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source: palm/trunk/SCRIPTS/palmrun @ 3570

Last change on this file since 3570 was 3570, checked in by kanani, 6 years ago
Fix too long lines (chemistry_model_mod, chem_emissions_mod), correct terminal message (palmrun)
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 3570 2018-11-27 17:44:21Z kanani $
[3570]	29	# Rename job-id by run_id
	30	#
	31	# 3555 2018-11-22 13:50:37Z raasch
[3555]	32	# sed-command to remove repeated space-characters replaced by tr-command, to
	33	# guarantee mac compatible
	34	#
	35	# 3549 2018-11-21 15:44:44Z raasch
[3549]	36	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	37	# of login messages on specific systems
	38	#
	39	# 3534 2018-11-19 15:35:16Z raasch
[3534]	40	# batch_scp for sending back the job protocol file is called via login-node if
	41	# a login-node has been set in the config-file
	42	# ssh-calls rearranged to avoid output of system/user-profile messages
	43	#
	44	# 3505 2018-11-08 09:14:30Z raasch
[3505]	45	# job folders are created in case that they do not exist
	46	#
	47	# 3455 2018-10-30 14:12:31Z raasch
[3455]	48	# options -h and -d renamed -c and -r, respectively
	49	#
	50	# 3402 2018-10-23 11:49:24Z knoop
[3346]	51	# job_id is set for compatibility reasons with older versions of config files
	52	#
	53	# 3313 2018-10-06 15:22:48Z knoop
[3294]	54	# more detailed error message for outdated fileconnection file
	55	#
	56	# 3236 2018-09-10 09:07:06Z raasch
[3236]	57	# warning issued in case of file connection file version mismatch,
	58	# host_configuration renamed configuration_identifier,
	59	# "host identifier" in header output renamed "config. identifier",
	60	# jobname renamed run_identifier,
	61	# run_id renamed run_id_number
	62	# job_id renamed run_id
	63	# option -r renamed -i
	64	#
	65	# 3151 2018-07-19 08:45:38Z raasch
[3151]	66	# removed additional listing of files to be compiled, print PALM code revision
	67	# in header
	68	#
	69	# 3132 2018-07-16 11:44:58Z raasch
[3132]	70	# create consistent error messages in case of failed restarts,
	71	# check existence of remote job catalog
	72	#
	73	# 3043 2018-05-25 10:47:54Z raasch
[3043]	74	# check for setting of fast_io_catalog
	75	#
	76	# 3033 2018-05-23 15:26:19Z raasch
[3025]	77	# -T option not required for interactive runs (tasks per node =
	78	# total number of cores is assumed as default, if option is not given),
	79	# reformatting of a few messages,
	80	# bugfix: destination output directory is created if attribute "pe" is set in
	81	# .palm.iofiles
	82	#
	83	# 2718 2018-01-02 08:49:38Z maronga
[2993]	84	# bugfix of r2990
	85	#
	86	# 2718 2018-01-02 08:49:38Z maronga
[2990]	87	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	88	# not in the working directory from where palmrun is called
	89	#
	90	# 2718 2018-01-02 08:49:38Z maronga
[2957]	91	# svfout in the activation string will be replaced now by svfin in case of
	92	# automatic restarts
	93	#
	94	# 2718 2018-01-02 08:49:38Z maronga
[2906]	95	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	96	# the possible output or input of sky view factors
	97	#
	98	# 2718 2018-01-02 08:49:38Z maronga
[2834]	99	# "fname" renamed to "jobname"
	100	#
	101	# 2718 2018-01-02 08:49:38Z maronga
[2799]	102	# parameters are allowed in output commands (OC:)
	103	#
	104	# 2718 2018-01-02 08:49:38Z maronga
[2789]	105	# bugfix: exit if no queue has been given neither with option -q nor in the
	106	# configuration file
	107	#
	108	# 2718 2018-01-02 08:49:38Z maronga
[2762]	109	# file connection file from trunk/SCRIPTS is taken by default
	110	#
	111	# 2718 2018-01-02 08:49:38Z maronga
[2716]	112	# Corrected "Former revisions" section
	113	#
	114	# 2696 2017-12-14 17:12:51Z kanani
	115	# Change in file header (GPL part)
	116	#
	117	# 2693 2017-12-13 12:33:49Z raasch
[2693]	118	# replacement of variables given by {{<variable>}} in configuration file is now
	119	# done in a more general way, variable names are written in small letters
	120	#
	121	# 2670 2017-12-06 16:32:19Z raasch
[2670]	122	# test printouts removed
	123	#
	124	# 2669 2017-12-06 16:03:27Z raasch
[2669]	125	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	126	# removed,
	127	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	128	# files,
	129	# informative messages in case of missing optional input files shortened
	130	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	131	#
	132	# 2638 2017-11-23 12:44:23Z raasch
[2610]	133	# use of wildcards in file connection statements enabled
	134	#
	135	# 2605 2017-11-09 15:31:46Z raasch
[2605]	136	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	137	# will not be sent with the job file any more, but copied into the
[2610]	138	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	139	#
	140	# 2600 2017-11-01 14:11:20Z raasch
[2600]	141	# cycle numbers are made three digits wide
	142	#
	143	# 2566 2017-10-20 08:50:47Z raasch
[2566]	144	# execute command for combine_plot_fields added
	145	# "TEMPDIR" renamed "tempdir"
	146	# temporary working directory for local batch jobs is created immediately within
	147	# the user's palmrun call, due to a requirement of the "grid engine" batch
	148	# system, where the working directory is given with batch directive -wd and must
	149	# already exist when the job is submitted,
	150	# informative messages in non-trace mode reduced and partly reformatted
	151	#
	152	# 2551 2017-10-18 07:25:11Z raasch
[2551]	153	# TEMPDIR added as replacement string to be used in batch directives
	154	#
	155	# 2512 2017-10-04 08:26:59Z raasch
[2507]	156	# bugfix for determining cycle numbers of NetCDF input files
	157	#
	158	# 2506 2017-09-29 08:30:37Z raasch
[2506]	159	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	160	# host configuration added to SOURCES_FOR_RUN_... folder name
	161	# host_identifier renamed host_configuration
	162	# option -W added to allow for job dependencies
	163	#
	164	# 2501 2017-09-26 11:41:55Z raasch
[2501]	165	# default value for number of cores (option -X) set to 1
	166	# bugfix for mechanism which overwrites configuration file settings with values
	167	# provided by palmrun options
	168	#
	169	# 2499 2017-09-22 16:47:58Z kanani
[2499]	170	# option -h named configuration identifier
	171	#
	172	# 2480 2017-09-19 06:24:14Z maronga
[2480]	173	# bugfix for last revision
	174	#
	175	# 2479 2017-09-19 06:12:16Z raasch
[2479]	176	# option -A (project account number) added
	177	#
	178	# 2422 2017-09-08 08:25:41Z raasch
[2410]	179	# initial revision
[2380]	180	#
	181	#--------------------------------------------------------------------------------#
	182	# palmrun - script for running PALM jobs on local and remote hosts
	183	#--------------------------------------------------------------------------------#
	184
	185
	186
	187	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	188
	189	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	190	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	191	# (TOO MANY ARGUMENTS - PROBLEM)
	192	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	193
[2610]	194	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	195	typeset -i nr_of_output_files=0
[2380]	196	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	197	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	198	# SCRIPT-OPTION ARGUMENTS
	199	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	200	typeset -i icycle inode ival maxcycle mpi_tasks
	201	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	202
	203	activation_string_list=""
	204	AddFilenames=""
	205	combine_plot_fields=true
	206	compiler_name=""
	207	compiler_name_ser=""
	208	compiler_options=""
[3236]	209	configuration_identifier="default"
[2501]	210	cores=1
[2380]	211	cores_atmos=0
	212	cores_ocean=0
	213	coupled_dist=""
	214	cpp_options=""
	215	cpumax=0
[2506]	216	create_batch_job=false
[2380]	217	create_jobfile_only=false
	218	create_remote_batch_job=false
	219	dashes=" ----------------------------------------------------------------------------"
	220	defaultqueue=""
[2506]	221	delete_temporary_catalog=true
[2380]	222	do_compile=true
	223	do_trace=false
	224	executable=""
	225	execute_command=""
	226	execution_error=false
[2762]	227	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	228	global_revision=""
	229	hostfile=""
	230	hp=""
	231	keep_data_from_previous_run=false
	232	link_local_input=false
	233	link_local_output=false
[2388]	234	linker_options=""
[2385]	235	local_jobcatalog=""
[2380]	236	locat=normal
	237	makefile=""
	238	max_par_io_str=""
	239	prc=$0
	240	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	241	do
	242	prc=`echo $prc \| cut -f2- -d"/"`
	243	done
	244	module_calls=""
[2506]	245	palmrun_memory=""
[2380]	246	palmrun_script_name=$prc
	247	openmp=false
[2506]	248	previous_job=""
[2479]	249	project_account=""
[2380]	250	queue=none
[2906]	251	read_svf=""
[2380]	252	restart_run=false
	253	return_address=""
[2385]	254	remote_jobcatalog=""
[2380]	255	remote_username=""
	256	running_in_batch_mode=false
[3313]	257	running_in_test_mode=false
[2380]	258	run_coupled_model=false
	259	run_id=""
[3236]	260	run_id_number=""
	261	run_identifier=test
[2380]	262	silent=false
	263	source_list=""
	264	source_path=""
[2501]	265	tasks_per_node=0
[2380]	266	threads_per_task=1
	267	transfer_problems=false
[2384]	268	user_source_path=""
[2506]	269	use_existing_sources_folder=""
[2380]	270	use_openmp=false
[3033]	271	version="palmrun 1.0 Rev$Rev: 3570 $"
[2380]	272	working_directory=`pwd`
	273	write_binary=""
[2906]	274	write_svf=""
[2380]	275
	276
	277	# ERROR HANDLING IN CASE OF EXIT
[2404]	278	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	279	then
	280
	281	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	282	(( i = 0 ))
	283	while (( i < iec ))
	284	do
	285	(( i = i + 1 ))
	286	printf "\n *** Execution of ERROR-command:\n"
	287	printf " >>> ${err_command[$i]}\n"
	288	eval ${err_command[$i]}
	289	done
[2566]	290	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	291	printf "\n\n+++ palmrun crashed \n\n"
	292	exit 1
	293	elif [[ $locat != normal ]]
[2380]	294	then
[3312]	295	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	296	printf "\n+++ palmrun killed by \"^C\" \n\n"
	297	exit 2
	298	else
[2566]	299	printf "\n --> palmrun finished\n\n"
[3312]	300	exit 0
[2380]	301	fi' exit
	302
	303
	304	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	305	trap 'locat=control_c
	306	exit 1
[2380]	307	' 2
	308
	309
	310	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	311	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	312	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]	313	do
	314	case $option in
	315	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	316	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	317	(b) create_batch_job=true; prc="$prc -b";;
	318	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	319	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	320	(C) restart_run=true; prc="$prc -C";;
	321	(F) create_jobfile_only=true;;
	322	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	323	(i) run_id_number=$OPTARG;;
[2380]	324	(j) running_in_batch_mode=true;;
	325	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	326	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	327	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	328	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	329	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	330	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	331	(R) return_address=$OPTARG;;
	332	(s) source_list=$OPTARG;;
[2501]	333	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	334	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	335	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	336	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	337	(v) silent=true; prc="$prc -v";;
[2506]	338	(V) use_existing_sources_folder="-V";;
[2380]	339	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	340	(W) previous_job=$OPTARG;;
[2380]	341	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	342	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	343	(y) ocean_file_appendix=true; prc="$prc -y";;
	344	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	345	(z) running_in_test_mode=true;;
[2380]	346	(Z) combine_plot_fields=false; prc="$prc -Z";;
	347	(\?) printf "\n +++ unknown option $OPTARG \n"
	348	printf "\n --> type \"$0 ?\" for available options \n"
	349	locat=parameter;exit;;
	350	esac
	351	done
	352
	353
	354	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	355	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	356	(( to_shift = $OPTIND - 1 ))
	357	shift $to_shift
	358
	359	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	360	if [[ "$1" = "?" ]]
	361	then
	362	(printf "\n *** Description of available palmrun options:\n"
	363	printf "\n Option Description Default-Value"
	364	printf "\n -a activation string list \"\" "
[2479]	365	printf "\n -A project account number ---"
[2380]	366	printf "\n -b batch-job on local machine ---"
	367	printf "\n -B do not delete temporary directory at end ---"
[3455]	368	printf "\n -c configuration identifier \"default\" "
[2380]	369	printf "\n -F create batch job file only ---"
	370	printf "\n -k keep data from previous run"
	371	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	372	printf "\n -M Makefile name Makefile"
	373	printf "\n -O threads per openMP task ---"
	374	printf "\n -q queue \"$queue\" "
[3455]	375	printf "\n -r run identifier test"
[2380]	376	printf "\n -s filenames of routines to be compiled \"\" "
	377	printf "\n must end with .f, .f90, .F, or .c !"
	378	printf "\n use \"..\" for more than one file and wildcards"
	379	printf "\n -s LM compiles all locally modified files"
	380	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	381	printf "\n -T tasks per node ---"
[2380]	382	printf "\n -u username on remote machine \"\" "
	383	printf "\n -v no prompt for confirmation ---"
[2506]	384	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	385	printf "\n -w maximum parallel io streams as given by -X"
[2506]	386	printf "\n -W name of job to wait for ---"
[2380]	387	printf "\n -x tracing of palmrun for debug purposes ---"
	388	printf "\n -X # of processors (on parallel machines) 1"
	389	printf "\n -y add appendix \"_O\" to all local output"
	390	printf "\n files (ocean precursor runs followed by"
	391	printf "\n coupled atmosphere-ocean runs) ---"
	392	printf "\n -Y run coupled model, \"#1 #2\" with"
	393	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	394	printf "\n -Z skip combine_plot_fields at the end of "
	395	printf "\n the simulation ---"
	396	printf "\n "
	397	printf "\n Possible values of positional parameter <modus>:"
	398	printf "\n \"?\" - this outline \n\n") \| more
	399	exit
	400	elif [[ "$1" != "" ]]
	401	then
	402	printf "\n +++ positional parameter $1 unknown \n"
	403	locat=parameter; exit
	404	fi
	405
	406
	407
	408	# SHORT STARTING MESSAGE
	409	printf "\n*** $version "
	410	printf "\n will be executed. Please wait ..."
	411
	412
[2506]	413	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	414	config_file=.palm.config.$configuration_identifier
	415	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	416
	417
	418	# CHECK, IF CONFIGURATION FILE EXISTS
	419	if [[ ! -f $config_file ]]
	420	then
	421	printf "\n\n +++ configuration file: "
	422	printf "\n $config_file"
	423	printf "\n does not exist"
	424	locat=connect; exit
	425	fi
	426
	427
[2762]	428	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	429	if [[ -f .palm.iofiles ]]
	430	then
[3236]	431
	432	# CHECK VERSION MISMATCH
	433	if [[ $running_in_batch_mode != true ]]
	434	then
	435	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	436	then
	437	printf "\n\n +++ WARNING: A file connection file has been found in your"
	438	printf "\n working directory, but its revision does not match"
	439	printf "\n the revision of the default (trunk) version."
[3294]	440	printf "\n You may need to update your connection file"
	441	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	442	fi
	443	fi
	444
[2762]	445	fileconnection_file=.palm.iofiles
[3236]	446
[2762]	447	fi
	448
	449
[2380]	450	# CHECK, IF FILE CONNECTION FILE EXISTS
	451	if [[ ! -f $fileconnection_file ]]
	452	then
	453	printf "\n\n +++ file connection file: "
	454	printf "\n $fileconnection_file"
	455	printf "\n does not exist"
	456	locat=connect; exit
	457	fi
	458
	459
[2404]	460	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	461	if [[ "$activation_string_list" = "" ]]
	462	then
	463	printf "\n\n +++ no activation string list given: "
	464	printf "\n please set palmrun option \"-a\" "
	465	locat=palmrun_option; exit
	466	fi
	467
	468
	469	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	470	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	471	then
	472	write_binary=true
	473	else
	474	write_binary=false
	475	fi
	476
[2906]	477	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	478	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	479	then
	480	write_svf=true
	481	else
	482	write_svf=false
	483	fi
[2404]	484
[2906]	485	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	486	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	487	then
	488	read_svf=true
	489	else
	490	read_svf=false
	491	fi
	492
	493
[2380]	494	# READ AND EVALUATE THE CONFIGURATION-FILE
	495	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	496
	497	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	498	while read line
	499	do
	500
	501	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	502	eval line=\"$line\"
	503
	504
	505	# INTERPRET THE LINE
	506	if [[ "$(echo $line)" = "" ]]
	507	then
	508
	509	# EMPTY LINE, NO ACTION
	510	continue
	511
	512	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	513	then
	514
	515	# LINE IS A COMMENT LINE
	516	continue
	517
	518	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	519	then
	520
	521	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	522	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	523	value=`echo $line \| cut -d" " -s -f2-`
	524
	525
	526	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	527	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	528	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	529	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	530	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	531	# CONFIGURATION-FILE.
	532	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	533	then
	534	eval export $var="\$value"
	535
	536	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	537	if [[ $do_trace = true ]]
	538	then
	539	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	540	fi
	541	fi
	542
	543	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	544	then
	545
	546	# LINE DEFINES BATCH-DIRECTIVE
	547	(( ibd = ibd + 1 ))
	548	line=$(echo $line \| cut -c4-)
	549	batch_directive[$ibd]="$line"
	550
	551	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	552	then
	553
	554	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	555	# REMOTE TO A LOCAL HOST
	556	(( ibdt = ibdt + 1 ))
	557	line=$(echo $line \| cut -c5-)
	558	batch_directive_transfer[$ibdt]="$line"
	559
	560	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	561	then
	562
	563	# LINE DEFINES ERROR-COMMAND
	564	(( iec = iec + 1 ))
	565	line=$(echo $line \| cut -c4-)
	566	err_command[$iec]="$line"
	567
	568	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	569	then
	570
	571	# LINE DEFINES INPUT-COMMAND
	572	(( iic = iic + 1 ))
	573	line=$(echo $line \| cut -c4-)
	574	in_command[$iic]="$line"
	575
	576	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	577	then
	578
	579	# LINE DEFINES OUTPUT-COMMAND
	580	(( ioc = ioc + 1 ))
	581	line=$(echo $line \| cut -c4-)
	582	out_command[$ioc]="$line"
	583
	584	else
	585
	586	# SKIP ALL OTHER LINES
	587	continue
	588
	589	fi
	590
	591	done < $config_file
	592
	593
	594	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	595	if [[ "$fast_io_catalog" = "" ]]
	596	then
	597	printf "\n +++ no fast_io_catalog found in $config_file"
	598	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	599	locat=config_file; exit
	600	fi
[2380]	601	if [[ "$compiler_name" = "" ]]
	602	then
	603	printf "\n +++ no compiler name found in $config_file"
	604	printf "\n Please add line \"compiler_name ...\" to that file."
	605	locat=config_file; exit
	606	fi
	607	if [[ "$compiler_name_ser" = "" ]]
	608	then
	609	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	610	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	611	locat=config_file; exit
	612	fi
	613	if [[ "$compiler_options" = "" ]]
	614	then
	615	printf "\n +++ no compiler options found in $config_file"
	616	printf "\n Please add line \"compiler_options ...\" to that file."
	617	locat=config_file; exit
	618	fi
[2388]	619	if [[ "$linker_options" = "" ]]
[2380]	620	then
[2388]	621	printf "\n +++ no linker options found in $config_file"
	622	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	623	locat=config_file; exit
	624	fi
	625	if [[ "$execute_command" = "" ]]
	626	then
	627	printf "\n +++ no execute command found in $config_file"
	628	printf "\n Please add line \"execute_command ...\" to that file."
	629	locat=config_file; exit
	630	fi
	631
	632	if [[ "$hostfile" != "" ]]
	633	then
	634	if [[ $hostfile != auto && ! -f $hostfile ]]
	635	then
	636	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	637	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	638	locat=config_file; exit
	639	fi
	640	fi
	641
	642
	643	# DETERMINE THE CALL STATUS
	644	if [[ "$return_address" != "" ]]
	645	then
	646
	647	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	648	# BATCH MODE AND ...
	649	running_on_remote=true
	650
	651	else
	652
	653	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	654	if [[ "$remote_ip" != "" ]]
	655	then
	656
	657	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	658	create_remote_batch_job=true
	659
[3132]	660	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	661	if [[ "$remote_jobcatalog" = "" ]]
	662	then
	663	printf "\n +++ no remote jobcatalog found in $config_file"
	664	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	665	locat=config_file; exit
	666	fi
	667
	668
[2380]	669	fi
	670	running_on_remote=false
	671	fi
	672
	673
	674
	675	# READ AND EVALUATE THE I/O-FILE LIST
	676	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	677
	678	# READ THE FILE CONNECTION FILE LINE BY LINE
	679	while read line
	680	do
	681
[2669]	682	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
[3555]	683	# HERE, TR IS USED INSTEAD OF SED TO GUARANTEE MAC COMPATIBILITY
	684	line=`echo "$line" \| tr -s " "`
[2380]	685
	686	# INTERPRET THE LINE
	687	if [[ "$(echo $line)" = "" ]]
	688	then
	689	# EMPTY LINE, NO ACTION
	690	continue
	691
	692	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	693	then
	694
	695	# LINE IS A COMMENT LINE
	696	true
	697
	698	else
	699
	700	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	701	# s2a: in/out - field
[2669]	702	# s2b: action - field (optional)
	703	s1=`echo "$line" \| cut -d" " -f1`
	704	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	705	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	706	then
[2669]	707	s2a=$s2
[2380]	708	s2b=""
	709	else
[2669]	710	s2a=`echo $s2 \| cut -d":" -f1`
	711	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	712	fi
[2669]	713	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	714	s4=`echo "$line" \| cut -d" " -s -f4`
	715	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	716	s5=`echo "$line" \| cut -d" " -s -f5`
	717	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	718
	719
	720	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	721	# INPUT- OR OUTPUT-LIST.
	722	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	723	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	724	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	725	# IS NOT CHECKED AND STORED.
[2610]	726	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	727	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	728	then
	729	found=false
	730	for actual in $activation_string_list
	731	do
	732	for formal in $s3
	733	do
	734	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	735	done
	736	done
	737	if [[ $found = true ]]
	738	then
	739	(( iin = iin + 1 ))
[2669]	740	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	741	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	742	if [[ "$s2a" = inopt ]]
	743	then
	744	optin_pre[$iin]=yes
	745	else
	746	optin_pre[$iin]=no
	747	fi
[2605]	748
	749	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	750	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	751	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	752	then
[2610]	753	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	754	fi
	755
[2610]	756	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	757	# THE WILDCARD FROM THE ENDING
	758	if [[ "${s5: -1}" = "*" ]]
	759	then
[2669]	760	if [[ "$s2b" = "di" ]]
[2610]	761	then
	762	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	763	printf "\n see file \"$fileconnection_file\", line"
	764	printf "\n$line"
	765	locat=iofiles_file; exit
	766	fi
	767	multin[$iin]=true
	768	string=${endin_pre[$iin]}
	769	endin_pre[$iin]="${string%?}"
	770	else
	771	multin[$iin]=false
	772	fi
[2380]	773	fi
[2669]	774	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	775	then
	776	found=false
	777	for actual in $activation_string_list
	778	do
	779	for formal in $s3
	780	do
[2670]	781	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	782	done
	783	done
	784	if [[ $found = true ]]
	785	then
	786	(( iout = iout + 1 ))
[2669]	787	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	788	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	789
[2669]	790	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	791	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	792	if [[ $formal = wildcard ]]
	793	then
	794	warnout_pre[$iout]=false
	795	else
	796	warnout_pre[$iout]=true
	797	fi
	798
[2610]	799	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	800	# THE WILDCARD FROM THE LOCAL FILENAME
	801	if [[ "${s1: -1}" = "*" ]]
	802	then
[2669]	803	if [[ "$s2b" = "di" ]]
[2610]	804	then
	805	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	806	printf "\n see file \"$fileconnection_file\", line"
	807	printf "\n$line"
	808	locat=iofiles_file; exit
	809	fi
	810	multout[$iout]=true
	811	string=${localout_pre[$iout]}
	812	localout_pre[$iout]="${string%?}"
	813	else
	814	multout[$iout]=false
	815	fi
[2380]	816	fi
[2669]	817	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	818	then
[2669]	819	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	820	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	821	locat=connect; exit
	822	fi
	823	IFS="$IFSALT"
	824	fi
	825
	826	done < $fileconnection_file
	827
	828
	829
[2501]	830	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	831	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	832	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	833	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	834	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	835	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	836
	837
	838
[2380]	839	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	840	if [[ $run_coupled_model = true ]]
	841	then
	842
	843	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	844	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	845
	846	if (( $cores_ocean + $cores_atmos != $cores ))
	847	then
	848
	849	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	850	printf "\n PEs (total) : $cores"
	851	printf "\n PEs (atmosphere): $cores_atmos"
	852	printf "\n PEs (ocean) : $cores_ocean"
	853	locat=coupling; exit
	854
	855	fi
	856
	857	fi
	858
	859
	860	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	861	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	862	# FOLDER
	863	if [[ $running_in_batch_mode = true ]]
	864	then
	865
[2506]	866	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	867	then
[2506]	868	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	869	printf "\n Please check the output of the palmrun-call"
	870	printf "\n that you did on your local host."
	871	locat=SOURCES_FOR_RUN; exit
	872	fi
	873
	874	else
	875
	876	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	877	# AUTOMATIC RESTART RUN
	878	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	879	if [[ $restart_run = false ]]
	880	then
	881
	882	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	883	# THE LOCAL HOST
	884	if [[ ! -d $source_path ]]
	885	then
	886	printf "\n\n +++ source path \"$source_path\" on local host"
	887	printf "\n \"$(hostname)\" does not exist"
	888	locat=source_path; exit
	889	fi
	890
[2990]	891	rm -rf ${base_directory}/${sources_for_run_catalog}
	892	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	893
	894	if [[ "$source_list" = LM ]]
	895	then
	896
	897	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	898	source_list=""
	899	cd $source_path
	900
	901
[2512]	902	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	903	if [[ ! -d ../.svn ]]
[2380]	904	then
	905	printf "\n\n +++ source directory"
	906	printf "\n \"$source_path\" "
	907	printf "\n is not under control of \"subversion\"."
[2512]	908	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	909	fi
	910
	911
	912	# LIST ALL MODIFIED SOURCE CODE FILES
	913	Filenames=""
[2404]	914	svn status > tmp_svnstatus
[2380]	915	while read line
	916	do
	917	firstc=`echo $line \| cut -c1`
	918	if [[ $firstc = M \|\| $firstc = "?" ]]
	919	then
	920	Name=`echo "$line" \| cut -c8-`
	921	extension=`echo $Name \| cut -d. -f2`
	922	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	923	then
	924	Filenames="$Filenames "$Name
	925	fi
	926	fi
[2404]	927	done < tmp_svnstatus
	928	rm -rf tmp_svnstatus
[2380]	929
	930
	931	# COPY FILES TO SOURCES_FOR_RUN_...
	932	for filename in $Filenames
	933	do
[2990]	934	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	935	source_list=$source_list"$filename "
	936	done
	937
	938	cd - > /dev/null
	939
	940
	941	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	942	elif [[ "$source_list" != "" ]]
	943	then
	944
	945	cd $source_path
	946
	947	for filename in $source_list
	948	do
	949
	950	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	951	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	952	then
	953	printf "\n +++ source code file: $filename"
	954	printf "\n must not contain (\"/\") "
	955	locat=source; exit
	956	fi
	957
	958	if [[ ! -f $filename ]]
	959	then
	960	printf "\n +++ source code file: $filename"
	961	printf "\n does not exist"
	962	locat=source; exit
	963	else
[2990]	964	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	965	fi
	966
	967	done
	968
	969	cd - > /dev/null
	970
	971	fi
	972
	973	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	974	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	975	if [[ ! -f $makefile ]]
	976	then
	977	printf "\n +++ file \"$makefile\" does not exist"
	978	locat=make; exit
	979	else
[2990]	980	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	981	fi
	982
	983
	984	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	985	if [[ "$user_source_path" != "" ]]
[2380]	986	then
	987
	988	# DOES THE DIRECTORY EXIST?
[2384]	989	if [[ ! -d $user_source_path ]]
[2380]	990	then
	991
	992	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	993	printf "\n \"$user_source_path\" "
[2380]	994	printf "\n does not exist or is not a directory."
	995	printf "\n No source code will be used from this directory!\n"
[2384]	996	user_source_path=""
[2380]	997	if [[ $silent == false ]]
	998	then
	999	sleep 2
	1000	fi
	1001
	1002	else
	1003
[2384]	1004	cd $user_source_path
[2380]	1005
	1006	Names=$(ls -1 *.f90 2>&1)
	1007	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1008	Names=$(ls -1 *.F90 2>&1)
	1009	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1010	Names=$(ls -1 *.F 2>&1)
	1011	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1012	Names=$(ls -1 *.f 2>&1)
	1013	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1014	Names=$(ls -1 *.c 2>&1)
	1015	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1016
	1017	cd - > /dev/null
[2990]	1018	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1019
	1020	# COPY MAKEFILE IF EXISTING
[2384]	1021	if [[ -f $user_source_path/Makefile ]]
[2380]	1022	then
	1023	printf "\n\n *** user Makefile from directory"
[2384]	1024	printf "\n \"$user_source_path\" is used \n"
[2380]	1025	if [[ $silent == false ]]
	1026	then
	1027	sleep 1
	1028	fi
[2384]	1029	cp $user_source_path/Makefile .
[2380]	1030	fi
	1031
	1032	for filename in $AddFilenames
	1033	do
	1034	if [[ -f $filename ]]
	1035	then
	1036	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1037	printf "\n source code directory \"$user_source_path\" "
[2380]	1038	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1039	printf "\n from directory \"$source_path\"."
	1040	locat=source; exit
	1041	fi
	1042
[2384]	1043	cp $user_source_path/$filename .
[2380]	1044	source_list="$source_list $filename"
	1045
	1046	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1047	if [[ $(grep -c $filename Makefile) = 0 ]]
	1048	then
	1049	printf "\n\n +++ user file \"$filename\" "
	1050	printf "\n is not listed in Makefile \n"
	1051	locat=source; exit
	1052	fi
	1053	done
	1054	cd - > /dev/null
	1055	fi
	1056	fi
	1057
	1058	# COPY CONFIGURATION FILES
[2990]	1059	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1060	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1061
	1062	# COPY SHELLSCRIPTS
[2990]	1063	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1064	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1065
	1066	fi
	1067
	1068	fi
	1069
[2605]	1070
[2380]	1071	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1072	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1073	if [[ "$global_revision" = "" ]]
	1074	then
	1075	global_revision=`svnversion $source_path 2>/dev/null`
	1076	global_revision="Rev: $global_revision"
	1077	fi
	1078
	1079
	1080	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1081	if [[ -n $cores ]]
	1082	then
	1083
	1084	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1085	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1086	if [[ $tasks_per_node = 0 ]]
[2380]	1087	then
[3025]	1088	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1089	then
	1090	printf "\n"
	1091	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1092	printf "\n set -T option or define tasks_per_node in the config file"
	1093	locat=tasks_per_node; (( iec = 0 )); exit
	1094	else
	1095	# DEFAULT FOR INTERACTIVE RUN
	1096	tasks_per_node=$cores
	1097	fi
[2380]	1098	fi
	1099
	1100	if (( cores < tasks_per_node ))
	1101	then
	1102	printf "\n"
	1103	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1104	printf "\n given values: -T $tasks_per_node -X $cores"
	1105	locat=tasks_per_node; (( iec = 0 )); exit
	1106	fi
	1107
	1108	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1109	(( mpi_tasks = cores / threads_per_task ))
	1110	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1111	(( ii = cores / tasks_per_node ))
	1112	(( remaining_cores = cores - ii * tasks_per_node ))
	1113	if (( remaining_cores > 0 ))
	1114	then
	1115	printf "\n"
	1116	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1117	printf "\n divisor of the total number of cores (option \"-X\")"
	1118	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1119	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1120	(( nodes = nodes + 1 ))
	1121	fi
	1122
	1123	fi
	1124
	1125
	1126	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1127	if [[ "$maximum_parallel_io_streams" = "" ]]
	1128	then
	1129	maximum_parallel_io_streams=$cores
	1130	fi
	1131
	1132
	1133	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1134	if [[ "$scp_port" != "" ]]
	1135	then
	1136	PORTOPT="-P $scp_port"
	1137	SSH_PORTOPT="-p $scp_port"
	1138	fi
	1139
	1140
	1141	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1142	# CONFIG-FILE
	1143	if [[ "$ssh_key" != "" ]]
	1144	then
	1145	ssh_key="-i $HOME/.ssh/$ssh_key"
	1146	fi
	1147
	1148
	1149	# SET QUEUE, IF NOT GIVEN
	1150	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1151	then
	1152
	1153	if [[ $queue = none && "$defaultqueue" = "" ]]
	1154	then
	1155	printf "\n"
	1156	printf "\n +++ no default queue given in configuration file and no queue"
	1157	printf "\n given with option -q"
[2789]	1158	locat=queue; exit
[2380]	1159	fi
	1160	if [[ $queue = none ]]
	1161	then
	1162	queue=$defaultqueue
	1163	fi
	1164
	1165	fi
	1166
	1167
	1168	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1169	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1170	(( i = 0 ))
[2610]	1171	(( nr_of_input_files = 0 ))
[2380]	1172	while (( i < iin ))
	1173	do
	1174	(( i = i + 1 ))
	1175
	1176	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1177	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1178	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1179	then
[2610]	1180	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1181	else
[3236]	1182	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1183	fi
	1184
[2610]	1185
[2380]	1186	# CHECK IF FILE EXISTS
	1187	if ! ls $filename* 1>/dev/null 2>&1
	1188	then
	1189
[2669]	1190	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1191	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1192	then
	1193	printf "\n\n +++ INPUT-file: "
[2610]	1194	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1195	then
	1196	printf "\n $filename"
	1197	else
[2610]	1198	printf "\n $filename.${extin_pre[$i]}"
[2380]	1199	fi
	1200	printf "\n does not exist\n"
	1201	locat=input; exit
	1202	else
[2610]	1203	(( nr_of_input_files = nr_of_input_files + 1 ))
	1204	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1205	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1206	actionin[$nr_of_input_files]="unavailable"
[2610]	1207	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1208	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1209	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1210	fi
[2605]	1211
[2380]	1212	else
	1213
[3236]	1214	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1215	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1216	# ENDINGS
[2610]	1217	if [[ "${multin[$i]}" = true ]]
	1218	then
	1219	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1220	ls -1 -d ${filename} > filelist 2>/dev/null
	1221	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1222	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1223
[2610]	1224	endings=""
	1225	while read line
	1226	do
	1227	# filename without path (i.e. after the last "/")
	1228	basefilename=$(basename ${line})
[2380]	1229
[2610]	1230	# check if there is an extension and remove it
	1231	ext=${basefilename##*.}
	1232	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1233	then
	1234	basefilename=${basefilename%.*}
	1235	fi
[2380]	1236
[2610]	1237	# check for an existing cycle number and remove it
	1238	cycle=${basefilename##*.}
	1239	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1240	then
	1241	basefilename=${basefilename%.*}
	1242	fi
[2600]	1243
[3236]	1244	# remove the run_identifier from the beginning
	1245	length_run_identifier=${#run_identifier}
	1246	ending=${basefilename:${length_run_identifier}}
[2610]	1247
	1248	# remove the ending given in the .iofiles from the beginning
	1249	endingstring="${endin_pre[$i]}"
	1250	length_ending=${#endingstring}
	1251	ending=${ending:${length_ending}}
	1252
	1253	if [[ "$ending" = "" ]]
[2600]	1254	then
[2610]	1255	# standard ending as given in the .iofiles
	1256	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1257	then
	1258	endings="$endings DEFAULT"
	1259	fi
[2600]	1260	else
[2610]	1261	# ending must start with "_", otherwise its a different file
	1262	if [[ "${ending:0:1}" = "_" ]]
	1263	then
	1264	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1265	then
	1266	endings="$endings $ending"
	1267	fi
	1268	fi
[2600]	1269	fi
[2610]	1270
	1271	done <filelist
[2380]	1272
[2610]	1273	rm filelist
[2380]	1274
[2600]	1275	else
[2610]	1276
	1277	# SINGLE NAME
	1278	endings=DEFAULT
	1279
[2600]	1280	fi
	1281
[2610]	1282	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1283	for ending in $endings
	1284	do
	1285
	1286	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1287	if [[ $ending = DEFAULT ]]
[2380]	1288	then
[2610]	1289	ending=""
	1290	fi
	1291
	1292	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1293	(( nr_of_input_files = nr_of_input_files + 1 ))
	1294	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1295	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1296	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1297	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1298	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1299	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1300
	1301
	1302	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1303	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1304	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1305	then
	1306	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1307	else
[3236]	1308	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1309	fi
[2610]	1310
	1311	# DETERMINE THE FILE'S CYCLE NUMBER
	1312	(( maxcycle = 0 ))
	1313	ls -1 -d $filename > filelist 2>/dev/null
	1314	ls -1 -d $filename.* >> filelist 2>/dev/null
	1315	while read line
	1316	do
	1317	# filename without path (i.e. after the last "/")
	1318	basefilename=$(basename ${line})
	1319
	1320	# check if there is an extension
	1321	extension=${basefilename##*.}
	1322	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1323	then
	1324	basefilename=${basefilename%.*}
	1325	fi
	1326
	1327	# check for an existing cycle number
	1328	cycle=${basefilename##*.}
	1329	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1330	then
[2669]	1331	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1332	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1333	(( icycle = $((10#$cycle)) ))
[2610]	1334	else
	1335	(( icycle = 0 ))
	1336	fi
	1337
	1338	if (( icycle > maxcycle ))
	1339	then
	1340	(( maxcycle = icycle ))
	1341
	1342	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1343	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1344	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1345	then
	1346	leading_zero=true
	1347	else
	1348	leading_zero=false
	1349	fi
	1350	fi
	1351
	1352	done <filelist
	1353	rm filelist
	1354
	1355	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1356	if [[ $leading_zero = true ]]
[2380]	1357	then
[2610]	1358	cyclestring=`printf "%03d" $maxcycle`
	1359	else
	1360	cyclestring=$maxcycle
[2380]	1361	fi
[2610]	1362
	1363	# APPEND CYCLE NUMBER TO FILENAME
	1364	if (( maxcycle > 0 ))
[2380]	1365	then
[2610]	1366	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1367	then
	1368	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1369	else
	1370	filename=${filename}.$cyclestring
	1371	fi
[2380]	1372	else
[2610]	1373	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1374	then
	1375	filename=${filename}.${extin[$nr_of_input_files]}
	1376	fi
[2380]	1377	fi
[2610]	1378
	1379	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1380	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1381	absnamein[$nr_of_input_files]=$filename
	1382	if (( maxcycle > 0 ))
[2380]	1383	then
[2610]	1384	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1385	then
	1386	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1387	else
[3236]	1388	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1389	fi
[2380]	1390	else
[2610]	1391	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1392	then
	1393	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1394	else
[3236]	1395	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1396	fi
[2380]	1397	fi
	1398
[2610]	1399	done
	1400
[2380]	1401	fi
[2610]	1402
[2380]	1403	done
	1404
[2610]	1405
[2380]	1406	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1407	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1408	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1409	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1410	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1411	# REMOTE HOST)
	1412	(( i = 0 ))
	1413	while (( i < iout ))
	1414	do
	1415	(( i = i + 1 ))
[2610]	1416	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1417	then
[2610]	1418	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1419	then
[2610]	1420	actionout_pre[$i]=""
	1421	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1422	then
[2610]	1423	actionout_pre[$i]=pe
	1424	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1425	then
[2610]	1426	actionout_pre[$i]=a
[2380]	1427	fi
	1428	(( maxcycle = 0 ))
[3236]	1429	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1430	eval catalogname=${pathout_pre[$i]}
[2380]	1431	if ! ls $filename* 1>/dev/null 2>&1
	1432	then
	1433
	1434	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1435	if cat /dev/null > $filename
	1436	then
	1437	rm $filename
	1438	else
	1439
	1440	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1441	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1442	if [[ ! -d $catalogname ]]
	1443	then
	1444	if mkdir -p $catalogname
	1445	then
	1446	printf "\n\n *** directory:"
	1447	printf "\n $catalogname"
	1448	printf "\n was created\n"
	1449	else
	1450	printf "\n\n +++ OUTPUT-file:"
	1451	printf "\n $filename"
	1452	printf "\n cannot be created, because directory does not exist"
	1453	printf "\n and cannot be created either"
	1454	printf "\n"
	1455	locat=output ; exit
	1456	fi 2>/dev/null
	1457	else
	1458	printf "\n\n +++ OUTPUT-file:"
	1459	printf "\n $filename"
	1460	printf "\n cannot be created, although directory exists"
	1461	printf "\n"
	1462	locat=output ; exit
	1463	fi
	1464	fi 2>/dev/null
	1465
	1466	fi
	1467
	1468	fi
	1469	done
	1470
	1471
	1472	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1473	if [[ $running_in_batch_mode = false ]]
	1474	then
[3236]	1475	run_id_number=$RANDOM
	1476	run_id=${run_identifier}.$run_id_number
[2380]	1477
[3236]	1478	tempdir=$fast_io_catalog/$run_id
[3346]	1479
	1480	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1481	export job_id=$run_id
	1482
[2380]	1483	fi
	1484
	1485
	1486	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1487	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1488	then
	1489
	1490	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1491	if [[ $ibd = 0 ]]
	1492	then
	1493	printf "\n"
	1494	printf "\n +++ no batch directives found in configuration file"
	1495	locat=config_file_batch_directives; (( iec = 0 )); exit
	1496	fi
	1497
	1498	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1499	done=false
[2384]	1500	cputime=$cpumax
[2380]	1501	while [[ $done = false ]]
	1502	do
[2384]	1503	if (( cputime == 0 ))
[2380]	1504	then
	1505	printf "\n +++ cpu-time is undefined"
	1506	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1507	printf "\n >>> "
[2384]	1508	read cputime 1>/dev/null 2>&1
[2380]	1509	else
	1510	done=true
	1511	fi
	1512	done
[2420]	1513	cpumax=$cputime
[2380]	1514
	1515	# CHECK THE MEMORY DEMAND
	1516	done=false
	1517	while [[ $done = false ]]
	1518	do
	1519	if (( memory == 0 ))
	1520	then
	1521	printf "\n +++ memory demand is undefined"
	1522	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1523	printf "\n >>> "
	1524	read memory 1>/dev/null 2>&1
	1525	else
	1526	done=true
	1527	fi
	1528	done
	1529
	1530	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1531	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1532	then
	1533	while [[ -z $remote_username ]]
	1534	do
[2420]	1535	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1536	printf "\n >>> Please type username:"
	1537	printf "\n >>> "
	1538	read remote_username
	1539	done
	1540	fi
	1541
	1542	else
	1543
[2420]	1544	if [[ $running_in_batch_mode = false ]]
	1545	then
	1546	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1547	cpumax=$cputime
	1548	else
	1549	cputime=$cpumax
	1550	fi
[2380]	1551
	1552	fi
	1553
	1554
	1555	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1556	(( cpu_hours = cputime / 3600 ))
	1557	(( resttime = cputime - cpu_hours * 3600 ))
	1558	(( cpu_minutes = resttime / 60 ))
	1559	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1560	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1561
	1562
	1563	# OUTPUT OF THE PALMRUN-HEADER
	1564	calltime=$(date)
	1565	printf "\n"
	1566	printf "#------------------------------------------------------------------------# \n"
	1567	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1568	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1569	printf "\| \| \n"
	1570	column1="called on:"; column2=$(hostname)
	1571	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1572	if [[ $create_remote_batch_job = true ]]
	1573	then
[3236]	1574	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1575	else
	1576	if [[ $running_on_remote = true ]]
	1577	then
[3236]	1578	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1579	else
[3236]	1580	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1581	fi
	1582	fi
	1583	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1584
	1585	column1="running in:"
	1586	if [[ $running_in_batch_mode = true ]]
	1587	then
	1588	column2="batch job mode"
	1589	else
	1590	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1591	then
	1592	column2="job creation mode"
	1593	else
	1594	column2="interactive run mode"
	1595	fi
	1596	fi
	1597	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1598
[2479]	1599	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1600	then
[2480]	1601	if [[ "$project_account" != "" ]]
[2479]	1602	then
	1603	column1="project account number:"
	1604	column2="$project_account"
	1605	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1606	fi
	1607	fi
	1608
[2380]	1609	if [[ -n $cores ]]
	1610	then
	1611	if [[ $run_coupled_model = false ]]
	1612	then
	1613	column1="number of cores:"; column2=$cores
	1614	else
	1615	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1616	fi
	1617	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1618	fi
	1619	if [[ -n $tasks_per_node ]]
	1620	then
	1621	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1622	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1623	if (( remaining_cores > 0 ))
	1624	then
	1625	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1626	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1627	fi
	1628	fi
	1629	if [[ $maximum_parallel_io_streams != $cores ]]
	1630	then
	1631	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1632	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1633	fi
	1634	if [[ $use_openmp = true ]]
	1635	then
	1636	column1="threads per task:"; column2="$threads_per_task"
	1637	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1638	fi
[2384]	1639	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1640	then
[2506]	1641	column1="memory demand / PE":; column2="$memory MB"
	1642	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1643	column1="job cpu time (h:m:s):"; column2="$timestring"
	1644	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1645	fi
[2380]	1646	printf "\| \| \n"
	1647	if [[ "$source_list" != "" ]]
	1648	then
	1649	if [[ "$make_options" != "" ]]
	1650	then
	1651	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1652	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1653	line=$(echo "$make_options" \| cut -c46-)
	1654	while [[ "$line" != "" ]]
	1655	do
	1656	column1=""
	1657	column2=$(echo "$line" \| cut -c-45)
	1658	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1659	line=$(echo "$line" \| cut -c46-)
	1660	done
	1661	fi
	1662	fi
	1663
	1664	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1665	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1666	line=$(echo "$cpp_options" \| cut -c46-)
	1667	while [[ "$line" != "" ]]
	1668	do
	1669	column1=""
	1670	column2=$(echo "$line" \| cut -c-45)
	1671	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1672	line=$(echo "$line" \| cut -c46-)
	1673	done
	1674
	1675	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1676	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1677	line=$(echo "$compiler_options" \| cut -c46-)
	1678	while [[ "$line" != "" ]]
	1679	do
	1680	column1=""
	1681	column2=$(echo "$line" \| cut -c-45)
	1682	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1683	line=$(echo "$line" \| cut -c46-)
	1684	done
	1685
[2388]	1686	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1687	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1688	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1689	while [[ "$line" != "" ]]
	1690	do
	1691	column1=""
	1692	column2=$(echo "$line" \| cut -c-45)
	1693	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1694	line=$(echo "$line" \| cut -c46-)
	1695	done
	1696
	1697	if [[ "$login_init_cmd" != "" ]]
	1698	then
	1699	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1700	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1701	line=$(echo "$login_init_cmd" \| cut -c46-)
	1702	while [[ "$line" != "" ]]
	1703	do
	1704	column1=""
	1705	column2=$(echo "$line" \| cut -c-45)
	1706	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1707	line=$(echo "$line" \| cut -c46-)
	1708	done
	1709	fi
	1710
	1711	if [[ "$module_commands" != "" ]]
	1712	then
	1713	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1714	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1715	line=$(echo "$module_commands" \| cut -c46-)
	1716	while [[ "$line" != "" ]]
	1717	do
	1718	column1=""
	1719	column2=$(echo "$line" \| cut -c-45)
	1720	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1721	line=$(echo "$line" \| cut -c46-)
	1722	done
	1723	fi
	1724	printf "\| \| \n"
[3236]	1725	column1="run identifier:"; column2=$run_identifier
[2380]	1726	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1727	column1="activation string list:"; column2=$(echo $activation_string_list)
	1728	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1729
	1730	if [[ "$ocean_file_appendix" = true ]]
	1731	then
	1732	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1733	fi
	1734
	1735	if [[ "$source_list" != "" ]]
	1736	then
	1737	printf "\| \| \n"
	1738	printf "\| Files to be compiled: \| \n"
	1739	line=$source_list
	1740	while [[ "$line" != "" ]]
	1741	do
	1742	linestart=$(echo $line \| cut -c-70)
	1743	printf "\| %-70s \| \n" "$linestart"
	1744	line=$(echo "$line" \| cut -c71-)
	1745	done
	1746	fi
	1747	printf "#------------------------------------------------------------------------#"
	1748
	1749
	1750
	1751	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1752	if [[ $do_trace = true ]]
	1753	then
	1754	(( i = 0 ))
[2610]	1755	while (( i < nr_of_input_files ))
[2380]	1756	do
	1757	(( i = i + 1 ))
	1758	if (( i == 1 ))
	1759	then
	1760	printf "\n\n >>> INPUT-file assignments:\n"
	1761	fi
	1762	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1763	done
	1764	(( i = 0 ))
	1765	while (( i < iout ))
	1766	do
	1767	(( i = i + 1 ))
	1768	if (( i == 1 ))
	1769	then
	1770	printf "\n\n >>> OUTPUT-file assignments:\n"
	1771	fi
	1772	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1773	done
	1774	(( i = 0 ))
	1775	while (( i < iic ))
	1776	do
	1777	(( i = i + 1 ))
	1778	if (( i == 1 ))
	1779	then
	1780	printf "\n\n >>> INPUT-commands:\n"
	1781	fi
	1782	printf "\n ${in_command[$i]}"
	1783	done
	1784	(( i = 0 ))
	1785	while (( i < ioc ))
	1786	do
	1787	(( i = i + 1 ))
	1788	if (( i == 1 ))
	1789	then
	1790	printf "\n\n >>> OUTPUT-commands:\n"
	1791	fi
	1792	printf "\n ${out_command[$i]}"
	1793	done
	1794	fi
	1795
	1796	# QUERY FOR CONTINUE
	1797	if [[ $silent = false && $running_in_batch_mode = false ]]
	1798	then
	1799	antwort=dummy
	1800	printf "\n\n"
	1801	printf " >>> everything o.k. (y/n) ? "
	1802	while read antwort
	1803	do
	1804	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1805	then
	1806	printf " >>> everything o.k. (y/n) ? "
	1807	else
	1808	break
	1809	fi
	1810	done
	1811	if [[ $antwort = n \|\| $antwort = N ]]
	1812	then
	1813	locat=user_abort; (( iec = 0 )); exit
	1814	fi
	1815	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1816	then
[2566]	1817	printf "\n *** batch-job will be created and submitted"
[2380]	1818	else
[2566]	1819	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1820	fi
	1821	fi
	1822
	1823
	1824
	1825	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1826	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1827	then
	1828
	1829	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1830	then
[2566]	1831	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1832	else
[2566]	1833	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1834	fi
	1835
[2422]	1836	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1837	# IT SHALL BE CREATED
	1838	ask_for_make_depository=false
	1839	if [[ $create_remote_batch_job = true ]]
	1840	then
	1841
	1842	line=`grep %base_directory $config_file`
[3236]	1843	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1844	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1845
[3236]	1846	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1847	then
	1848	printf "\n\n +++ make depository \"${make_depository}\""
	1849	printf "\n on remote host not found!"
	1850	ask_for_make_depository=true
	1851	fi
[3236]	1852	rm ${configuration_identifier}_last_make_protokoll
[2422]	1853
	1854	else
	1855
	1856	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1857	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1858	if [[ ! -d ${make_depository} ]]
	1859	then
	1860	printf "\n\n +++ make depository \"${make_depository}\""
	1861	printf "\n on local host not found!"
	1862	ask_for_make_depository=true
	1863	fi
	1864
	1865	fi
	1866
	1867	if [[ $ask_for_make_depository = true ]]
	1868	then
	1869
	1870	antwort=dummy
	1871	printf "\n\n"
	1872	printf " >>> Create a new one (y/n) ? "
	1873	while read antwort
	1874	do
	1875	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1876	then
	1877	printf " >>> Create a new one (y/n) ? "
	1878	else
	1879	break
	1880	fi
	1881	done
	1882	if [[ $antwort = n \|\| $antwort = N ]]
	1883	then
	1884	locat=user_abort; (( iec = 0 )); exit
	1885	fi
	1886
[2566]	1887	if [[ $do_trace = true ]]
	1888	then
[3455]	1889	palmbuild -c $configuration_identifier
[2566]	1890	else
[3455]	1891	palmbuild -v -c $configuration_identifier
[2566]	1892	fi
[2422]	1893
[3312]	1894	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1895	then
	1896
	1897	# ABORT IN CASE OF COMPILATION PROBLEMS
	1898	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1899	locat=make_depository
	1900	exit
	1901	else
	1902	echo " *** now continue with creating executable and other sources"
	1903	fi
	1904
	1905	fi
	1906
[2566]	1907	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1908	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1909
[3312]	1910	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1911	then
	1912
	1913	# ABORT IN CASE OF COMPILATION PROBLEMS
	1914	printf "\n +++ error while creating executable and/or other sources"
	1915	locat=execution
[2990]	1916	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1917	exit
	1918
	1919	else
	1920
[2566]	1921	printf " *** executable and other sources created\n"
[2990]	1922	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1923
	1924	fi
	1925
	1926	fi
	1927
	1928
[2669]	1929	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1930	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1931	if [[ $create_remote_batch_job = true ]]
	1932	then
	1933	(( i = 0 ))
[2610]	1934	while (( i < nr_of_input_files ))
[2605]	1935	do
	1936	(( i = i + 1 ))
[2669]	1937	if [[ "${actionin[$i]}" = tr ]]
[2605]	1938	then
	1939	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1940	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1941	fi
	1942	done
	1943	if (( i > 0 ))
	1944	then
[3025]	1945	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1946	fi
	1947	fi
	1948
	1949
[2380]	1950	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1951	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1952	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1953	then
	1954
	1955	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1956	if [[ $running_in_batch_mode = false ]]
	1957	then
	1958	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1959	# FOLDER
[2566]	1960	mkdir -p $tempdir
	1961	chmod go+rx $tempdir
	1962	cd $tempdir
	1963	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1964	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1965
	1966	else
	1967
	1968	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1969	printf "\n *** running in temporary directory: $tempdir"
[2380]	1970
	1971	fi
	1972
	1973
	1974	# PROVIDE THE INPUT FILES
	1975	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1976	optional_files_missing=false
[2380]	1977	(( i = 0 ))
[2610]	1978	while (( i < nr_of_input_files ))
[2380]	1979	do
	1980	(( i = i + 1 ))
	1981	if (( i == 1 ))
	1982	then
	1983	printf "\n\n *** providing INPUT-files:\n$dashes"
	1984	fi
	1985
	1986
	1987	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1988	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1989	then
[2669]	1990	optional_files_missing=true
[2380]	1991	continue
	1992	fi
	1993
	1994	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1995	files_for_cores=false; filetype=file
	1996	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1997	then
	1998	files_for_cores=true; filetype=files
	1999	actionin[$i]=""
	2000	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	2001	then
	2002	actionin[$i]=""
	2003	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	2004	then
	2005	files_for_cores=true; filetype=files
	2006	actionin[$i]="ln"
	2007	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2008	then
	2009	actionin[$i]="ln"
	2010	fi
	2011
	2012	if [[ $files_for_cores = true ]]
	2013	then
	2014	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2015	else
	2016	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2017	fi
	2018
	2019	# INPUT-FILES TO BE LINKED
	2020	if [[ "${actionin[$i]}" = ln ]]
	2021	then
	2022
	2023	printf "\n $filetype will be linked"
	2024	if [[ $files_for_cores = false ]]
	2025	then
	2026	if [[ -f "${absnamein[$i]}" ]]
	2027	then
	2028	ln ${absnamein[$i]} ${localin[$i]}
	2029	got_tmp[$i]=true
	2030	fi
	2031	else
	2032	if [[ -d "${absnamein[$i]}" ]]
	2033	then
[2396]	2034	mkdir -p ${localin[$i]}
[2380]	2035	cd ${absnamein[$i]}
	2036	for file in $(ls *)
	2037	do
[2566]	2038	ln $file $tempdir/${localin[$i]}
[2380]	2039	done >\|/dev/null 2>&1
[2566]	2040	cd $tempdir
[2380]	2041	fi
	2042
	2043	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2044	if [[ ! -f "${localin[$i]}/_000000" ]]
	2045	then
	2046	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2047	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2048	fi
	2049
	2050	got_tmp[$i]=true
	2051	fi
	2052	fi
	2053
	2054	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2055	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2056	then
	2057
	2058	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2059	then
	2060
	2061	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2062	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2063	printf "\n file will be provided for $cores processors"
[2396]	2064	mkdir -p ${localin[$i]}
[2380]	2065	ival=$cores
	2066	(( ii = 0 ))
	2067	while (( ii <= ival-1 ))
	2068	do
	2069	if (( ii < 10 ))
	2070	then
	2071	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2072	elif (( ii < 100 ))
	2073	then
	2074	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2075	elif (( ii < 1000 ))
	2076	then
	2077	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2078	else
	2079	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2080	fi
	2081	(( ii = ii + 1 ))
	2082	done
	2083
	2084	else
	2085
	2086	if [[ $files_for_cores = true ]]
	2087	then
	2088
	2089	# PROVIDE FILES FOR EACH CORE
	2090	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2091	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2092	printf "\n providing $cores files for the respective cores"
[2396]	2093	mkdir -p ${localin[$i]}
[2380]	2094	if [[ $link_local_input = true ]]
	2095	then
	2096	printf " files will be linked\n"
	2097	cd ${absnamein[$i]}
	2098	for file in $(ls *)
	2099	do
	2100	ln -f $file ${localin[$i]}
	2101	done
[2566]	2102	cd $tempdir
[2380]	2103	fi
	2104
	2105	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2106	if [[ ! -f "${localin[$i]}/_000000" ]]
	2107	then
	2108	if [[ $link_local_input = true ]]
	2109	then
	2110	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2111	fi
	2112	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2113	fi
	2114
	2115	else
	2116
	2117	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2118	if [[ $link_local_input = true ]]
	2119	then
	2120	printf " file will be linked\n"
	2121	ln -f ${absnamein[$i]} ${localin[$i]}
	2122	fi
[2605]	2123	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2124	if [[ ! -f "${localin[$i]}" ]]
	2125	then
	2126	if [[ $link_local_input = true ]]
	2127	then
	2128	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2129	fi
[2669]	2130	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2131	then
	2132	mv ${absnamein[$i]} ${localin[$i]}
	2133	else
	2134	cp ${absnamein[$i]} ${localin[$i]}
	2135	fi
[2380]	2136	fi
	2137	fi
	2138	fi
	2139	fi
	2140
	2141	done
	2142	if (( i != 0 ))
	2143	then
[2669]	2144	if [[ $optional_files_missing = true ]]
	2145	then
	2146	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2147	fi
[2380]	2148	printf "\n$dashes\n *** all INPUT-files provided \n"
	2149	fi
	2150
	2151
	2152	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2153	(( i = 0 ))
	2154	while (( i < iic ))
	2155	do
	2156	(( i = i + 1 ))
	2157	if (( i == 1 ))
	2158	then
	2159	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2160	fi
	2161	printf "\n >>> ${in_command[$i]}"
	2162	eval ${in_command[$i]}
	2163	if (( i == iic ))
	2164	then
	2165	printf "\n$dashes\n"
	2166	fi
	2167	done
	2168
	2169
[3313]	2170	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2171	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2172	then
	2173	progress_bar_disabled=true
	2174	else
	2175	progress_bar_disabled=false
	2176	fi
	2177
	2178
[2380]	2179	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2180	# (FILE ENVPAR WILL BE READ BY PALM)
	2181	cat > ENVPAR << EOF
[3236]	2182	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2183	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2184	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2185	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2186	maximum_cpu_time_allowed = ${cpumax}.,
	2187	revision = '$global_revision',
[3313]	2188	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2189
	2190	EOF
	2191
	2192
	2193	# STARTING THE EXECUTABLE
	2194	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2195	PATH=$PATH:$tempdir
[2380]	2196
	2197
	2198	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2199	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2200	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2201	eval line=\"$line\"
	2202	execute_command="$line"
	2203
	2204
	2205	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2206	if [[ "$execute_command_for_combine" = "" ]]
	2207	then
	2208	eval line2=\"$line2\"
	2209	execute_command_for_combine="$line2"
	2210	fi
	2211
[2380]	2212
	2213
	2214	# PROVIDE A HOSTFILE, IF REQUIRED
	2215	if [[ "$hostfile" != "" ]]
	2216	then
	2217
	2218	if [[ $hostfile = auto ]]
	2219	then
	2220	# CREATE A NEW HOSTFILE
	2221	(( ii = 1 ))
	2222	while (( ii <= cores / threads_per_task ))
	2223	do
	2224	echo $(hostname) >> hostfile
	2225	(( ii = ii + 1 ))
	2226	done
	2227	if (( cores / threads_per_task == 0 ))
	2228	then
	2229	echo $(hostname) >> hostfile
	2230	fi
	2231
	2232	else
	2233	cp $hostfile hostfile
	2234	fi
	2235	eval line=\"`head -n $ii hostfile`\"
	2236	printf "\n *** running on: $line"
	2237	fi
	2238
	2239
	2240
	2241	# SET THE NUMBER OF OPENMP-THREADS
	2242	if [[ $use_openmp = true ]]
	2243	then
	2244	export OMP_NUM_THREADS=$threads_per_task
	2245	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2246	else
	2247	export OMP_NUM_THREADS=1
	2248	fi
	2249
	2250
[2610]	2251	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2252	if [[ $run_coupled_model = false ]]
	2253	then
	2254	if [[ "$ocean_file_appendix" = true ]]
	2255	then
	2256	echo "precursor_ocean" > coupling_steering
	2257	else
	2258	echo "precursor_atmos" > coupling_steering
	2259	fi
	2260	else
	2261	(( iia = $cores_atmos / $threads_per_task ))
	2262	(( iio = $cores_ocean / $threads_per_task ))
	2263	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2264	printf "\n\n"
	2265	echo "coupled_run $iia $iio" > coupling_steering
	2266	fi
	2267
	2268	printf "\n *** execute command:"
	2269	printf "\n \"$execute_command\" \n\n"
	2270
	2271
[3393]	2272	if [[ $progress_bar_disabled = true ]]
[2380]	2273	then
[3402]	2274	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2275	exit_code=${PIPESTATUS[0]}
	2276	else
	2277	$execute_command < coupling_steering &> >(tee STDOUT)
	2278	exit_code=${PIPESTATUS[0]}
	2279	fi
[2380]	2280
[3393]	2281	if [[ ${exit_code} != 0 ]]
	2282	then
	2283
[2380]	2284	# ABORT IN CASE OF RUNTIME ERRORS
	2285	printf "\n +++ runtime error occured"
	2286	locat=execution
	2287	exit
	2288
	2289	else
	2290
	2291	printf "\n$dashes\n *** execution finished \n"
	2292
	2293	fi
	2294
	2295
	2296	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2297	# BY EACH CORE INTO ONE FILE
	2298	if [[ ! -f combine_plot_fields.x ]]
	2299	then
	2300
	2301	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2302	printf "\n 2d- and/or 3d-data may be incomplete!"
	2303	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2304
	2305	elif [[ "$combine_plot_fields" == true ]]
	2306	then
	2307
	2308	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2309	$execute_command_for_combine
	2310
	2311	else
	2312
	2313	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2314	# DATA OUTPUT
[2380]	2315	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2316	fi
	2317
	2318
	2319
	2320	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2321	(( i = 0 ))
	2322	while (( i < ioc ))
	2323	do
	2324	(( i = i + 1 ))
	2325	if (( i == 1 ))
	2326	then
	2327	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2328	fi
[2799]	2329
	2330	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2331	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2332
[2380]	2333	printf "\n >>> ${out_command[$i]}"
	2334	eval ${out_command[$i]}
	2335	if (( i == ioc ))
	2336	then
	2337	printf "\n$dashes\n"
	2338	fi
	2339	done
	2340
	2341
[2610]	2342	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2343	# WILDCARDS
[2380]	2344	(( i = 0 ))
[2610]	2345	(( nr_of_output_files = 0 ))
	2346
[2380]	2347	while (( i < iout ))
	2348	do
[2610]	2349
[2380]	2350	(( i = i + 1 ))
[2610]	2351
	2352	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2353	# CREATE A LIST FOR THE DETECTED ENDINGS
	2354	if [[ "${multout[$i]}" = true ]]
	2355	then
	2356	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2357	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2358	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2359
	2360	endings="DEFAULT"
	2361	while read line
	2362	do
	2363	# remove the local name from the beginning
	2364	localnamestring="${localout_pre[$i]}"
	2365	length_localname=${#localnamestring}
	2366	ending=${line:${length_localname}}
	2367
	2368	if [[ "$ending" != "" ]]
	2369	then
	2370	endings="$endings $ending"
	2371	fi
	2372
	2373	done <filelist
	2374
	2375	rm filelist
	2376
	2377	else
	2378
	2379	# SINGLE NAME
	2380	endings=DEFAULT
	2381
	2382	fi
	2383
	2384	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2385	for ending in $endings
	2386	do
	2387
	2388	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2389	if [[ $ending = DEFAULT ]]
	2390	then
	2391	ending=""
	2392	fi
	2393
	2394	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2395	(( nr_of_output_files = nr_of_output_files + 1 ))
	2396	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2397	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2398	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2399	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2400	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2401	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2402	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2403
	2404	done
	2405
	2406	done
	2407
	2408
	2409
	2410
	2411	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2412	(( i = 0 ))
	2413	while (( i < nr_of_output_files ))
	2414	do
	2415	(( i = i + 1 ))
[2380]	2416	if (( i == 1 ))
	2417	then
	2418	printf "\n\n *** saving OUTPUT-files:"
	2419
	2420	# GET RUN NUMBER ASSIGNED BY PALM
	2421	if [[ -f RUN_NUMBER ]]
	2422	then
	2423	read run_number < RUN_NUMBER
	2424	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2425	usecycle_option="-U $run_number"
	2426	else
	2427	run_number=0
	2428	usecycle_option=""
	2429	fi
	2430	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2431	then
[2404]	2432	printf "\n *** in case of SCP transfers to local host"
	2433	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2434	fi
	2435	printf "\n$dashes"
	2436	fi
	2437
	2438	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2439	then
	2440
[3236]	2441	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2442
	2443	# DETERMINE THE CYCLE NUMBER
	2444	ls -1 -d $filename > filelist 2>/dev/null
	2445	ls -1 -d $filename.* >> filelist 2>/dev/null
	2446	while read line
	2447	do
	2448
	2449	# filename without path (i.e. after the last "/")
	2450	basefilename=$(basename ${line})
	2451
	2452	# check if there is an extension
	2453	extension=${basefilename##*.}
	2454	if [[ "$extension" = "${extout[$i]}" ]]
	2455	then
	2456	basefilename=${basefilename%.*}
	2457	fi
	2458
	2459	# check for an existing cycle number
	2460	cycle=${basefilename##*.}
	2461	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2462	then
[2669]	2463	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2464	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2465	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2466	else
	2467	(( icycle = 1 ))
	2468	fi
	2469
	2470	if (( icycle > maxcycle ))
	2471	then
	2472	(( maxcycle = icycle ))
	2473	fi
	2474
	2475	done <filelist
	2476	rm filelist
	2477
	2478
	2479	# SET THE CYCLE NUMBER
	2480	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2481	if [[ "${actionout[$i]}" = a ]]
	2482	then
	2483	(( maxcycle = maxcycle - 1 ))
	2484	fi
	2485
	2486	(( cycnum[$i] = maxcycle ))
	2487	pathout[$i]=$filename
	2488
	2489
	2490	# ADD CYCLE NUMBER TO FILENAME
	2491	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2492	if [[ "${actionout[$i]}" != "a" ]]
	2493	then
	2494	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2495	# WITH AN EXISTING CYCLE NUMBER
	2496	if (( run_number >= cycnum[$i] ))
	2497	then
	2498	(( cycnum[$i] = run_number ))
	2499	else
	2500	if (( run_number > 0 ))
	2501	then
	2502	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2503	fi
	2504	fi
	2505	fi
	2506	if (( cycnum[$i] > 0 ))
	2507	then
[2600]	2508	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2509	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2510	fi
	2511	fi
	2512
	2513	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2514	files_for_cores=false; filetype=file
	2515	link_local_output=false
	2516	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2517	then
	2518	files_for_cores=true; filetype=directory
	2519	actionout[$i]=""
	2520	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2521	then
	2522	actionout[$i]=""
	2523	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2524	then
	2525	files_for_cores=true; filetype=directory
	2526	link_local_output=true
	2527	actionout[$i]=""
	2528	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2529	then
	2530	link_local_output
	2531	actionout[$i]=""
	2532	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2533	then
	2534	files_for_cores=true; filetype=directory
	2535	actionout[$i]="tr"
	2536	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2537	then
	2538	actionout[$i]="tr"
	2539	fi
	2540
	2541	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2542	then
[2669]	2543	if [[ ${warnout[$i]} = true ]]
	2544	then
	2545	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2546	fi
[2380]	2547	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2548	then
[2669]	2549	if [[ ${warnout[$i]} = true ]]
	2550	then
	2551	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2552	fi
[2380]	2553	else
	2554
	2555
	2556	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2557	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2558	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2559	then
	2560	if [[ $running_on_remote = true ]]
	2561	then
	2562
	2563	# SET OPTIONS FOR TRANSFER
	2564	if [[ "${actionout[$i]}" = tr ]]
	2565	then
	2566	if [[ $files_for_cores = false ]]
	2567	then
	2568	catalog_option=""
	2569	catalog_string=""
	2570	else
	2571	catalog_option="-c"
	2572	catalog_string="/"
	2573	fi
	2574	append_option=""
	2575	append_string=""
	2576	else
	2577	append_option="-A"
	2578	append_string="append"
	2579	fi
	2580
	2581	transfer_failed=false
	2582	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2583	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2584
	2585	# TRANSFER VIA SCP
	2586	if [[ "$remote_loginnode" != "" ]]
	2587	then
[3534]	2588	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]	2589	else
[3236]	2590	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]	2591	fi
[3312]	2592	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2593
	2594
	2595	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2596	if [[ $transfer_failed = true ]]
	2597	then
	2598	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2599	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2600
	2601	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2602	eval local_catalog=${pathout[$i]}
	2603	if [[ ! -d $local_catalog ]]
	2604	then
	2605	printf " *** local directory does not exist. Trying to create:\n"
	2606	printf " $local_catalog \n"
	2607	mkdir -p $local_catalog
	2608	fi
[3236]	2609	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2610	transfer_problems=true
	2611	fi
	2612
	2613	else
	2614
	2615	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2616	# BE COPIED OR APPENDED ON THIS MACHINE
	2617	if [[ "${actionout[$i]}" = tr ]]
	2618	then
	2619	actionout[$i]=""
	2620	else
	2621	actionout[$i]="a"
	2622	fi
	2623	fi
	2624	fi
	2625
	2626
	2627	# APPEND ON THIS MACHINE
	2628	if [[ "${actionout[$i]}" = "a" ]]
	2629	then
	2630	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2631	then
	2632	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2633	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2634	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2635	else
	2636	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2637	printf "\n ${pathout[$i]}\n"
	2638	cat ${localout[$i]} >> ${pathout[$i]}
	2639	fi
	2640	fi
	2641
	2642	# COPY ON THIS MACHINE
	2643	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2644	# ON DIFFERENT FILE-SYSTEMS
	2645	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2646	then
	2647
	2648	# COPY IN CASE OF RUNS ON SINGLE CORES
	2649	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2650	then
	2651	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2652	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2653	if [[ $link_local_output = true ]]
	2654	then
	2655	printf " file will be linked\n"
	2656	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2657	fi
	2658	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2659	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2660	then
	2661	if [[ $link_local_output = true ]]
	2662	then
	2663	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2664	fi
	2665	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2666	else
	2667	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2668	fi
	2669	else
	2670	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2671	printf "\n ${pathout[$i]}\n"
	2672	if [[ $link_local_output = true ]]
	2673	then
	2674	printf " file will be linked\n"
	2675	ln -f ${localout[$i]} ${pathout[$i]}
	2676	fi
	2677	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2678	if [[ ! -f "${pathout[$i]}" ]]
	2679	then
	2680	if [[ $link_local_output = true ]]
	2681	then
	2682	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2683	fi
	2684	cp ${localout[$i]} ${pathout[$i]}
	2685	else
	2686	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2687	fi
	2688	fi
	2689
	2690	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2691	then
	2692
	2693	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2694	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2695	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2696	printf "\n ${pathout[$i]}\n"
	2697	if [[ $link_local_output = true ]]
	2698	then
	2699	printf " files will be linked\n"
[2396]	2700	mkdir -p ${pathout[$i]}
[2380]	2701	cd ${localout[$i]}
	2702	for file in $(ls *)
	2703	do
	2704	ln -f $file ${pathout[$i]}
	2705	done >\|/dev/null 2>&1
[2566]	2706	cd $tempdir
[2380]	2707	fi
	2708
	2709	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2710	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2711	then
	2712	if [[ $link_local_output = true ]]
	2713	then
	2714	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2715	fi
[3025]	2716	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2717	cp -r ${localout[$i]}/* ${pathout[$i]}
	2718	fi
	2719
	2720	fi
	2721	fi
	2722	done
	2723
	2724	if (( i != 0 ))
	2725	then
	2726	if [[ $transfer_problems = true ]]
	2727	then
	2728	printf "\n$dashes\n *** OUTPUT-files saved"
	2729	printf "\n +++ WARNING: some data transfers failed! \n"
	2730	else
	2731	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2732	fi
	2733	fi
	2734
	2735
	2736	# IF REQUIRED, START A RESTART-JOB
	2737	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2738	if [[ -f CONTINUE_RUN ]]
	2739	then
	2740
	2741	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2742	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2743	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2744	# -b START A BATCH JOB
	2745	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2746	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2747	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2748
[2957]	2749	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2750	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2751	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2752	then
	2753	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2754	fi
[2380]	2755
	2756	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2757	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2758	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2759	then
[2381]	2760	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2761	fi
	2762
	2763
	2764	# START THE RESTART-JOB
	2765	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2766	echo " $prc"
	2767	printf "\n$dashes\n"
	2768	if [[ $running_on_remote = true ]]
	2769	then
	2770
	2771	echo "*** ssh will be used to initiate restart-runs!"
	2772	echo " return_address=\"$return_address\" "
	2773	echo " return_username=\"$local_username\" "
	2774
	2775	if [[ "$remote_loginnode" != "" ]]
	2776	then
[3534]	2777	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]	2778	else
[3534]	2779	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2780	fi
	2781
	2782	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2783	sleep 30
	2784
	2785	else
	2786
	2787	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2788	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2789	cd - > /dev/null
	2790
	2791	fi
	2792
[3132]	2793	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2794	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2795	then
	2796	printf "\n$dashes\n +++ creating restart run failed \n"
	2797	locat=create_restart
[3455]	2798	rm palmrun_restart.log
[3132]	2799	exit
	2800	else
	2801	printf "\n$dashes\n *** restart run initiated \n"
	2802	rm palmrun_restart.log
	2803	fi
[2380]	2804
[3132]	2805
[2380]	2806	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2807	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2808	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2809	# MAY BE VERY HUGE)
	2810	(( i = 0 ))
[2610]	2811	while (( i < nr_of_input_files ))
[2380]	2812	do
	2813	(( i = i + 1 ))
	2814	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2815	then
	2816	rm -r ${absnamein[$i]}
	2817	fi
	2818	done
	2819
	2820	fi
	2821
	2822
	2823	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2824	cd $HOME
[2566]	2825	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2826
	2827
	2828	else
	2829
	2830
	2831	# PREPARING ACTIONS,
	2832	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2833
	2834	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2835	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2836	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2837	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2838	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2839	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2840	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2841	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2842	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2843	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2844	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2845	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2846	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2847	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2848	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2849	if [[ $create_remote_batch_job = true ]]
	2850	then
	2851	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2852	if [[ $do_trace = true ]]
	2853	then
	2854	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2855	fi
[2380]	2856	elif [[ $create_batch_job = true ]]
	2857	then
	2858	palmrun_com=${palmrun_com}" -j"
[2420]	2859	if [[ $do_trace = true ]]
	2860	then
	2861	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2862	fi
[2380]	2863	fi
	2864
	2865
	2866	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2867	# REMOTE HOST
[3236]	2868	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2869	job_protocol_file=$job_protocol_file_local
	2870	if [[ $create_remote_batch_job = true ]]
	2871	then
[3236]	2872	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2873	job_protocol_file=$job_protocol_file_remote
	2874	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2875	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2876	fi
	2877
	2878
	2879	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2880	jobfile=jobfile.$run_id_number
[2380]	2881
	2882
	2883	# FIRST CREATE THE BATCH DIRECTIVES
	2884	(( i = 0 ))
	2885	while (( i < ibd ))
	2886	do
	2887	(( i = i + 1 ))
[2693]	2888	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2889	eval line=\"$line\"
	2890	echo "$line" >> $jobfile
	2891	done
	2892	echo " " >> $jobfile
	2893
	2894
	2895	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2896	# PROTOCOL
	2897	if [[ $create_remote_batch_job = true ]]
	2898	then
[3236]	2899	echo "set +vx" >> $jobfile
	2900	echo "trap '" >> $jobfile
	2901	echo "set +vx" >> $jobfile
	2902	echo "cd ${remote_jobcatalog}" >> $jobfile
	2903	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2904
	2905	# ADD THE BATCH DIRECTIVES
	2906	(( i = 0 ))
	2907	while (( i < ibdt ))
	2908	do
	2909	(( i = i + 1 ))
[2693]	2910	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2911	eval line=\"$line\"
	2912	echo "$line" >> $jobfile
	2913	done
	2914	echo " " >> $jobfile
	2915
	2916	echo "set -x" >> $jobfile
[3534]	2917	if [[ "$remote_loginnode" != "" ]]
	2918	then
	2919	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}\" " >> $jobfile
	2920	else
	2921	echo "${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
	2922	fi
[2380]	2923	echo "%%END%%" >> $jobfile
	2924	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2925	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2926	echo "rm $scpjob_file" >> $jobfile
[2404]	2927	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2928	echo "set -x" >> $jobfile
	2929	echo " ' exit" >> $jobfile
	2930	fi
	2931
	2932
	2933	# ACTIVATE ERROR-TRACEBACK
	2934	if [[ $do_trace = true ]]
	2935	then
	2936	echo "set -x" >> $jobfile
	2937	else
	2938	echo "set +vx" >> $jobfile
	2939	fi
	2940
	2941
	2942	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2943	if [[ "$login_init_cmd" != "" ]]
	2944	then
	2945	echo "$login_init_cmd" >> $jobfile
	2946	fi
	2947	if [[ "$module_commands" != "" ]]
	2948	then
	2949	echo "$module_commands" >> $jobfile
	2950	fi
	2951
	2952
	2953	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2954	if [[ $create_remote_batch_job = true ]]
	2955	then
	2956	echo "mkdir $tempdir" >> $jobfile
	2957	echo "chmod go+rx $tempdir" >> $jobfile
	2958	else
	2959	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2960	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2961	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2962	mkdir $tempdir
	2963	chmod go+rx $tempdir
	2964	fi
	2965	echo "cd $tempdir" >> $jobfile
	2966	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2967	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2968	echo "export PATH=.:\$PATH" >> $jobfile
	2969	echo "export execute_palmrun=true" >> $jobfile
	2970
	2971
	2972	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2973	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2974	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2975	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2976	echo "export LOCAL_PWD" >> $jobfile
	2977
	2978
	2979	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2980	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2981	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2982
	2983
	2984	# CALL PALMRUN WITHIN THE JOB
	2985	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2986	echo "set -x" >> $jobfile
	2987	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2988
	2989
	2990	# TRANSFER JOBFILE TO THE TARGET HOST
	2991	if [[ $create_jobfile_only = false ]]
	2992	then
	2993
[3505]	2994	# CREATE LOCAL JOB FOLDER
	2995	eval local_jobcatalog=$local_jobcatalog
	2996	if [[ ! -d $local_jobcatalog ]]
	2997	then
	2998	echo " "
	2999	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	3000	mkdir $local_jobcatalog
	3001	fi
	3002
[2380]	3003	if [[ $create_remote_batch_job = true ]]
	3004	then
	3005
[2420]	3006	echo " "
[2566]	3007	echo " *** transfer of job to remote host via scp"
[3505]	3008
	3009	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3010	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3011
	3012	# COPY THE JOB FILE
[2420]	3013	if [[ $do_trace = true ]]
	3014	then
[3236]	3015	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3016	fi
[3236]	3017	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3018
[3505]	3019	# SUBMIT THE JOB
[3570]	3020	printf " *** submit the job (output of submit command, e.g. the run_id, may follow) \n"
[2420]	3021	if [[ $do_trace = true ]]
	3022	then
[3549]	3023	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]	3024	fi
[3549]	3025	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]	3026
	3027	elif [[ $create_batch_job = true ]]
	3028	then
	3029
[2385]	3030	eval local_jobcatalog=$local_jobcatalog
[3236]	3031	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3032	cd $local_jobcatalog
[2380]	3033	echo " "
[2420]	3034	echo " *** submit the job"
	3035	if [[ $do_trace = true ]]
	3036	then
[3236]	3037	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3038	fi
[3236]	3039	$submit_command ${configuration_identifier}_${run_id}
	3040	rm ${configuration_identifier}_${run_id}
[2380]	3041	cd - > /dev/null
	3042
	3043	fi
	3044
	3045	rm -rf $jobfile
	3046
	3047	else
	3048
	3049	printf "\n *** jobfile created under name \"$jobfile\" "
	3050	printf "\n no batch-job has been sent!"
	3051
	3052	fi
	3053
	3054	fi # END OF REMOTE-PART

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