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source: palm/trunk/SCRIPTS/palmrun @ 3558

Last change on this file since 3558 was 3555, checked in by raasch, 6 years ago
sed-command to remove repeated space-characters replaced by tr-command, to guarantee mac compatible
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 102.4 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 3555 2018-11-22 13:50:37Z kanani $
[3555]	29	# sed-command to remove repeated space-characters replaced by tr-command, to
	30	# guarantee mac compatible
	31	#
	32	# 3549 2018-11-21 15:44:44Z raasch
[3549]	33	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	34	# of login messages on specific systems
	35	#
	36	# 3534 2018-11-19 15:35:16Z raasch
[3534]	37	# batch_scp for sending back the job protocol file is called via login-node if
	38	# a login-node has been set in the config-file
	39	# ssh-calls rearranged to avoid output of system/user-profile messages
	40	#
	41	# 3505 2018-11-08 09:14:30Z raasch
[3505]	42	# job folders are created in case that they do not exist
	43	#
	44	# 3455 2018-10-30 14:12:31Z raasch
[3455]	45	# options -h and -d renamed -c and -r, respectively
	46	#
	47	# 3402 2018-10-23 11:49:24Z knoop
[3346]	48	# job_id is set for compatibility reasons with older versions of config files
	49	#
	50	# 3313 2018-10-06 15:22:48Z knoop
[3294]	51	# more detailed error message for outdated fileconnection file
	52	#
	53	# 3236 2018-09-10 09:07:06Z raasch
[3236]	54	# warning issued in case of file connection file version mismatch,
	55	# host_configuration renamed configuration_identifier,
	56	# "host identifier" in header output renamed "config. identifier",
	57	# jobname renamed run_identifier,
	58	# run_id renamed run_id_number
	59	# job_id renamed run_id
	60	# option -r renamed -i
	61	#
	62	# 3151 2018-07-19 08:45:38Z raasch
[3151]	63	# removed additional listing of files to be compiled, print PALM code revision
	64	# in header
	65	#
	66	# 3132 2018-07-16 11:44:58Z raasch
[3132]	67	# create consistent error messages in case of failed restarts,
	68	# check existence of remote job catalog
	69	#
	70	# 3043 2018-05-25 10:47:54Z raasch
[3043]	71	# check for setting of fast_io_catalog
	72	#
	73	# 3033 2018-05-23 15:26:19Z raasch
[3025]	74	# -T option not required for interactive runs (tasks per node =
	75	# total number of cores is assumed as default, if option is not given),
	76	# reformatting of a few messages,
	77	# bugfix: destination output directory is created if attribute "pe" is set in
	78	# .palm.iofiles
	79	#
	80	# 2718 2018-01-02 08:49:38Z maronga
[2993]	81	# bugfix of r2990
	82	#
	83	# 2718 2018-01-02 08:49:38Z maronga
[2990]	84	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	85	# not in the working directory from where palmrun is called
	86	#
	87	# 2718 2018-01-02 08:49:38Z maronga
[2957]	88	# svfout in the activation string will be replaced now by svfin in case of
	89	# automatic restarts
	90	#
	91	# 2718 2018-01-02 08:49:38Z maronga
[2906]	92	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	93	# the possible output or input of sky view factors
	94	#
	95	# 2718 2018-01-02 08:49:38Z maronga
[2834]	96	# "fname" renamed to "jobname"
	97	#
	98	# 2718 2018-01-02 08:49:38Z maronga
[2799]	99	# parameters are allowed in output commands (OC:)
	100	#
	101	# 2718 2018-01-02 08:49:38Z maronga
[2789]	102	# bugfix: exit if no queue has been given neither with option -q nor in the
	103	# configuration file
	104	#
	105	# 2718 2018-01-02 08:49:38Z maronga
[2762]	106	# file connection file from trunk/SCRIPTS is taken by default
	107	#
	108	# 2718 2018-01-02 08:49:38Z maronga
[2716]	109	# Corrected "Former revisions" section
	110	#
	111	# 2696 2017-12-14 17:12:51Z kanani
	112	# Change in file header (GPL part)
	113	#
	114	# 2693 2017-12-13 12:33:49Z raasch
[2693]	115	# replacement of variables given by {{<variable>}} in configuration file is now
	116	# done in a more general way, variable names are written in small letters
	117	#
	118	# 2670 2017-12-06 16:32:19Z raasch
[2670]	119	# test printouts removed
	120	#
	121	# 2669 2017-12-06 16:03:27Z raasch
[2669]	122	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	123	# removed,
	124	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	125	# files,
	126	# informative messages in case of missing optional input files shortened
	127	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	128	#
	129	# 2638 2017-11-23 12:44:23Z raasch
[2610]	130	# use of wildcards in file connection statements enabled
	131	#
	132	# 2605 2017-11-09 15:31:46Z raasch
[2605]	133	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	134	# will not be sent with the job file any more, but copied into the
[2610]	135	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	136	#
	137	# 2600 2017-11-01 14:11:20Z raasch
[2600]	138	# cycle numbers are made three digits wide
	139	#
	140	# 2566 2017-10-20 08:50:47Z raasch
[2566]	141	# execute command for combine_plot_fields added
	142	# "TEMPDIR" renamed "tempdir"
	143	# temporary working directory for local batch jobs is created immediately within
	144	# the user's palmrun call, due to a requirement of the "grid engine" batch
	145	# system, where the working directory is given with batch directive -wd and must
	146	# already exist when the job is submitted,
	147	# informative messages in non-trace mode reduced and partly reformatted
	148	#
	149	# 2551 2017-10-18 07:25:11Z raasch
[2551]	150	# TEMPDIR added as replacement string to be used in batch directives
	151	#
	152	# 2512 2017-10-04 08:26:59Z raasch
[2507]	153	# bugfix for determining cycle numbers of NetCDF input files
	154	#
	155	# 2506 2017-09-29 08:30:37Z raasch
[2506]	156	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	157	# host configuration added to SOURCES_FOR_RUN_... folder name
	158	# host_identifier renamed host_configuration
	159	# option -W added to allow for job dependencies
	160	#
	161	# 2501 2017-09-26 11:41:55Z raasch
[2501]	162	# default value for number of cores (option -X) set to 1
	163	# bugfix for mechanism which overwrites configuration file settings with values
	164	# provided by palmrun options
	165	#
	166	# 2499 2017-09-22 16:47:58Z kanani
[2499]	167	# option -h named configuration identifier
	168	#
	169	# 2480 2017-09-19 06:24:14Z maronga
[2480]	170	# bugfix for last revision
	171	#
	172	# 2479 2017-09-19 06:12:16Z raasch
[2479]	173	# option -A (project account number) added
	174	#
	175	# 2422 2017-09-08 08:25:41Z raasch
[2410]	176	# initial revision
[2380]	177	#
	178	#--------------------------------------------------------------------------------#
	179	# palmrun - script for running PALM jobs on local and remote hosts
	180	#--------------------------------------------------------------------------------#
	181
	182
	183
	184	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	185
	186	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	187	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	188	# (TOO MANY ARGUMENTS - PROBLEM)
	189	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	190
[2610]	191	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	192	typeset -i nr_of_output_files=0
[2380]	193	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	194	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	195	# SCRIPT-OPTION ARGUMENTS
	196	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	197	typeset -i icycle inode ival maxcycle mpi_tasks
	198	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	199
	200	activation_string_list=""
	201	AddFilenames=""
	202	combine_plot_fields=true
	203	compiler_name=""
	204	compiler_name_ser=""
	205	compiler_options=""
[3236]	206	configuration_identifier="default"
[2501]	207	cores=1
[2380]	208	cores_atmos=0
	209	cores_ocean=0
	210	coupled_dist=""
	211	cpp_options=""
	212	cpumax=0
[2506]	213	create_batch_job=false
[2380]	214	create_jobfile_only=false
	215	create_remote_batch_job=false
	216	dashes=" ----------------------------------------------------------------------------"
	217	defaultqueue=""
[2506]	218	delete_temporary_catalog=true
[2380]	219	do_compile=true
	220	do_trace=false
	221	executable=""
	222	execute_command=""
	223	execution_error=false
[2762]	224	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	225	global_revision=""
	226	hostfile=""
	227	hp=""
	228	keep_data_from_previous_run=false
	229	link_local_input=false
	230	link_local_output=false
[2388]	231	linker_options=""
[2385]	232	local_jobcatalog=""
[2380]	233	locat=normal
	234	makefile=""
	235	max_par_io_str=""
	236	prc=$0
	237	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	238	do
	239	prc=`echo $prc \| cut -f2- -d"/"`
	240	done
	241	module_calls=""
[2506]	242	palmrun_memory=""
[2380]	243	palmrun_script_name=$prc
	244	openmp=false
[2506]	245	previous_job=""
[2479]	246	project_account=""
[2380]	247	queue=none
[2906]	248	read_svf=""
[2380]	249	restart_run=false
	250	return_address=""
[2385]	251	remote_jobcatalog=""
[2380]	252	remote_username=""
	253	running_in_batch_mode=false
[3313]	254	running_in_test_mode=false
[2380]	255	run_coupled_model=false
	256	run_id=""
[3236]	257	run_id_number=""
	258	run_identifier=test
[2380]	259	silent=false
	260	source_list=""
	261	source_path=""
[2501]	262	tasks_per_node=0
[2380]	263	threads_per_task=1
	264	transfer_problems=false
[2384]	265	user_source_path=""
[2506]	266	use_existing_sources_folder=""
[2380]	267	use_openmp=false
[3033]	268	version="palmrun 1.0 Rev$Rev: 3555 $"
[2380]	269	working_directory=`pwd`
	270	write_binary=""
[2906]	271	write_svf=""
[2380]	272
	273
	274	# ERROR HANDLING IN CASE OF EXIT
[2404]	275	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	276	then
	277
	278	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	279	(( i = 0 ))
	280	while (( i < iec ))
	281	do
	282	(( i = i + 1 ))
	283	printf "\n *** Execution of ERROR-command:\n"
	284	printf " >>> ${err_command[$i]}\n"
	285	eval ${err_command[$i]}
	286	done
[2566]	287	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	288	printf "\n\n+++ palmrun crashed \n\n"
	289	exit 1
	290	elif [[ $locat != normal ]]
[2380]	291	then
[3312]	292	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	293	printf "\n+++ palmrun killed by \"^C\" \n\n"
	294	exit 2
	295	else
[2566]	296	printf "\n --> palmrun finished\n\n"
[3312]	297	exit 0
[2380]	298	fi' exit
	299
	300
	301	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	302	trap 'locat=control_c
	303	exit 1
[2380]	304	' 2
	305
	306
	307	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	308	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	309	while getopts :a:A:bBc:CFG:i:jkm:M:O:q:r:R:s:t:T:u:U:vVw:W:xX:yY:zZ option
[2380]	310	do
	311	case $option in
	312	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	313	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	314	(b) create_batch_job=true; prc="$prc -b";;
	315	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	316	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	317	(C) restart_run=true; prc="$prc -C";;
	318	(F) create_jobfile_only=true;;
	319	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	320	(i) run_id_number=$OPTARG;;
[2380]	321	(j) running_in_batch_mode=true;;
	322	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	323	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	324	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	325	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	326	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	327	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	328	(R) return_address=$OPTARG;;
	329	(s) source_list=$OPTARG;;
[2501]	330	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	331	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	332	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	333	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	334	(v) silent=true; prc="$prc -v";;
[2506]	335	(V) use_existing_sources_folder="-V";;
[2380]	336	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	337	(W) previous_job=$OPTARG;;
[2380]	338	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	339	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	340	(y) ocean_file_appendix=true; prc="$prc -y";;
	341	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	342	(z) running_in_test_mode=true;;
[2380]	343	(Z) combine_plot_fields=false; prc="$prc -Z";;
	344	(\?) printf "\n +++ unknown option $OPTARG \n"
	345	printf "\n --> type \"$0 ?\" for available options \n"
	346	locat=parameter;exit;;
	347	esac
	348	done
	349
	350
	351	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	352	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	353	(( to_shift = $OPTIND - 1 ))
	354	shift $to_shift
	355
	356	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	357	if [[ "$1" = "?" ]]
	358	then
	359	(printf "\n *** Description of available palmrun options:\n"
	360	printf "\n Option Description Default-Value"
	361	printf "\n -a activation string list \"\" "
[2479]	362	printf "\n -A project account number ---"
[2380]	363	printf "\n -b batch-job on local machine ---"
	364	printf "\n -B do not delete temporary directory at end ---"
[3455]	365	printf "\n -c configuration identifier \"default\" "
[2380]	366	printf "\n -F create batch job file only ---"
	367	printf "\n -k keep data from previous run"
	368	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	369	printf "\n -M Makefile name Makefile"
	370	printf "\n -O threads per openMP task ---"
	371	printf "\n -q queue \"$queue\" "
[3455]	372	printf "\n -r run identifier test"
[2380]	373	printf "\n -s filenames of routines to be compiled \"\" "
	374	printf "\n must end with .f, .f90, .F, or .c !"
	375	printf "\n use \"..\" for more than one file and wildcards"
	376	printf "\n -s LM compiles all locally modified files"
	377	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	378	printf "\n -T tasks per node ---"
[2380]	379	printf "\n -u username on remote machine \"\" "
	380	printf "\n -v no prompt for confirmation ---"
[2506]	381	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	382	printf "\n -w maximum parallel io streams as given by -X"
[2506]	383	printf "\n -W name of job to wait for ---"
[2380]	384	printf "\n -x tracing of palmrun for debug purposes ---"
	385	printf "\n -X # of processors (on parallel machines) 1"
	386	printf "\n -y add appendix \"_O\" to all local output"
	387	printf "\n files (ocean precursor runs followed by"
	388	printf "\n coupled atmosphere-ocean runs) ---"
	389	printf "\n -Y run coupled model, \"#1 #2\" with"
	390	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	391	printf "\n -Z skip combine_plot_fields at the end of "
	392	printf "\n the simulation ---"
	393	printf "\n "
	394	printf "\n Possible values of positional parameter <modus>:"
	395	printf "\n \"?\" - this outline \n\n") \| more
	396	exit
	397	elif [[ "$1" != "" ]]
	398	then
	399	printf "\n +++ positional parameter $1 unknown \n"
	400	locat=parameter; exit
	401	fi
	402
	403
	404
	405	# SHORT STARTING MESSAGE
	406	printf "\n*** $version "
	407	printf "\n will be executed. Please wait ..."
	408
	409
[2506]	410	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	411	config_file=.palm.config.$configuration_identifier
	412	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	413
	414
	415	# CHECK, IF CONFIGURATION FILE EXISTS
	416	if [[ ! -f $config_file ]]
	417	then
	418	printf "\n\n +++ configuration file: "
	419	printf "\n $config_file"
	420	printf "\n does not exist"
	421	locat=connect; exit
	422	fi
	423
	424
[2762]	425	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	426	if [[ -f .palm.iofiles ]]
	427	then
[3236]	428
	429	# CHECK VERSION MISMATCH
	430	if [[ $running_in_batch_mode != true ]]
	431	then
	432	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	433	then
	434	printf "\n\n +++ WARNING: A file connection file has been found in your"
	435	printf "\n working directory, but its revision does not match"
	436	printf "\n the revision of the default (trunk) version."
[3294]	437	printf "\n You may need to update your connection file"
	438	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	439	fi
	440	fi
	441
[2762]	442	fileconnection_file=.palm.iofiles
[3236]	443
[2762]	444	fi
	445
	446
[2380]	447	# CHECK, IF FILE CONNECTION FILE EXISTS
	448	if [[ ! -f $fileconnection_file ]]
	449	then
	450	printf "\n\n +++ file connection file: "
	451	printf "\n $fileconnection_file"
	452	printf "\n does not exist"
	453	locat=connect; exit
	454	fi
	455
	456
[2404]	457	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	458	if [[ "$activation_string_list" = "" ]]
	459	then
	460	printf "\n\n +++ no activation string list given: "
	461	printf "\n please set palmrun option \"-a\" "
	462	locat=palmrun_option; exit
	463	fi
	464
	465
	466	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	467	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	468	then
	469	write_binary=true
	470	else
	471	write_binary=false
	472	fi
	473
[2906]	474	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	475	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	476	then
	477	write_svf=true
	478	else
	479	write_svf=false
	480	fi
[2404]	481
[2906]	482	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	483	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	484	then
	485	read_svf=true
	486	else
	487	read_svf=false
	488	fi
	489
	490
[2380]	491	# READ AND EVALUATE THE CONFIGURATION-FILE
	492	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	493
	494	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	495	while read line
	496	do
	497
	498	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	499	eval line=\"$line\"
	500
	501
	502	# INTERPRET THE LINE
	503	if [[ "$(echo $line)" = "" ]]
	504	then
	505
	506	# EMPTY LINE, NO ACTION
	507	continue
	508
	509	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	510	then
	511
	512	# LINE IS A COMMENT LINE
	513	continue
	514
	515	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	516	then
	517
	518	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	519	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	520	value=`echo $line \| cut -d" " -s -f2-`
	521
	522
	523	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	524	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	525	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	526	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	527	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	528	# CONFIGURATION-FILE.
	529	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	530	then
	531	eval export $var="\$value"
	532
	533	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	534	if [[ $do_trace = true ]]
	535	then
	536	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	537	fi
	538	fi
	539
	540	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	541	then
	542
	543	# LINE DEFINES BATCH-DIRECTIVE
	544	(( ibd = ibd + 1 ))
	545	line=$(echo $line \| cut -c4-)
	546	batch_directive[$ibd]="$line"
	547
	548	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	549	then
	550
	551	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	552	# REMOTE TO A LOCAL HOST
	553	(( ibdt = ibdt + 1 ))
	554	line=$(echo $line \| cut -c5-)
	555	batch_directive_transfer[$ibdt]="$line"
	556
	557	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	558	then
	559
	560	# LINE DEFINES ERROR-COMMAND
	561	(( iec = iec + 1 ))
	562	line=$(echo $line \| cut -c4-)
	563	err_command[$iec]="$line"
	564
	565	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	566	then
	567
	568	# LINE DEFINES INPUT-COMMAND
	569	(( iic = iic + 1 ))
	570	line=$(echo $line \| cut -c4-)
	571	in_command[$iic]="$line"
	572
	573	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	574	then
	575
	576	# LINE DEFINES OUTPUT-COMMAND
	577	(( ioc = ioc + 1 ))
	578	line=$(echo $line \| cut -c4-)
	579	out_command[$ioc]="$line"
	580
	581	else
	582
	583	# SKIP ALL OTHER LINES
	584	continue
	585
	586	fi
	587
	588	done < $config_file
	589
	590
	591	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	592	if [[ "$fast_io_catalog" = "" ]]
	593	then
	594	printf "\n +++ no fast_io_catalog found in $config_file"
	595	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	596	locat=config_file; exit
	597	fi
[2380]	598	if [[ "$compiler_name" = "" ]]
	599	then
	600	printf "\n +++ no compiler name found in $config_file"
	601	printf "\n Please add line \"compiler_name ...\" to that file."
	602	locat=config_file; exit
	603	fi
	604	if [[ "$compiler_name_ser" = "" ]]
	605	then
	606	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	607	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	608	locat=config_file; exit
	609	fi
	610	if [[ "$compiler_options" = "" ]]
	611	then
	612	printf "\n +++ no compiler options found in $config_file"
	613	printf "\n Please add line \"compiler_options ...\" to that file."
	614	locat=config_file; exit
	615	fi
[2388]	616	if [[ "$linker_options" = "" ]]
[2380]	617	then
[2388]	618	printf "\n +++ no linker options found in $config_file"
	619	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	620	locat=config_file; exit
	621	fi
	622	if [[ "$execute_command" = "" ]]
	623	then
	624	printf "\n +++ no execute command found in $config_file"
	625	printf "\n Please add line \"execute_command ...\" to that file."
	626	locat=config_file; exit
	627	fi
	628
	629	if [[ "$hostfile" != "" ]]
	630	then
	631	if [[ $hostfile != auto && ! -f $hostfile ]]
	632	then
	633	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	634	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	635	locat=config_file; exit
	636	fi
	637	fi
	638
	639
	640	# DETERMINE THE CALL STATUS
	641	if [[ "$return_address" != "" ]]
	642	then
	643
	644	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	645	# BATCH MODE AND ...
	646	running_on_remote=true
	647
	648	else
	649
	650	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	651	if [[ "$remote_ip" != "" ]]
	652	then
	653
	654	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	655	create_remote_batch_job=true
	656
[3132]	657	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	658	if [[ "$remote_jobcatalog" = "" ]]
	659	then
	660	printf "\n +++ no remote jobcatalog found in $config_file"
	661	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	662	locat=config_file; exit
	663	fi
	664
	665
[2380]	666	fi
	667	running_on_remote=false
	668	fi
	669
	670
	671
	672	# READ AND EVALUATE THE I/O-FILE LIST
	673	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	674
	675	# READ THE FILE CONNECTION FILE LINE BY LINE
	676	while read line
	677	do
	678
[2669]	679	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
[3555]	680	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
	681	line=`echo "$line" \| tr -s " "`
[2380]	682
	683	# INTERPRET THE LINE
	684	if [[ "$(echo $line)" = "" ]]
	685	then
	686	# EMPTY LINE, NO ACTION
	687	continue
	688
	689	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	690	then
	691
	692	# LINE IS A COMMENT LINE
	693	true
	694
	695	else
	696
	697	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	698	# s2a: in/out - field
[2669]	699	# s2b: action - field (optional)
	700	s1=`echo "$line" \| cut -d" " -f1`
	701	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	702	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	703	then
[2669]	704	s2a=$s2
[2380]	705	s2b=""
	706	else
[2669]	707	s2a=`echo $s2 \| cut -d":" -f1`
	708	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	709	fi
[2669]	710	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	711	s4=`echo "$line" \| cut -d" " -s -f4`
	712	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	713	s5=`echo "$line" \| cut -d" " -s -f5`
	714	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	715
	716
	717	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	718	# INPUT- OR OUTPUT-LIST.
	719	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	720	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	721	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	722	# IS NOT CHECKED AND STORED.
[2610]	723	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	724	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	725	then
	726	found=false
	727	for actual in $activation_string_list
	728	do
	729	for formal in $s3
	730	do
	731	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	732	done
	733	done
	734	if [[ $found = true ]]
	735	then
	736	(( iin = iin + 1 ))
[2669]	737	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	738	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	739	if [[ "$s2a" = inopt ]]
	740	then
	741	optin_pre[$iin]=yes
	742	else
	743	optin_pre[$iin]=no
	744	fi
[2605]	745
	746	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	747	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	748	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	749	then
[2610]	750	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	751	fi
	752
[2610]	753	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	754	# THE WILDCARD FROM THE ENDING
	755	if [[ "${s5: -1}" = "*" ]]
	756	then
[2669]	757	if [[ "$s2b" = "di" ]]
[2610]	758	then
	759	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	760	printf "\n see file \"$fileconnection_file\", line"
	761	printf "\n$line"
	762	locat=iofiles_file; exit
	763	fi
	764	multin[$iin]=true
	765	string=${endin_pre[$iin]}
	766	endin_pre[$iin]="${string%?}"
	767	else
	768	multin[$iin]=false
	769	fi
[2380]	770	fi
[2669]	771	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	772	then
	773	found=false
	774	for actual in $activation_string_list
	775	do
	776	for formal in $s3
	777	do
[2670]	778	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	779	done
	780	done
	781	if [[ $found = true ]]
	782	then
	783	(( iout = iout + 1 ))
[2669]	784	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	785	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	786
[2669]	787	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	788	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	789	if [[ $formal = wildcard ]]
	790	then
	791	warnout_pre[$iout]=false
	792	else
	793	warnout_pre[$iout]=true
	794	fi
	795
[2610]	796	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	797	# THE WILDCARD FROM THE LOCAL FILENAME
	798	if [[ "${s1: -1}" = "*" ]]
	799	then
[2669]	800	if [[ "$s2b" = "di" ]]
[2610]	801	then
	802	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	803	printf "\n see file \"$fileconnection_file\", line"
	804	printf "\n$line"
	805	locat=iofiles_file; exit
	806	fi
	807	multout[$iout]=true
	808	string=${localout_pre[$iout]}
	809	localout_pre[$iout]="${string%?}"
	810	else
	811	multout[$iout]=false
	812	fi
[2380]	813	fi
[2669]	814	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	815	then
[2669]	816	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	817	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	818	locat=connect; exit
	819	fi
	820	IFS="$IFSALT"
	821	fi
	822
	823	done < $fileconnection_file
	824
	825
	826
[2501]	827	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	828	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	829	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	830	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	831	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	832	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	833
	834
	835
[2380]	836	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	837	if [[ $run_coupled_model = true ]]
	838	then
	839
	840	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	841	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	842
	843	if (( $cores_ocean + $cores_atmos != $cores ))
	844	then
	845
	846	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	847	printf "\n PEs (total) : $cores"
	848	printf "\n PEs (atmosphere): $cores_atmos"
	849	printf "\n PEs (ocean) : $cores_ocean"
	850	locat=coupling; exit
	851
	852	fi
	853
	854	fi
	855
	856
	857	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	858	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	859	# FOLDER
	860	if [[ $running_in_batch_mode = true ]]
	861	then
	862
[2506]	863	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	864	then
[2506]	865	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	866	printf "\n Please check the output of the palmrun-call"
	867	printf "\n that you did on your local host."
	868	locat=SOURCES_FOR_RUN; exit
	869	fi
	870
	871	else
	872
	873	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	874	# AUTOMATIC RESTART RUN
	875	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	876	if [[ $restart_run = false ]]
	877	then
	878
	879	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	880	# THE LOCAL HOST
	881	if [[ ! -d $source_path ]]
	882	then
	883	printf "\n\n +++ source path \"$source_path\" on local host"
	884	printf "\n \"$(hostname)\" does not exist"
	885	locat=source_path; exit
	886	fi
	887
[2990]	888	rm -rf ${base_directory}/${sources_for_run_catalog}
	889	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	890
	891	if [[ "$source_list" = LM ]]
	892	then
	893
	894	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	895	source_list=""
	896	cd $source_path
	897
	898
[2512]	899	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	900	if [[ ! -d ../.svn ]]
[2380]	901	then
	902	printf "\n\n +++ source directory"
	903	printf "\n \"$source_path\" "
	904	printf "\n is not under control of \"subversion\"."
[2512]	905	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	906	fi
	907
	908
	909	# LIST ALL MODIFIED SOURCE CODE FILES
	910	Filenames=""
[2404]	911	svn status > tmp_svnstatus
[2380]	912	while read line
	913	do
	914	firstc=`echo $line \| cut -c1`
	915	if [[ $firstc = M \|\| $firstc = "?" ]]
	916	then
	917	Name=`echo "$line" \| cut -c8-`
	918	extension=`echo $Name \| cut -d. -f2`
	919	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	920	then
	921	Filenames="$Filenames "$Name
	922	fi
	923	fi
[2404]	924	done < tmp_svnstatus
	925	rm -rf tmp_svnstatus
[2380]	926
	927
	928	# COPY FILES TO SOURCES_FOR_RUN_...
	929	for filename in $Filenames
	930	do
[2990]	931	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	932	source_list=$source_list"$filename "
	933	done
	934
	935	cd - > /dev/null
	936
	937
	938	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	939	elif [[ "$source_list" != "" ]]
	940	then
	941
	942	cd $source_path
	943
	944	for filename in $source_list
	945	do
	946
	947	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	948	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	949	then
	950	printf "\n +++ source code file: $filename"
	951	printf "\n must not contain (\"/\") "
	952	locat=source; exit
	953	fi
	954
	955	if [[ ! -f $filename ]]
	956	then
	957	printf "\n +++ source code file: $filename"
	958	printf "\n does not exist"
	959	locat=source; exit
	960	else
[2990]	961	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	962	fi
	963
	964	done
	965
	966	cd - > /dev/null
	967
	968	fi
	969
	970	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	971	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	972	if [[ ! -f $makefile ]]
	973	then
	974	printf "\n +++ file \"$makefile\" does not exist"
	975	locat=make; exit
	976	else
[2990]	977	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	978	fi
	979
	980
	981	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	982	if [[ "$user_source_path" != "" ]]
[2380]	983	then
	984
	985	# DOES THE DIRECTORY EXIST?
[2384]	986	if [[ ! -d $user_source_path ]]
[2380]	987	then
	988
	989	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	990	printf "\n \"$user_source_path\" "
[2380]	991	printf "\n does not exist or is not a directory."
	992	printf "\n No source code will be used from this directory!\n"
[2384]	993	user_source_path=""
[2380]	994	if [[ $silent == false ]]
	995	then
	996	sleep 2
	997	fi
	998
	999	else
	1000
[2384]	1001	cd $user_source_path
[2380]	1002
	1003	Names=$(ls -1 *.f90 2>&1)
	1004	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1005	Names=$(ls -1 *.F90 2>&1)
	1006	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1007	Names=$(ls -1 *.F 2>&1)
	1008	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1009	Names=$(ls -1 *.f 2>&1)
	1010	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1011	Names=$(ls -1 *.c 2>&1)
	1012	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1013
	1014	cd - > /dev/null
[2990]	1015	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1016
	1017	# COPY MAKEFILE IF EXISTING
[2384]	1018	if [[ -f $user_source_path/Makefile ]]
[2380]	1019	then
	1020	printf "\n\n *** user Makefile from directory"
[2384]	1021	printf "\n \"$user_source_path\" is used \n"
[2380]	1022	if [[ $silent == false ]]
	1023	then
	1024	sleep 1
	1025	fi
[2384]	1026	cp $user_source_path/Makefile .
[2380]	1027	fi
	1028
	1029	for filename in $AddFilenames
	1030	do
	1031	if [[ -f $filename ]]
	1032	then
	1033	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1034	printf "\n source code directory \"$user_source_path\" "
[2380]	1035	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1036	printf "\n from directory \"$source_path\"."
	1037	locat=source; exit
	1038	fi
	1039
[2384]	1040	cp $user_source_path/$filename .
[2380]	1041	source_list="$source_list $filename"
	1042
	1043	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1044	if [[ $(grep -c $filename Makefile) = 0 ]]
	1045	then
	1046	printf "\n\n +++ user file \"$filename\" "
	1047	printf "\n is not listed in Makefile \n"
	1048	locat=source; exit
	1049	fi
	1050	done
	1051	cd - > /dev/null
	1052	fi
	1053	fi
	1054
	1055	# COPY CONFIGURATION FILES
[2990]	1056	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1057	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1058
	1059	# COPY SHELLSCRIPTS
[2990]	1060	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1061	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1062
	1063	fi
	1064
	1065	fi
	1066
[2605]	1067
[2380]	1068	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1069	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1070	if [[ "$global_revision" = "" ]]
	1071	then
	1072	global_revision=`svnversion $source_path 2>/dev/null`
	1073	global_revision="Rev: $global_revision"
	1074	fi
	1075
	1076
	1077	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1078	if [[ -n $cores ]]
	1079	then
	1080
	1081	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1082	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1083	if [[ $tasks_per_node = 0 ]]
[2380]	1084	then
[3025]	1085	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1086	then
	1087	printf "\n"
	1088	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1089	printf "\n set -T option or define tasks_per_node in the config file"
	1090	locat=tasks_per_node; (( iec = 0 )); exit
	1091	else
	1092	# DEFAULT FOR INTERACTIVE RUN
	1093	tasks_per_node=$cores
	1094	fi
[2380]	1095	fi
	1096
	1097	if (( cores < tasks_per_node ))
	1098	then
	1099	printf "\n"
	1100	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1101	printf "\n given values: -T $tasks_per_node -X $cores"
	1102	locat=tasks_per_node; (( iec = 0 )); exit
	1103	fi
	1104
	1105	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1106	(( mpi_tasks = cores / threads_per_task ))
	1107	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1108	(( ii = cores / tasks_per_node ))
	1109	(( remaining_cores = cores - ii * tasks_per_node ))
	1110	if (( remaining_cores > 0 ))
	1111	then
	1112	printf "\n"
	1113	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1114	printf "\n divisor of the total number of cores (option \"-X\")"
	1115	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1116	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1117	(( nodes = nodes + 1 ))
	1118	fi
	1119
	1120	fi
	1121
	1122
	1123	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1124	if [[ "$maximum_parallel_io_streams" = "" ]]
	1125	then
	1126	maximum_parallel_io_streams=$cores
	1127	fi
	1128
	1129
	1130	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1131	if [[ "$scp_port" != "" ]]
	1132	then
	1133	PORTOPT="-P $scp_port"
	1134	SSH_PORTOPT="-p $scp_port"
	1135	fi
	1136
	1137
	1138	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1139	# CONFIG-FILE
	1140	if [[ "$ssh_key" != "" ]]
	1141	then
	1142	ssh_key="-i $HOME/.ssh/$ssh_key"
	1143	fi
	1144
	1145
	1146	# SET QUEUE, IF NOT GIVEN
	1147	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1148	then
	1149
	1150	if [[ $queue = none && "$defaultqueue" = "" ]]
	1151	then
	1152	printf "\n"
	1153	printf "\n +++ no default queue given in configuration file and no queue"
	1154	printf "\n given with option -q"
[2789]	1155	locat=queue; exit
[2380]	1156	fi
	1157	if [[ $queue = none ]]
	1158	then
	1159	queue=$defaultqueue
	1160	fi
	1161
	1162	fi
	1163
	1164
	1165	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1166	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1167	(( i = 0 ))
[2610]	1168	(( nr_of_input_files = 0 ))
[2380]	1169	while (( i < iin ))
	1170	do
	1171	(( i = i + 1 ))
	1172
	1173	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1174	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1175	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1176	then
[2610]	1177	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1178	else
[3236]	1179	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1180	fi
	1181
[2610]	1182
[2380]	1183	# CHECK IF FILE EXISTS
	1184	if ! ls $filename* 1>/dev/null 2>&1
	1185	then
	1186
[2669]	1187	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1188	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1189	then
	1190	printf "\n\n +++ INPUT-file: "
[2610]	1191	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1192	then
	1193	printf "\n $filename"
	1194	else
[2610]	1195	printf "\n $filename.${extin_pre[$i]}"
[2380]	1196	fi
	1197	printf "\n does not exist\n"
	1198	locat=input; exit
	1199	else
[2610]	1200	(( nr_of_input_files = nr_of_input_files + 1 ))
	1201	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1202	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1203	actionin[$nr_of_input_files]="unavailable"
[2610]	1204	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1205	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1206	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1207	fi
[2605]	1208
[2380]	1209	else
	1210
[3236]	1211	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1212	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1213	# ENDINGS
[2610]	1214	if [[ "${multin[$i]}" = true ]]
	1215	then
	1216	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1217	ls -1 -d ${filename} > filelist 2>/dev/null
	1218	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1219	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1220
[2610]	1221	endings=""
	1222	while read line
	1223	do
	1224	# filename without path (i.e. after the last "/")
	1225	basefilename=$(basename ${line})
[2380]	1226
[2610]	1227	# check if there is an extension and remove it
	1228	ext=${basefilename##*.}
	1229	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1230	then
	1231	basefilename=${basefilename%.*}
	1232	fi
[2380]	1233
[2610]	1234	# check for an existing cycle number and remove it
	1235	cycle=${basefilename##*.}
	1236	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1237	then
	1238	basefilename=${basefilename%.*}
	1239	fi
[2600]	1240
[3236]	1241	# remove the run_identifier from the beginning
	1242	length_run_identifier=${#run_identifier}
	1243	ending=${basefilename:${length_run_identifier}}
[2610]	1244
	1245	# remove the ending given in the .iofiles from the beginning
	1246	endingstring="${endin_pre[$i]}"
	1247	length_ending=${#endingstring}
	1248	ending=${ending:${length_ending}}
	1249
	1250	if [[ "$ending" = "" ]]
[2600]	1251	then
[2610]	1252	# standard ending as given in the .iofiles
	1253	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1254	then
	1255	endings="$endings DEFAULT"
	1256	fi
[2600]	1257	else
[2610]	1258	# ending must start with "_", otherwise its a different file
	1259	if [[ "${ending:0:1}" = "_" ]]
	1260	then
	1261	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1262	then
	1263	endings="$endings $ending"
	1264	fi
	1265	fi
[2600]	1266	fi
[2610]	1267
	1268	done <filelist
[2380]	1269
[2610]	1270	rm filelist
[2380]	1271
[2600]	1272	else
[2610]	1273
	1274	# SINGLE NAME
	1275	endings=DEFAULT
	1276
[2600]	1277	fi
	1278
[2610]	1279	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1280	for ending in $endings
	1281	do
	1282
	1283	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1284	if [[ $ending = DEFAULT ]]
[2380]	1285	then
[2610]	1286	ending=""
	1287	fi
	1288
	1289	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1290	(( nr_of_input_files = nr_of_input_files + 1 ))
	1291	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1292	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1293	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1294	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1295	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1296	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1297
	1298
	1299	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1300	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1301	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1302	then
	1303	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1304	else
[3236]	1305	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1306	fi
[2610]	1307
	1308	# DETERMINE THE FILE'S CYCLE NUMBER
	1309	(( maxcycle = 0 ))
	1310	ls -1 -d $filename > filelist 2>/dev/null
	1311	ls -1 -d $filename.* >> filelist 2>/dev/null
	1312	while read line
	1313	do
	1314	# filename without path (i.e. after the last "/")
	1315	basefilename=$(basename ${line})
	1316
	1317	# check if there is an extension
	1318	extension=${basefilename##*.}
	1319	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1320	then
	1321	basefilename=${basefilename%.*}
	1322	fi
	1323
	1324	# check for an existing cycle number
	1325	cycle=${basefilename##*.}
	1326	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1327	then
[2669]	1328	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1329	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1330	(( icycle = $((10#$cycle)) ))
[2610]	1331	else
	1332	(( icycle = 0 ))
	1333	fi
	1334
	1335	if (( icycle > maxcycle ))
	1336	then
	1337	(( maxcycle = icycle ))
	1338
	1339	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1340	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1341	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1342	then
	1343	leading_zero=true
	1344	else
	1345	leading_zero=false
	1346	fi
	1347	fi
	1348
	1349	done <filelist
	1350	rm filelist
	1351
	1352	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1353	if [[ $leading_zero = true ]]
[2380]	1354	then
[2610]	1355	cyclestring=`printf "%03d" $maxcycle`
	1356	else
	1357	cyclestring=$maxcycle
[2380]	1358	fi
[2610]	1359
	1360	# APPEND CYCLE NUMBER TO FILENAME
	1361	if (( maxcycle > 0 ))
[2380]	1362	then
[2610]	1363	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1364	then
	1365	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1366	else
	1367	filename=${filename}.$cyclestring
	1368	fi
[2380]	1369	else
[2610]	1370	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1371	then
	1372	filename=${filename}.${extin[$nr_of_input_files]}
	1373	fi
[2380]	1374	fi
[2610]	1375
	1376	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1377	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1378	absnamein[$nr_of_input_files]=$filename
	1379	if (( maxcycle > 0 ))
[2380]	1380	then
[2610]	1381	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1382	then
	1383	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1384	else
[3236]	1385	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1386	fi
[2380]	1387	else
[2610]	1388	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1389	then
	1390	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1391	else
[3236]	1392	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1393	fi
[2380]	1394	fi
	1395
[2610]	1396	done
	1397
[2380]	1398	fi
[2610]	1399
[2380]	1400	done
	1401
[2610]	1402
[2380]	1403	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1404	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1405	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1406	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1407	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1408	# REMOTE HOST)
	1409	(( i = 0 ))
	1410	while (( i < iout ))
	1411	do
	1412	(( i = i + 1 ))
[2610]	1413	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1414	then
[2610]	1415	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1416	then
[2610]	1417	actionout_pre[$i]=""
	1418	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1419	then
[2610]	1420	actionout_pre[$i]=pe
	1421	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1422	then
[2610]	1423	actionout_pre[$i]=a
[2380]	1424	fi
	1425	(( maxcycle = 0 ))
[3236]	1426	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1427	eval catalogname=${pathout_pre[$i]}
[2380]	1428	if ! ls $filename* 1>/dev/null 2>&1
	1429	then
	1430
	1431	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1432	if cat /dev/null > $filename
	1433	then
	1434	rm $filename
	1435	else
	1436
	1437	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1438	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1439	if [[ ! -d $catalogname ]]
	1440	then
	1441	if mkdir -p $catalogname
	1442	then
	1443	printf "\n\n *** directory:"
	1444	printf "\n $catalogname"
	1445	printf "\n was created\n"
	1446	else
	1447	printf "\n\n +++ OUTPUT-file:"
	1448	printf "\n $filename"
	1449	printf "\n cannot be created, because directory does not exist"
	1450	printf "\n and cannot be created either"
	1451	printf "\n"
	1452	locat=output ; exit
	1453	fi 2>/dev/null
	1454	else
	1455	printf "\n\n +++ OUTPUT-file:"
	1456	printf "\n $filename"
	1457	printf "\n cannot be created, although directory exists"
	1458	printf "\n"
	1459	locat=output ; exit
	1460	fi
	1461	fi 2>/dev/null
	1462
	1463	fi
	1464
	1465	fi
	1466	done
	1467
	1468
	1469	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1470	if [[ $running_in_batch_mode = false ]]
	1471	then
[3236]	1472	run_id_number=$RANDOM
	1473	run_id=${run_identifier}.$run_id_number
[2380]	1474
[3236]	1475	tempdir=$fast_io_catalog/$run_id
[3346]	1476
	1477	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1478	export job_id=$run_id
	1479
[2380]	1480	fi
	1481
	1482
	1483	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1484	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1485	then
	1486
	1487	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1488	if [[ $ibd = 0 ]]
	1489	then
	1490	printf "\n"
	1491	printf "\n +++ no batch directives found in configuration file"
	1492	locat=config_file_batch_directives; (( iec = 0 )); exit
	1493	fi
	1494
	1495	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1496	done=false
[2384]	1497	cputime=$cpumax
[2380]	1498	while [[ $done = false ]]
	1499	do
[2384]	1500	if (( cputime == 0 ))
[2380]	1501	then
	1502	printf "\n +++ cpu-time is undefined"
	1503	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1504	printf "\n >>> "
[2384]	1505	read cputime 1>/dev/null 2>&1
[2380]	1506	else
	1507	done=true
	1508	fi
	1509	done
[2420]	1510	cpumax=$cputime
[2380]	1511
	1512	# CHECK THE MEMORY DEMAND
	1513	done=false
	1514	while [[ $done = false ]]
	1515	do
	1516	if (( memory == 0 ))
	1517	then
	1518	printf "\n +++ memory demand is undefined"
	1519	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1520	printf "\n >>> "
	1521	read memory 1>/dev/null 2>&1
	1522	else
	1523	done=true
	1524	fi
	1525	done
	1526
	1527	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1528	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1529	then
	1530	while [[ -z $remote_username ]]
	1531	do
[2420]	1532	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1533	printf "\n >>> Please type username:"
	1534	printf "\n >>> "
	1535	read remote_username
	1536	done
	1537	fi
	1538
	1539	else
	1540
[2420]	1541	if [[ $running_in_batch_mode = false ]]
	1542	then
	1543	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1544	cpumax=$cputime
	1545	else
	1546	cputime=$cpumax
	1547	fi
[2380]	1548
	1549	fi
	1550
	1551
	1552	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1553	(( cpu_hours = cputime / 3600 ))
	1554	(( resttime = cputime - cpu_hours * 3600 ))
	1555	(( cpu_minutes = resttime / 60 ))
	1556	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1557	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1558
	1559
	1560	# OUTPUT OF THE PALMRUN-HEADER
	1561	calltime=$(date)
	1562	printf "\n"
	1563	printf "#------------------------------------------------------------------------# \n"
	1564	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1565	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1566	printf "\| \| \n"
	1567	column1="called on:"; column2=$(hostname)
	1568	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1569	if [[ $create_remote_batch_job = true ]]
	1570	then
[3236]	1571	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1572	else
	1573	if [[ $running_on_remote = true ]]
	1574	then
[3236]	1575	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1576	else
[3236]	1577	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1578	fi
	1579	fi
	1580	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1581
	1582	column1="running in:"
	1583	if [[ $running_in_batch_mode = true ]]
	1584	then
	1585	column2="batch job mode"
	1586	else
	1587	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1588	then
	1589	column2="job creation mode"
	1590	else
	1591	column2="interactive run mode"
	1592	fi
	1593	fi
	1594	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1595
[2479]	1596	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1597	then
[2480]	1598	if [[ "$project_account" != "" ]]
[2479]	1599	then
	1600	column1="project account number:"
	1601	column2="$project_account"
	1602	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1603	fi
	1604	fi
	1605
[2380]	1606	if [[ -n $cores ]]
	1607	then
	1608	if [[ $run_coupled_model = false ]]
	1609	then
	1610	column1="number of cores:"; column2=$cores
	1611	else
	1612	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1613	fi
	1614	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1615	fi
	1616	if [[ -n $tasks_per_node ]]
	1617	then
	1618	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1619	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1620	if (( remaining_cores > 0 ))
	1621	then
	1622	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1623	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1624	fi
	1625	fi
	1626	if [[ $maximum_parallel_io_streams != $cores ]]
	1627	then
	1628	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1629	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1630	fi
	1631	if [[ $use_openmp = true ]]
	1632	then
	1633	column1="threads per task:"; column2="$threads_per_task"
	1634	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1635	fi
[2384]	1636	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1637	then
[2506]	1638	column1="memory demand / PE":; column2="$memory MB"
	1639	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1640	column1="job cpu time (h:m:s):"; column2="$timestring"
	1641	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1642	fi
[2380]	1643	printf "\| \| \n"
	1644	if [[ "$source_list" != "" ]]
	1645	then
	1646	if [[ "$make_options" != "" ]]
	1647	then
	1648	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1649	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1650	line=$(echo "$make_options" \| cut -c46-)
	1651	while [[ "$line" != "" ]]
	1652	do
	1653	column1=""
	1654	column2=$(echo "$line" \| cut -c-45)
	1655	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1656	line=$(echo "$line" \| cut -c46-)
	1657	done
	1658	fi
	1659	fi
	1660
	1661	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1662	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1663	line=$(echo "$cpp_options" \| cut -c46-)
	1664	while [[ "$line" != "" ]]
	1665	do
	1666	column1=""
	1667	column2=$(echo "$line" \| cut -c-45)
	1668	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1669	line=$(echo "$line" \| cut -c46-)
	1670	done
	1671
	1672	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1673	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1674	line=$(echo "$compiler_options" \| cut -c46-)
	1675	while [[ "$line" != "" ]]
	1676	do
	1677	column1=""
	1678	column2=$(echo "$line" \| cut -c-45)
	1679	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1680	line=$(echo "$line" \| cut -c46-)
	1681	done
	1682
[2388]	1683	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1684	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1685	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1686	while [[ "$line" != "" ]]
	1687	do
	1688	column1=""
	1689	column2=$(echo "$line" \| cut -c-45)
	1690	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1691	line=$(echo "$line" \| cut -c46-)
	1692	done
	1693
	1694	if [[ "$login_init_cmd" != "" ]]
	1695	then
	1696	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1697	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1698	line=$(echo "$login_init_cmd" \| cut -c46-)
	1699	while [[ "$line" != "" ]]
	1700	do
	1701	column1=""
	1702	column2=$(echo "$line" \| cut -c-45)
	1703	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1704	line=$(echo "$line" \| cut -c46-)
	1705	done
	1706	fi
	1707
	1708	if [[ "$module_commands" != "" ]]
	1709	then
	1710	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1711	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1712	line=$(echo "$module_commands" \| cut -c46-)
	1713	while [[ "$line" != "" ]]
	1714	do
	1715	column1=""
	1716	column2=$(echo "$line" \| cut -c-45)
	1717	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1718	line=$(echo "$line" \| cut -c46-)
	1719	done
	1720	fi
	1721	printf "\| \| \n"
[3236]	1722	column1="run identifier:"; column2=$run_identifier
[2380]	1723	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1724	column1="activation string list:"; column2=$(echo $activation_string_list)
	1725	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1726
	1727	if [[ "$ocean_file_appendix" = true ]]
	1728	then
	1729	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1730	fi
	1731
	1732	if [[ "$source_list" != "" ]]
	1733	then
	1734	printf "\| \| \n"
	1735	printf "\| Files to be compiled: \| \n"
	1736	line=$source_list
	1737	while [[ "$line" != "" ]]
	1738	do
	1739	linestart=$(echo $line \| cut -c-70)
	1740	printf "\| %-70s \| \n" "$linestart"
	1741	line=$(echo "$line" \| cut -c71-)
	1742	done
	1743	fi
	1744	printf "#------------------------------------------------------------------------#"
	1745
	1746
	1747
	1748	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1749	if [[ $do_trace = true ]]
	1750	then
	1751	(( i = 0 ))
[2610]	1752	while (( i < nr_of_input_files ))
[2380]	1753	do
	1754	(( i = i + 1 ))
	1755	if (( i == 1 ))
	1756	then
	1757	printf "\n\n >>> INPUT-file assignments:\n"
	1758	fi
	1759	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1760	done
	1761	(( i = 0 ))
	1762	while (( i < iout ))
	1763	do
	1764	(( i = i + 1 ))
	1765	if (( i == 1 ))
	1766	then
	1767	printf "\n\n >>> OUTPUT-file assignments:\n"
	1768	fi
	1769	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1770	done
	1771	(( i = 0 ))
	1772	while (( i < iic ))
	1773	do
	1774	(( i = i + 1 ))
	1775	if (( i == 1 ))
	1776	then
	1777	printf "\n\n >>> INPUT-commands:\n"
	1778	fi
	1779	printf "\n ${in_command[$i]}"
	1780	done
	1781	(( i = 0 ))
	1782	while (( i < ioc ))
	1783	do
	1784	(( i = i + 1 ))
	1785	if (( i == 1 ))
	1786	then
	1787	printf "\n\n >>> OUTPUT-commands:\n"
	1788	fi
	1789	printf "\n ${out_command[$i]}"
	1790	done
	1791	fi
	1792
	1793	# QUERY FOR CONTINUE
	1794	if [[ $silent = false && $running_in_batch_mode = false ]]
	1795	then
	1796	antwort=dummy
	1797	printf "\n\n"
	1798	printf " >>> everything o.k. (y/n) ? "
	1799	while read antwort
	1800	do
	1801	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1802	then
	1803	printf " >>> everything o.k. (y/n) ? "
	1804	else
	1805	break
	1806	fi
	1807	done
	1808	if [[ $antwort = n \|\| $antwort = N ]]
	1809	then
	1810	locat=user_abort; (( iec = 0 )); exit
	1811	fi
	1812	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1813	then
[2566]	1814	printf "\n *** batch-job will be created and submitted"
[2380]	1815	else
[2566]	1816	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1817	fi
	1818	fi
	1819
	1820
	1821
	1822	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1823	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1824	then
	1825
	1826	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1827	then
[2566]	1828	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1829	else
[2566]	1830	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1831	fi
	1832
[2422]	1833	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1834	# IT SHALL BE CREATED
	1835	ask_for_make_depository=false
	1836	if [[ $create_remote_batch_job = true ]]
	1837	then
	1838
	1839	line=`grep %base_directory $config_file`
[3236]	1840	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1841	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1842
[3236]	1843	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1844	then
	1845	printf "\n\n +++ make depository \"${make_depository}\""
	1846	printf "\n on remote host not found!"
	1847	ask_for_make_depository=true
	1848	fi
[3236]	1849	rm ${configuration_identifier}_last_make_protokoll
[2422]	1850
	1851	else
	1852
	1853	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1854	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1855	if [[ ! -d ${make_depository} ]]
	1856	then
	1857	printf "\n\n +++ make depository \"${make_depository}\""
	1858	printf "\n on local host not found!"
	1859	ask_for_make_depository=true
	1860	fi
	1861
	1862	fi
	1863
	1864	if [[ $ask_for_make_depository = true ]]
	1865	then
	1866
	1867	antwort=dummy
	1868	printf "\n\n"
	1869	printf " >>> Create a new one (y/n) ? "
	1870	while read antwort
	1871	do
	1872	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1873	then
	1874	printf " >>> Create a new one (y/n) ? "
	1875	else
	1876	break
	1877	fi
	1878	done
	1879	if [[ $antwort = n \|\| $antwort = N ]]
	1880	then
	1881	locat=user_abort; (( iec = 0 )); exit
	1882	fi
	1883
[2566]	1884	if [[ $do_trace = true ]]
	1885	then
[3455]	1886	palmbuild -c $configuration_identifier
[2566]	1887	else
[3455]	1888	palmbuild -v -c $configuration_identifier
[2566]	1889	fi
[2422]	1890
[3312]	1891	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1892	then
	1893
	1894	# ABORT IN CASE OF COMPILATION PROBLEMS
	1895	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1896	locat=make_depository
	1897	exit
	1898	else
	1899	echo " *** now continue with creating executable and other sources"
	1900	fi
	1901
	1902	fi
	1903
[2566]	1904	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1905	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1906
[3312]	1907	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1908	then
	1909
	1910	# ABORT IN CASE OF COMPILATION PROBLEMS
	1911	printf "\n +++ error while creating executable and/or other sources"
	1912	locat=execution
[2990]	1913	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1914	exit
	1915
	1916	else
	1917
[2566]	1918	printf " *** executable and other sources created\n"
[2990]	1919	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1920
	1921	fi
	1922
	1923	fi
	1924
	1925
[2669]	1926	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1927	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1928	if [[ $create_remote_batch_job = true ]]
	1929	then
	1930	(( i = 0 ))
[2610]	1931	while (( i < nr_of_input_files ))
[2605]	1932	do
	1933	(( i = i + 1 ))
[2669]	1934	if [[ "${actionin[$i]}" = tr ]]
[2605]	1935	then
	1936	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1937	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1938	fi
	1939	done
	1940	if (( i > 0 ))
	1941	then
[3025]	1942	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1943	fi
	1944	fi
	1945
	1946
[2380]	1947	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1948	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1949	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1950	then
	1951
	1952	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1953	if [[ $running_in_batch_mode = false ]]
	1954	then
	1955	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1956	# FOLDER
[2566]	1957	mkdir -p $tempdir
	1958	chmod go+rx $tempdir
	1959	cd $tempdir
	1960	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1961	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1962
	1963	else
	1964
	1965	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1966	printf "\n *** running in temporary directory: $tempdir"
[2380]	1967
	1968	fi
	1969
	1970
	1971	# PROVIDE THE INPUT FILES
	1972	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1973	optional_files_missing=false
[2380]	1974	(( i = 0 ))
[2610]	1975	while (( i < nr_of_input_files ))
[2380]	1976	do
	1977	(( i = i + 1 ))
	1978	if (( i == 1 ))
	1979	then
	1980	printf "\n\n *** providing INPUT-files:\n$dashes"
	1981	fi
	1982
	1983
	1984	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1985	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1986	then
[2669]	1987	optional_files_missing=true
[2380]	1988	continue
	1989	fi
	1990
	1991	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1992	files_for_cores=false; filetype=file
	1993	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1994	then
	1995	files_for_cores=true; filetype=files
	1996	actionin[$i]=""
	1997	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1998	then
	1999	actionin[$i]=""
	2000	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	2001	then
	2002	files_for_cores=true; filetype=files
	2003	actionin[$i]="ln"
	2004	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2005	then
	2006	actionin[$i]="ln"
	2007	fi
	2008
	2009	if [[ $files_for_cores = true ]]
	2010	then
	2011	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2012	else
	2013	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2014	fi
	2015
	2016	# INPUT-FILES TO BE LINKED
	2017	if [[ "${actionin[$i]}" = ln ]]
	2018	then
	2019
	2020	printf "\n $filetype will be linked"
	2021	if [[ $files_for_cores = false ]]
	2022	then
	2023	if [[ -f "${absnamein[$i]}" ]]
	2024	then
	2025	ln ${absnamein[$i]} ${localin[$i]}
	2026	got_tmp[$i]=true
	2027	fi
	2028	else
	2029	if [[ -d "${absnamein[$i]}" ]]
	2030	then
[2396]	2031	mkdir -p ${localin[$i]}
[2380]	2032	cd ${absnamein[$i]}
	2033	for file in $(ls *)
	2034	do
[2566]	2035	ln $file $tempdir/${localin[$i]}
[2380]	2036	done >\|/dev/null 2>&1
[2566]	2037	cd $tempdir
[2380]	2038	fi
	2039
	2040	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2041	if [[ ! -f "${localin[$i]}/_000000" ]]
	2042	then
	2043	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2044	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2045	fi
	2046
	2047	got_tmp[$i]=true
	2048	fi
	2049	fi
	2050
	2051	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2052	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2053	then
	2054
	2055	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2056	then
	2057
	2058	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2059	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2060	printf "\n file will be provided for $cores processors"
[2396]	2061	mkdir -p ${localin[$i]}
[2380]	2062	ival=$cores
	2063	(( ii = 0 ))
	2064	while (( ii <= ival-1 ))
	2065	do
	2066	if (( ii < 10 ))
	2067	then
	2068	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2069	elif (( ii < 100 ))
	2070	then
	2071	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2072	elif (( ii < 1000 ))
	2073	then
	2074	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2075	else
	2076	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2077	fi
	2078	(( ii = ii + 1 ))
	2079	done
	2080
	2081	else
	2082
	2083	if [[ $files_for_cores = true ]]
	2084	then
	2085
	2086	# PROVIDE FILES FOR EACH CORE
	2087	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2088	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2089	printf "\n providing $cores files for the respective cores"
[2396]	2090	mkdir -p ${localin[$i]}
[2380]	2091	if [[ $link_local_input = true ]]
	2092	then
	2093	printf " files will be linked\n"
	2094	cd ${absnamein[$i]}
	2095	for file in $(ls *)
	2096	do
	2097	ln -f $file ${localin[$i]}
	2098	done
[2566]	2099	cd $tempdir
[2380]	2100	fi
	2101
	2102	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2103	if [[ ! -f "${localin[$i]}/_000000" ]]
	2104	then
	2105	if [[ $link_local_input = true ]]
	2106	then
	2107	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2108	fi
	2109	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2110	fi
	2111
	2112	else
	2113
	2114	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2115	if [[ $link_local_input = true ]]
	2116	then
	2117	printf " file will be linked\n"
	2118	ln -f ${absnamein[$i]} ${localin[$i]}
	2119	fi
[2605]	2120	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2121	if [[ ! -f "${localin[$i]}" ]]
	2122	then
	2123	if [[ $link_local_input = true ]]
	2124	then
	2125	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2126	fi
[2669]	2127	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2128	then
	2129	mv ${absnamein[$i]} ${localin[$i]}
	2130	else
	2131	cp ${absnamein[$i]} ${localin[$i]}
	2132	fi
[2380]	2133	fi
	2134	fi
	2135	fi
	2136	fi
	2137
	2138	done
	2139	if (( i != 0 ))
	2140	then
[2669]	2141	if [[ $optional_files_missing = true ]]
	2142	then
	2143	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2144	fi
[2380]	2145	printf "\n$dashes\n *** all INPUT-files provided \n"
	2146	fi
	2147
	2148
	2149	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2150	(( i = 0 ))
	2151	while (( i < iic ))
	2152	do
	2153	(( i = i + 1 ))
	2154	if (( i == 1 ))
	2155	then
	2156	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2157	fi
	2158	printf "\n >>> ${in_command[$i]}"
	2159	eval ${in_command[$i]}
	2160	if (( i == iic ))
	2161	then
	2162	printf "\n$dashes\n"
	2163	fi
	2164	done
	2165
	2166
[3313]	2167	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2168	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2169	then
	2170	progress_bar_disabled=true
	2171	else
	2172	progress_bar_disabled=false
	2173	fi
	2174
	2175
[2380]	2176	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2177	# (FILE ENVPAR WILL BE READ BY PALM)
	2178	cat > ENVPAR << EOF
[3236]	2179	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2180	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2181	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2182	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2183	maximum_cpu_time_allowed = ${cpumax}.,
	2184	revision = '$global_revision',
[3313]	2185	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2186
	2187	EOF
	2188
	2189
	2190	# STARTING THE EXECUTABLE
	2191	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2192	PATH=$PATH:$tempdir
[2380]	2193
	2194
	2195	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2196	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2197	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2198	eval line=\"$line\"
	2199	execute_command="$line"
	2200
	2201
	2202	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2203	if [[ "$execute_command_for_combine" = "" ]]
	2204	then
	2205	eval line2=\"$line2\"
	2206	execute_command_for_combine="$line2"
	2207	fi
	2208
[2380]	2209
	2210
	2211	# PROVIDE A HOSTFILE, IF REQUIRED
	2212	if [[ "$hostfile" != "" ]]
	2213	then
	2214
	2215	if [[ $hostfile = auto ]]
	2216	then
	2217	# CREATE A NEW HOSTFILE
	2218	(( ii = 1 ))
	2219	while (( ii <= cores / threads_per_task ))
	2220	do
	2221	echo $(hostname) >> hostfile
	2222	(( ii = ii + 1 ))
	2223	done
	2224	if (( cores / threads_per_task == 0 ))
	2225	then
	2226	echo $(hostname) >> hostfile
	2227	fi
	2228
	2229	else
	2230	cp $hostfile hostfile
	2231	fi
	2232	eval line=\"`head -n $ii hostfile`\"
	2233	printf "\n *** running on: $line"
	2234	fi
	2235
	2236
	2237
	2238	# SET THE NUMBER OF OPENMP-THREADS
	2239	if [[ $use_openmp = true ]]
	2240	then
	2241	export OMP_NUM_THREADS=$threads_per_task
	2242	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2243	else
	2244	export OMP_NUM_THREADS=1
	2245	fi
	2246
	2247
[2610]	2248	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2249	if [[ $run_coupled_model = false ]]
	2250	then
	2251	if [[ "$ocean_file_appendix" = true ]]
	2252	then
	2253	echo "precursor_ocean" > coupling_steering
	2254	else
	2255	echo "precursor_atmos" > coupling_steering
	2256	fi
	2257	else
	2258	(( iia = $cores_atmos / $threads_per_task ))
	2259	(( iio = $cores_ocean / $threads_per_task ))
	2260	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2261	printf "\n\n"
	2262	echo "coupled_run $iia $iio" > coupling_steering
	2263	fi
	2264
	2265	printf "\n *** execute command:"
	2266	printf "\n \"$execute_command\" \n\n"
	2267
	2268
[3393]	2269	if [[ $progress_bar_disabled = true ]]
[2380]	2270	then
[3402]	2271	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2272	exit_code=${PIPESTATUS[0]}
	2273	else
	2274	$execute_command < coupling_steering &> >(tee STDOUT)
	2275	exit_code=${PIPESTATUS[0]}
	2276	fi
[2380]	2277
[3393]	2278	if [[ ${exit_code} != 0 ]]
	2279	then
	2280
[2380]	2281	# ABORT IN CASE OF RUNTIME ERRORS
	2282	printf "\n +++ runtime error occured"
	2283	locat=execution
	2284	exit
	2285
	2286	else
	2287
	2288	printf "\n$dashes\n *** execution finished \n"
	2289
	2290	fi
	2291
	2292
	2293	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2294	# BY EACH CORE INTO ONE FILE
	2295	if [[ ! -f combine_plot_fields.x ]]
	2296	then
	2297
	2298	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2299	printf "\n 2d- and/or 3d-data may be incomplete!"
	2300	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2301
	2302	elif [[ "$combine_plot_fields" == true ]]
	2303	then
	2304
	2305	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2306	$execute_command_for_combine
	2307
	2308	else
	2309
	2310	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2311	# DATA OUTPUT
[2380]	2312	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2313	fi
	2314
	2315
	2316
	2317	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2318	(( i = 0 ))
	2319	while (( i < ioc ))
	2320	do
	2321	(( i = i + 1 ))
	2322	if (( i == 1 ))
	2323	then
	2324	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2325	fi
[2799]	2326
	2327	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2328	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2329
[2380]	2330	printf "\n >>> ${out_command[$i]}"
	2331	eval ${out_command[$i]}
	2332	if (( i == ioc ))
	2333	then
	2334	printf "\n$dashes\n"
	2335	fi
	2336	done
	2337
	2338
[2610]	2339	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2340	# WILDCARDS
[2380]	2341	(( i = 0 ))
[2610]	2342	(( nr_of_output_files = 0 ))
	2343
[2380]	2344	while (( i < iout ))
	2345	do
[2610]	2346
[2380]	2347	(( i = i + 1 ))
[2610]	2348
	2349	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2350	# CREATE A LIST FOR THE DETECTED ENDINGS
	2351	if [[ "${multout[$i]}" = true ]]
	2352	then
	2353	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2354	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2355	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2356
	2357	endings="DEFAULT"
	2358	while read line
	2359	do
	2360	# remove the local name from the beginning
	2361	localnamestring="${localout_pre[$i]}"
	2362	length_localname=${#localnamestring}
	2363	ending=${line:${length_localname}}
	2364
	2365	if [[ "$ending" != "" ]]
	2366	then
	2367	endings="$endings $ending"
	2368	fi
	2369
	2370	done <filelist
	2371
	2372	rm filelist
	2373
	2374	else
	2375
	2376	# SINGLE NAME
	2377	endings=DEFAULT
	2378
	2379	fi
	2380
	2381	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2382	for ending in $endings
	2383	do
	2384
	2385	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2386	if [[ $ending = DEFAULT ]]
	2387	then
	2388	ending=""
	2389	fi
	2390
	2391	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2392	(( nr_of_output_files = nr_of_output_files + 1 ))
	2393	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2394	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2395	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2396	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2397	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2398	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2399	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2400
	2401	done
	2402
	2403	done
	2404
	2405
	2406
	2407
	2408	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2409	(( i = 0 ))
	2410	while (( i < nr_of_output_files ))
	2411	do
	2412	(( i = i + 1 ))
[2380]	2413	if (( i == 1 ))
	2414	then
	2415	printf "\n\n *** saving OUTPUT-files:"
	2416
	2417	# GET RUN NUMBER ASSIGNED BY PALM
	2418	if [[ -f RUN_NUMBER ]]
	2419	then
	2420	read run_number < RUN_NUMBER
	2421	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2422	usecycle_option="-U $run_number"
	2423	else
	2424	run_number=0
	2425	usecycle_option=""
	2426	fi
	2427	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2428	then
[2404]	2429	printf "\n *** in case of SCP transfers to local host"
	2430	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2431	fi
	2432	printf "\n$dashes"
	2433	fi
	2434
	2435	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2436	then
	2437
[3236]	2438	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2439
	2440	# DETERMINE THE CYCLE NUMBER
	2441	ls -1 -d $filename > filelist 2>/dev/null
	2442	ls -1 -d $filename.* >> filelist 2>/dev/null
	2443	while read line
	2444	do
	2445
	2446	# filename without path (i.e. after the last "/")
	2447	basefilename=$(basename ${line})
	2448
	2449	# check if there is an extension
	2450	extension=${basefilename##*.}
	2451	if [[ "$extension" = "${extout[$i]}" ]]
	2452	then
	2453	basefilename=${basefilename%.*}
	2454	fi
	2455
	2456	# check for an existing cycle number
	2457	cycle=${basefilename##*.}
	2458	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2459	then
[2669]	2460	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2461	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2462	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2463	else
	2464	(( icycle = 1 ))
	2465	fi
	2466
	2467	if (( icycle > maxcycle ))
	2468	then
	2469	(( maxcycle = icycle ))
	2470	fi
	2471
	2472	done <filelist
	2473	rm filelist
	2474
	2475
	2476	# SET THE CYCLE NUMBER
	2477	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2478	if [[ "${actionout[$i]}" = a ]]
	2479	then
	2480	(( maxcycle = maxcycle - 1 ))
	2481	fi
	2482
	2483	(( cycnum[$i] = maxcycle ))
	2484	pathout[$i]=$filename
	2485
	2486
	2487	# ADD CYCLE NUMBER TO FILENAME
	2488	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2489	if [[ "${actionout[$i]}" != "a" ]]
	2490	then
	2491	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2492	# WITH AN EXISTING CYCLE NUMBER
	2493	if (( run_number >= cycnum[$i] ))
	2494	then
	2495	(( cycnum[$i] = run_number ))
	2496	else
	2497	if (( run_number > 0 ))
	2498	then
	2499	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2500	fi
	2501	fi
	2502	fi
	2503	if (( cycnum[$i] > 0 ))
	2504	then
[2600]	2505	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2506	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2507	fi
	2508	fi
	2509
	2510	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2511	files_for_cores=false; filetype=file
	2512	link_local_output=false
	2513	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2514	then
	2515	files_for_cores=true; filetype=directory
	2516	actionout[$i]=""
	2517	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2518	then
	2519	actionout[$i]=""
	2520	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2521	then
	2522	files_for_cores=true; filetype=directory
	2523	link_local_output=true
	2524	actionout[$i]=""
	2525	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2526	then
	2527	link_local_output
	2528	actionout[$i]=""
	2529	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2530	then
	2531	files_for_cores=true; filetype=directory
	2532	actionout[$i]="tr"
	2533	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2534	then
	2535	actionout[$i]="tr"
	2536	fi
	2537
	2538	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2539	then
[2669]	2540	if [[ ${warnout[$i]} = true ]]
	2541	then
	2542	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2543	fi
[2380]	2544	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2545	then
[2669]	2546	if [[ ${warnout[$i]} = true ]]
	2547	then
	2548	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2549	fi
[2380]	2550	else
	2551
	2552
	2553	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2554	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2555	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2556	then
	2557	if [[ $running_on_remote = true ]]
	2558	then
	2559
	2560	# SET OPTIONS FOR TRANSFER
	2561	if [[ "${actionout[$i]}" = tr ]]
	2562	then
	2563	if [[ $files_for_cores = false ]]
	2564	then
	2565	catalog_option=""
	2566	catalog_string=""
	2567	else
	2568	catalog_option="-c"
	2569	catalog_string="/"
	2570	fi
	2571	append_option=""
	2572	append_string=""
	2573	else
	2574	append_option="-A"
	2575	append_string="append"
	2576	fi
	2577
	2578	transfer_failed=false
	2579	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2580	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2581
	2582	# TRANSFER VIA SCP
	2583	if [[ "$remote_loginnode" != "" ]]
	2584	then
[3534]	2585	ssh -q $remote_username@$remote_loginnode "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}"
[2380]	2586	else
[3236]	2587	batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} "${pathout[$i]}" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}
[2380]	2588	fi
[3312]	2589	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2590
	2591
	2592	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2593	if [[ $transfer_failed = true ]]
	2594	then
	2595	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2596	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2597
	2598	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2599	eval local_catalog=${pathout[$i]}
	2600	if [[ ! -d $local_catalog ]]
	2601	then
	2602	printf " *** local directory does not exist. Trying to create:\n"
	2603	printf " $local_catalog \n"
	2604	mkdir -p $local_catalog
	2605	fi
[3236]	2606	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2607	transfer_problems=true
	2608	fi
	2609
	2610	else
	2611
	2612	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2613	# BE COPIED OR APPENDED ON THIS MACHINE
	2614	if [[ "${actionout[$i]}" = tr ]]
	2615	then
	2616	actionout[$i]=""
	2617	else
	2618	actionout[$i]="a"
	2619	fi
	2620	fi
	2621	fi
	2622
	2623
	2624	# APPEND ON THIS MACHINE
	2625	if [[ "${actionout[$i]}" = "a" ]]
	2626	then
	2627	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2628	then
	2629	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2630	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2631	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2632	else
	2633	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2634	printf "\n ${pathout[$i]}\n"
	2635	cat ${localout[$i]} >> ${pathout[$i]}
	2636	fi
	2637	fi
	2638
	2639	# COPY ON THIS MACHINE
	2640	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2641	# ON DIFFERENT FILE-SYSTEMS
	2642	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2643	then
	2644
	2645	# COPY IN CASE OF RUNS ON SINGLE CORES
	2646	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2647	then
	2648	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2649	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2650	if [[ $link_local_output = true ]]
	2651	then
	2652	printf " file will be linked\n"
	2653	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2654	fi
	2655	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2656	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2657	then
	2658	if [[ $link_local_output = true ]]
	2659	then
	2660	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2661	fi
	2662	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2663	else
	2664	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2665	fi
	2666	else
	2667	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2668	printf "\n ${pathout[$i]}\n"
	2669	if [[ $link_local_output = true ]]
	2670	then
	2671	printf " file will be linked\n"
	2672	ln -f ${localout[$i]} ${pathout[$i]}
	2673	fi
	2674	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2675	if [[ ! -f "${pathout[$i]}" ]]
	2676	then
	2677	if [[ $link_local_output = true ]]
	2678	then
	2679	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2680	fi
	2681	cp ${localout[$i]} ${pathout[$i]}
	2682	else
	2683	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2684	fi
	2685	fi
	2686
	2687	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2688	then
	2689
	2690	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2691	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2692	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2693	printf "\n ${pathout[$i]}\n"
	2694	if [[ $link_local_output = true ]]
	2695	then
	2696	printf " files will be linked\n"
[2396]	2697	mkdir -p ${pathout[$i]}
[2380]	2698	cd ${localout[$i]}
	2699	for file in $(ls *)
	2700	do
	2701	ln -f $file ${pathout[$i]}
	2702	done >\|/dev/null 2>&1
[2566]	2703	cd $tempdir
[2380]	2704	fi
	2705
	2706	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2707	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2708	then
	2709	if [[ $link_local_output = true ]]
	2710	then
	2711	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2712	fi
[3025]	2713	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2714	cp -r ${localout[$i]}/* ${pathout[$i]}
	2715	fi
	2716
	2717	fi
	2718	fi
	2719	done
	2720
	2721	if (( i != 0 ))
	2722	then
	2723	if [[ $transfer_problems = true ]]
	2724	then
	2725	printf "\n$dashes\n *** OUTPUT-files saved"
	2726	printf "\n +++ WARNING: some data transfers failed! \n"
	2727	else
	2728	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2729	fi
	2730	fi
	2731
	2732
	2733	# IF REQUIRED, START A RESTART-JOB
	2734	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2735	if [[ -f CONTINUE_RUN ]]
	2736	then
	2737
	2738	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2739	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2740	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2741	# -b START A BATCH JOB
	2742	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2743	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2744	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2745
[2957]	2746	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2747	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2748	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2749	then
	2750	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2751	fi
[2380]	2752
	2753	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2754	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2755	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2756	then
[2381]	2757	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2758	fi
	2759
	2760
	2761	# START THE RESTART-JOB
	2762	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2763	echo " $prc"
	2764	printf "\n$dashes\n"
	2765	if [[ $running_on_remote = true ]]
	2766	then
	2767
	2768	echo "*** ssh will be used to initiate restart-runs!"
	2769	echo " return_address=\"$return_address\" "
	2770	echo " return_username=\"$local_username\" "
	2771
	2772	if [[ "$remote_loginnode" != "" ]]
	2773	then
[3534]	2774	ssh -q $remote_username@$remote_loginnode "ssh -q $SSH_PORTOPT $local_username@$return_address \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" " \| tee palmrun_restart.log
[2380]	2775	else
[3534]	2776	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2777	fi
	2778
	2779	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2780	sleep 30
	2781
	2782	else
	2783
	2784	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2785	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2786	cd - > /dev/null
	2787
	2788	fi
	2789
[3132]	2790	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2791	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2792	then
	2793	printf "\n$dashes\n +++ creating restart run failed \n"
	2794	locat=create_restart
[3455]	2795	rm palmrun_restart.log
[3132]	2796	exit
	2797	else
	2798	printf "\n$dashes\n *** restart run initiated \n"
	2799	rm palmrun_restart.log
	2800	fi
[2380]	2801
[3132]	2802
[2380]	2803	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2804	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2805	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2806	# MAY BE VERY HUGE)
	2807	(( i = 0 ))
[2610]	2808	while (( i < nr_of_input_files ))
[2380]	2809	do
	2810	(( i = i + 1 ))
	2811	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2812	then
	2813	rm -r ${absnamein[$i]}
	2814	fi
	2815	done
	2816
	2817	fi
	2818
	2819
	2820	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2821	cd $HOME
[2566]	2822	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2823
	2824
	2825	else
	2826
	2827
	2828	# PREPARING ACTIONS,
	2829	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2830
	2831	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2832	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2833	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2834	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2835	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2836	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2837	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2838	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2839	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2840	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2841	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2842	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2843	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2844	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2845	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2846	if [[ $create_remote_batch_job = true ]]
	2847	then
	2848	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2849	if [[ $do_trace = true ]]
	2850	then
	2851	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2852	fi
[2380]	2853	elif [[ $create_batch_job = true ]]
	2854	then
	2855	palmrun_com=${palmrun_com}" -j"
[2420]	2856	if [[ $do_trace = true ]]
	2857	then
	2858	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2859	fi
[2380]	2860	fi
	2861
	2862
	2863	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2864	# REMOTE HOST
[3236]	2865	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2866	job_protocol_file=$job_protocol_file_local
	2867	if [[ $create_remote_batch_job = true ]]
	2868	then
[3236]	2869	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2870	job_protocol_file=$job_protocol_file_remote
	2871	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2872	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2873	fi
	2874
	2875
	2876	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2877	jobfile=jobfile.$run_id_number
[2380]	2878
	2879
	2880	# FIRST CREATE THE BATCH DIRECTIVES
	2881	(( i = 0 ))
	2882	while (( i < ibd ))
	2883	do
	2884	(( i = i + 1 ))
[2693]	2885	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2886	eval line=\"$line\"
	2887	echo "$line" >> $jobfile
	2888	done
	2889	echo " " >> $jobfile
	2890
	2891
	2892	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2893	# PROTOCOL
	2894	if [[ $create_remote_batch_job = true ]]
	2895	then
[3236]	2896	echo "set +vx" >> $jobfile
	2897	echo "trap '" >> $jobfile
	2898	echo "set +vx" >> $jobfile
	2899	echo "cd ${remote_jobcatalog}" >> $jobfile
	2900	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2901
	2902	# ADD THE BATCH DIRECTIVES
	2903	(( i = 0 ))
	2904	while (( i < ibdt ))
	2905	do
	2906	(( i = i + 1 ))
[2693]	2907	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2908	eval line=\"$line\"
	2909	echo "$line" >> $jobfile
	2910	done
	2911	echo " " >> $jobfile
	2912
	2913	echo "set -x" >> $jobfile
[3534]	2914	if [[ "$remote_loginnode" != "" ]]
	2915	then
	2916	echo "ssh -q $remote_username@$remote_loginnode \"cd ${remote_jobcatalog}; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \\\"$local_jobcatalog\\\" ${configuration_identifier}_${run_identifier}\" " >> $jobfile
	2917	else
	2918	echo "${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT -d -w 10 -u $local_username $local_ip $job_protocol_file_remote \"$local_jobcatalog\" ${configuration_identifier}_${run_identifier}" >> $jobfile
	2919	fi
[2380]	2920	echo "%%END%%" >> $jobfile
	2921	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2922	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2923	echo "rm $scpjob_file" >> $jobfile
[2404]	2924	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2925	echo "set -x" >> $jobfile
	2926	echo " ' exit" >> $jobfile
	2927	fi
	2928
	2929
	2930	# ACTIVATE ERROR-TRACEBACK
	2931	if [[ $do_trace = true ]]
	2932	then
	2933	echo "set -x" >> $jobfile
	2934	else
	2935	echo "set +vx" >> $jobfile
	2936	fi
	2937
	2938
	2939	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2940	if [[ "$login_init_cmd" != "" ]]
	2941	then
	2942	echo "$login_init_cmd" >> $jobfile
	2943	fi
	2944	if [[ "$module_commands" != "" ]]
	2945	then
	2946	echo "$module_commands" >> $jobfile
	2947	fi
	2948
	2949
	2950	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2951	if [[ $create_remote_batch_job = true ]]
	2952	then
	2953	echo "mkdir $tempdir" >> $jobfile
	2954	echo "chmod go+rx $tempdir" >> $jobfile
	2955	else
	2956	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2957	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2958	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2959	mkdir $tempdir
	2960	chmod go+rx $tempdir
	2961	fi
	2962	echo "cd $tempdir" >> $jobfile
	2963	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2964	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2965	echo "export PATH=.:\$PATH" >> $jobfile
	2966	echo "export execute_palmrun=true" >> $jobfile
	2967
	2968
	2969	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2970	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2971	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2972	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2973	echo "export LOCAL_PWD" >> $jobfile
	2974
	2975
	2976	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2977	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2978	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2979
	2980
	2981	# CALL PALMRUN WITHIN THE JOB
	2982	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2983	echo "set -x" >> $jobfile
	2984	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2985
	2986
	2987	# TRANSFER JOBFILE TO THE TARGET HOST
	2988	if [[ $create_jobfile_only = false ]]
	2989	then
	2990
[3505]	2991	# CREATE LOCAL JOB FOLDER
	2992	eval local_jobcatalog=$local_jobcatalog
	2993	if [[ ! -d $local_jobcatalog ]]
	2994	then
	2995	echo " "
	2996	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	2997	mkdir $local_jobcatalog
	2998	fi
	2999
[2380]	3000	if [[ $create_remote_batch_job = true ]]
	3001	then
	3002
[2420]	3003	echo " "
[2566]	3004	echo " *** transfer of job to remote host via scp"
[3505]	3005
	3006	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3007	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3008
	3009	# COPY THE JOB FILE
[2420]	3010	if [[ $do_trace = true ]]
	3011	then
[3236]	3012	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3013	fi
[3236]	3014	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3015
[3505]	3016	# SUBMIT THE JOB
[3549]	3017	printf " *** submit the job (output of submit command, e.g. the job-id, may follow) \n"
[2420]	3018	if [[ $do_trace = true ]]
	3019	then
[3549]	3020	echo " echo \"cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}\" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>/dev/null"
[2420]	3021	fi
[3549]	3022	echo "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>/dev/null
[2380]	3023
	3024	elif [[ $create_batch_job = true ]]
	3025	then
	3026
[2385]	3027	eval local_jobcatalog=$local_jobcatalog
[3236]	3028	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3029	cd $local_jobcatalog
[2380]	3030	echo " "
[2420]	3031	echo " *** submit the job"
	3032	if [[ $do_trace = true ]]
	3033	then
[3236]	3034	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3035	fi
[3236]	3036	$submit_command ${configuration_identifier}_${run_id}
	3037	rm ${configuration_identifier}_${run_id}
[2380]	3038	cd - > /dev/null
	3039
	3040	fi
	3041
	3042	rm -rf $jobfile
	3043
	3044	else
	3045
	3046	printf "\n *** jobfile created under name \"$jobfile\" "
	3047	printf "\n no batch-job has been sent!"
	3048
	3049	fi
	3050
	3051	fi # END OF REMOTE-PART

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