FILE LINE BY LINE
	607	while read line
	608	do
	609
[2669]	610	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	611	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	612
	613	# INTERPRET THE LINE
	614	if [[ "$(echo $line)" = "" ]]
	615	then
	616	# EMPTY LINE, NO ACTION
	617	continue
	618
	619	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	620	then
	621
	622	# LINE IS A COMMENT LINE
	623	true
	624
	625	else
	626
	627	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	628	# s2a: in/out - field
[2669]	629	# s2b: action - field (optional)
	630	s1=`echo "$line" \| cut -d" " -f1`
	631	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	632	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	633	then
[2669]	634	s2a=$s2
[2380]	635	s2b=""
	636	else
[2669]	637	s2a=`echo $s2 \| cut -d":" -f1`
	638	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	639	fi
[2669]	640	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	641	s4=`echo "$line" \| cut -d" " -s -f4`
	642	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	643	s5=`echo "$line" \| cut -d" " -s -f5`
	644	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	645
	646
	647	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	648	# INPUT- OR OUTPUT-LIST.
	649	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	650	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	651	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	652	# IS NOT CHECKED AND STORED.
[2610]	653	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	654	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	655	then
	656	found=false
	657	for actual in $activation_string_list
	658	do
	659	for formal in $s3
	660	do
	661	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	662	done
	663	done
	664	if [[ $found = true ]]
	665	then
	666	(( iin = iin + 1 ))
[2669]	667	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	668	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	669	if [[ "$s2a" = inopt ]]
	670	then
	671	optin_pre[$iin]=yes
	672	else
	673	optin_pre[$iin]=no
	674	fi
[2605]	675
	676	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	677	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	678	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	679	then
[2610]	680	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	681	fi
	682
[2610]	683	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	684	# THE WILDCARD FROM THE ENDING
	685	if [[ "${s5: -1}" = "*" ]]
	686	then
[2669]	687	if [[ "$s2b" = "di" ]]
[2610]	688	then
	689	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	690	printf "\n see file \"$fileconnection_file\", line"
	691	printf "\n$line"
	692	locat=iofiles_file; exit
	693	fi
	694	multin[$iin]=true
	695	string=${endin_pre[$iin]}
	696	endin_pre[$iin]="${string%?}"
	697	else
	698	multin[$iin]=false
	699	fi
[2380]	700	fi
[2669]	701	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	702	then
	703	found=false
	704	for actual in $activation_string_list
	705	do
	706	for formal in $s3
	707	do
[2670]	708	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	709	done
	710	done
	711	if [[ $found = true ]]
	712	then
	713	(( iout = iout + 1 ))
[2669]	714	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	715	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	716
[2669]	717	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	718	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	719	if [[ $formal = wildcard ]]
	720	then
	721	warnout_pre[$iout]=false
	722	else
	723	warnout_pre[$iout]=true
	724	fi
	725
[2610]	726	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	727	# THE WILDCARD FROM THE LOCAL FILENAME
	728	if [[ "${s1: -1}" = "*" ]]
	729	then
[2669]	730	if [[ "$s2b" = "di" ]]
[2610]	731	then
	732	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	733	printf "\n see file \"$fileconnection_file\", line"
	734	printf "\n$line"
	735	locat=iofiles_file; exit
	736	fi
	737	multout[$iout]=true
	738	string=${localout_pre[$iout]}
	739	localout_pre[$iout]="${string%?}"
	740	else
	741	multout[$iout]=false
	742	fi
[2380]	743	fi
[2669]	744	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	745	then
[2669]	746	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	747	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	748	locat=connect; exit
	749	fi
	750	IFS="$IFSALT"
	751	fi
	752
	753	done < $fileconnection_file
	754
	755
	756
[2501]	757	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	758	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	759	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	760	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	761	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	762	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	763
	764
	765
[2380]	766	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	767	if [[ $run_coupled_model = true ]]
	768	then
	769
	770	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	771	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	772
	773	if (( $cores_ocean + $cores_atmos != $cores ))
	774	then
	775
	776	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	777	printf "\n PEs (total) : $cores"
	778	printf "\n PEs (atmosphere): $cores_atmos"
	779	printf "\n PEs (ocean) : $cores_ocean"
	780	locat=coupling; exit
	781
	782	fi
	783
	784	fi
	785
	786
	787	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	788	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	789	# FOLDER
	790	if [[ $running_in_batch_mode = true ]]
	791	then
	792
[2506]	793	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	794	then
[2506]	795	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	796	printf "\n Please check the output of the palmrun-call"
	797	printf "\n that you did on your local host."
	798	locat=SOURCES_FOR_RUN; exit
	799	fi
	800
	801	else
	802
	803	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	804	# AUTOMATIC RESTART RUN
	805	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	806	if [[ $restart_run = false ]]
	807	then
	808
	809	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	810	# THE LOCAL HOST
	811	if [[ ! -d $source_path ]]
	812	then
	813	printf "\n\n +++ source path \"$source_path\" on local host"
	814	printf "\n \"$(hostname)\" does not exist"
	815	locat=source_path; exit
	816	fi
	817
[2990]	818	rm -rf ${base_directory}/${sources_for_run_catalog}
	819	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	820
	821	if [[ "$source_list" = LM ]]
	822	then
	823
	824	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	825	source_list=""
	826	cd $source_path
	827
	828
[2512]	829	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	830	if [[ ! -d ../.svn ]]
[2380]	831	then
	832	printf "\n\n +++ source directory"
	833	printf "\n \"$source_path\" "
	834	printf "\n is not under control of \"subversion\"."
[2512]	835	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	836	fi
	837
	838
	839	# LIST ALL MODIFIED SOURCE CODE FILES
	840	Filenames=""
[2404]	841	svn status > tmp_svnstatus
[2380]	842	while read line
	843	do
	844	firstc=`echo $line \| cut -c1`
	845	if [[ $firstc = M \|\| $firstc = "?" ]]
	846	then
	847	Name=`echo "$line" \| cut -c8-`
	848	extension=`echo $Name \| cut -d. -f2`
	849	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	850	then
	851	Filenames="$Filenames "$Name
	852	fi
	853	fi
[2404]	854	done < tmp_svnstatus
	855	rm -rf tmp_svnstatus
[2380]	856
	857
	858	# COPY FILES TO SOURCES_FOR_RUN_...
	859	for filename in $Filenames
	860	do
[2990]	861	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	862	source_list=$source_list"$filename "
	863	done
	864
	865	cd - > /dev/null
	866
	867
	868	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	869	elif [[ "$source_list" != "" ]]
	870	then
	871
	872	cd $source_path
	873
	874	for filename in $source_list
	875	do
	876
	877	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	878	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	879	then
	880	printf "\n +++ source code file: $filename"
	881	printf "\n must not contain (\"/\") "
	882	locat=source; exit
	883	fi
	884
	885	if [[ ! -f $filename ]]
	886	then
	887	printf "\n +++ source code file: $filename"
	888	printf "\n does not exist"
	889	locat=source; exit
	890	else
[2990]	891	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	892	fi
	893
	894	done
	895
	896	cd - > /dev/null
	897
	898	fi
	899
	900	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	901	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	902	if [[ ! -f $makefile ]]
	903	then
	904	printf "\n +++ file \"$makefile\" does not exist"
	905	locat=make; exit
	906	else
[2990]	907	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	908	fi
	909
	910
	911	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	912	if [[ "$user_source_path" != "" ]]
[2380]	913	then
	914
	915	# DOES THE DIRECTORY EXIST?
[2384]	916	if [[ ! -d $user_source_path ]]
[2380]	917	then
	918
	919	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	920	printf "\n \"$user_source_path\" "
[2380]	921	printf "\n does not exist or is not a directory."
	922	printf "\n No source code will be used from this directory!\n"
[2384]	923	user_source_path=""
[2380]	924	if [[ $silent == false ]]
	925	then
	926	sleep 2
	927	fi
	928
	929	else
	930
[2384]	931	cd $user_source_path
[2380]	932	found=false
	933
	934	Names=$(ls -1 *.f90 2>&1)
	935	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	936	Names=$(ls -1 *.F90 2>&1)
	937	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	938	Names=$(ls -1 *.F 2>&1)
	939	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	940	Names=$(ls -1 *.f 2>&1)
	941	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	942	Names=$(ls -1 *.c 2>&1)
	943	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	944
	945	cd - > /dev/null
[2990]	946	cd ${base_directory}/${sources_for_run_catalog}
[2380]	947
	948	# COPY MAKEFILE IF EXISTING
[2384]	949	if [[ -f $user_source_path/Makefile ]]
[2380]	950	then
	951	printf "\n\n *** user Makefile from directory"
[2384]	952	printf "\n \"$user_source_path\" is used \n"
[2380]	953	if [[ $silent == false ]]
	954	then
	955	sleep 1
	956	fi
[2384]	957	cp $user_source_path/Makefile .
[2380]	958	fi
	959
	960	for filename in $AddFilenames
	961	do
	962	if [[ -f $filename ]]
	963	then
	964	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	965	printf "\n source code directory \"$user_source_path\" "
[2380]	966	printf "\n but was also given with option \"-s\" which means that it should be taken"
	967	printf "\n from directory \"$source_path\"."
	968	locat=source; exit
	969	fi
	970
[2384]	971	cp $user_source_path/$filename .
[2380]	972	source_list="$source_list $filename"
	973
	974	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	975	if [[ $(grep -c $filename Makefile) = 0 ]]
	976	then
	977	printf "\n\n +++ user file \"$filename\" "
	978	printf "\n is not listed in Makefile \n"
	979	locat=source; exit
	980	else
	981
	982	if [[ $found = false ]]
	983	then
	984	found=true
	985	printf "\n\n *** following user file(s) added to the"
	986	printf " files to be translated:\n "
	987	fi
	988	printf "$filename "
	989	if [[ $silent == false ]]
	990	then
	991	sleep 0.5
	992	fi
	993
	994	fi
	995	done
	996	[[ $found = true ]] && printf "\n"
	997	cd - > /dev/null
	998	fi
	999	fi
	1000
	1001	# COPY CONFIGURATION FILES
[2990]	1002	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1003	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1004
	1005	# COPY SHELLSCRIPTS
[2990]	1006	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1007	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1008
	1009	fi
	1010
	1011	fi
	1012
[2605]	1013
[2380]	1014	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1015	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1016	if [[ "$global_revision" = "" ]]
	1017	then
	1018	global_revision=`svnversion $source_path 2>/dev/null`
	1019	global_revision="Rev: $global_revision"
	1020	fi
	1021
	1022
	1023	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1024	if [[ -n $cores ]]
	1025	then
	1026
	1027	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1028	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1029	if [[ $tasks_per_node = 0 ]]
[2380]	1030	then
[3025]	1031	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1032	then
	1033	printf "\n"
	1034	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1035	printf "\n set -T option or define tasks_per_node in the config file"
	1036	locat=tasks_per_node; (( iec = 0 )); exit
	1037	else
	1038	# DEFAULT FOR INTERACTIVE RUN
	1039	tasks_per_node=$cores
	1040	fi
[2380]	1041	fi
	1042
	1043	if (( cores < tasks_per_node ))
	1044	then
	1045	printf "\n"
	1046	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1047	printf "\n given values: -T $tasks_per_node -X $cores"
	1048	locat=tasks_per_node; (( iec = 0 )); exit
	1049	fi
	1050
	1051	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1052	(( mpi_tasks = cores / threads_per_task ))
	1053	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1054	(( ii = cores / tasks_per_node ))
	1055	(( remaining_cores = cores - ii * tasks_per_node ))
	1056	if (( remaining_cores > 0 ))
	1057	then
	1058	printf "\n"
	1059	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1060	printf "\n divisor of the total number of cores (option \"-X\")"
	1061	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1062	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1063	(( nodes = nodes + 1 ))
	1064	fi
	1065
	1066	fi
	1067
	1068
	1069	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1070	if [[ "$maximum_parallel_io_streams" = "" ]]
	1071	then
	1072	maximum_parallel_io_streams=$cores
	1073	fi
	1074
	1075
	1076	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1077	if [[ "$scp_port" != "" ]]
	1078	then
	1079	PORTOPT="-P $scp_port"
	1080	SSH_PORTOPT="-p $scp_port"
	1081	fi
	1082
	1083
	1084	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1085	# CONFIG-FILE
	1086	if [[ "$ssh_key" != "" ]]
	1087	then
	1088	ssh_key="-i $HOME/.ssh/$ssh_key"
	1089	fi
	1090
	1091
	1092	# SET QUEUE, IF NOT GIVEN
	1093	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1094	then
	1095
	1096	if [[ $queue = none && "$defaultqueue" = "" ]]
	1097	then
	1098	printf "\n"
	1099	printf "\n +++ no default queue given in configuration file and no queue"
	1100	printf "\n given with option -q"
[2789]	1101	locat=queue; exit
[2380]	1102	fi
	1103	if [[ $queue = none ]]
	1104	then
	1105	queue=$defaultqueue
	1106	fi
	1107
	1108	fi
	1109
	1110
	1111	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1112	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1113	(( i = 0 ))
[2610]	1114	(( nr_of_input_files = 0 ))
[2380]	1115	while (( i < iin ))
	1116	do
	1117	(( i = i + 1 ))
	1118
	1119	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1120	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1121	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1122	then
[2610]	1123	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1124	else
[2834]	1125	eval filename=${pathin_pre[$i]}/${jobname}${endin_pre[$i]}
[2380]	1126	fi
	1127
[2610]	1128
[2380]	1129	# CHECK IF FILE EXISTS
	1130	if ! ls $filename* 1>/dev/null 2>&1
	1131	then
	1132
[2669]	1133	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1134	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1135	then
	1136	printf "\n\n +++ INPUT-file: "
[2610]	1137	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1138	then
	1139	printf "\n $filename"
	1140	else
[2610]	1141	printf "\n $filename.${extin_pre[$i]}"
[2380]	1142	fi
	1143	printf "\n does not exist\n"
	1144	locat=input; exit
	1145	else
[2610]	1146	(( nr_of_input_files = nr_of_input_files + 1 ))
	1147	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1148	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1149	actionin[$nr_of_input_files]="unavailable"
[2610]	1150	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1151	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1152	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1153	fi
[2605]	1154
[2380]	1155	else
	1156
[2834]	1157	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME ($jobname) AND
[2610]	1158	# CREATE A LIST FOR THE DETECTED BASENAME ENDINGS
	1159	if [[ "${multin[$i]}" = true ]]
	1160	then
	1161	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1162	ls -1 -d ${filename} > filelist 2>/dev/null
	1163	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1164	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1165
[2610]	1166	endings=""
	1167	while read line
	1168	do
	1169	# filename without path (i.e. after the last "/")
	1170	basefilename=$(basename ${line})
[2380]	1171
[2610]	1172	# check if there is an extension and remove it
	1173	ext=${basefilename##*.}
	1174	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1175	then
	1176	basefilename=${basefilename%.*}
	1177	fi
[2380]	1178
[2610]	1179	# check for an existing cycle number and remove it
	1180	cycle=${basefilename##*.}
	1181	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1182	then
	1183	basefilename=${basefilename%.*}
	1184	fi
[2600]	1185
[2834]	1186	# remove the jobname from the beginning
	1187	length_jobname=${#jobname}
	1188	ending=${basefilename:${length_jobname}}
[2610]	1189
	1190	# remove the ending given in the .iofiles from the beginning
	1191	endingstring="${endin_pre[$i]}"
	1192	length_ending=${#endingstring}
	1193	ending=${ending:${length_ending}}
	1194
	1195	if [[ "$ending" = "" ]]
[2600]	1196	then
[2610]	1197	# standard ending as given in the .iofiles
	1198	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1199	then
	1200	endings="$endings DEFAULT"
	1201	fi
[2600]	1202	else
[2610]	1203	# ending must start with "_", otherwise its a different file
	1204	if [[ "${ending:0:1}" = "_" ]]
	1205	then
	1206	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1207	then
	1208	endings="$endings $ending"
	1209	fi
	1210	fi
[2600]	1211	fi
[2610]	1212
	1213	done <filelist
[2380]	1214
[2610]	1215	rm filelist
[2380]	1216
[2600]	1217	else
[2610]	1218
	1219	# SINGLE NAME
	1220	endings=DEFAULT
	1221
[2600]	1222	fi
	1223
[2610]	1224	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1225	for ending in $endings
	1226	do
	1227
	1228	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1229	if [[ $ending = DEFAULT ]]
[2380]	1230	then
[2610]	1231	ending=""
	1232	fi
	1233
	1234	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1235	(( nr_of_input_files = nr_of_input_files + 1 ))
	1236	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1237	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1238	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1239	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1240	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1241	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1242
	1243
	1244	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1245	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1246	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1247	then
	1248	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1249	else
[2834]	1250	eval filename=${pathin[$nr_of_input_files]}/${jobname}${endin[$nr_of_input_files]}
[2380]	1251	fi
[2610]	1252
	1253	# DETERMINE THE FILE'S CYCLE NUMBER
	1254	(( maxcycle = 0 ))
	1255	ls -1 -d $filename > filelist 2>/dev/null
	1256	ls -1 -d $filename.* >> filelist 2>/dev/null
	1257	while read line
	1258	do
	1259	# filename without path (i.e. after the last "/")
	1260	basefilename=$(basename ${line})
	1261
	1262	# check if there is an extension
	1263	extension=${basefilename##*.}
	1264	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1265	then
	1266	basefilename=${basefilename%.*}
	1267	fi
	1268
	1269	# check for an existing cycle number
	1270	cycle=${basefilename##*.}
	1271	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1272	then
[2669]	1273	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1274	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1275	(( icycle = $((10#$cycle)) ))
[2610]	1276	else
	1277	(( icycle = 0 ))
	1278	fi
	1279
	1280	if (( icycle > maxcycle ))
	1281	then
	1282	(( maxcycle = icycle ))
	1283
	1284	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1285	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1286	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1287	then
	1288	leading_zero=true
	1289	else
	1290	leading_zero=false
	1291	fi
	1292	fi
	1293
	1294	done <filelist
	1295	rm filelist
	1296
	1297	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1298	if [[ $leading_zero = true ]]
[2380]	1299	then
[2610]	1300	cyclestring=`printf "%03d" $maxcycle`
	1301	else
	1302	cyclestring=$maxcycle
[2380]	1303	fi
[2610]	1304
	1305	# APPEND CYCLE NUMBER TO FILENAME
	1306	if (( maxcycle > 0 ))
[2380]	1307	then
[2610]	1308	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1309	then
	1310	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1311	else
	1312	filename=${filename}.$cyclestring
	1313	fi
[2380]	1314	else
[2610]	1315	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1316	then
	1317	filename=${filename}.${extin[$nr_of_input_files]}
	1318	fi
[2380]	1319	fi
[2610]	1320
	1321	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1322	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1323	absnamein[$nr_of_input_files]=$filename
	1324	if (( maxcycle > 0 ))
[2380]	1325	then
[2610]	1326	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1327	then
	1328	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1329	else
[2834]	1330	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1331	fi
[2380]	1332	else
[2610]	1333	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1334	then
	1335	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1336	else
[2834]	1337	frelin[$nr_of_input_files]=${jobname}${endin[$nr_of_input_files]}
[2610]	1338	fi
[2380]	1339	fi
	1340
[2610]	1341	done
	1342
[2380]	1343	fi
[2610]	1344
[2380]	1345	done
	1346
[2610]	1347
[2380]	1348	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1349	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1350	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1351	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1352	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1353	# REMOTE HOST)
	1354	(( i = 0 ))
	1355	while (( i < iout ))
	1356	do
	1357	(( i = i + 1 ))
[2610]	1358	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1359	then
[2610]	1360	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1361	then
[2610]	1362	actionout_pre[$i]=""
	1363	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1364	then
[2610]	1365	actionout_pre[$i]=pe
	1366	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1367	then
[2610]	1368	actionout_pre[$i]=a
[2380]	1369	fi
	1370	(( maxcycle = 0 ))
[2834]	1371	eval filename=${pathout_pre[$i]}/${jobname}${endout_pre[$i]}
[2610]	1372	eval catalogname=${pathout_pre[$i]}
[2380]	1373	if ! ls $filename* 1>/dev/null 2>&1
	1374	then
	1375
	1376	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1377	if cat /dev/null > $filename
	1378	then
	1379	rm $filename
	1380	else
	1381
	1382	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1383	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1384	if [[ ! -d $catalogname ]]
	1385	then
	1386	if mkdir -p $catalogname
	1387	then
	1388	printf "\n\n *** directory:"
	1389	printf "\n $catalogname"
	1390	printf "\n was created\n"
	1391	else
	1392	printf "\n\n +++ OUTPUT-file:"
	1393	printf "\n $filename"
	1394	printf "\n cannot be created, because directory does not exist"
	1395	printf "\n and cannot be created either"
	1396	printf "\n"
	1397	locat=output ; exit
	1398	fi 2>/dev/null
	1399	else
	1400	printf "\n\n +++ OUTPUT-file:"
	1401	printf "\n $filename"
	1402	printf "\n cannot be created, although directory exists"
	1403	printf "\n"
	1404	locat=output ; exit
	1405	fi
	1406	fi 2>/dev/null
	1407
	1408	fi
	1409
	1410	fi
	1411	done
	1412
	1413
	1414	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1415	if [[ $running_in_batch_mode = false ]]
	1416	then
	1417	run_id=$RANDOM
[2834]	1418	job_id=${jobname}.$run_id
[2380]	1419
[2566]	1420	tempdir=$fast_io_catalog/$job_id
[2380]	1421	fi
	1422
	1423
	1424	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1425	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1426	then
	1427
	1428	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1429	if [[ $ibd = 0 ]]
	1430	then
	1431	printf "\n"
	1432	printf "\n +++ no batch directives found in configuration file"
	1433	locat=config_file_batch_directives; (( iec = 0 )); exit
	1434	fi
	1435
	1436	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1437	done=false
[2384]	1438	cputime=$cpumax
[2380]	1439	while [[ $done = false ]]
	1440	do
[2384]	1441	if (( cputime == 0 ))
[2380]	1442	then
	1443	printf "\n +++ cpu-time is undefined"
	1444	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1445	printf "\n >>> "
[2384]	1446	read cputime 1>/dev/null 2>&1
[2380]	1447	else
	1448	done=true
	1449	fi
	1450	done
[2420]	1451	cpumax=$cputime
[2380]	1452
	1453	# CHECK THE MEMORY DEMAND
	1454	done=false
	1455	while [[ $done = false ]]
	1456	do
	1457	if (( memory == 0 ))
	1458	then
	1459	printf "\n +++ memory demand is undefined"
	1460	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1461	printf "\n >>> "
	1462	read memory 1>/dev/null 2>&1
	1463	else
	1464	done=true
	1465	fi
	1466	done
	1467
	1468	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1469	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1470	then
	1471	while [[ -z $remote_username ]]
	1472	do
[2420]	1473	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1474	printf "\n >>> Please type username:"
	1475	printf "\n >>> "
	1476	read remote_username
	1477	done
	1478	fi
	1479
	1480	else
	1481
[2420]	1482	if [[ $running_in_batch_mode = false ]]
	1483	then
	1484	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1485	cpumax=$cputime
	1486	else
	1487	cputime=$cpumax
	1488	fi
[2380]	1489
	1490	fi
	1491
	1492
	1493	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1494	(( cpu_hours = cputime / 3600 ))
	1495	(( resttime = cputime - cpu_hours * 3600 ))
	1496	(( cpu_minutes = resttime / 60 ))
	1497	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1498	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1499
	1500
	1501	# OUTPUT OF THE PALMRUN-HEADER
	1502	calltime=$(date)
	1503	printf "\n"
	1504	printf "#------------------------------------------------------------------------# \n"
	1505	printf "\| %-35s%35s \| \n" "$version" "$calltime"
	1506	printf "\| \| \n"
	1507	column1="called on:"; column2=$(hostname)
	1508	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1509	if [[ $create_remote_batch_job = true ]]
	1510	then
[2506]	1511	column1="execution on:"; column2="$host_configuration (username: $remote_username)"
[2380]	1512	else
	1513	if [[ $running_on_remote = true ]]
	1514	then
[3025]	1515	column1="host identifier:"; column2="$host_configuration (execute on IP: $remote_ip)"
[2380]	1516	else
[3025]	1517	column1="host identifier:"; column2="$host_configuration (execute on IP: $local_ip)"
[2380]	1518	fi
	1519	fi
	1520	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1521
	1522	column1="running in:"
	1523	if [[ $running_in_batch_mode = true ]]
	1524	then
	1525	column2="batch job mode"
	1526	else
	1527	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1528	then
	1529	column2="job creation mode"
	1530	else
	1531	column2="interactive run mode"
	1532	fi
	1533	fi
	1534	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1535
[2479]	1536	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1537	then
[2480]	1538	if [[ "$project_account" != "" ]]
[2479]	1539	then
	1540	column1="project account number:"
	1541	column2="$project_account"
	1542	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1543	fi
	1544	fi
	1545
[2380]	1546	if [[ -n $cores ]]
	1547	then
	1548	if [[ $run_coupled_model = false ]]
	1549	then
	1550	column1="number of cores:"; column2=$cores
	1551	else
	1552	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1553	fi
	1554	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1555	fi
	1556	if [[ -n $tasks_per_node ]]
	1557	then
	1558	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1559	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1560	if (( remaining_cores > 0 ))
	1561	then
	1562	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1563	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1564	fi
	1565	fi
	1566	if [[ $maximum_parallel_io_streams != $cores ]]
	1567	then
	1568	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1569	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1570	fi
	1571	if [[ $use_openmp = true ]]
	1572	then
	1573	column1="threads per task:"; column2="$threads_per_task"
	1574	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1575	fi
[2384]	1576	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1577	then
[2506]	1578	column1="memory demand / PE":; column2="$memory MB"
	1579	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1580	column1="job cpu time (h:m:s):"; column2="$timestring"
	1581	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1582	fi
[2380]	1583	printf "\| \| \n"
	1584	if [[ "$source_list" != "" ]]
	1585	then
	1586	if [[ "$make_options" != "" ]]
	1587	then
	1588	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1589	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1590	line=$(echo "$make_options" \| cut -c46-)
	1591	while [[ "$line" != "" ]]
	1592	do
	1593	column1=""
	1594	column2=$(echo "$line" \| cut -c-45)
	1595	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1596	line=$(echo "$line" \| cut -c46-)
	1597	done
	1598	fi
	1599	fi
	1600
	1601	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1603	line=$(echo "$cpp_options" \| cut -c46-)
	1604	while [[ "$line" != "" ]]
	1605	do
	1606	column1=""
	1607	column2=$(echo "$line" \| cut -c-45)
	1608	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1609	line=$(echo "$line" \| cut -c46-)
	1610	done
	1611
	1612	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1613	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1614	line=$(echo "$compiler_options" \| cut -c46-)
	1615	while [[ "$line" != "" ]]
	1616	do
	1617	column1=""
	1618	column2=$(echo "$line" \| cut -c-45)
	1619	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1620	line=$(echo "$line" \| cut -c46-)
	1621	done
	1622
[2388]	1623	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1624	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1625	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1626	while [[ "$line" != "" ]]
	1627	do
	1628	column1=""
	1629	column2=$(echo "$line" \| cut -c-45)
	1630	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1631	line=$(echo "$line" \| cut -c46-)
	1632	done
	1633
	1634	if [[ "$login_init_cmd" != "" ]]
	1635	then
	1636	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1637	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1638	line=$(echo "$login_init_cmd" \| cut -c46-)
	1639	while [[ "$line" != "" ]]
	1640	do
	1641	column1=""
	1642	column2=$(echo "$line" \| cut -c-45)
	1643	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1644	line=$(echo "$line" \| cut -c46-)
	1645	done
	1646	fi
	1647
	1648	if [[ "$module_commands" != "" ]]
	1649	then
	1650	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1651	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1652	line=$(echo "$module_commands" \| cut -c46-)
	1653	while [[ "$line" != "" ]]
	1654	do
	1655	column1=""
	1656	column2=$(echo "$line" \| cut -c-45)
	1657	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1658	line=$(echo "$line" \| cut -c46-)
	1659	done
	1660	fi
	1661	printf "\| \| \n"
[3025]	1662	column1="run identifier:"; column2=$jobname
[2380]	1663	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1664	column1="activation string list:"; column2=$(echo $activation_string_list)
	1665	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1666
	1667	if [[ "$ocean_file_appendix" = true ]]
	1668	then
	1669	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1670	fi
	1671
	1672	if [[ "$source_list" != "" ]]
	1673	then
	1674	printf "\| \| \n"
	1675	printf "\| Files to be compiled: \| \n"
	1676	line=$source_list
	1677	while [[ "$line" != "" ]]
	1678	do
	1679	linestart=$(echo $line \| cut -c-70)
	1680	printf "\| %-70s \| \n" "$linestart"
	1681	line=$(echo "$line" \| cut -c71-)
	1682	done
	1683	fi
	1684	printf "#------------------------------------------------------------------------#"
	1685
	1686
	1687
	1688	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1689	if [[ $do_trace = true ]]
	1690	then
	1691	(( i = 0 ))
[2610]	1692	while (( i < nr_of_input_files ))
[2380]	1693	do
	1694	(( i = i + 1 ))
	1695	if (( i == 1 ))
	1696	then
	1697	printf "\n\n >>> INPUT-file assignments:\n"
	1698	fi
	1699	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1700	done
	1701	(( i = 0 ))
	1702	while (( i < iout ))
	1703	do
	1704	(( i = i + 1 ))
	1705	if (( i == 1 ))
	1706	then
	1707	printf "\n\n >>> OUTPUT-file assignments:\n"
	1708	fi
	1709	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1710	done
	1711	(( i = 0 ))
	1712	while (( i < iic ))
	1713	do
	1714	(( i = i + 1 ))
	1715	if (( i == 1 ))
	1716	then
	1717	printf "\n\n >>> INPUT-commands:\n"
	1718	fi
	1719	printf "\n ${in_command[$i]}"
	1720	done
	1721	(( i = 0 ))
	1722	while (( i < ioc ))
	1723	do
	1724	(( i = i + 1 ))
	1725	if (( i == 1 ))
	1726	then
	1727	printf "\n\n >>> OUTPUT-commands:\n"
	1728	fi
	1729	printf "\n ${out_command[$i]}"
	1730	done
	1731	fi
	1732
	1733	# QUERY FOR CONTINUE
	1734	if [[ $silent = false && $running_in_batch_mode = false ]]
	1735	then
	1736	antwort=dummy
	1737	printf "\n\n"
	1738	printf " >>> everything o.k. (y/n) ? "
	1739	while read antwort
	1740	do
	1741	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1742	then
	1743	printf " >>> everything o.k. (y/n) ? "
	1744	else
	1745	break
	1746	fi
	1747	done
	1748	if [[ $antwort = n \|\| $antwort = N ]]
	1749	then
	1750	locat=user_abort; (( iec = 0 )); exit
	1751	fi
	1752	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1753	then
[2566]	1754	printf "\n *** batch-job will be created and submitted"
[2380]	1755	else
[2566]	1756	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1757	fi
	1758	fi
	1759
	1760
	1761
	1762	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1763	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1764	then
	1765
	1766	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1767	then
[2566]	1768	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1769	else
[2566]	1770	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1771	fi
	1772
[2422]	1773	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1774	# IT SHALL BE CREATED
	1775	ask_for_make_depository=false
	1776	if [[ $create_remote_batch_job = true ]]
	1777	then
	1778
	1779	line=`grep %base_directory $config_file`
[2506]	1780	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${host_configuration}
	1781	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]	1782
[2506]	1783	if [[ $(grep -c "depository not found" ${host_configuration}_last_make_protokoll) != 0 ]]
[2422]	1784	then
	1785	printf "\n\n +++ make depository \"${make_depository}\""
	1786	printf "\n on remote host not found!"
	1787	ask_for_make_depository=true
	1788	fi
[2506]	1789	rm ${host_configuration}_last_make_protokoll
[2422]	1790
	1791	else
	1792
	1793	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[2506]	1794	make_depository=${base_directory}/MAKE_DEPOSITORY_${host_configuration}
[2422]	1795	if [[ ! -d ${make_depository} ]]
	1796	then
	1797	printf "\n\n +++ make depository \"${make_depository}\""
	1798	printf "\n on local host not found!"
	1799	ask_for_make_depository=true
	1800	fi
	1801
	1802	fi
	1803
	1804	if [[ $ask_for_make_depository = true ]]
	1805	then
	1806
	1807	antwort=dummy
	1808	printf "\n\n"
	1809	printf " >>> Create a new one (y/n) ? "
	1810	while read antwort
	1811	do
	1812	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1813	then
	1814	printf " >>> Create a new one (y/n) ? "
	1815	else
	1816	break
	1817	fi
	1818	done
	1819	if [[ $antwort = n \|\| $antwort = N ]]
	1820	then
	1821	locat=user_abort; (( iec = 0 )); exit
	1822	fi
	1823
[2566]	1824	if [[ $do_trace = true ]]
	1825	then
	1826	palmbuild -h $host_configuration
	1827	else
	1828	palmbuild -v -h $host_configuration
	1829	fi
[2422]	1830
	1831	if [[ $? != 0 ]]
	1832	then
	1833
	1834	# ABORT IN CASE OF COMPILATION PROBLEMS
	1835	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1836	locat=make_depository
	1837	exit
	1838	else
	1839	echo " *** now continue with creating executable and other sources"
	1840	fi
	1841
	1842	fi
	1843
[2566]	1844	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[2993]	1845	palmbuild -v $use_existing_sources_folder -h $host_configuration -d $jobname
[2380]	1846
	1847	if [[ $? != 0 ]]
	1848	then
	1849
	1850	# ABORT IN CASE OF COMPILATION PROBLEMS
	1851	printf "\n +++ error while creating executable and/or other sources"
	1852	locat=execution
[2990]	1853	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1854	exit
	1855
	1856	else
	1857
[2566]	1858	printf " *** executable and other sources created\n"
[2990]	1859	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1860
	1861	fi
	1862
	1863	fi
	1864
	1865
[2669]	1866	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1867	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1868	if [[ $create_remote_batch_job = true ]]
	1869	then
	1870	(( i = 0 ))
[2610]	1871	while (( i < nr_of_input_files ))
[2605]	1872	do
	1873	(( i = i + 1 ))
[2669]	1874	if [[ "${actionin[$i]}" = tr ]]
[2605]	1875	then
	1876	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1877	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1878	fi
	1879	done
	1880	if (( i > 0 ))
	1881	then
[3025]	1882	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1883	fi
	1884	fi
	1885
	1886
[2380]	1887	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1888	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1889	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1890	then
	1891
	1892	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1893	if [[ $running_in_batch_mode = false ]]
	1894	then
	1895	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1896	# FOLDER
[2566]	1897	mkdir -p $tempdir
	1898	chmod go+rx $tempdir
	1899	cd $tempdir
	1900	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1901	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1902
	1903	else
	1904
	1905	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1906	printf "\n *** running in temporary directory: $tempdir"
[2380]	1907
	1908	fi
	1909
	1910
	1911	# PROVIDE THE INPUT FILES
	1912	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1913	optional_files_missing=false
[2380]	1914	(( i = 0 ))
[2610]	1915	while (( i < nr_of_input_files ))
[2380]	1916	do
	1917	(( i = i + 1 ))
	1918	if (( i == 1 ))
	1919	then
	1920	printf "\n\n *** providing INPUT-files:\n$dashes"
	1921	fi
	1922
	1923
	1924	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1925	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1926	then
[2669]	1927	optional_files_missing=true
[2380]	1928	continue
	1929	fi
	1930
	1931	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1932	files_for_cores=false; filetype=file
	1933	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1934	then
	1935	files_for_cores=true; filetype=files
	1936	actionin[$i]=""
	1937	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1938	then
	1939	actionin[$i]=""
	1940	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1941	then
	1942	files_for_cores=true; filetype=files
	1943	actionin[$i]="ln"
	1944	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1945	then
	1946	actionin[$i]="ln"
	1947	fi
	1948
	1949	if [[ $files_for_cores = true ]]
	1950	then
	1951	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	1952	else
	1953	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	1954	fi
	1955
	1956	# INPUT-FILES TO BE LINKED
	1957	if [[ "${actionin[$i]}" = ln ]]
	1958	then
	1959
	1960	printf "\n $filetype will be linked"
	1961	if [[ $files_for_cores = false ]]
	1962	then
	1963	if [[ -f "${absnamein[$i]}" ]]
	1964	then
	1965	ln ${absnamein[$i]} ${localin[$i]}
	1966	got_tmp[$i]=true
	1967	fi
	1968	else
	1969	if [[ -d "${absnamein[$i]}" ]]
	1970	then
[2396]	1971	mkdir -p ${localin[$i]}
[2380]	1972	cd ${absnamein[$i]}
	1973	for file in $(ls *)
	1974	do
[2566]	1975	ln $file $tempdir/${localin[$i]}
[2380]	1976	done >\|/dev/null 2>&1
[2566]	1977	cd $tempdir
[2380]	1978	fi
	1979
	1980	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	1981	if [[ ! -f "${localin[$i]}/_000000" ]]
	1982	then
	1983	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	1984	cp -r ${absnamein[$i]}/* ${localin[$i]}
	1985	fi
	1986
	1987	got_tmp[$i]=true
	1988	fi
	1989	fi
	1990
	1991	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	1992	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	1993	then
	1994
	1995	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	1996	then
	1997
	1998	# FILE COPIES ARE PROVIDED FOR ALL CORES
	1999	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2000	printf "\n file will be provided for $cores processors"
[2396]	2001	mkdir -p ${localin[$i]}
[2380]	2002	ival=$cores
	2003	(( ii = 0 ))
	2004	while (( ii <= ival-1 ))
	2005	do
	2006	if (( ii < 10 ))
	2007	then
	2008	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2009	elif (( ii < 100 ))
	2010	then
	2011	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2012	elif (( ii < 1000 ))
	2013	then
	2014	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2015	else
	2016	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2017	fi
	2018	(( ii = ii + 1 ))
	2019	done
	2020
	2021	else
	2022
	2023	if [[ $files_for_cores = true ]]
	2024	then
	2025
	2026	# PROVIDE FILES FOR EACH CORE
	2027	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2028	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2029	printf "\n providing $cores files for the respective cores"
[2396]	2030	mkdir -p ${localin[$i]}
[2380]	2031	if [[ $link_local_input = true ]]
	2032	then
	2033	printf " files will be linked\n"
	2034	cd ${absnamein[$i]}
	2035	for file in $(ls *)
	2036	do
	2037	ln -f $file ${localin[$i]}
	2038	done
[2566]	2039	cd $tempdir
[2380]	2040	fi
	2041
	2042	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2043	if [[ ! -f "${localin[$i]}/_000000" ]]
	2044	then
	2045	if [[ $link_local_input = true ]]
	2046	then
	2047	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2048	fi
	2049	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2050	fi
	2051
	2052	else
	2053
	2054	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2055	if [[ $link_local_input = true ]]
	2056	then
	2057	printf " file will be linked\n"
	2058	ln -f ${absnamein[$i]} ${localin[$i]}
	2059	fi
[2605]	2060	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2061	if [[ ! -f "${localin[$i]}" ]]
	2062	then
	2063	if [[ $link_local_input = true ]]
	2064	then
	2065	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2066	fi
[2669]	2067	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2068	then
	2069	mv ${absnamein[$i]} ${localin[$i]}
	2070	else
	2071	cp ${absnamein[$i]} ${localin[$i]}
	2072	fi
[2380]	2073	fi
	2074	fi
	2075	fi
	2076	fi
	2077
	2078	done
	2079	if (( i != 0 ))
	2080	then
[2669]	2081	if [[ $optional_files_missing = true ]]
	2082	then
	2083	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2084	fi
[2380]	2085	printf "\n$dashes\n *** all INPUT-files provided \n"
	2086	fi
	2087
	2088
	2089	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2090	(( i = 0 ))
	2091	while (( i < iic ))
	2092	do
	2093	(( i = i + 1 ))
	2094	if (( i == 1 ))
	2095	then
	2096	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2097	fi
	2098	printf "\n >>> ${in_command[$i]}"
	2099	eval ${in_command[$i]}
	2100	if (( i == iic ))
	2101	then
	2102	printf "\n$dashes\n"
	2103	fi
	2104	done
	2105
	2106
	2107	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2108	# (FILE ENVPAR WILL BE READ BY PALM)
	2109	cat > ENVPAR << EOF
[2834]	2110	&envpar run_identifier = '$jobname', host = '$host_configuration',
[2906]	2111	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2112	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2113	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2114	maximum_cpu_time_allowed = ${cpumax}.,
	2115	revision = '$global_revision',
	2116	batch_job = .${running_in_batch_mode}. /
	2117
	2118	EOF
	2119
	2120
	2121	# STARTING THE EXECUTABLE
	2122	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2123	PATH=$PATH:$tempdir
[2380]	2124
	2125
	2126	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2127	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2128	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2129	eval line=\"$line\"
	2130	execute_command="$line"
	2131
	2132
	2133	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2134	if [[ "$execute_command_for_combine" = "" ]]
	2135	then
	2136	eval line2=\"$line2\"
	2137	execute_command_for_combine="$line2"
	2138	fi
	2139
[2380]	2140
	2141
	2142	# PROVIDE A HOSTFILE, IF REQUIRED
	2143	if [[ "$hostfile" != "" ]]
	2144	then
	2145
	2146	if [[ $hostfile = auto ]]
	2147	then
	2148	# CREATE A NEW HOSTFILE
	2149	(( ii = 1 ))
	2150	while (( ii <= cores / threads_per_task ))
	2151	do
	2152	echo $(hostname) >> hostfile
	2153	(( ii = ii + 1 ))
	2154	done
	2155	if (( cores / threads_per_task == 0 ))
	2156	then
	2157	echo $(hostname) >> hostfile
	2158	fi
	2159
	2160	else
	2161	cp $hostfile hostfile
	2162	fi
	2163	eval line=\"`head -n $ii hostfile`\"
	2164	printf "\n *** running on: $line"
	2165	fi
	2166
	2167
	2168
	2169	# SET THE NUMBER OF OPENMP-THREADS
	2170	if [[ $use_openmp = true ]]
	2171	then
	2172	export OMP_NUM_THREADS=$threads_per_task
	2173	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2174	else
	2175	export OMP_NUM_THREADS=1
	2176	fi
	2177
	2178
[2610]	2179	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2180	if [[ $run_coupled_model = false ]]
	2181	then
	2182	if [[ "$ocean_file_appendix" = true ]]
	2183	then
	2184	echo "precursor_ocean" > coupling_steering
	2185	else
	2186	echo "precursor_atmos" > coupling_steering
	2187	fi
	2188	else
	2189	(( iia = $cores_atmos / $threads_per_task ))
	2190	(( iio = $cores_ocean / $threads_per_task ))
	2191	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2192	printf "\n\n"
	2193	echo "coupled_run $iia $iio" > coupling_steering
	2194	fi
	2195
	2196	printf "\n *** execute command:"
	2197	printf "\n \"$execute_command\" \n\n"
	2198
	2199	$execute_command < coupling_steering
	2200
	2201	if [[ $? != 0 ]]
	2202	then
	2203
	2204	# ABORT IN CASE OF RUNTIME ERRORS
	2205	printf "\n +++ runtime error occured"
	2206	locat=execution
	2207	exit
	2208
	2209	else
	2210
	2211	printf "\n$dashes\n *** execution finished \n"
	2212
	2213	fi
	2214
	2215
	2216	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2217	# BY EACH CORE INTO ONE FILE
	2218	if [[ ! -f combine_plot_fields.x ]]
	2219	then
	2220
	2221	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2222	printf "\n 2d- and/or 3d-data may be incomplete!"
	2223	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2224
	2225	elif [[ "$combine_plot_fields" == true ]]
	2226	then
	2227
	2228	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2229	$execute_command_for_combine
	2230
	2231	else
	2232
	2233	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2234	# DATA OUTPUT
[2380]	2235	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2236	fi
	2237
	2238
	2239
	2240	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2241	(( i = 0 ))
	2242	while (( i < ioc ))
	2243	do
	2244	(( i = i + 1 ))
	2245	if (( i == 1 ))
	2246	then
	2247	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2248	fi
[2799]	2249
	2250	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2251	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2252
[2380]	2253	printf "\n >>> ${out_command[$i]}"
	2254	eval ${out_command[$i]}
	2255	if (( i == ioc ))
	2256	then
	2257	printf "\n$dashes\n"
	2258	fi
	2259	done
	2260
	2261
[2610]	2262	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2263	# WILDCARDS
[2380]	2264	(( i = 0 ))
[2610]	2265	(( nr_of_output_files = 0 ))
	2266
[2380]	2267	while (( i < iout ))
	2268	do
[2610]	2269
[2380]	2270	(( i = i + 1 ))
[2610]	2271
	2272	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2273	# CREATE A LIST FOR THE DETECTED ENDINGS
	2274	if [[ "${multout[$i]}" = true ]]
	2275	then
	2276	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2277	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2278	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2279
	2280	endings="DEFAULT"
	2281	while read line
	2282	do
	2283	# remove the local name from the beginning
	2284	localnamestring="${localout_pre[$i]}"
	2285	length_localname=${#localnamestring}
	2286	ending=${line:${length_localname}}
	2287
	2288	if [[ "$ending" != "" ]]
	2289	then
	2290	endings="$endings $ending"
	2291	fi
	2292
	2293	done <filelist
	2294
	2295	rm filelist
	2296
	2297	else
	2298
	2299	# SINGLE NAME
	2300	endings=DEFAULT
	2301
	2302	fi
	2303
	2304	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2305	for ending in $endings
	2306	do
	2307
	2308	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2309	if [[ $ending = DEFAULT ]]
	2310	then
	2311	ending=""
	2312	fi
	2313
	2314	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2315	(( nr_of_output_files = nr_of_output_files + 1 ))
	2316	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2317	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2318	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2319	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2320	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2321	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2322	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2323
	2324	done
	2325
	2326	done
	2327
	2328
	2329
	2330
	2331	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2332	(( i = 0 ))
	2333	while (( i < nr_of_output_files ))
	2334	do
	2335	(( i = i + 1 ))
[2380]	2336	if (( i == 1 ))
	2337	then
	2338	printf "\n\n *** saving OUTPUT-files:"
	2339
	2340	# GET RUN NUMBER ASSIGNED BY PALM
	2341	if [[ -f RUN_NUMBER ]]
	2342	then
	2343	read run_number < RUN_NUMBER
	2344	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2345	usecycle_option="-U $run_number"
	2346	else
	2347	run_number=0
	2348	usecycle_option=""
	2349	fi
	2350	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2351	then
[2404]	2352	printf "\n *** in case of SCP transfers to local host"
	2353	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2354	fi
	2355	printf "\n$dashes"
	2356	fi
	2357
	2358	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2359	then
	2360
[2834]	2361	eval filename=${pathout[$i]}/${jobname}${endout[$i]}
[2610]	2362
	2363	# DETERMINE THE CYCLE NUMBER
	2364	ls -1 -d $filename > filelist 2>/dev/null
	2365	ls -1 -d $filename.* >> filelist 2>/dev/null
	2366	while read line
	2367	do
	2368
	2369	# filename without path (i.e. after the last "/")
	2370	basefilename=$(basename ${line})
	2371
	2372	# check if there is an extension
	2373	extension=${basefilename##*.}
	2374	if [[ "$extension" = "${extout[$i]}" ]]
	2375	then
	2376	basefilename=${basefilename%.*}
	2377	fi
	2378
	2379	# check for an existing cycle number
	2380	cycle=${basefilename##*.}
	2381	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2382	then
[2669]	2383	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2384	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2385	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2386	else
	2387	(( icycle = 1 ))
	2388	fi
	2389
	2390	if (( icycle > maxcycle ))
	2391	then
	2392	(( maxcycle = icycle ))
	2393	fi
	2394
	2395	done <filelist
	2396	rm filelist
	2397
	2398
	2399	# SET THE CYCLE NUMBER
	2400	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2401	if [[ "${actionout[$i]}" = a ]]
	2402	then
	2403	(( maxcycle = maxcycle - 1 ))
	2404	fi
	2405
	2406	(( cycnum[$i] = maxcycle ))
	2407	pathout[$i]=$filename
	2408
	2409
	2410	# ADD CYCLE NUMBER TO FILENAME
	2411	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2412	if [[ "${actionout[$i]}" != "a" ]]
	2413	then
	2414	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2415	# WITH AN EXISTING CYCLE NUMBER
	2416	if (( run_number >= cycnum[$i] ))
	2417	then
	2418	(( cycnum[$i] = run_number ))
	2419	else
	2420	if (( run_number > 0 ))
	2421	then
	2422	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2423	fi
	2424	fi
	2425	fi
	2426	if (( cycnum[$i] > 0 ))
	2427	then
[2600]	2428	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2429	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2430	fi
	2431	fi
	2432
	2433	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2434	files_for_cores=false; filetype=file
	2435	link_local_output=false
	2436	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2437	then
	2438	files_for_cores=true; filetype=directory
	2439	actionout[$i]=""
	2440	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2441	then
	2442	actionout[$i]=""
	2443	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2444	then
	2445	files_for_cores=true; filetype=directory
	2446	link_local_output=true
	2447	actionout[$i]=""
	2448	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2449	then
	2450	link_local_output
	2451	actionout[$i]=""
	2452	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2453	then
	2454	files_for_cores=true; filetype=directory
	2455	actionout[$i]="tr"
	2456	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2457	then
	2458	actionout[$i]="tr"
	2459	fi
	2460
	2461	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2462	then
[2669]	2463	if [[ ${warnout[$i]} = true ]]
	2464	then
	2465	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2466	fi
[2380]	2467	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2468	then
[2669]	2469	if [[ ${warnout[$i]} = true ]]
	2470	then
	2471	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2472	fi
[2380]	2473	else
	2474
	2475
	2476	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2477	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2478	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2479	then
	2480	if [[ $running_on_remote = true ]]
	2481	then
	2482
	2483	# SET OPTIONS FOR TRANSFER
	2484	if [[ "${actionout[$i]}" = tr ]]
	2485	then
	2486	if [[ $files_for_cores = false ]]
	2487	then
	2488	catalog_option=""
	2489	catalog_string=""
	2490	else
	2491	catalog_option="-c"
	2492	catalog_string="/"
	2493	fi
	2494	append_option=""
	2495	append_string=""
	2496	else
	2497	append_option="-A"
	2498	append_string="append"
	2499	fi
	2500
	2501	transfer_failed=false
	2502	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[2834]	2503	printf "\n ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}$catalog_string\n"
[2380]	2504
	2505	# TRANSFER VIA SCP
	2506	if [[ "$remote_loginnode" != "" ]]
	2507	then
[2834]	2508	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]	2509	else
[2834]	2510	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]	2511	fi
	2512	[[ $? != 0 ]] && transfer_failed=true
	2513
	2514
	2515	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2516	if [[ $transfer_failed = true ]]
	2517	then
	2518	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[2834]	2519	printf " ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id\n"
[2380]	2520
	2521	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2522	eval local_catalog=${pathout[$i]}
	2523	if [[ ! -d $local_catalog ]]
	2524	then
	2525	printf " *** local directory does not exist. Trying to create:\n"
	2526	printf " $local_catalog \n"
	2527	mkdir -p $local_catalog
	2528	fi
[2834]	2529	eval cp ${localout[$i]} ${pathout[$i]}/${host_configuration}_${jobname}${endout[$i]}_$run_id
[2380]	2530	transfer_problems=true
	2531	fi
	2532
	2533	else
	2534
	2535	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2536	# BE COPIED OR APPENDED ON THIS MACHINE
	2537	if [[ "${actionout[$i]}" = tr ]]
	2538	then
	2539	actionout[$i]=""
	2540	else
	2541	actionout[$i]="a"
	2542	fi
	2543	fi
	2544	fi
	2545
	2546
	2547	# APPEND ON THIS MACHINE
	2548	if [[ "${actionout[$i]}" = "a" ]]
	2549	then
	2550	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2551	then
	2552	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2553	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2554	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2555	else
	2556	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2557	printf "\n ${pathout[$i]}\n"
	2558	cat ${localout[$i]} >> ${pathout[$i]}
	2559	fi
	2560	fi
	2561
	2562	# COPY ON THIS MACHINE
	2563	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2564	# ON DIFFERENT FILE-SYSTEMS
	2565	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2566	then
	2567
	2568	# COPY IN CASE OF RUNS ON SINGLE CORES
	2569	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2570	then
	2571	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2572	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2573	if [[ $link_local_output = true ]]
	2574	then
	2575	printf " file will be linked\n"
	2576	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2577	fi
	2578	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2579	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2580	then
	2581	if [[ $link_local_output = true ]]
	2582	then
	2583	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2584	fi
	2585	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2586	else
	2587	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2588	fi
	2589	else
	2590	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2591	printf "\n ${pathout[$i]}\n"
	2592	if [[ $link_local_output = true ]]
	2593	then
	2594	printf " file will be linked\n"
	2595	ln -f ${localout[$i]} ${pathout[$i]}
	2596	fi
	2597	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2598	if [[ ! -f "${pathout[$i]}" ]]
	2599	then
	2600	if [[ $link_local_output = true ]]
	2601	then
	2602	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2603	fi
	2604	cp ${localout[$i]} ${pathout[$i]}
	2605	else
	2606	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2607	fi
	2608	fi
	2609
	2610	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2611	then
	2612
	2613	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2614	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2615	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2616	printf "\n ${pathout[$i]}\n"
	2617	if [[ $link_local_output = true ]]
	2618	then
	2619	printf " files will be linked\n"
[2396]	2620	mkdir -p ${pathout[$i]}
[2380]	2621	cd ${localout[$i]}
	2622	for file in $(ls *)
	2623	do
	2624	ln -f $file ${pathout[$i]}
	2625	done >\|/dev/null 2>&1
[2566]	2626	cd $tempdir
[2380]	2627	fi
	2628
	2629	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2630	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2631	then
	2632	if [[ $link_local_output = true ]]
	2633	then
	2634	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2635	fi
[3025]	2636	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2637	cp -r ${localout[$i]}/* ${pathout[$i]}
	2638	fi
	2639
	2640	fi
	2641	fi
	2642	done
	2643
	2644	if (( i != 0 ))
	2645	then
	2646	if [[ $transfer_problems = true ]]
	2647	then
	2648	printf "\n$dashes\n *** OUTPUT-files saved"
	2649	printf "\n +++ WARNING: some data transfers failed! \n"
	2650	else
	2651	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2652	fi
	2653	fi
	2654
	2655
	2656	# IF REQUIRED, START A RESTART-JOB
	2657	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2658	if [[ -f CONTINUE_RUN ]]
	2659	then
	2660
	2661	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2662	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2663	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2664	# -b START A BATCH JOB
	2665	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2666	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2667	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2668
[2957]	2669	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2670	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2671	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2672	then
	2673	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2674	fi
[2380]	2675
	2676	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2677	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2678	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2679	then
[2381]	2680	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2681	fi
	2682
	2683
	2684	# START THE RESTART-JOB
	2685	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2686	echo " $prc"
	2687	printf "\n$dashes\n"
	2688	if [[ $running_on_remote = true ]]
	2689	then
	2690
	2691	echo "*** ssh will be used to initiate restart-runs!"
	2692	echo " return_address=\"$return_address\" "
	2693	echo " return_username=\"$local_username\" "
	2694
	2695	if [[ "$remote_loginnode" != "" ]]
	2696	then
[2420]	2697	echo "echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address " \| ssh -q $remote_username@$remote_loginnode
[2380]	2698	else
[2420]	2699	echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address
[2380]	2700	fi
	2701
	2702	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2703	sleep 30
	2704
	2705	else
	2706
	2707	# START THE RESTART JOB ON THE LOCAL HOST
	2708	eval $prc # THE ' MUST BE EVALUATED
	2709	cd - > /dev/null
	2710
	2711	fi
	2712	printf "\n$dashes\n *** restart-run initiated \n"
	2713
	2714
	2715	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2716	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2717	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2718	# MAY BE VERY HUGE)
	2719	(( i = 0 ))
[2610]	2720	while (( i < nr_of_input_files ))
[2380]	2721	do
	2722	(( i = i + 1 ))
	2723	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2724	then
	2725	rm -r ${absnamein[$i]}
	2726	fi
	2727	done
	2728
	2729	fi
	2730
	2731
	2732	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2733	cd $HOME
[2566]	2734	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2735
	2736
	2737	else
	2738
	2739
	2740	# PREPARING ACTIONS,
	2741	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2742
	2743	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[2834]	2744	palmrun_com="$palmrun_script_name -d $jobname -h $host_configuration -m $memory -t $cpumax -q $queue -r $run_id -U $local_username"
[2380]	2745	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2746	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2747	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2748	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2749	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2750	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2751	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2752	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2753	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2754	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2755	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2756	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2757	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2758	if [[ $create_remote_batch_job = true ]]
	2759	then
	2760	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2761	if [[ $do_trace = true ]]
	2762	then
	2763	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2764	fi
[2380]	2765	elif [[ $create_batch_job = true ]]
	2766	then
	2767	palmrun_com=${palmrun_com}" -j"
[2420]	2768	if [[ $do_trace = true ]]
	2769	then
	2770	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2771	fi
[2380]	2772	fi
	2773
	2774
	2775	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2776	# REMOTE HOST
[2506]	2777	job_protocol_file_local=${local_jobcatalog}/${host_configuration}_${job_id}
[2380]	2778	job_protocol_file=$job_protocol_file_local
	2779	if [[ $create_remote_batch_job = true ]]
	2780	then
[2506]	2781	job_protocol_file_remote=${remote_jobcatalog}/${host_configuration}_${job_id}
[2380]	2782	job_protocol_file=$job_protocol_file_remote
	2783	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
	2784	scpjob_file=${remote_jobcatalog}/scpjob.$run_id
	2785	fi
	2786
	2787
	2788	# BUILD THE JOB-SCRIPTS ON FILE jobfile
	2789	jobfile=jobfile.$run_id
	2790
	2791
	2792	# FIRST CREATE THE BATCH DIRECTIVES
	2793	(( i = 0 ))
	2794	while (( i < ibd ))
	2795	do
	2796	(( i = i + 1 ))
[2693]	2797	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2798	eval line=\"$line\"
	2799	echo "$line" >> $jobfile
	2800	done
	2801	echo " " >> $jobfile
	2802
	2803
	2804	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2805	# PROTOCOL
	2806	if [[ $create_remote_batch_job = true ]]
	2807	then
	2808	echo "set +vx" >> $jobfile
	2809	echo "trap '" >> $jobfile
	2810	echo "set +vx" >> $jobfile
	2811	echo "cd ${remote_jobcatalog}" >> $jobfile
	2812	echo "cat > scpjob.$run_id << %%END%%" >> $jobfile
	2813
	2814	# ADD THE BATCH DIRECTIVES
	2815	(( i = 0 ))
	2816	while (( i < ibdt ))
	2817	do
	2818	(( i = i + 1 ))
[2693]	2819	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2820	eval line=\"$line\"
	2821	echo "$line" >> $jobfile
	2822	done
	2823	echo " " >> $jobfile
	2824
	2825	echo "set -x" >> $jobfile
[2834]	2826	echo "${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]	2827	echo "%%END%%" >> $jobfile
	2828	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
	2829	echo "$submit_command $scpjob_file" >> $jobfile
	2830	echo "rm $scpjob_file" >> $jobfile
[2404]	2831	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2832	echo "set -x" >> $jobfile
	2833	echo " ' exit" >> $jobfile
	2834	fi
	2835
	2836
	2837	# ACTIVATE ERROR-TRACEBACK
	2838	if [[ $do_trace = true ]]
	2839	then
	2840	echo "set -x" >> $jobfile
	2841	else
	2842	echo "set +vx" >> $jobfile
	2843	fi
	2844
	2845
	2846	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2847	if [[ "$login_init_cmd" != "" ]]
	2848	then
	2849	echo "$login_init_cmd" >> $jobfile
	2850	fi
	2851	if [[ "$module_commands" != "" ]]
	2852	then
	2853	echo "$module_commands" >> $jobfile
	2854	fi
	2855
	2856
	2857	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2858	if [[ $create_remote_batch_job = true ]]
	2859	then
	2860	echo "mkdir $tempdir" >> $jobfile
	2861	echo "chmod go+rx $tempdir" >> $jobfile
	2862	else
	2863	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2864	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2865	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2866	mkdir $tempdir
	2867	chmod go+rx $tempdir
	2868	fi
	2869	echo "cd $tempdir" >> $jobfile
	2870	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2871	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2872	echo "export PATH=.:\$PATH" >> $jobfile
	2873	echo "export execute_palmrun=true" >> $jobfile
	2874
	2875
	2876	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2877	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2878	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2879	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2880	echo "export LOCAL_PWD" >> $jobfile
	2881
	2882
	2883	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2884	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2885	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2886
	2887
	2888	# CALL PALMRUN WITHIN THE JOB
	2889	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2890	echo "set -x" >> $jobfile
	2891	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2892
	2893
	2894	# TRANSFER JOBFILE TO THE TARGET HOST
	2895	if [[ $create_jobfile_only = false ]]
	2896	then
	2897
	2898	if [[ $create_remote_batch_job = true ]]
	2899	then
	2900
[2420]	2901	echo " "
[2566]	2902	echo " *** transfer of job to remote host via scp"
[2420]	2903	if [[ $do_trace = true ]]
	2904	then
[2506]	2905	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id}"
[2420]	2906	fi
[2566]	2907	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${host_configuration}_${job_id} > /dev/null
[2380]	2908
[2566]	2909	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	2910	if [[ $do_trace = true ]]
	2911	then
[2506]	2912	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]	2913	fi
[2506]	2914	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]	2915
	2916	elif [[ $create_batch_job = true ]]
	2917	then
	2918
[2385]	2919	eval local_jobcatalog=$local_jobcatalog
[2506]	2920	cp $jobfile ${local_jobcatalog}/${host_configuration}_${job_id}
[2385]	2921	cd $local_jobcatalog
[2380]	2922	echo " "
[2420]	2923	echo " *** submit the job"
	2924	if [[ $do_trace = true ]]
	2925	then
[2506]	2926	echo "$submit_command ${host_configuration}_${job_id}"
[2420]	2927	fi
[2506]	2928	$submit_command ${host_configuration}_${job_id}
	2929	rm ${host_configuration}_${job_id}
[2380]	2930	cd - > /dev/null
	2931
	2932	fi
	2933
	2934	rm -rf $jobfile
	2935
	2936	else
	2937
	2938	printf "\n *** jobfile created under name \"$jobfile\" "
	2939	printf "\n no batch-job has been sent!"
	2940
	2941	fi
	2942
	2943	fi # END OF REMOTE-PART

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