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source: palm/trunk/SCRIPTS/palmrun @ 3551

Last change on this file since 3551 was 3549, checked in by raasch, 6 years ago
ssh-call for submitting batch jobs on remote systems modified to avoid output of login messages on specific systems, ssh-calls for compilations on remote systems modified to avoid output of login messages on specific systems, english translation of german comments / variable names
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 102.2 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 3549 2018-11-21 15:44:44Z suehring $
[3549]	29	# ssh-call for submitting batch jobs on remote systems modified to avoid output
	30	# of login messages on specific systems
	31	#
	32	# 3534 2018-11-19 15:35:16Z raasch
[3534]	33	# batch_scp for sending back the job protocol file is called via login-node if
	34	# a login-node has been set in the config-file
	35	# ssh-calls rearranged to avoid output of system/user-profile messages
	36	#
	37	# 3505 2018-11-08 09:14:30Z raasch
[3505]	38	# job folders are created in case that they do not exist
	39	#
	40	# 3455 2018-10-30 14:12:31Z raasch
[3455]	41	# options -h and -d renamed -c and -r, respectively
	42	#
	43	# 3402 2018-10-23 11:49:24Z knoop
[3346]	44	# job_id is set for compatibility reasons with older versions of config files
	45	#
	46	# 3313 2018-10-06 15:22:48Z knoop
[3294]	47	# more detailed error message for outdated fileconnection file
	48	#
	49	# 3236 2018-09-10 09:07:06Z raasch
[3236]	50	# warning issued in case of file connection file version mismatch,
	51	# host_configuration renamed configuration_identifier,
	52	# "host identifier" in header output renamed "config. identifier",
	53	# jobname renamed run_identifier,
	54	# run_id renamed run_id_number
	55	# job_id renamed run_id
	56	# option -r renamed -i
	57	#
	58	# 3151 2018-07-19 08:45:38Z raasch
[3151]	59	# removed additional listing of files to be compiled, print PALM code revision
	60	# in header
	61	#
	62	# 3132 2018-07-16 11:44:58Z raasch
[3132]	63	# create consistent error messages in case of failed restarts,
	64	# check existence of remote job catalog
	65	#
	66	# 3043 2018-05-25 10:47:54Z raasch
[3043]	67	# check for setting of fast_io_catalog
	68	#
	69	# 3033 2018-05-23 15:26:19Z raasch
[3025]	70	# -T option not required for interactive runs (tasks per node =
	71	# total number of cores is assumed as default, if option is not given),
	72	# reformatting of a few messages,
	73	# bugfix: destination output directory is created if attribute "pe" is set in
	74	# .palm.iofiles
	75	#
	76	# 2718 2018-01-02 08:49:38Z maronga
[2993]	77	# bugfix of r2990
	78	#
	79	# 2718 2018-01-02 08:49:38Z maronga
[2990]	80	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	81	# not in the working directory from where palmrun is called
	82	#
	83	# 2718 2018-01-02 08:49:38Z maronga
[2957]	84	# svfout in the activation string will be replaced now by svfin in case of
	85	# automatic restarts
	86	#
	87	# 2718 2018-01-02 08:49:38Z maronga
[2906]	88	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	89	# the possible output or input of sky view factors
	90	#
	91	# 2718 2018-01-02 08:49:38Z maronga
[2834]	92	# "fname" renamed to "jobname"
	93	#
	94	# 2718 2018-01-02 08:49:38Z maronga
[2799]	95	# parameters are allowed in output commands (OC:)
	96	#
	97	# 2718 2018-01-02 08:49:38Z maronga
[2789]	98	# bugfix: exit if no queue has been given neither with option -q nor in the
	99	# configuration file
	100	#
	101	# 2718 2018-01-02 08:49:38Z maronga
[2762]	102	# file connection file from trunk/SCRIPTS is taken by default
	103	#
	104	# 2718 2018-01-02 08:49:38Z maronga
[2716]	105	# Corrected "Former revisions" section
	106	#
	107	# 2696 2017-12-14 17:12:51Z kanani
	108	# Change in file header (GPL part)
	109	#
	110	# 2693 2017-12-13 12:33:49Z raasch
[2693]	111	# replacement of variables given by {{<variable>}} in configuration file is now
	112	# done in a more general way, variable names are written in small letters
	113	#
	114	# 2670 2017-12-06 16:32:19Z raasch
[2670]	115	# test printouts removed
	116	#
	117	# 2669 2017-12-06 16:03:27Z raasch
[2669]	118	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	119	# removed,
	120	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	121	# files,
	122	# informative messages in case of missing optional input files shortened
	123	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	124	#
	125	# 2638 2017-11-23 12:44:23Z raasch
[2610]	126	# use of wildcards in file connection statements enabled
	127	#
	128	# 2605 2017-11-09 15:31:46Z raasch
[2605]	129	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	130	# will not be sent with the job file any more, but copied into the
[2610]	131	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	132	#
	133	# 2600 2017-11-01 14:11:20Z raasch
[2600]	134	# cycle numbers are made three digits wide
	135	#
	136	# 2566 2017-10-20 08:50:47Z raasch
[2566]	137	# execute command for combine_plot_fields added
	138	# "TEMPDIR" renamed "tempdir"
	139	# temporary working directory for local batch jobs is created immediately within
	140	# the user's palmrun call, due to a requirement of the "grid engine" batch
	141	# system, where the working directory is given with batch directive -wd and must
	142	# already exist when the job is submitted,
	143	# informative messages in non-trace mode reduced and partly reformatted
	144	#
	145	# 2551 2017-10-18 07:25:11Z raasch
[2551]	146	# TEMPDIR added as replacement string to be used in batch directives
	147	#
	148	# 2512 2017-10-04 08:26:59Z raasch
[2507]	149	# bugfix for determining cycle numbers of NetCDF input files
	150	#
	151	# 2506 2017-09-29 08:30:37Z raasch
[2506]	152	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	153	# host configuration added to SOURCES_FOR_RUN_... folder name
	154	# host_identifier renamed host_configuration
	155	# option -W added to allow for job dependencies
	156	#
	157	# 2501 2017-09-26 11:41:55Z raasch
[2501]	158	# default value for number of cores (option -X) set to 1
	159	# bugfix for mechanism which overwrites configuration file settings with values
	160	# provided by palmrun options
	161	#
	162	# 2499 2017-09-22 16:47:58Z kanani
[2499]	163	# option -h named configuration identifier
	164	#
	165	# 2480 2017-09-19 06:24:14Z maronga
[2480]	166	# bugfix for last revision
	167	#
	168	# 2479 2017-09-19 06:12:16Z raasch
[2479]	169	# option -A (project account number) added
	170	#
	171	# 2422 2017-09-08 08:25:41Z raasch
[2410]	172	# initial revision
[2380]	173	#
	174	#--------------------------------------------------------------------------------#
	175	# palmrun - script for running PALM jobs on local and remote hosts
	176	#--------------------------------------------------------------------------------#
	177
	178
	179
	180	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	181
	182	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	183	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	184	# (TOO MANY ARGUMENTS - PROBLEM)
	185	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	186
[2610]	187	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	188	typeset -i nr_of_output_files=0
[2380]	189	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	190	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	191	# SCRIPT-OPTION ARGUMENTS
	192	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	193	typeset -i icycle inode ival maxcycle mpi_tasks
	194	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	195
	196	activation_string_list=""
	197	AddFilenames=""
	198	combine_plot_fields=true
	199	compiler_name=""
	200	compiler_name_ser=""
	201	compiler_options=""
[3236]	202	configuration_identifier="default"
[2501]	203	cores=1
[2380]	204	cores_atmos=0
	205	cores_ocean=0
	206	coupled_dist=""
	207	cpp_options=""
	208	cpumax=0
[2506]	209	create_batch_job=false
[2380]	210	create_jobfile_only=false
	211	create_remote_batch_job=false
	212	dashes=" ----------------------------------------------------------------------------"
	213	defaultqueue=""
[2506]	214	delete_temporary_catalog=true
[2380]	215	do_compile=true
	216	do_trace=false
	217	executable=""
	218	execute_command=""
	219	execution_error=false
[2762]	220	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	221	global_revision=""
	222	hostfile=""
	223	hp=""
	224	keep_data_from_previous_run=false
	225	link_local_input=false
	226	link_local_output=false
[2388]	227	linker_options=""
[2385]	228	local_jobcatalog=""
[2380]	229	locat=normal
	230	makefile=""
	231	max_par_io_str=""
	232	prc=$0
	233	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	234	do
	235	prc=`echo $prc \| cut -f2- -d"/"`
	236	done
	237	module_calls=""
[2506]	238	palmrun_memory=""
[2380]	239	palmrun_script_name=$prc
	240	openmp=false
[2506]	241	previous_job=""
[2479]	242	project_account=""
[2380]	243	queue=none
[2906]	244	read_svf=""
[2380]	245	restart_run=false
	246	return_address=""
[2385]	247	remote_jobcatalog=""
[2380]	248	remote_username=""
	249	running_in_batch_mode=false
[3313]	250	running_in_test_mode=false
[2380]	251	run_coupled_model=false
	252	run_id=""
[3236]	253	run_id_number=""
	254	run_identifier=test
[2380]	255	silent=false
	256	source_list=""
	257	source_path=""
[2501]	258	tasks_per_node=0
[2380]	259	threads_per_task=1
	260	transfer_problems=false
[2384]	261	user_source_path=""
[2506]	262	use_existing_sources_folder=""
[2380]	263	use_openmp=false
[3033]	264	version="palmrun 1.0 Rev$Rev: 3549 $"
[2380]	265	working_directory=`pwd`
	266	write_binary=""
[2906]	267	write_svf=""
[2380]	268
	269
	270	# ERROR HANDLING IN CASE OF EXIT
[2404]	271	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	272	then
	273
	274	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	275	(( i = 0 ))
	276	while (( i < iec ))
	277	do
	278	(( i = i + 1 ))
	279	printf "\n *** Execution of ERROR-command:\n"
	280	printf " >>> ${err_command[$i]}\n"
	281	eval ${err_command[$i]}
	282	done
[2566]	283	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	284	printf "\n\n+++ palmrun crashed \n\n"
	285	exit 1
	286	elif [[ $locat != normal ]]
[2380]	287	then
[3312]	288	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	289	printf "\n+++ palmrun killed by \"^C\" \n\n"
	290	exit 2
	291	else
[2566]	292	printf "\n --> palmrun finished\n\n"
[3312]	293	exit 0
[2380]	294	fi' exit
	295
	296
	297	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	298	trap 'locat=control_c
	299	exit 1
[2380]	300	' 2
	301
	302
	303	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	304	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	305	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]	306	do
	307	case $option in
	308	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	309	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	310	(b) create_batch_job=true; prc="$prc -b";;
	311	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	312	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	313	(C) restart_run=true; prc="$prc -C";;
	314	(F) create_jobfile_only=true;;
	315	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	316	(i) run_id_number=$OPTARG;;
[2380]	317	(j) running_in_batch_mode=true;;
	318	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	319	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	320	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	321	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	322	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	323	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	324	(R) return_address=$OPTARG;;
	325	(s) source_list=$OPTARG;;
[2501]	326	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	327	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	328	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	329	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	330	(v) silent=true; prc="$prc -v";;
[2506]	331	(V) use_existing_sources_folder="-V";;
[2380]	332	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	333	(W) previous_job=$OPTARG;;
[2380]	334	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	335	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	336	(y) ocean_file_appendix=true; prc="$prc -y";;
	337	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	338	(z) running_in_test_mode=true;;
[2380]	339	(Z) combine_plot_fields=false; prc="$prc -Z";;
	340	(\?) printf "\n +++ unknown option $OPTARG \n"
	341	printf "\n --> type \"$0 ?\" for available options \n"
	342	locat=parameter;exit;;
	343	esac
	344	done
	345
	346
	347	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	348	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	349	(( to_shift = $OPTIND - 1 ))
	350	shift $to_shift
	351
	352	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	353	if [[ "$1" = "?" ]]
	354	then
	355	(printf "\n *** Description of available palmrun options:\n"
	356	printf "\n Option Description Default-Value"
	357	printf "\n -a activation string list \"\" "
[2479]	358	printf "\n -A project account number ---"
[2380]	359	printf "\n -b batch-job on local machine ---"
	360	printf "\n -B do not delete temporary directory at end ---"
[3455]	361	printf "\n -c configuration identifier \"default\" "
[2380]	362	printf "\n -F create batch job file only ---"
	363	printf "\n -k keep data from previous run"
	364	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	365	printf "\n -M Makefile name Makefile"
	366	printf "\n -O threads per openMP task ---"
	367	printf "\n -q queue \"$queue\" "
[3455]	368	printf "\n -r run identifier test"
[2380]	369	printf "\n -s filenames of routines to be compiled \"\" "
	370	printf "\n must end with .f, .f90, .F, or .c !"
	371	printf "\n use \"..\" for more than one file and wildcards"
	372	printf "\n -s LM compiles all locally modified files"
	373	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	374	printf "\n -T tasks per node ---"
[2380]	375	printf "\n -u username on remote machine \"\" "
	376	printf "\n -v no prompt for confirmation ---"
[2506]	377	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	378	printf "\n -w maximum parallel io streams as given by -X"
[2506]	379	printf "\n -W name of job to wait for ---"
[2380]	380	printf "\n -x tracing of palmrun for debug purposes ---"
	381	printf "\n -X # of processors (on parallel machines) 1"
	382	printf "\n -y add appendix \"_O\" to all local output"
	383	printf "\n files (ocean precursor runs followed by"
	384	printf "\n coupled atmosphere-ocean runs) ---"
	385	printf "\n -Y run coupled model, \"#1 #2\" with"
	386	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	387	printf "\n -Z skip combine_plot_fields at the end of "
	388	printf "\n the simulation ---"
	389	printf "\n "
	390	printf "\n Possible values of positional parameter <modus>:"
	391	printf "\n \"?\" - this outline \n\n") \| more
	392	exit
	393	elif [[ "$1" != "" ]]
	394	then
	395	printf "\n +++ positional parameter $1 unknown \n"
	396	locat=parameter; exit
	397	fi
	398
	399
	400
	401	# SHORT STARTING MESSAGE
	402	printf "\n*** $version "
	403	printf "\n will be executed. Please wait ..."
	404
	405
[2506]	406	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	407	config_file=.palm.config.$configuration_identifier
	408	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	409
	410
	411	# CHECK, IF CONFIGURATION FILE EXISTS
	412	if [[ ! -f $config_file ]]
	413	then
	414	printf "\n\n +++ configuration file: "
	415	printf "\n $config_file"
	416	printf "\n does not exist"
	417	locat=connect; exit
	418	fi
	419
	420
[2762]	421	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	422	if [[ -f .palm.iofiles ]]
	423	then
[3236]	424
	425	# CHECK VERSION MISMATCH
	426	if [[ $running_in_batch_mode != true ]]
	427	then
	428	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	429	then
	430	printf "\n\n +++ WARNING: A file connection file has been found in your"
	431	printf "\n working directory, but its revision does not match"
	432	printf "\n the revision of the default (trunk) version."
[3294]	433	printf "\n You may need to update your connection file"
	434	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	435	fi
	436	fi
	437
[2762]	438	fileconnection_file=.palm.iofiles
[3236]	439
[2762]	440	fi
	441
	442
[2380]	443	# CHECK, IF FILE CONNECTION FILE EXISTS
	444	if [[ ! -f $fileconnection_file ]]
	445	then
	446	printf "\n\n +++ file connection file: "
	447	printf "\n $fileconnection_file"
	448	printf "\n does not exist"
	449	locat=connect; exit
	450	fi
	451
	452
[2404]	453	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	454	if [[ "$activation_string_list" = "" ]]
	455	then
	456	printf "\n\n +++ no activation string list given: "
	457	printf "\n please set palmrun option \"-a\" "
	458	locat=palmrun_option; exit
	459	fi
	460
	461
	462	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	463	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	464	then
	465	write_binary=true
	466	else
	467	write_binary=false
	468	fi
	469
[2906]	470	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	471	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	472	then
	473	write_svf=true
	474	else
	475	write_svf=false
	476	fi
[2404]	477
[2906]	478	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	479	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	480	then
	481	read_svf=true
	482	else
	483	read_svf=false
	484	fi
	485
	486
[2380]	487	# READ AND EVALUATE THE CONFIGURATION-FILE
	488	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	489
	490	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	491	while read line
	492	do
	493
	494	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	495	eval line=\"$line\"
	496
	497
	498	# INTERPRET THE LINE
	499	if [[ "$(echo $line)" = "" ]]
	500	then
	501
	502	# EMPTY LINE, NO ACTION
	503	continue
	504
	505	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	506	then
	507
	508	# LINE IS A COMMENT LINE
	509	continue
	510
	511	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	512	then
	513
	514	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	515	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	516	value=`echo $line \| cut -d" " -s -f2-`
	517
	518
	519	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	520	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	521	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	522	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	523	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	524	# CONFIGURATION-FILE.
	525	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	526	then
	527	eval export $var="\$value"
	528
	529	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	530	if [[ $do_trace = true ]]
	531	then
	532	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	533	fi
	534	fi
	535
	536	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	537	then
	538
	539	# LINE DEFINES BATCH-DIRECTIVE
	540	(( ibd = ibd + 1 ))
	541	line=$(echo $line \| cut -c4-)
	542	batch_directive[$ibd]="$line"
	543
	544	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	545	then
	546
	547	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	548	# REMOTE TO A LOCAL HOST
	549	(( ibdt = ibdt + 1 ))
	550	line=$(echo $line \| cut -c5-)
	551	batch_directive_transfer[$ibdt]="$line"
	552
	553	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	554	then
	555
	556	# LINE DEFINES ERROR-COMMAND
	557	(( iec = iec + 1 ))
	558	line=$(echo $line \| cut -c4-)
	559	err_command[$iec]="$line"
	560
	561	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	562	then
	563
	564	# LINE DEFINES INPUT-COMMAND
	565	(( iic = iic + 1 ))
	566	line=$(echo $line \| cut -c4-)
	567	in_command[$iic]="$line"
	568
	569	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	570	then
	571
	572	# LINE DEFINES OUTPUT-COMMAND
	573	(( ioc = ioc + 1 ))
	574	line=$(echo $line \| cut -c4-)
	575	out_command[$ioc]="$line"
	576
	577	else
	578
	579	# SKIP ALL OTHER LINES
	580	continue
	581
	582	fi
	583
	584	done < $config_file
	585
	586
	587	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	588	if [[ "$fast_io_catalog" = "" ]]
	589	then
	590	printf "\n +++ no fast_io_catalog found in $config_file"
	591	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	592	locat=config_file; exit
	593	fi
[2380]	594	if [[ "$compiler_name" = "" ]]
	595	then
	596	printf "\n +++ no compiler name found in $config_file"
	597	printf "\n Please add line \"compiler_name ...\" to that file."
	598	locat=config_file; exit
	599	fi
	600	if [[ "$compiler_name_ser" = "" ]]
	601	then
	602	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	603	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	604	locat=config_file; exit
	605	fi
	606	if [[ "$compiler_options" = "" ]]
	607	then
	608	printf "\n +++ no compiler options found in $config_file"
	609	printf "\n Please add line \"compiler_options ...\" to that file."
	610	locat=config_file; exit
	611	fi
[2388]	612	if [[ "$linker_options" = "" ]]
[2380]	613	then
[2388]	614	printf "\n +++ no linker options found in $config_file"
	615	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	616	locat=config_file; exit
	617	fi
	618	if [[ "$execute_command" = "" ]]
	619	then
	620	printf "\n +++ no execute command found in $config_file"
	621	printf "\n Please add line \"execute_command ...\" to that file."
	622	locat=config_file; exit
	623	fi
	624
	625	if [[ "$hostfile" != "" ]]
	626	then
	627	if [[ $hostfile != auto && ! -f $hostfile ]]
	628	then
	629	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	630	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	631	locat=config_file; exit
	632	fi
	633	fi
	634
	635
	636	# DETERMINE THE CALL STATUS
	637	if [[ "$return_address" != "" ]]
	638	then
	639
	640	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	641	# BATCH MODE AND ...
	642	running_on_remote=true
	643
	644	else
	645
	646	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	647	if [[ "$remote_ip" != "" ]]
	648	then
	649
	650	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	651	create_remote_batch_job=true
	652
[3132]	653	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	654	if [[ "$remote_jobcatalog" = "" ]]
	655	then
	656	printf "\n +++ no remote jobcatalog found in $config_file"
	657	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	658	locat=config_file; exit
	659	fi
	660
	661
[2380]	662	fi
	663	running_on_remote=false
	664	fi
	665
	666
	667
	668	# READ AND EVALUATE THE I/O-FILE LIST
	669	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	670
	671	# READ THE FILE CONNECTION FILE LINE BY LINE
	672	while read line
	673	do
	674
[2669]	675	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	676	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	677
	678	# INTERPRET THE LINE
	679	if [[ "$(echo $line)" = "" ]]
	680	then
	681	# EMPTY LINE, NO ACTION
	682	continue
	683
	684	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	685	then
	686
	687	# LINE IS A COMMENT LINE
	688	true
	689
	690	else
	691
	692	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	693	# s2a: in/out - field
[2669]	694	# s2b: action - field (optional)
	695	s1=`echo "$line" \| cut -d" " -f1`
	696	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	697	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	698	then
[2669]	699	s2a=$s2
[2380]	700	s2b=""
	701	else
[2669]	702	s2a=`echo $s2 \| cut -d":" -f1`
	703	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	704	fi
[2669]	705	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	706	s4=`echo "$line" \| cut -d" " -s -f4`
	707	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	708	s5=`echo "$line" \| cut -d" " -s -f5`
	709	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	710
	711
	712	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	713	# INPUT- OR OUTPUT-LIST.
	714	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	715	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	716	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	717	# IS NOT CHECKED AND STORED.
[2610]	718	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	719	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	720	then
	721	found=false
	722	for actual in $activation_string_list
	723	do
	724	for formal in $s3
	725	do
	726	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	727	done
	728	done
	729	if [[ $found = true ]]
	730	then
	731	(( iin = iin + 1 ))
[2669]	732	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	733	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	734	if [[ "$s2a" = inopt ]]
	735	then
	736	optin_pre[$iin]=yes
	737	else
	738	optin_pre[$iin]=no
	739	fi
[2605]	740
	741	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	742	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	743	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	744	then
[2610]	745	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	746	fi
	747
[2610]	748	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	749	# THE WILDCARD FROM THE ENDING
	750	if [[ "${s5: -1}" = "*" ]]
	751	then
[2669]	752	if [[ "$s2b" = "di" ]]
[2610]	753	then
	754	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	755	printf "\n see file \"$fileconnection_file\", line"
	756	printf "\n$line"
	757	locat=iofiles_file; exit
	758	fi
	759	multin[$iin]=true
	760	string=${endin_pre[$iin]}
	761	endin_pre[$iin]="${string%?}"
	762	else
	763	multin[$iin]=false
	764	fi
[2380]	765	fi
[2669]	766	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	767	then
	768	found=false
	769	for actual in $activation_string_list
	770	do
	771	for formal in $s3
	772	do
[2670]	773	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	774	done
	775	done
	776	if [[ $found = true ]]
	777	then
	778	(( iout = iout + 1 ))
[2669]	779	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	780	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	781
[2669]	782	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	783	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	784	if [[ $formal = wildcard ]]
	785	then
	786	warnout_pre[$iout]=false
	787	else
	788	warnout_pre[$iout]=true
	789	fi
	790
[2610]	791	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	792	# THE WILDCARD FROM THE LOCAL FILENAME
	793	if [[ "${s1: -1}" = "*" ]]
	794	then
[2669]	795	if [[ "$s2b" = "di" ]]
[2610]	796	then
	797	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	798	printf "\n see file \"$fileconnection_file\", line"
	799	printf "\n$line"
	800	locat=iofiles_file; exit
	801	fi
	802	multout[$iout]=true
	803	string=${localout_pre[$iout]}
	804	localout_pre[$iout]="${string%?}"
	805	else
	806	multout[$iout]=false
	807	fi
[2380]	808	fi
[2669]	809	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	810	then
[2669]	811	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	812	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	813	locat=connect; exit
	814	fi
	815	IFS="$IFSALT"
	816	fi
	817
	818	done < $fileconnection_file
	819
	820
	821
[2501]	822	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	823	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	824	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	825	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	826	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	827	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	828
	829
	830
[2380]	831	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	832	if [[ $run_coupled_model = true ]]
	833	then
	834
	835	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	836	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	837
	838	if (( $cores_ocean + $cores_atmos != $cores ))
	839	then
	840
	841	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	842	printf "\n PEs (total) : $cores"
	843	printf "\n PEs (atmosphere): $cores_atmos"
	844	printf "\n PEs (ocean) : $cores_ocean"
	845	locat=coupling; exit
	846
	847	fi
	848
	849	fi
	850
	851
	852	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	853	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	854	# FOLDER
	855	if [[ $running_in_batch_mode = true ]]
	856	then
	857
[2506]	858	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	859	then
[2506]	860	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	861	printf "\n Please check the output of the palmrun-call"
	862	printf "\n that you did on your local host."
	863	locat=SOURCES_FOR_RUN; exit
	864	fi
	865
	866	else
	867
	868	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	869	# AUTOMATIC RESTART RUN
	870	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	871	if [[ $restart_run = false ]]
	872	then
	873
	874	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	875	# THE LOCAL HOST
	876	if [[ ! -d $source_path ]]
	877	then
	878	printf "\n\n +++ source path \"$source_path\" on local host"
	879	printf "\n \"$(hostname)\" does not exist"
	880	locat=source_path; exit
	881	fi
	882
[2990]	883	rm -rf ${base_directory}/${sources_for_run_catalog}
	884	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	885
	886	if [[ "$source_list" = LM ]]
	887	then
	888
	889	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	890	source_list=""
	891	cd $source_path
	892
	893
[2512]	894	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	895	if [[ ! -d ../.svn ]]
[2380]	896	then
	897	printf "\n\n +++ source directory"
	898	printf "\n \"$source_path\" "
	899	printf "\n is not under control of \"subversion\"."
[2512]	900	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	901	fi
	902
	903
	904	# LIST ALL MODIFIED SOURCE CODE FILES
	905	Filenames=""
[2404]	906	svn status > tmp_svnstatus
[2380]	907	while read line
	908	do
	909	firstc=`echo $line \| cut -c1`
	910	if [[ $firstc = M \|\| $firstc = "?" ]]
	911	then
	912	Name=`echo "$line" \| cut -c8-`
	913	extension=`echo $Name \| cut -d. -f2`
	914	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	915	then
	916	Filenames="$Filenames "$Name
	917	fi
	918	fi
[2404]	919	done < tmp_svnstatus
	920	rm -rf tmp_svnstatus
[2380]	921
	922
	923	# COPY FILES TO SOURCES_FOR_RUN_...
	924	for filename in $Filenames
	925	do
[2990]	926	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	927	source_list=$source_list"$filename "
	928	done
	929
	930	cd - > /dev/null
	931
	932
	933	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	934	elif [[ "$source_list" != "" ]]
	935	then
	936
	937	cd $source_path
	938
	939	for filename in $source_list
	940	do
	941
	942	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	943	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	944	then
	945	printf "\n +++ source code file: $filename"
	946	printf "\n must not contain (\"/\") "
	947	locat=source; exit
	948	fi
	949
	950	if [[ ! -f $filename ]]
	951	then
	952	printf "\n +++ source code file: $filename"
	953	printf "\n does not exist"
	954	locat=source; exit
	955	else
[2990]	956	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	957	fi
	958
	959	done
	960
	961	cd - > /dev/null
	962
	963	fi
	964
	965	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	966	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	967	if [[ ! -f $makefile ]]
	968	then
	969	printf "\n +++ file \"$makefile\" does not exist"
	970	locat=make; exit
	971	else
[2990]	972	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	973	fi
	974
	975
	976	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	977	if [[ "$user_source_path" != "" ]]
[2380]	978	then
	979
	980	# DOES THE DIRECTORY EXIST?
[2384]	981	if [[ ! -d $user_source_path ]]
[2380]	982	then
	983
	984	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	985	printf "\n \"$user_source_path\" "
[2380]	986	printf "\n does not exist or is not a directory."
	987	printf "\n No source code will be used from this directory!\n"
[2384]	988	user_source_path=""
[2380]	989	if [[ $silent == false ]]
	990	then
	991	sleep 2
	992	fi
	993
	994	else
	995
[2384]	996	cd $user_source_path
[2380]	997
	998	Names=$(ls -1 *.f90 2>&1)
	999	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	1000	Names=$(ls -1 *.F90 2>&1)
	1001	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1002	Names=$(ls -1 *.F 2>&1)
	1003	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1004	Names=$(ls -1 *.f 2>&1)
	1005	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1006	Names=$(ls -1 *.c 2>&1)
	1007	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1008
	1009	cd - > /dev/null
[2990]	1010	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1011
	1012	# COPY MAKEFILE IF EXISTING
[2384]	1013	if [[ -f $user_source_path/Makefile ]]
[2380]	1014	then
	1015	printf "\n\n *** user Makefile from directory"
[2384]	1016	printf "\n \"$user_source_path\" is used \n"
[2380]	1017	if [[ $silent == false ]]
	1018	then
	1019	sleep 1
	1020	fi
[2384]	1021	cp $user_source_path/Makefile .
[2380]	1022	fi
	1023
	1024	for filename in $AddFilenames
	1025	do
	1026	if [[ -f $filename ]]
	1027	then
	1028	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1029	printf "\n source code directory \"$user_source_path\" "
[2380]	1030	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1031	printf "\n from directory \"$source_path\"."
	1032	locat=source; exit
	1033	fi
	1034
[2384]	1035	cp $user_source_path/$filename .
[2380]	1036	source_list="$source_list $filename"
	1037
	1038	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1039	if [[ $(grep -c $filename Makefile) = 0 ]]
	1040	then
	1041	printf "\n\n +++ user file \"$filename\" "
	1042	printf "\n is not listed in Makefile \n"
	1043	locat=source; exit
	1044	fi
	1045	done
	1046	cd - > /dev/null
	1047	fi
	1048	fi
	1049
	1050	# COPY CONFIGURATION FILES
[2990]	1051	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1052	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1053
	1054	# COPY SHELLSCRIPTS
[2990]	1055	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1056	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1057
	1058	fi
	1059
	1060	fi
	1061
[2605]	1062
[2380]	1063	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1064	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1065	if [[ "$global_revision" = "" ]]
	1066	then
	1067	global_revision=`svnversion $source_path 2>/dev/null`
	1068	global_revision="Rev: $global_revision"
	1069	fi
	1070
	1071
	1072	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1073	if [[ -n $cores ]]
	1074	then
	1075
	1076	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1077	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1078	if [[ $tasks_per_node = 0 ]]
[2380]	1079	then
[3025]	1080	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1081	then
	1082	printf "\n"
	1083	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1084	printf "\n set -T option or define tasks_per_node in the config file"
	1085	locat=tasks_per_node; (( iec = 0 )); exit
	1086	else
	1087	# DEFAULT FOR INTERACTIVE RUN
	1088	tasks_per_node=$cores
	1089	fi
[2380]	1090	fi
	1091
	1092	if (( cores < tasks_per_node ))
	1093	then
	1094	printf "\n"
	1095	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1096	printf "\n given values: -T $tasks_per_node -X $cores"
	1097	locat=tasks_per_node; (( iec = 0 )); exit
	1098	fi
	1099
	1100	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1101	(( mpi_tasks = cores / threads_per_task ))
	1102	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1103	(( ii = cores / tasks_per_node ))
	1104	(( remaining_cores = cores - ii * tasks_per_node ))
	1105	if (( remaining_cores > 0 ))
	1106	then
	1107	printf "\n"
	1108	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1109	printf "\n divisor of the total number of cores (option \"-X\")"
	1110	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1111	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1112	(( nodes = nodes + 1 ))
	1113	fi
	1114
	1115	fi
	1116
	1117
	1118	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1119	if [[ "$maximum_parallel_io_streams" = "" ]]
	1120	then
	1121	maximum_parallel_io_streams=$cores
	1122	fi
	1123
	1124
	1125	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1126	if [[ "$scp_port" != "" ]]
	1127	then
	1128	PORTOPT="-P $scp_port"
	1129	SSH_PORTOPT="-p $scp_port"
	1130	fi
	1131
	1132
	1133	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1134	# CONFIG-FILE
	1135	if [[ "$ssh_key" != "" ]]
	1136	then
	1137	ssh_key="-i $HOME/.ssh/$ssh_key"
	1138	fi
	1139
	1140
	1141	# SET QUEUE, IF NOT GIVEN
	1142	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1143	then
	1144
	1145	if [[ $queue = none && "$defaultqueue" = "" ]]
	1146	then
	1147	printf "\n"
	1148	printf "\n +++ no default queue given in configuration file and no queue"
	1149	printf "\n given with option -q"
[2789]	1150	locat=queue; exit
[2380]	1151	fi
	1152	if [[ $queue = none ]]
	1153	then
	1154	queue=$defaultqueue
	1155	fi
	1156
	1157	fi
	1158
	1159
	1160	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1161	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1162	(( i = 0 ))
[2610]	1163	(( nr_of_input_files = 0 ))
[2380]	1164	while (( i < iin ))
	1165	do
	1166	(( i = i + 1 ))
	1167
	1168	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1169	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1170	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1171	then
[2610]	1172	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1173	else
[3236]	1174	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1175	fi
	1176
[2610]	1177
[2380]	1178	# CHECK IF FILE EXISTS
	1179	if ! ls $filename* 1>/dev/null 2>&1
	1180	then
	1181
[2669]	1182	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1183	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1184	then
	1185	printf "\n\n +++ INPUT-file: "
[2610]	1186	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1187	then
	1188	printf "\n $filename"
	1189	else
[2610]	1190	printf "\n $filename.${extin_pre[$i]}"
[2380]	1191	fi
	1192	printf "\n does not exist\n"
	1193	locat=input; exit
	1194	else
[2610]	1195	(( nr_of_input_files = nr_of_input_files + 1 ))
	1196	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1197	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1198	actionin[$nr_of_input_files]="unavailable"
[2610]	1199	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1200	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1201	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1202	fi
[2605]	1203
[2380]	1204	else
	1205
[3236]	1206	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1207	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1208	# ENDINGS
[2610]	1209	if [[ "${multin[$i]}" = true ]]
	1210	then
	1211	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1212	ls -1 -d ${filename} > filelist 2>/dev/null
	1213	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1214	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1215
[2610]	1216	endings=""
	1217	while read line
	1218	do
	1219	# filename without path (i.e. after the last "/")
	1220	basefilename=$(basename ${line})
[2380]	1221
[2610]	1222	# check if there is an extension and remove it
	1223	ext=${basefilename##*.}
	1224	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1225	then
	1226	basefilename=${basefilename%.*}
	1227	fi
[2380]	1228
[2610]	1229	# check for an existing cycle number and remove it
	1230	cycle=${basefilename##*.}
	1231	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1232	then
	1233	basefilename=${basefilename%.*}
	1234	fi
[2600]	1235
[3236]	1236	# remove the run_identifier from the beginning
	1237	length_run_identifier=${#run_identifier}
	1238	ending=${basefilename:${length_run_identifier}}
[2610]	1239
	1240	# remove the ending given in the .iofiles from the beginning
	1241	endingstring="${endin_pre[$i]}"
	1242	length_ending=${#endingstring}
	1243	ending=${ending:${length_ending}}
	1244
	1245	if [[ "$ending" = "" ]]
[2600]	1246	then
[2610]	1247	# standard ending as given in the .iofiles
	1248	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1249	then
	1250	endings="$endings DEFAULT"
	1251	fi
[2600]	1252	else
[2610]	1253	# ending must start with "_", otherwise its a different file
	1254	if [[ "${ending:0:1}" = "_" ]]
	1255	then
	1256	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1257	then
	1258	endings="$endings $ending"
	1259	fi
	1260	fi
[2600]	1261	fi
[2610]	1262
	1263	done <filelist
[2380]	1264
[2610]	1265	rm filelist
[2380]	1266
[2600]	1267	else
[2610]	1268
	1269	# SINGLE NAME
	1270	endings=DEFAULT
	1271
[2600]	1272	fi
	1273
[2610]	1274	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1275	for ending in $endings
	1276	do
	1277
	1278	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1279	if [[ $ending = DEFAULT ]]
[2380]	1280	then
[2610]	1281	ending=""
	1282	fi
	1283
	1284	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1285	(( nr_of_input_files = nr_of_input_files + 1 ))
	1286	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1287	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1288	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1289	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1290	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1291	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1292
	1293
	1294	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1295	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1296	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1297	then
	1298	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1299	else
[3236]	1300	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1301	fi
[2610]	1302
	1303	# DETERMINE THE FILE'S CYCLE NUMBER
	1304	(( maxcycle = 0 ))
	1305	ls -1 -d $filename > filelist 2>/dev/null
	1306	ls -1 -d $filename.* >> filelist 2>/dev/null
	1307	while read line
	1308	do
	1309	# filename without path (i.e. after the last "/")
	1310	basefilename=$(basename ${line})
	1311
	1312	# check if there is an extension
	1313	extension=${basefilename##*.}
	1314	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1315	then
	1316	basefilename=${basefilename%.*}
	1317	fi
	1318
	1319	# check for an existing cycle number
	1320	cycle=${basefilename##*.}
	1321	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1322	then
[2669]	1323	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1324	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1325	(( icycle = $((10#$cycle)) ))
[2610]	1326	else
	1327	(( icycle = 0 ))
	1328	fi
	1329
	1330	if (( icycle > maxcycle ))
	1331	then
	1332	(( maxcycle = icycle ))
	1333
	1334	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1335	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1336	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1337	then
	1338	leading_zero=true
	1339	else
	1340	leading_zero=false
	1341	fi
	1342	fi
	1343
	1344	done <filelist
	1345	rm filelist
	1346
	1347	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1348	if [[ $leading_zero = true ]]
[2380]	1349	then
[2610]	1350	cyclestring=`printf "%03d" $maxcycle`
	1351	else
	1352	cyclestring=$maxcycle
[2380]	1353	fi
[2610]	1354
	1355	# APPEND CYCLE NUMBER TO FILENAME
	1356	if (( maxcycle > 0 ))
[2380]	1357	then
[2610]	1358	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1359	then
	1360	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1361	else
	1362	filename=${filename}.$cyclestring
	1363	fi
[2380]	1364	else
[2610]	1365	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1366	then
	1367	filename=${filename}.${extin[$nr_of_input_files]}
	1368	fi
[2380]	1369	fi
[2610]	1370
	1371	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1372	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1373	absnamein[$nr_of_input_files]=$filename
	1374	if (( maxcycle > 0 ))
[2380]	1375	then
[2610]	1376	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1377	then
	1378	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1379	else
[3236]	1380	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1381	fi
[2380]	1382	else
[2610]	1383	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1384	then
	1385	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1386	else
[3236]	1387	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1388	fi
[2380]	1389	fi
	1390
[2610]	1391	done
	1392
[2380]	1393	fi
[2610]	1394
[2380]	1395	done
	1396
[2610]	1397
[2380]	1398	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1399	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1400	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1401	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1402	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1403	# REMOTE HOST)
	1404	(( i = 0 ))
	1405	while (( i < iout ))
	1406	do
	1407	(( i = i + 1 ))
[2610]	1408	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1409	then
[2610]	1410	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1411	then
[2610]	1412	actionout_pre[$i]=""
	1413	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1414	then
[2610]	1415	actionout_pre[$i]=pe
	1416	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1417	then
[2610]	1418	actionout_pre[$i]=a
[2380]	1419	fi
	1420	(( maxcycle = 0 ))
[3236]	1421	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1422	eval catalogname=${pathout_pre[$i]}
[2380]	1423	if ! ls $filename* 1>/dev/null 2>&1
	1424	then
	1425
	1426	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1427	if cat /dev/null > $filename
	1428	then
	1429	rm $filename
	1430	else
	1431
	1432	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1433	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1434	if [[ ! -d $catalogname ]]
	1435	then
	1436	if mkdir -p $catalogname
	1437	then
	1438	printf "\n\n *** directory:"
	1439	printf "\n $catalogname"
	1440	printf "\n was created\n"
	1441	else
	1442	printf "\n\n +++ OUTPUT-file:"
	1443	printf "\n $filename"
	1444	printf "\n cannot be created, because directory does not exist"
	1445	printf "\n and cannot be created either"
	1446	printf "\n"
	1447	locat=output ; exit
	1448	fi 2>/dev/null
	1449	else
	1450	printf "\n\n +++ OUTPUT-file:"
	1451	printf "\n $filename"
	1452	printf "\n cannot be created, although directory exists"
	1453	printf "\n"
	1454	locat=output ; exit
	1455	fi
	1456	fi 2>/dev/null
	1457
	1458	fi
	1459
	1460	fi
	1461	done
	1462
	1463
	1464	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1465	if [[ $running_in_batch_mode = false ]]
	1466	then
[3236]	1467	run_id_number=$RANDOM
	1468	run_id=${run_identifier}.$run_id_number
[2380]	1469
[3236]	1470	tempdir=$fast_io_catalog/$run_id
[3346]	1471
	1472	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1473	export job_id=$run_id
	1474
[2380]	1475	fi
	1476
	1477
	1478	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1479	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1480	then
	1481
	1482	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1483	if [[ $ibd = 0 ]]
	1484	then
	1485	printf "\n"
	1486	printf "\n +++ no batch directives found in configuration file"
	1487	locat=config_file_batch_directives; (( iec = 0 )); exit
	1488	fi
	1489
	1490	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1491	done=false
[2384]	1492	cputime=$cpumax
[2380]	1493	while [[ $done = false ]]
	1494	do
[2384]	1495	if (( cputime == 0 ))
[2380]	1496	then
	1497	printf "\n +++ cpu-time is undefined"
	1498	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1499	printf "\n >>> "
[2384]	1500	read cputime 1>/dev/null 2>&1
[2380]	1501	else
	1502	done=true
	1503	fi
	1504	done
[2420]	1505	cpumax=$cputime
[2380]	1506
	1507	# CHECK THE MEMORY DEMAND
	1508	done=false
	1509	while [[ $done = false ]]
	1510	do
	1511	if (( memory == 0 ))
	1512	then
	1513	printf "\n +++ memory demand is undefined"
	1514	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1515	printf "\n >>> "
	1516	read memory 1>/dev/null 2>&1
	1517	else
	1518	done=true
	1519	fi
	1520	done
	1521
	1522	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1523	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1524	then
	1525	while [[ -z $remote_username ]]
	1526	do
[2420]	1527	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1528	printf "\n >>> Please type username:"
	1529	printf "\n >>> "
	1530	read remote_username
	1531	done
	1532	fi
	1533
	1534	else
	1535
[2420]	1536	if [[ $running_in_batch_mode = false ]]
	1537	then
	1538	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1539	cpumax=$cputime
	1540	else
	1541	cputime=$cpumax
	1542	fi
[2380]	1543
	1544	fi
	1545
	1546
	1547	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1548	(( cpu_hours = cputime / 3600 ))
	1549	(( resttime = cputime - cpu_hours * 3600 ))
	1550	(( cpu_minutes = resttime / 60 ))
	1551	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1552	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1553
	1554
	1555	# OUTPUT OF THE PALMRUN-HEADER
	1556	calltime=$(date)
	1557	printf "\n"
	1558	printf "#------------------------------------------------------------------------# \n"
	1559	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1560	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1561	printf "\| \| \n"
	1562	column1="called on:"; column2=$(hostname)
	1563	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1564	if [[ $create_remote_batch_job = true ]]
	1565	then
[3236]	1566	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1567	else
	1568	if [[ $running_on_remote = true ]]
	1569	then
[3236]	1570	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1571	else
[3236]	1572	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1573	fi
	1574	fi
	1575	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1576
	1577	column1="running in:"
	1578	if [[ $running_in_batch_mode = true ]]
	1579	then
	1580	column2="batch job mode"
	1581	else
	1582	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1583	then
	1584	column2="job creation mode"
	1585	else
	1586	column2="interactive run mode"
	1587	fi
	1588	fi
	1589	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1590
[2479]	1591	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1592	then
[2480]	1593	if [[ "$project_account" != "" ]]
[2479]	1594	then
	1595	column1="project account number:"
	1596	column2="$project_account"
	1597	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1598	fi
	1599	fi
	1600
[2380]	1601	if [[ -n $cores ]]
	1602	then
	1603	if [[ $run_coupled_model = false ]]
	1604	then
	1605	column1="number of cores:"; column2=$cores
	1606	else
	1607	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1608	fi
	1609	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1610	fi
	1611	if [[ -n $tasks_per_node ]]
	1612	then
	1613	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1614	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1615	if (( remaining_cores > 0 ))
	1616	then
	1617	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1618	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1619	fi
	1620	fi
	1621	if [[ $maximum_parallel_io_streams != $cores ]]
	1622	then
	1623	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1624	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1625	fi
	1626	if [[ $use_openmp = true ]]
	1627	then
	1628	column1="threads per task:"; column2="$threads_per_task"
	1629	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1630	fi
[2384]	1631	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1632	then
[2506]	1633	column1="memory demand / PE":; column2="$memory MB"
	1634	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1635	column1="job cpu time (h:m:s):"; column2="$timestring"
	1636	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1637	fi
[2380]	1638	printf "\| \| \n"
	1639	if [[ "$source_list" != "" ]]
	1640	then
	1641	if [[ "$make_options" != "" ]]
	1642	then
	1643	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1644	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1645	line=$(echo "$make_options" \| cut -c46-)
	1646	while [[ "$line" != "" ]]
	1647	do
	1648	column1=""
	1649	column2=$(echo "$line" \| cut -c-45)
	1650	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1651	line=$(echo "$line" \| cut -c46-)
	1652	done
	1653	fi
	1654	fi
	1655
	1656	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1657	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1658	line=$(echo "$cpp_options" \| cut -c46-)
	1659	while [[ "$line" != "" ]]
	1660	do
	1661	column1=""
	1662	column2=$(echo "$line" \| cut -c-45)
	1663	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1664	line=$(echo "$line" \| cut -c46-)
	1665	done
	1666
	1667	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1668	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1669	line=$(echo "$compiler_options" \| cut -c46-)
	1670	while [[ "$line" != "" ]]
	1671	do
	1672	column1=""
	1673	column2=$(echo "$line" \| cut -c-45)
	1674	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1675	line=$(echo "$line" \| cut -c46-)
	1676	done
	1677
[2388]	1678	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1679	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1680	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1681	while [[ "$line" != "" ]]
	1682	do
	1683	column1=""
	1684	column2=$(echo "$line" \| cut -c-45)
	1685	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1686	line=$(echo "$line" \| cut -c46-)
	1687	done
	1688
	1689	if [[ "$login_init_cmd" != "" ]]
	1690	then
	1691	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1692	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1693	line=$(echo "$login_init_cmd" \| cut -c46-)
	1694	while [[ "$line" != "" ]]
	1695	do
	1696	column1=""
	1697	column2=$(echo "$line" \| cut -c-45)
	1698	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1699	line=$(echo "$line" \| cut -c46-)
	1700	done
	1701	fi
	1702
	1703	if [[ "$module_commands" != "" ]]
	1704	then
	1705	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1706	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1707	line=$(echo "$module_commands" \| cut -c46-)
	1708	while [[ "$line" != "" ]]
	1709	do
	1710	column1=""
	1711	column2=$(echo "$line" \| cut -c-45)
	1712	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1713	line=$(echo "$line" \| cut -c46-)
	1714	done
	1715	fi
	1716	printf "\| \| \n"
[3236]	1717	column1="run identifier:"; column2=$run_identifier
[2380]	1718	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1719	column1="activation string list:"; column2=$(echo $activation_string_list)
	1720	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1721
	1722	if [[ "$ocean_file_appendix" = true ]]
	1723	then
	1724	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1725	fi
	1726
	1727	if [[ "$source_list" != "" ]]
	1728	then
	1729	printf "\| \| \n"
	1730	printf "\| Files to be compiled: \| \n"
	1731	line=$source_list
	1732	while [[ "$line" != "" ]]
	1733	do
	1734	linestart=$(echo $line \| cut -c-70)
	1735	printf "\| %-70s \| \n" "$linestart"
	1736	line=$(echo "$line" \| cut -c71-)
	1737	done
	1738	fi
	1739	printf "#------------------------------------------------------------------------#"
	1740
	1741
	1742
	1743	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1744	if [[ $do_trace = true ]]
	1745	then
	1746	(( i = 0 ))
[2610]	1747	while (( i < nr_of_input_files ))
[2380]	1748	do
	1749	(( i = i + 1 ))
	1750	if (( i == 1 ))
	1751	then
	1752	printf "\n\n >>> INPUT-file assignments:\n"
	1753	fi
	1754	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1755	done
	1756	(( i = 0 ))
	1757	while (( i < iout ))
	1758	do
	1759	(( i = i + 1 ))
	1760	if (( i == 1 ))
	1761	then
	1762	printf "\n\n >>> OUTPUT-file assignments:\n"
	1763	fi
	1764	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1765	done
	1766	(( i = 0 ))
	1767	while (( i < iic ))
	1768	do
	1769	(( i = i + 1 ))
	1770	if (( i == 1 ))
	1771	then
	1772	printf "\n\n >>> INPUT-commands:\n"
	1773	fi
	1774	printf "\n ${in_command[$i]}"
	1775	done
	1776	(( i = 0 ))
	1777	while (( i < ioc ))
	1778	do
	1779	(( i = i + 1 ))
	1780	if (( i == 1 ))
	1781	then
	1782	printf "\n\n >>> OUTPUT-commands:\n"
	1783	fi
	1784	printf "\n ${out_command[$i]}"
	1785	done
	1786	fi
	1787
	1788	# QUERY FOR CONTINUE
	1789	if [[ $silent = false && $running_in_batch_mode = false ]]
	1790	then
	1791	antwort=dummy
	1792	printf "\n\n"
	1793	printf " >>> everything o.k. (y/n) ? "
	1794	while read antwort
	1795	do
	1796	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1797	then
	1798	printf " >>> everything o.k. (y/n) ? "
	1799	else
	1800	break
	1801	fi
	1802	done
	1803	if [[ $antwort = n \|\| $antwort = N ]]
	1804	then
	1805	locat=user_abort; (( iec = 0 )); exit
	1806	fi
	1807	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1808	then
[2566]	1809	printf "\n *** batch-job will be created and submitted"
[2380]	1810	else
[2566]	1811	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1812	fi
	1813	fi
	1814
	1815
	1816
	1817	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1818	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1819	then
	1820
	1821	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1822	then
[2566]	1823	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1824	else
[2566]	1825	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1826	fi
	1827
[2422]	1828	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1829	# IT SHALL BE CREATED
	1830	ask_for_make_depository=false
	1831	if [[ $create_remote_batch_job = true ]]
	1832	then
	1833
	1834	line=`grep %base_directory $config_file`
[3236]	1835	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1836	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1837
[3236]	1838	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1839	then
	1840	printf "\n\n +++ make depository \"${make_depository}\""
	1841	printf "\n on remote host not found!"
	1842	ask_for_make_depository=true
	1843	fi
[3236]	1844	rm ${configuration_identifier}_last_make_protokoll
[2422]	1845
	1846	else
	1847
	1848	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1849	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1850	if [[ ! -d ${make_depository} ]]
	1851	then
	1852	printf "\n\n +++ make depository \"${make_depository}\""
	1853	printf "\n on local host not found!"
	1854	ask_for_make_depository=true
	1855	fi
	1856
	1857	fi
	1858
	1859	if [[ $ask_for_make_depository = true ]]
	1860	then
	1861
	1862	antwort=dummy
	1863	printf "\n\n"
	1864	printf " >>> Create a new one (y/n) ? "
	1865	while read antwort
	1866	do
	1867	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1868	then
	1869	printf " >>> Create a new one (y/n) ? "
	1870	else
	1871	break
	1872	fi
	1873	done
	1874	if [[ $antwort = n \|\| $antwort = N ]]
	1875	then
	1876	locat=user_abort; (( iec = 0 )); exit
	1877	fi
	1878
[2566]	1879	if [[ $do_trace = true ]]
	1880	then
[3455]	1881	palmbuild -c $configuration_identifier
[2566]	1882	else
[3455]	1883	palmbuild -v -c $configuration_identifier
[2566]	1884	fi
[2422]	1885
[3312]	1886	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1887	then
	1888
	1889	# ABORT IN CASE OF COMPILATION PROBLEMS
	1890	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1891	locat=make_depository
	1892	exit
	1893	else
	1894	echo " *** now continue with creating executable and other sources"
	1895	fi
	1896
	1897	fi
	1898
[2566]	1899	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1900	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1901
[3312]	1902	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1903	then
	1904
	1905	# ABORT IN CASE OF COMPILATION PROBLEMS
	1906	printf "\n +++ error while creating executable and/or other sources"
	1907	locat=execution
[2990]	1908	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1909	exit
	1910
	1911	else
	1912
[2566]	1913	printf " *** executable and other sources created\n"
[2990]	1914	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1915
	1916	fi
	1917
	1918	fi
	1919
	1920
[2669]	1921	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1922	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1923	if [[ $create_remote_batch_job = true ]]
	1924	then
	1925	(( i = 0 ))
[2610]	1926	while (( i < nr_of_input_files ))
[2605]	1927	do
	1928	(( i = i + 1 ))
[2669]	1929	if [[ "${actionin[$i]}" = tr ]]
[2605]	1930	then
	1931	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1932	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1933	fi
	1934	done
	1935	if (( i > 0 ))
	1936	then
[3025]	1937	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1938	fi
	1939	fi
	1940
	1941
[2380]	1942	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1943	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1944	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1945	then
	1946
	1947	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1948	if [[ $running_in_batch_mode = false ]]
	1949	then
	1950	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1951	# FOLDER
[2566]	1952	mkdir -p $tempdir
	1953	chmod go+rx $tempdir
	1954	cd $tempdir
	1955	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1956	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1957
	1958	else
	1959
	1960	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1961	printf "\n *** running in temporary directory: $tempdir"
[2380]	1962
	1963	fi
	1964
	1965
	1966	# PROVIDE THE INPUT FILES
	1967	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1968	optional_files_missing=false
[2380]	1969	(( i = 0 ))
[2610]	1970	while (( i < nr_of_input_files ))
[2380]	1971	do
	1972	(( i = i + 1 ))
	1973	if (( i == 1 ))
	1974	then
	1975	printf "\n\n *** providing INPUT-files:\n$dashes"
	1976	fi
	1977
	1978
	1979	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1980	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1981	then
[2669]	1982	optional_files_missing=true
[2380]	1983	continue
	1984	fi
	1985
	1986	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1987	files_for_cores=false; filetype=file
	1988	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1989	then
	1990	files_for_cores=true; filetype=files
	1991	actionin[$i]=""
	1992	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1993	then
	1994	actionin[$i]=""
	1995	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1996	then
	1997	files_for_cores=true; filetype=files
	1998	actionin[$i]="ln"
	1999	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	2000	then
	2001	actionin[$i]="ln"
	2002	fi
	2003
	2004	if [[ $files_for_cores = true ]]
	2005	then
	2006	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2007	else
	2008	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2009	fi
	2010
	2011	# INPUT-FILES TO BE LINKED
	2012	if [[ "${actionin[$i]}" = ln ]]
	2013	then
	2014
	2015	printf "\n $filetype will be linked"
	2016	if [[ $files_for_cores = false ]]
	2017	then
	2018	if [[ -f "${absnamein[$i]}" ]]
	2019	then
	2020	ln ${absnamein[$i]} ${localin[$i]}
	2021	got_tmp[$i]=true
	2022	fi
	2023	else
	2024	if [[ -d "${absnamein[$i]}" ]]
	2025	then
[2396]	2026	mkdir -p ${localin[$i]}
[2380]	2027	cd ${absnamein[$i]}
	2028	for file in $(ls *)
	2029	do
[2566]	2030	ln $file $tempdir/${localin[$i]}
[2380]	2031	done >\|/dev/null 2>&1
[2566]	2032	cd $tempdir
[2380]	2033	fi
	2034
	2035	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2036	if [[ ! -f "${localin[$i]}/_000000" ]]
	2037	then
	2038	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2039	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2040	fi
	2041
	2042	got_tmp[$i]=true
	2043	fi
	2044	fi
	2045
	2046	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2047	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2048	then
	2049
	2050	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2051	then
	2052
	2053	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2054	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2055	printf "\n file will be provided for $cores processors"
[2396]	2056	mkdir -p ${localin[$i]}
[2380]	2057	ival=$cores
	2058	(( ii = 0 ))
	2059	while (( ii <= ival-1 ))
	2060	do
	2061	if (( ii < 10 ))
	2062	then
	2063	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2064	elif (( ii < 100 ))
	2065	then
	2066	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2067	elif (( ii < 1000 ))
	2068	then
	2069	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2070	else
	2071	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2072	fi
	2073	(( ii = ii + 1 ))
	2074	done
	2075
	2076	else
	2077
	2078	if [[ $files_for_cores = true ]]
	2079	then
	2080
	2081	# PROVIDE FILES FOR EACH CORE
	2082	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2083	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2084	printf "\n providing $cores files for the respective cores"
[2396]	2085	mkdir -p ${localin[$i]}
[2380]	2086	if [[ $link_local_input = true ]]
	2087	then
	2088	printf " files will be linked\n"
	2089	cd ${absnamein[$i]}
	2090	for file in $(ls *)
	2091	do
	2092	ln -f $file ${localin[$i]}
	2093	done
[2566]	2094	cd $tempdir
[2380]	2095	fi
	2096
	2097	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2098	if [[ ! -f "${localin[$i]}/_000000" ]]
	2099	then
	2100	if [[ $link_local_input = true ]]
	2101	then
	2102	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2103	fi
	2104	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2105	fi
	2106
	2107	else
	2108
	2109	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2110	if [[ $link_local_input = true ]]
	2111	then
	2112	printf " file will be linked\n"
	2113	ln -f ${absnamein[$i]} ${localin[$i]}
	2114	fi
[2605]	2115	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2116	if [[ ! -f "${localin[$i]}" ]]
	2117	then
	2118	if [[ $link_local_input = true ]]
	2119	then
	2120	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2121	fi
[2669]	2122	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2123	then
	2124	mv ${absnamein[$i]} ${localin[$i]}
	2125	else
	2126	cp ${absnamein[$i]} ${localin[$i]}
	2127	fi
[2380]	2128	fi
	2129	fi
	2130	fi
	2131	fi
	2132
	2133	done
	2134	if (( i != 0 ))
	2135	then
[2669]	2136	if [[ $optional_files_missing = true ]]
	2137	then
	2138	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2139	fi
[2380]	2140	printf "\n$dashes\n *** all INPUT-files provided \n"
	2141	fi
	2142
	2143
	2144	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2145	(( i = 0 ))
	2146	while (( i < iic ))
	2147	do
	2148	(( i = i + 1 ))
	2149	if (( i == 1 ))
	2150	then
	2151	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2152	fi
	2153	printf "\n >>> ${in_command[$i]}"
	2154	eval ${in_command[$i]}
	2155	if (( i == iic ))
	2156	then
	2157	printf "\n$dashes\n"
	2158	fi
	2159	done
	2160
	2161
[3313]	2162	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2163	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2164	then
	2165	progress_bar_disabled=true
	2166	else
	2167	progress_bar_disabled=false
	2168	fi
	2169
	2170
[2380]	2171	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2172	# (FILE ENVPAR WILL BE READ BY PALM)
	2173	cat > ENVPAR << EOF
[3236]	2174	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2175	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2176	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2177	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2178	maximum_cpu_time_allowed = ${cpumax}.,
	2179	revision = '$global_revision',
[3313]	2180	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2181
	2182	EOF
	2183
	2184
	2185	# STARTING THE EXECUTABLE
	2186	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2187	PATH=$PATH:$tempdir
[2380]	2188
	2189
	2190	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2191	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2192	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2193	eval line=\"$line\"
	2194	execute_command="$line"
	2195
	2196
	2197	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2198	if [[ "$execute_command_for_combine" = "" ]]
	2199	then
	2200	eval line2=\"$line2\"
	2201	execute_command_for_combine="$line2"
	2202	fi
	2203
[2380]	2204
	2205
	2206	# PROVIDE A HOSTFILE, IF REQUIRED
	2207	if [[ "$hostfile" != "" ]]
	2208	then
	2209
	2210	if [[ $hostfile = auto ]]
	2211	then
	2212	# CREATE A NEW HOSTFILE
	2213	(( ii = 1 ))
	2214	while (( ii <= cores / threads_per_task ))
	2215	do
	2216	echo $(hostname) >> hostfile
	2217	(( ii = ii + 1 ))
	2218	done
	2219	if (( cores / threads_per_task == 0 ))
	2220	then
	2221	echo $(hostname) >> hostfile
	2222	fi
	2223
	2224	else
	2225	cp $hostfile hostfile
	2226	fi
	2227	eval line=\"`head -n $ii hostfile`\"
	2228	printf "\n *** running on: $line"
	2229	fi
	2230
	2231
	2232
	2233	# SET THE NUMBER OF OPENMP-THREADS
	2234	if [[ $use_openmp = true ]]
	2235	then
	2236	export OMP_NUM_THREADS=$threads_per_task
	2237	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2238	else
	2239	export OMP_NUM_THREADS=1
	2240	fi
	2241
	2242
[2610]	2243	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2244	if [[ $run_coupled_model = false ]]
	2245	then
	2246	if [[ "$ocean_file_appendix" = true ]]
	2247	then
	2248	echo "precursor_ocean" > coupling_steering
	2249	else
	2250	echo "precursor_atmos" > coupling_steering
	2251	fi
	2252	else
	2253	(( iia = $cores_atmos / $threads_per_task ))
	2254	(( iio = $cores_ocean / $threads_per_task ))
	2255	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2256	printf "\n\n"
	2257	echo "coupled_run $iia $iio" > coupling_steering
	2258	fi
	2259
	2260	printf "\n *** execute command:"
	2261	printf "\n \"$execute_command\" \n\n"
	2262
	2263
[3393]	2264	if [[ $progress_bar_disabled = true ]]
[2380]	2265	then
[3402]	2266	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2267	exit_code=${PIPESTATUS[0]}
	2268	else
	2269	$execute_command < coupling_steering &> >(tee STDOUT)
	2270	exit_code=${PIPESTATUS[0]}
	2271	fi
[2380]	2272
[3393]	2273	if [[ ${exit_code} != 0 ]]
	2274	then
	2275
[2380]	2276	# ABORT IN CASE OF RUNTIME ERRORS
	2277	printf "\n +++ runtime error occured"
	2278	locat=execution
	2279	exit
	2280
	2281	else
	2282
	2283	printf "\n$dashes\n *** execution finished \n"
	2284
	2285	fi
	2286
	2287
	2288	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2289	# BY EACH CORE INTO ONE FILE
	2290	if [[ ! -f combine_plot_fields.x ]]
	2291	then
	2292
	2293	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2294	printf "\n 2d- and/or 3d-data may be incomplete!"
	2295	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2296
	2297	elif [[ "$combine_plot_fields" == true ]]
	2298	then
	2299
	2300	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2301	$execute_command_for_combine
	2302
	2303	else
	2304
	2305	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2306	# DATA OUTPUT
[2380]	2307	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2308	fi
	2309
	2310
	2311
	2312	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2313	(( i = 0 ))
	2314	while (( i < ioc ))
	2315	do
	2316	(( i = i + 1 ))
	2317	if (( i == 1 ))
	2318	then
	2319	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2320	fi
[2799]	2321
	2322	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2323	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2324
[2380]	2325	printf "\n >>> ${out_command[$i]}"
	2326	eval ${out_command[$i]}
	2327	if (( i == ioc ))
	2328	then
	2329	printf "\n$dashes\n"
	2330	fi
	2331	done
	2332
	2333
[2610]	2334	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2335	# WILDCARDS
[2380]	2336	(( i = 0 ))
[2610]	2337	(( nr_of_output_files = 0 ))
	2338
[2380]	2339	while (( i < iout ))
	2340	do
[2610]	2341
[2380]	2342	(( i = i + 1 ))
[2610]	2343
	2344	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2345	# CREATE A LIST FOR THE DETECTED ENDINGS
	2346	if [[ "${multout[$i]}" = true ]]
	2347	then
	2348	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2349	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2350	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2351
	2352	endings="DEFAULT"
	2353	while read line
	2354	do
	2355	# remove the local name from the beginning
	2356	localnamestring="${localout_pre[$i]}"
	2357	length_localname=${#localnamestring}
	2358	ending=${line:${length_localname}}
	2359
	2360	if [[ "$ending" != "" ]]
	2361	then
	2362	endings="$endings $ending"
	2363	fi
	2364
	2365	done <filelist
	2366
	2367	rm filelist
	2368
	2369	else
	2370
	2371	# SINGLE NAME
	2372	endings=DEFAULT
	2373
	2374	fi
	2375
	2376	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2377	for ending in $endings
	2378	do
	2379
	2380	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2381	if [[ $ending = DEFAULT ]]
	2382	then
	2383	ending=""
	2384	fi
	2385
	2386	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2387	(( nr_of_output_files = nr_of_output_files + 1 ))
	2388	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2389	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2390	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2391	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2392	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2393	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2394	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2395
	2396	done
	2397
	2398	done
	2399
	2400
	2401
	2402
	2403	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2404	(( i = 0 ))
	2405	while (( i < nr_of_output_files ))
	2406	do
	2407	(( i = i + 1 ))
[2380]	2408	if (( i == 1 ))
	2409	then
	2410	printf "\n\n *** saving OUTPUT-files:"
	2411
	2412	# GET RUN NUMBER ASSIGNED BY PALM
	2413	if [[ -f RUN_NUMBER ]]
	2414	then
	2415	read run_number < RUN_NUMBER
	2416	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2417	usecycle_option="-U $run_number"
	2418	else
	2419	run_number=0
	2420	usecycle_option=""
	2421	fi
	2422	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2423	then
[2404]	2424	printf "\n *** in case of SCP transfers to local host"
	2425	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2426	fi
	2427	printf "\n$dashes"
	2428	fi
	2429
	2430	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2431	then
	2432
[3236]	2433	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2434
	2435	# DETERMINE THE CYCLE NUMBER
	2436	ls -1 -d $filename > filelist 2>/dev/null
	2437	ls -1 -d $filename.* >> filelist 2>/dev/null
	2438	while read line
	2439	do
	2440
	2441	# filename without path (i.e. after the last "/")
	2442	basefilename=$(basename ${line})
	2443
	2444	# check if there is an extension
	2445	extension=${basefilename##*.}
	2446	if [[ "$extension" = "${extout[$i]}" ]]
	2447	then
	2448	basefilename=${basefilename%.*}
	2449	fi
	2450
	2451	# check for an existing cycle number
	2452	cycle=${basefilename##*.}
	2453	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2454	then
[2669]	2455	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2456	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2457	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2458	else
	2459	(( icycle = 1 ))
	2460	fi
	2461
	2462	if (( icycle > maxcycle ))
	2463	then
	2464	(( maxcycle = icycle ))
	2465	fi
	2466
	2467	done <filelist
	2468	rm filelist
	2469
	2470
	2471	# SET THE CYCLE NUMBER
	2472	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2473	if [[ "${actionout[$i]}" = a ]]
	2474	then
	2475	(( maxcycle = maxcycle - 1 ))
	2476	fi
	2477
	2478	(( cycnum[$i] = maxcycle ))
	2479	pathout[$i]=$filename
	2480
	2481
	2482	# ADD CYCLE NUMBER TO FILENAME
	2483	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2484	if [[ "${actionout[$i]}" != "a" ]]
	2485	then
	2486	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2487	# WITH AN EXISTING CYCLE NUMBER
	2488	if (( run_number >= cycnum[$i] ))
	2489	then
	2490	(( cycnum[$i] = run_number ))
	2491	else
	2492	if (( run_number > 0 ))
	2493	then
	2494	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2495	fi
	2496	fi
	2497	fi
	2498	if (( cycnum[$i] > 0 ))
	2499	then
[2600]	2500	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2501	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2502	fi
	2503	fi
	2504
	2505	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2506	files_for_cores=false; filetype=file
	2507	link_local_output=false
	2508	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2509	then
	2510	files_for_cores=true; filetype=directory
	2511	actionout[$i]=""
	2512	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2513	then
	2514	actionout[$i]=""
	2515	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2516	then
	2517	files_for_cores=true; filetype=directory
	2518	link_local_output=true
	2519	actionout[$i]=""
	2520	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2521	then
	2522	link_local_output
	2523	actionout[$i]=""
	2524	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2525	then
	2526	files_for_cores=true; filetype=directory
	2527	actionout[$i]="tr"
	2528	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2529	then
	2530	actionout[$i]="tr"
	2531	fi
	2532
	2533	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2534	then
[2669]	2535	if [[ ${warnout[$i]} = true ]]
	2536	then
	2537	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2538	fi
[2380]	2539	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2540	then
[2669]	2541	if [[ ${warnout[$i]} = true ]]
	2542	then
	2543	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2544	fi
[2380]	2545	else
	2546
	2547
	2548	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2549	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2550	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2551	then
	2552	if [[ $running_on_remote = true ]]
	2553	then
	2554
	2555	# SET OPTIONS FOR TRANSFER
	2556	if [[ "${actionout[$i]}" = tr ]]
	2557	then
	2558	if [[ $files_for_cores = false ]]
	2559	then
	2560	catalog_option=""
	2561	catalog_string=""
	2562	else
	2563	catalog_option="-c"
	2564	catalog_string="/"
	2565	fi
	2566	append_option=""
	2567	append_string=""
	2568	else
	2569	append_option="-A"
	2570	append_string="append"
	2571	fi
	2572
	2573	transfer_failed=false
	2574	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2575	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2576
	2577	# TRANSFER VIA SCP
	2578	if [[ "$remote_loginnode" != "" ]]
	2579	then
[3534]	2580	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]	2581	else
[3236]	2582	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]	2583	fi
[3312]	2584	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2585
	2586
	2587	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2588	if [[ $transfer_failed = true ]]
	2589	then
	2590	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2591	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2592
	2593	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2594	eval local_catalog=${pathout[$i]}
	2595	if [[ ! -d $local_catalog ]]
	2596	then
	2597	printf " *** local directory does not exist. Trying to create:\n"
	2598	printf " $local_catalog \n"
	2599	mkdir -p $local_catalog
	2600	fi
[3236]	2601	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2602	transfer_problems=true
	2603	fi
	2604
	2605	else
	2606
	2607	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2608	# BE COPIED OR APPENDED ON THIS MACHINE
	2609	if [[ "${actionout[$i]}" = tr ]]
	2610	then
	2611	actionout[$i]=""
	2612	else
	2613	actionout[$i]="a"
	2614	fi
	2615	fi
	2616	fi
	2617
	2618
	2619	# APPEND ON THIS MACHINE
	2620	if [[ "${actionout[$i]}" = "a" ]]
	2621	then
	2622	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2623	then
	2624	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2625	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2626	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2627	else
	2628	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2629	printf "\n ${pathout[$i]}\n"
	2630	cat ${localout[$i]} >> ${pathout[$i]}
	2631	fi
	2632	fi
	2633
	2634	# COPY ON THIS MACHINE
	2635	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2636	# ON DIFFERENT FILE-SYSTEMS
	2637	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2638	then
	2639
	2640	# COPY IN CASE OF RUNS ON SINGLE CORES
	2641	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2642	then
	2643	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2644	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2645	if [[ $link_local_output = true ]]
	2646	then
	2647	printf " file will be linked\n"
	2648	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2649	fi
	2650	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2651	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2652	then
	2653	if [[ $link_local_output = true ]]
	2654	then
	2655	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2656	fi
	2657	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2658	else
	2659	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2660	fi
	2661	else
	2662	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2663	printf "\n ${pathout[$i]}\n"
	2664	if [[ $link_local_output = true ]]
	2665	then
	2666	printf " file will be linked\n"
	2667	ln -f ${localout[$i]} ${pathout[$i]}
	2668	fi
	2669	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2670	if [[ ! -f "${pathout[$i]}" ]]
	2671	then
	2672	if [[ $link_local_output = true ]]
	2673	then
	2674	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2675	fi
	2676	cp ${localout[$i]} ${pathout[$i]}
	2677	else
	2678	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2679	fi
	2680	fi
	2681
	2682	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2683	then
	2684
	2685	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2686	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2687	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2688	printf "\n ${pathout[$i]}\n"
	2689	if [[ $link_local_output = true ]]
	2690	then
	2691	printf " files will be linked\n"
[2396]	2692	mkdir -p ${pathout[$i]}
[2380]	2693	cd ${localout[$i]}
	2694	for file in $(ls *)
	2695	do
	2696	ln -f $file ${pathout[$i]}
	2697	done >\|/dev/null 2>&1
[2566]	2698	cd $tempdir
[2380]	2699	fi
	2700
	2701	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2702	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2703	then
	2704	if [[ $link_local_output = true ]]
	2705	then
	2706	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2707	fi
[3025]	2708	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2709	cp -r ${localout[$i]}/* ${pathout[$i]}
	2710	fi
	2711
	2712	fi
	2713	fi
	2714	done
	2715
	2716	if (( i != 0 ))
	2717	then
	2718	if [[ $transfer_problems = true ]]
	2719	then
	2720	printf "\n$dashes\n *** OUTPUT-files saved"
	2721	printf "\n +++ WARNING: some data transfers failed! \n"
	2722	else
	2723	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2724	fi
	2725	fi
	2726
	2727
	2728	# IF REQUIRED, START A RESTART-JOB
	2729	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2730	if [[ -f CONTINUE_RUN ]]
	2731	then
	2732
	2733	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2734	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2735	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2736	# -b START A BATCH JOB
	2737	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2738	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2739	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2740
[2957]	2741	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2742	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2743	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2744	then
	2745	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2746	fi
[2380]	2747
	2748	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2749	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2750	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2751	then
[2381]	2752	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2753	fi
	2754
	2755
	2756	# START THE RESTART-JOB
	2757	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2758	echo " $prc"
	2759	printf "\n$dashes\n"
	2760	if [[ $running_on_remote = true ]]
	2761	then
	2762
	2763	echo "*** ssh will be used to initiate restart-runs!"
	2764	echo " return_address=\"$return_address\" "
	2765	echo " return_username=\"$local_username\" "
	2766
	2767	if [[ "$remote_loginnode" != "" ]]
	2768	then
[3534]	2769	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]	2770	else
[3534]	2771	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2772	fi
	2773
	2774	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2775	sleep 30
	2776
	2777	else
	2778
	2779	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2780	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2781	cd - > /dev/null
	2782
	2783	fi
	2784
[3132]	2785	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2786	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2787	then
	2788	printf "\n$dashes\n +++ creating restart run failed \n"
	2789	locat=create_restart
[3455]	2790	rm palmrun_restart.log
[3132]	2791	exit
	2792	else
	2793	printf "\n$dashes\n *** restart run initiated \n"
	2794	rm palmrun_restart.log
	2795	fi
[2380]	2796
[3132]	2797
[2380]	2798	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2799	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2800	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2801	# MAY BE VERY HUGE)
	2802	(( i = 0 ))
[2610]	2803	while (( i < nr_of_input_files ))
[2380]	2804	do
	2805	(( i = i + 1 ))
	2806	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2807	then
	2808	rm -r ${absnamein[$i]}
	2809	fi
	2810	done
	2811
	2812	fi
	2813
	2814
	2815	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2816	cd $HOME
[2566]	2817	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2818
	2819
	2820	else
	2821
	2822
	2823	# PREPARING ACTIONS,
	2824	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2825
	2826	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2827	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2828	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2829	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2830	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2831	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2832	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2833	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2834	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2835	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2836	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2837	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2838	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2839	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2840	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2841	if [[ $create_remote_batch_job = true ]]
	2842	then
	2843	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2844	if [[ $do_trace = true ]]
	2845	then
	2846	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2847	fi
[2380]	2848	elif [[ $create_batch_job = true ]]
	2849	then
	2850	palmrun_com=${palmrun_com}" -j"
[2420]	2851	if [[ $do_trace = true ]]
	2852	then
	2853	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2854	fi
[2380]	2855	fi
	2856
	2857
	2858	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2859	# REMOTE HOST
[3236]	2860	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2861	job_protocol_file=$job_protocol_file_local
	2862	if [[ $create_remote_batch_job = true ]]
	2863	then
[3236]	2864	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2865	job_protocol_file=$job_protocol_file_remote
	2866	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2867	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2868	fi
	2869
	2870
	2871	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2872	jobfile=jobfile.$run_id_number
[2380]	2873
	2874
	2875	# FIRST CREATE THE BATCH DIRECTIVES
	2876	(( i = 0 ))
	2877	while (( i < ibd ))
	2878	do
	2879	(( i = i + 1 ))
[2693]	2880	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2881	eval line=\"$line\"
	2882	echo "$line" >> $jobfile
	2883	done
	2884	echo " " >> $jobfile
	2885
	2886
	2887	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2888	# PROTOCOL
	2889	if [[ $create_remote_batch_job = true ]]
	2890	then
[3236]	2891	echo "set +vx" >> $jobfile
	2892	echo "trap '" >> $jobfile
	2893	echo "set +vx" >> $jobfile
	2894	echo "cd ${remote_jobcatalog}" >> $jobfile
	2895	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2896
	2897	# ADD THE BATCH DIRECTIVES
	2898	(( i = 0 ))
	2899	while (( i < ibdt ))
	2900	do
	2901	(( i = i + 1 ))
[2693]	2902	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2903	eval line=\"$line\"
	2904	echo "$line" >> $jobfile
	2905	done
	2906	echo " " >> $jobfile
	2907
	2908	echo "set -x" >> $jobfile
[3534]	2909	if [[ "$remote_loginnode" != "" ]]
	2910	then
	2911	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}\" " >> $jobfile
	2912	else
	2913	echo "${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
	2914	fi
[2380]	2915	echo "%%END%%" >> $jobfile
	2916	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2917	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2918	echo "rm $scpjob_file" >> $jobfile
[2404]	2919	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2920	echo "set -x" >> $jobfile
	2921	echo " ' exit" >> $jobfile
	2922	fi
	2923
	2924
	2925	# ACTIVATE ERROR-TRACEBACK
	2926	if [[ $do_trace = true ]]
	2927	then
	2928	echo "set -x" >> $jobfile
	2929	else
	2930	echo "set +vx" >> $jobfile
	2931	fi
	2932
	2933
	2934	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2935	if [[ "$login_init_cmd" != "" ]]
	2936	then
	2937	echo "$login_init_cmd" >> $jobfile
	2938	fi
	2939	if [[ "$module_commands" != "" ]]
	2940	then
	2941	echo "$module_commands" >> $jobfile
	2942	fi
	2943
	2944
	2945	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2946	if [[ $create_remote_batch_job = true ]]
	2947	then
	2948	echo "mkdir $tempdir" >> $jobfile
	2949	echo "chmod go+rx $tempdir" >> $jobfile
	2950	else
	2951	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2952	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2953	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2954	mkdir $tempdir
	2955	chmod go+rx $tempdir
	2956	fi
	2957	echo "cd $tempdir" >> $jobfile
	2958	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2959	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2960	echo "export PATH=.:\$PATH" >> $jobfile
	2961	echo "export execute_palmrun=true" >> $jobfile
	2962
	2963
	2964	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2965	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2966	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2967	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2968	echo "export LOCAL_PWD" >> $jobfile
	2969
	2970
	2971	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2972	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2973	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2974
	2975
	2976	# CALL PALMRUN WITHIN THE JOB
	2977	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2978	echo "set -x" >> $jobfile
	2979	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2980
	2981
	2982	# TRANSFER JOBFILE TO THE TARGET HOST
	2983	if [[ $create_jobfile_only = false ]]
	2984	then
	2985
[3505]	2986	# CREATE LOCAL JOB FOLDER
	2987	eval local_jobcatalog=$local_jobcatalog
	2988	if [[ ! -d $local_jobcatalog ]]
	2989	then
	2990	echo " "
	2991	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	2992	mkdir $local_jobcatalog
	2993	fi
	2994
[2380]	2995	if [[ $create_remote_batch_job = true ]]
	2996	then
	2997
[2420]	2998	echo " "
[2566]	2999	echo " *** transfer of job to remote host via scp"
[3505]	3000
	3001	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3002	ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" 2>&1
[3505]	3003
	3004	# COPY THE JOB FILE
[2420]	3005	if [[ $do_trace = true ]]
	3006	then
[3236]	3007	echo " scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id}"
[2420]	3008	fi
[3236]	3009	scp $ssh_key $PORTOPT $jobfile ${remote_username}@${remote_ip}:${remote_jobcatalog}/${configuration_identifier}_${run_id} > /dev/null
[2380]	3010
[3505]	3011	# SUBMIT THE JOB
[3549]	3012	printf " *** submit the job (output of submit command, e.g. the job-id, may follow) \n"
[2420]	3013	if [[ $do_trace = true ]]
	3014	then
[3549]	3015	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]	3016	fi
[3549]	3017	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]	3018
	3019	elif [[ $create_batch_job = true ]]
	3020	then
	3021
[2385]	3022	eval local_jobcatalog=$local_jobcatalog
[3236]	3023	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3024	cd $local_jobcatalog
[2380]	3025	echo " "
[2420]	3026	echo " *** submit the job"
	3027	if [[ $do_trace = true ]]
	3028	then
[3236]	3029	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3030	fi
[3236]	3031	$submit_command ${configuration_identifier}_${run_id}
	3032	rm ${configuration_identifier}_${run_id}
[2380]	3033	cd - > /dev/null
	3034
	3035	fi
	3036
	3037	rm -rf $jobfile
	3038
	3039	else
	3040
	3041	printf "\n *** jobfile created under name \"$jobfile\" "
	3042	printf "\n no batch-job has been sent!"
	3043
	3044	fi
	3045
	3046	fi # END OF REMOTE-PART

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