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source: palm/trunk/SCRIPTS/palmrun @ 3541

Last change on this file since 3541 was 3534, checked in by raasch, 6 years ago
inifor integrated in build mechanism, some bugfixes in inifor to avoid compile time errors, batch_scp for sending back the job protocol file is called via login-node if a login-node has been set in the config-file, ssh-calls rearranged to avoid output of system/user-profile messages
Property svn:executable set to ``* Property svn:keywords set to `Id Rev`
File size: 103.3 KB

Rev	Line
[2380]	1	#!/bin/bash
	2
	3	# palmrun - script for running PALM jobs
	4
	5	#--------------------------------------------------------------------------------#
[2696]	6	# This file is part of the PALM model system.
[2380]	7	#
	8	# PALM is free software: you can redistribute it and/or modify it under the terms
	9	# of the GNU General Public License as published by the Free Software Foundation,
	10	# either version 3 of the License, or (at your option) any later version.
	11	#
	12	# PALM is distributed in the hope that it will be useful, but WITHOUT ANY
	13	# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	14	# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	15	#
	16	# You should have received a copy of the GNU General Public License along with
	17	# PALM. If not, see <http://www.gnu.org/licenses/>.
	18	#
[2718]	19	# Copyright 2017-2018 Leibniz Universitaet Hannover
[2380]	20	#--------------------------------------------------------------------------------#
	21	#
	22	# Current revisions:
	23	# ------------------
	24	#
[2410]	25	#
[2380]	26	# Former revisions:
	27	# -----------------
[3032]	28	# $Id: palmrun 3534 2018-11-19 15:35:16Z gronemeier $
[3534]	29	# batch_scp for sending back the job protocol file is called via login-node if
	30	# a login-node has been set in the config-file
	31	# ssh-calls rearranged to avoid output of system/user-profile messages
	32	#
	33	# 3505 2018-11-08 09:14:30Z raasch
[3505]	34	# job folders are created in case that they do not exist
	35	#
	36	# 3455 2018-10-30 14:12:31Z raasch
[3455]	37	# options -h and -d renamed -c and -r, respectively
	38	#
	39	# 3402 2018-10-23 11:49:24Z knoop
[3346]	40	# job_id is set for compatibility reasons with older versions of config files
	41	#
	42	# 3313 2018-10-06 15:22:48Z knoop
[3294]	43	# more detailed error message for outdated fileconnection file
	44	#
	45	# 3236 2018-09-10 09:07:06Z raasch
[3236]	46	# warning issued in case of file connection file version mismatch,
	47	# host_configuration renamed configuration_identifier,
	48	# "host identifier" in header output renamed "config. identifier",
	49	# jobname renamed run_identifier,
	50	# run_id renamed run_id_number
	51	# job_id renamed run_id
	52	# option -r renamed -i
	53	#
	54	# 3151 2018-07-19 08:45:38Z raasch
[3151]	55	# removed additional listing of files to be compiled, print PALM code revision
	56	# in header
	57	#
	58	# 3132 2018-07-16 11:44:58Z raasch
[3132]	59	# create consistent error messages in case of failed restarts,
	60	# check existence of remote job catalog
	61	#
	62	# 3043 2018-05-25 10:47:54Z raasch
[3043]	63	# check for setting of fast_io_catalog
	64	#
	65	# 3033 2018-05-23 15:26:19Z raasch
[3025]	66	# -T option not required for interactive runs (tasks per node =
	67	# total number of cores is assumed as default, if option is not given),
	68	# reformatting of a few messages,
	69	# bugfix: destination output directory is created if attribute "pe" is set in
	70	# .palm.iofiles
	71	#
	72	# 2718 2018-01-02 08:49:38Z maronga
[2993]	73	# bugfix of r2990
	74	#
	75	# 2718 2018-01-02 08:49:38Z maronga
[2990]	76	# bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and
	77	# not in the working directory from where palmrun is called
	78	#
	79	# 2718 2018-01-02 08:49:38Z maronga
[2957]	80	# svfout in the activation string will be replaced now by svfin in case of
	81	# automatic restarts
	82	#
	83	# 2718 2018-01-02 08:49:38Z maronga
[2906]	84	# Introduction of new ENVIRONMENT variables read_svf and write_svf to consider
	85	# the possible output or input of sky view factors
	86	#
	87	# 2718 2018-01-02 08:49:38Z maronga
[2834]	88	# "fname" renamed to "jobname"
	89	#
	90	# 2718 2018-01-02 08:49:38Z maronga
[2799]	91	# parameters are allowed in output commands (OC:)
	92	#
	93	# 2718 2018-01-02 08:49:38Z maronga
[2789]	94	# bugfix: exit if no queue has been given neither with option -q nor in the
	95	# configuration file
	96	#
	97	# 2718 2018-01-02 08:49:38Z maronga
[2762]	98	# file connection file from trunk/SCRIPTS is taken by default
	99	#
	100	# 2718 2018-01-02 08:49:38Z maronga
[2716]	101	# Corrected "Former revisions" section
	102	#
	103	# 2696 2017-12-14 17:12:51Z kanani
	104	# Change in file header (GPL part)
	105	#
	106	# 2693 2017-12-13 12:33:49Z raasch
[2693]	107	# replacement of variables given by {{<variable>}} in configuration file is now
	108	# done in a more general way, variable names are written in small letters
	109	#
	110	# 2670 2017-12-06 16:32:19Z raasch
[2670]	111	# test printouts removed
	112	#
	113	# 2669 2017-12-06 16:03:27Z raasch
[2669]	114	# file attributes in .palm.iofiles restructured, "loc" attribute completely
	115	# removed,
	116	# wildcard (*) allowed in .palm.iofiles as file activation string for output
	117	# files,
	118	# informative messages in case of missing optional input files shortened
	119	# bugfix: variable cycle explicitly interpreted with 10 as the number base
	120	#
	121	# 2638 2017-11-23 12:44:23Z raasch
[2610]	122	# use of wildcards in file connection statements enabled
	123	#
	124	# 2605 2017-11-09 15:31:46Z raasch
[2605]	125	# in case of remote jobs, input files with "job" or "jobopt" (new) attribute
	126	# will not be sent with the job file any more, but copied into the
[2610]	127	# SOURCES_FOR_RUN... folder on the remote host, before the job is submitted
[2605]	128	#
	129	# 2600 2017-11-01 14:11:20Z raasch
[2600]	130	# cycle numbers are made three digits wide
	131	#
	132	# 2566 2017-10-20 08:50:47Z raasch
[2566]	133	# execute command for combine_plot_fields added
	134	# "TEMPDIR" renamed "tempdir"
	135	# temporary working directory for local batch jobs is created immediately within
	136	# the user's palmrun call, due to a requirement of the "grid engine" batch
	137	# system, where the working directory is given with batch directive -wd and must
	138	# already exist when the job is submitted,
	139	# informative messages in non-trace mode reduced and partly reformatted
	140	#
	141	# 2551 2017-10-18 07:25:11Z raasch
[2551]	142	# TEMPDIR added as replacement string to be used in batch directives
	143	#
	144	# 2512 2017-10-04 08:26:59Z raasch
[2507]	145	# bugfix for determining cycle numbers of NetCDF input files
	146	#
	147	# 2506 2017-09-29 08:30:37Z raasch
[2506]	148	# option -V added to check for an existing SOURCES_FOR_RUN_... folder
	149	# host configuration added to SOURCES_FOR_RUN_... folder name
	150	# host_identifier renamed host_configuration
	151	# option -W added to allow for job dependencies
	152	#
	153	# 2501 2017-09-26 11:41:55Z raasch
[2501]	154	# default value for number of cores (option -X) set to 1
	155	# bugfix for mechanism which overwrites configuration file settings with values
	156	# provided by palmrun options
	157	#
	158	# 2499 2017-09-22 16:47:58Z kanani
[2499]	159	# option -h named configuration identifier
	160	#
	161	# 2480 2017-09-19 06:24:14Z maronga
[2480]	162	# bugfix for last revision
	163	#
	164	# 2479 2017-09-19 06:12:16Z raasch
[2479]	165	# option -A (project account number) added
	166	#
	167	# 2422 2017-09-08 08:25:41Z raasch
[2410]	168	# initial revision
[2380]	169	#
	170	#--------------------------------------------------------------------------------#
	171	# palmrun - script for running PALM jobs on local and remote hosts
	172	#--------------------------------------------------------------------------------#
	173
	174
	175
	176	# DECLARATION OF VARIABLES AND THEIR DEFAULT VALUES
	177
	178	set +o allexport # SUPPRESS EXPORT OF ALL VARIABLES, SINCE IN THE PAST THIS
	179	# LEAD TO PROBLEMS IN ROUTINES CALLED BY PALMRUN
	180	# (TOO MANY ARGUMENTS - PROBLEM)
	181	set +o noclobber # EXISTING FILES ARE ALLOWED TO BE OVERWRITTEN
	182
[2610]	183	typeset -i ibd=0 ibdt=0 iec=0 iic=0 iin=0 ioc=0 iout=0 nr_of_input_files=0
	184	typeset -i nr_of_output_files=0
[2380]	185	typeset -x -i memory=0 # HAS TO BE EXPORTED HERE, OTHERWISE AN UNKNOWN SIDE
	186	# SIDE EFFECT MAY CAUSE DATA LOSS WHEN GETOPTS IS READING THE
	187	# SCRIPT-OPTION ARGUMENTS
	188	typeset -i cores cputime cpu_hours cpu_minutes cpu_seconds i ii iia iii iio
	189	typeset -i icycle inode ival maxcycle mpi_tasks
	190	typeset -i nodes remaining_cores run_number tasks_per_node threads_per_task
	191
	192	activation_string_list=""
	193	AddFilenames=""
	194	combine_plot_fields=true
	195	compiler_name=""
	196	compiler_name_ser=""
	197	compiler_options=""
[3236]	198	configuration_identifier="default"
[2501]	199	cores=1
[2380]	200	cores_atmos=0
	201	cores_ocean=0
	202	coupled_dist=""
	203	cpp_options=""
	204	cpumax=0
[2506]	205	create_batch_job=false
[2380]	206	create_jobfile_only=false
	207	create_remote_batch_job=false
	208	dashes=" ----------------------------------------------------------------------------"
	209	defaultqueue=""
[2506]	210	delete_temporary_catalog=true
[2380]	211	do_compile=true
	212	do_trace=false
	213	executable=""
	214	execute_command=""
	215	execution_error=false
[2762]	216	fileconnection_file=trunk/SCRIPTS/.palm.iofiles
[2380]	217	global_revision=""
	218	hostfile=""
	219	hp=""
	220	keep_data_from_previous_run=false
	221	link_local_input=false
	222	link_local_output=false
[2388]	223	linker_options=""
[2385]	224	local_jobcatalog=""
[2380]	225	locat=normal
	226	makefile=""
	227	max_par_io_str=""
	228	prc=$0
	229	while [[ $(echo $prc \| grep -c "/") != 0 ]]
	230	do
	231	prc=`echo $prc \| cut -f2- -d"/"`
	232	done
	233	module_calls=""
[2506]	234	palmrun_memory=""
[2380]	235	palmrun_script_name=$prc
	236	openmp=false
[2506]	237	previous_job=""
[2479]	238	project_account=""
[2380]	239	queue=none
[2906]	240	read_svf=""
[2380]	241	restart_run=false
	242	return_address=""
[2385]	243	remote_jobcatalog=""
[2380]	244	remote_username=""
	245	running_in_batch_mode=false
[3313]	246	running_in_test_mode=false
[2380]	247	run_coupled_model=false
	248	run_id=""
[3236]	249	run_id_number=""
	250	run_identifier=test
[2380]	251	silent=false
	252	source_list=""
	253	source_path=""
[2501]	254	tasks_per_node=0
[2380]	255	threads_per_task=1
	256	transfer_problems=false
[2384]	257	user_source_path=""
[2506]	258	use_existing_sources_folder=""
[2380]	259	use_openmp=false
[3033]	260	version="palmrun 1.0 Rev$Rev: 3534 $"
[2380]	261	working_directory=`pwd`
	262	write_binary=""
[2906]	263	write_svf=""
[2380]	264
	265
	266	# ERROR HANDLING IN CASE OF EXIT
[2404]	267	trap 'if [[ $locat != normal && $locat != control_c ]]
[2380]	268	then
	269
	270	# CARRY OUT ERROR-COMMANDS GIVEN IN THE CONFIGURATION FILE (EC:)
	271	(( i = 0 ))
	272	while (( i < iec ))
	273	do
	274	(( i = i + 1 ))
	275	printf "\n *** Execution of ERROR-command:\n"
	276	printf " >>> ${err_command[$i]}\n"
	277	eval ${err_command[$i]}
	278	done
[2566]	279	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
[3312]	280	printf "\n\n+++ palmrun crashed \n\n"
	281	exit 1
	282	elif [[ $locat != normal ]]
[2380]	283	then
[3312]	284	[[ $delete_temporary_catalog = true ]] && (cd; rm -rf $tempdir)
	285	printf "\n+++ palmrun killed by \"^C\" \n\n"
	286	exit 2
	287	else
[2566]	288	printf "\n --> palmrun finished\n\n"
[3312]	289	exit 0
[2380]	290	fi' exit
	291
	292
	293	# ACTIONS IN CASE OF TERMINAL-BREAK (CONTROL-C):
[3312]	294	trap 'locat=control_c
	295	exit 1
[2380]	296	' 2
	297
	298
	299	# READ SHELLSCRIPT-OPTIONS AND REBUILD THE PALMRUN-COMMAND STRING (prc),
	300	# WHICH WILL BE USED TO START RESTART-JOBS
[3455]	301	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]	302	do
	303	case $option in
	304	(a) activation_string_list=$OPTARG; prc="$prc -a'$OPTARG'";;
[2479]	305	(A) project_account=$OPTARG; prc="$prc -A'$OPTARG'";;
[2380]	306	(b) create_batch_job=true; prc="$prc -b";;
	307	(B) delete_temporary_catalog=false; prc="$prc -B";;
[3455]	308	(c) configuration_identifier=$OPTARG; prc="$prc -c$OPTARG";;
[2380]	309	(C) restart_run=true; prc="$prc -C";;
	310	(F) create_jobfile_only=true;;
	311	(G) global_revision=$OPTARG; prc="$prc -G'$OPTARG'";;
[3236]	312	(i) run_id_number=$OPTARG;;
[2380]	313	(j) running_in_batch_mode=true;;
	314	(k) keep_data_from_previous_run=true; prc="$prc -k";;
[2501]	315	(m) palmrun_memory=$OPTARG; prc="$prc -m$OPTARG";;
[2380]	316	(M) makefile=$OPTARG; prc="$prc -M$OPTARG";;
	317	(O) use_openmp=true; threads_per_task=$OPTARG; prc="$prc -O$OPTARG";;
	318	(q) queue=$OPTARG; prc="$prc -q$OPTARG";;
[3455]	319	(r) run_identifier=$OPTARG; prc="$prc -r$OPTARG";;
[2380]	320	(R) return_address=$OPTARG;;
	321	(s) source_list=$OPTARG;;
[2501]	322	(t) palmrun_cpumax=$OPTARG; prc="$prc -t$OPTARG";;
[2380]	323	(T) palmrun_tasks_per_node=$OPTARG; prc="$prc -T$OPTARG";;
	324	(u) remote_username=$OPTARG; prc="$prc -u$OPTARG";;
	325	(U) return_username=$OPTARG; prc="$prc -U$OPTARG";;
	326	(v) silent=true; prc="$prc -v";;
[2506]	327	(V) use_existing_sources_folder="-V";;
[2380]	328	(w) max_par_io_str=$OPTARG; prc="$prc -w$OPTARG";;
[2506]	329	(W) previous_job=$OPTARG;;
[2380]	330	(x) do_trace=true;set -x; prc="$prc -x";;
[2501]	331	(X) palmrun_cores=$OPTARG; prc="$prc -X$OPTARG";;
[2380]	332	(y) ocean_file_appendix=true; prc="$prc -y";;
	333	(Y) run_coupled_model=true; coupled_dist=$OPTARG; prc="$prc -Y'$OPTARG'";;
[3313]	334	(z) running_in_test_mode=true;;
[2380]	335	(Z) combine_plot_fields=false; prc="$prc -Z";;
	336	(\?) printf "\n +++ unknown option $OPTARG \n"
	337	printf "\n --> type \"$0 ?\" for available options \n"
	338	locat=parameter;exit;;
	339	esac
	340	done
	341
	342
	343	# SKIP GIVEN OPTIONS TO READ POSITIONAL PARAMETER, IF GIVEN
	344	# CURRENTLY ONLY PARAMETER ? (TO OUTPUT A SHORT COMMAND INFO) IS ALLOWED
	345	(( to_shift = $OPTIND - 1 ))
	346	shift $to_shift
	347
	348	# PRINT SHORT DESCRIPTION OF PALMRUN OPTIONS
	349	if [[ "$1" = "?" ]]
	350	then
	351	(printf "\n *** Description of available palmrun options:\n"
	352	printf "\n Option Description Default-Value"
	353	printf "\n -a activation string list \"\" "
[2479]	354	printf "\n -A project account number ---"
[2380]	355	printf "\n -b batch-job on local machine ---"
	356	printf "\n -B do not delete temporary directory at end ---"
[3455]	357	printf "\n -c configuration identifier \"default\" "
[2380]	358	printf "\n -F create batch job file only ---"
	359	printf "\n -k keep data from previous run"
	360	printf "\n -m memory demand in MB (batch-jobs) 0 MB"
	361	printf "\n -M Makefile name Makefile"
	362	printf "\n -O threads per openMP task ---"
	363	printf "\n -q queue \"$queue\" "
[3455]	364	printf "\n -r run identifier test"
[2380]	365	printf "\n -s filenames of routines to be compiled \"\" "
	366	printf "\n must end with .f, .f90, .F, or .c !"
	367	printf "\n use \"..\" for more than one file and wildcards"
	368	printf "\n -s LM compiles all locally modified files"
	369	printf "\n -t allowed cpu-time in seconds (batch) 0"
[2384]	370	printf "\n -T tasks per node ---"
[2380]	371	printf "\n -u username on remote machine \"\" "
	372	printf "\n -v no prompt for confirmation ---"
[2506]	373	printf "\n -V check if SOURCES_FOR_RUN_... exists ---"
[2380]	374	printf "\n -w maximum parallel io streams as given by -X"
[2506]	375	printf "\n -W name of job to wait for ---"
[2380]	376	printf "\n -x tracing of palmrun for debug purposes ---"
	377	printf "\n -X # of processors (on parallel machines) 1"
	378	printf "\n -y add appendix \"_O\" to all local output"
	379	printf "\n files (ocean precursor runs followed by"
	380	printf "\n coupled atmosphere-ocean runs) ---"
	381	printf "\n -Y run coupled model, \"#1 #2\" with"
	382	printf "\n #1 atmosphere and #2 ocean processors \"#/2 #/2\" depending on -X"
	383	printf "\n -Z skip combine_plot_fields at the end of "
	384	printf "\n the simulation ---"
	385	printf "\n "
	386	printf "\n Possible values of positional parameter <modus>:"
	387	printf "\n \"?\" - this outline \n\n") \| more
	388	exit
	389	elif [[ "$1" != "" ]]
	390	then
	391	printf "\n +++ positional parameter $1 unknown \n"
	392	locat=parameter; exit
	393	fi
	394
	395
	396
	397	# SHORT STARTING MESSAGE
	398	printf "\n*** $version "
	399	printf "\n will be executed. Please wait ..."
	400
	401
[2506]	402	# BUILD THE CONFIGURATION-FILE NAME AND THE SOURCES_FOR_RUN-FOLDER NAME
[3236]	403	config_file=.palm.config.$configuration_identifier
	404	sources_for_run_catalog=SOURCES_FOR_RUN_${configuration_identifier}_$run_identifier
[2380]	405
	406
	407	# CHECK, IF CONFIGURATION FILE EXISTS
	408	if [[ ! -f $config_file ]]
	409	then
	410	printf "\n\n +++ configuration file: "
	411	printf "\n $config_file"
	412	printf "\n does not exist"
	413	locat=connect; exit
	414	fi
	415
	416
[2762]	417	# CHECK, IF USER PROVIDES OWN FILE CONNECTION FILE
	418	if [[ -f .palm.iofiles ]]
	419	then
[3236]	420
	421	# CHECK VERSION MISMATCH
	422	if [[ $running_in_batch_mode != true ]]
	423	then
	424	if [[ $(head -n1 $fileconnection_file) != $(head -n1 .palm.iofiles) ]]
	425	then
	426	printf "\n\n +++ WARNING: A file connection file has been found in your"
	427	printf "\n working directory, but its revision does not match"
	428	printf "\n the revision of the default (trunk) version."
[3294]	429	printf "\n You may need to update your connection file"
	430	printf "\n \"${working_directory}/.palm.iofiles\" !"
[3236]	431	fi
	432	fi
	433
[2762]	434	fileconnection_file=.palm.iofiles
[3236]	435
[2762]	436	fi
	437
	438
[2380]	439	# CHECK, IF FILE CONNECTION FILE EXISTS
	440	if [[ ! -f $fileconnection_file ]]
	441	then
	442	printf "\n\n +++ file connection file: "
	443	printf "\n $fileconnection_file"
	444	printf "\n does not exist"
	445	locat=connect; exit
	446	fi
	447
	448
[2404]	449	# CHECK, IF THE ACTIVATION_STRING_LIST HAS BEEN GIVEN
	450	if [[ "$activation_string_list" = "" ]]
	451	then
	452	printf "\n\n +++ no activation string list given: "
	453	printf "\n please set palmrun option \"-a\" "
	454	locat=palmrun_option; exit
	455	fi
	456
	457
	458	# SET VARIABLE TO ACTIVATE PALM BINARY OUTPUT FOR RESTARTS
	459	if [[ $(echo $activation_string_list \| grep -c "restart") != 0 ]]
	460	then
	461	write_binary=true
	462	else
	463	write_binary=false
	464	fi
	465
[2906]	466	# SET VARIABLE TO ACTIVATE WRITING OF SVF DATA
	467	if [[ $(echo $activation_string_list \| grep -c "svfout") != 0 ]]
	468	then
	469	write_svf=true
	470	else
	471	write_svf=false
	472	fi
[2404]	473
[2906]	474	# SET VARIABLE TO ACTIVATE READING OF SVF DATA
	475	if [[ $(echo $activation_string_list \| grep -c "svfin") != 0 ]]
	476	then
	477	read_svf=true
	478	else
	479	read_svf=false
	480	fi
	481
	482
[2380]	483	# READ AND EVALUATE THE CONFIGURATION-FILE
	484	[[ $silent = false ]] && printf "\n\n Reading the configuration file... "
	485
	486	# READ VARIABLE SETTINGS FROM CONFIG FILE LINE BY LINE
	487	while read line
	488	do
	489
	490	# FIRST REPLACE ENVIRONMENT-VARIABLES BY THEIR RESPECTIVE VALUES
	491	eval line=\"$line\"
	492
	493
	494	# INTERPRET THE LINE
	495	if [[ "$(echo $line)" = "" ]]
	496	then
	497
	498	# EMPTY LINE, NO ACTION
	499	continue
	500
	501	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	502	then
	503
	504	# LINE IS A COMMENT LINE
	505	continue
	506
	507	elif [[ "$(echo $line \| cut -c1)" = "%" ]]
	508	then
	509
	510	# LINE DEFINES AN ENVIRONMENT-VARIABLE
	511	var=`echo $line \| cut -d" " -s -f1 \| cut -c2-`
	512	value=`echo $line \| cut -d" " -s -f2-`
	513
	514
	515	# VALUE FROM THE CONFIGURATION-FILE IS ASSIGNED TO THE
	516	# ENVIRONMENT-VARIABLE, BUT ONLY IF NO VALUE HAS BEEN ALREADY
	517	# ASSIGNED WITHIN THIS SCRIPT (E.G. BY SCRIPT-OPTIONS).
	518	# NON-ASSIGNED VARIABLES HAVE VALUE "" OR 0 (IN CASE OF INTEGER).
	519	# HENCE THE GENERAL RULE IS: SCRIPT-OPTION OVERWRITES THE
	520	# CONFIGURATION-FILE.
	521	if [[ "$(eval echo \$$var)" = "" \|\| "$(eval echo \$$var)" = "0" ]]
	522	then
	523	eval export $var="\$value"
	524
	525	# TERMINAL OUTPUT OF ENVIRONMENT-VARIABLES, IF TRACEBACK IS SWITCHED on
	526	if [[ $do_trace = true ]]
	527	then
	528	printf "\n*** ENVIRONMENT-VARIABLE $var = $value"
	529	fi
	530	fi
	531
	532	elif [[ "$(echo $line \| cut -c1-3)" = "BD:" ]]
	533	then
	534
	535	# LINE DEFINES BATCH-DIRECTIVE
	536	(( ibd = ibd + 1 ))
	537	line=$(echo $line \| cut -c4-)
	538	batch_directive[$ibd]="$line"
	539
	540	elif [[ "$(echo $line \| cut -c1-4)" = "BDT:" ]]
	541	then
	542
	543	# LINE DEFINES BATCH-DIRECTIVE FOR SENDING BACK THE JOBFILE FROM A
	544	# REMOTE TO A LOCAL HOST
	545	(( ibdt = ibdt + 1 ))
	546	line=$(echo $line \| cut -c5-)
	547	batch_directive_transfer[$ibdt]="$line"
	548
	549	elif [[ "$(echo $line \| cut -c1-3)" = "EC:" ]]
	550	then
	551
	552	# LINE DEFINES ERROR-COMMAND
	553	(( iec = iec + 1 ))
	554	line=$(echo $line \| cut -c4-)
	555	err_command[$iec]="$line"
	556
	557	elif [[ "$(echo $line \| cut -c1-3)" = "IC:" ]]
	558	then
	559
	560	# LINE DEFINES INPUT-COMMAND
	561	(( iic = iic + 1 ))
	562	line=$(echo $line \| cut -c4-)
	563	in_command[$iic]="$line"
	564
	565	elif [[ "$(echo $line \| cut -c1-3)" = "OC:" ]]
	566	then
	567
	568	# LINE DEFINES OUTPUT-COMMAND
	569	(( ioc = ioc + 1 ))
	570	line=$(echo $line \| cut -c4-)
	571	out_command[$ioc]="$line"
	572
	573	else
	574
	575	# SKIP ALL OTHER LINES
	576	continue
	577
	578	fi
	579
	580	done < $config_file
	581
	582
	583	# CHECK SETTING OF REQUIRED PARAMETERS
[3043]	584	if [[ "$fast_io_catalog" = "" ]]
	585	then
	586	printf "\n +++ no fast_io_catalog found in $config_file"
	587	printf "\n Please add line \"fast_io_catalog ...\" to that file."
	588	locat=config_file; exit
	589	fi
[2380]	590	if [[ "$compiler_name" = "" ]]
	591	then
	592	printf "\n +++ no compiler name found in $config_file"
	593	printf "\n Please add line \"compiler_name ...\" to that file."
	594	locat=config_file; exit
	595	fi
	596	if [[ "$compiler_name_ser" = "" ]]
	597	then
	598	printf "\n +++ no compiler name for non-paralle compilation found in $config_file"
	599	printf "\n Please add line \"compiler_name_ser ...\" to that file."
	600	locat=config_file; exit
	601	fi
	602	if [[ "$compiler_options" = "" ]]
	603	then
	604	printf "\n +++ no compiler options found in $config_file"
	605	printf "\n Please add line \"compiler_options ...\" to that file."
	606	locat=config_file; exit
	607	fi
[2388]	608	if [[ "$linker_options" = "" ]]
[2380]	609	then
[2388]	610	printf "\n +++ no linker options found in $config_file"
	611	printf "\n Please add line \"linker_options ...\" to that file."
[2380]	612	locat=config_file; exit
	613	fi
	614	if [[ "$execute_command" = "" ]]
	615	then
	616	printf "\n +++ no execute command found in $config_file"
	617	printf "\n Please add line \"execute_command ...\" to that file."
	618	locat=config_file; exit
	619	fi
	620
	621	if [[ "$hostfile" != "" ]]
	622	then
	623	if [[ $hostfile != auto && ! -f $hostfile ]]
	624	then
	625	printf "\n +++ no hostfile \"$hostfile\" found"
[3151]	626	printf "\n Please check line \"hostfile ...\" in $config_file"
[2380]	627	locat=config_file; exit
	628	fi
	629	fi
	630
	631
	632	# DETERMINE THE CALL STATUS
	633	if [[ "$return_address" != "" ]]
	634	then
	635
	636	# I AM RUNNING ON A REMOTE HOST, WHICH ALSO MEANS THAT I AM RUNNING IN
	637	# BATCH MODE AND ...
	638	running_on_remote=true
	639
	640	else
	641
	642	# I HAVE BEEN CALLED INTERACTIVELY ON THIS HOST
	643	if [[ "$remote_ip" != "" ]]
	644	then
	645
	646	# I HAVE TO CREATE A BATCH JOB TO RUN PALM ON THE REMOTE HOST
	647	create_remote_batch_job=true
	648
[3132]	649	# CHECK THAT THE REMOTE JOBCATALOG HAS BEEN SET
	650	if [[ "$remote_jobcatalog" = "" ]]
	651	then
	652	printf "\n +++ no remote jobcatalog found in $config_file"
	653	printf "\n Please add line \"remote_jobcatalog ...\" to that file."
	654	locat=config_file; exit
	655	fi
	656
	657
[2380]	658	fi
	659	running_on_remote=false
	660	fi
	661
	662
	663
	664	# READ AND EVALUATE THE I/O-FILE LIST
	665	[[ $silent = false ]] && printf "\n Reading the I/O files... "
	666
	667	# READ THE FILE CONNECTION FILE LINE BY LINE
	668	while read line
	669	do
	670
[2669]	671	# REPLACE REPEATING SPACES BETWEEN THE COLUMNS BY A SINGLE SPACE
	672	line=`echo "$line" \| sed -e "s/\s\{1,\}/ /g"`
[2380]	673
	674	# INTERPRET THE LINE
	675	if [[ "$(echo $line)" = "" ]]
	676	then
	677	# EMPTY LINE, NO ACTION
	678	continue
	679
	680	elif [[ "$(echo $line \| cut -c1)" = "#" ]]
	681	then
	682
	683	# LINE IS A COMMENT LINE
	684	true
	685
	686	else
	687
	688	# LINE DEFINES FILE CONNECTION. READ THE FILE ATTRIBUTES.
	689	# s2a: in/out - field
[2669]	690	# s2b: action - field (optional)
	691	s1=`echo "$line" \| cut -d" " -f1`
	692	s2=`echo "$line" \| cut -d" " -s -f2`
[2380]	693	if [[ $(echo $s2 \| grep -c ":") = 0 ]]
	694	then
[2669]	695	s2a=$s2
[2380]	696	s2b=""
	697	else
[2669]	698	s2a=`echo $s2 \| cut -d":" -f1`
	699	s2b=`echo $s2 \| cut -d":" -f2`
[2380]	700	fi
[2669]	701	s3=`echo "$line" \| cut -d" " -f3 \| sed 's/*/wildcard /g'`
	702	s4=`echo "$line" \| cut -d" " -s -f4`
	703	eval s4=\"$s4\" # REPLACE ENVIRONMENT-VARIABLES IN PATH BY THEIR RESPECTIVE VALUES
	704	s5=`echo "$line" \| cut -d" " -s -f5`
	705	s6=`echo "$line" \| cut -d" " -s -f6`
[2380]	706
	707
	708	# STORE FILE CONNECTION, IF ACTIVATED BY ACTIVATION-STRING FROM
	709	# INPUT- OR OUTPUT-LIST.
	710	# VARIABLE S3 MAY CONTAIN A LIST OF ACTIVATION STRINGS (FIELD-SEPERATOR ":").
	711	# IF EXECUTION IS SCHEDULED FOR A REMOTE-MACHINE AND THE FILE IS ONLY
[2669]	712	# LOCALLY REQUIRED ON THAT MACHINE (I.E. s2b != tr), THE FILE CONNECTION
[2380]	713	# IS NOT CHECKED AND STORED.
[2610]	714	IFSALT="$IFS"; IFS="$IFS:" # ADD ":" AS FIELD SEPARATOR
[2669]	715	if [[ ( "$s2a" = in \|\| "$s2a" = inopt ) && ! ( $create_remote_batch_job = true && "$s2b" != tr ) ]]
[2380]	716	then
	717	found=false
	718	for actual in $activation_string_list
	719	do
	720	for formal in $s3
	721	do
	722	[[ $actual = $formal \|\| "$formal" = "-" ]] && found=true
	723	done
	724	done
	725	if [[ $found = true ]]
	726	then
	727	(( iin = iin + 1 ))
[2669]	728	localin_pre[$iin]=$s1; actionin_pre[$iin]=$s2b;
[2610]	729	pathin_pre[$iin]=$s4; endin_pre[$iin]=$s5; extin_pre[$iin]=$s6
[2669]	730	if [[ "$s2a" = inopt ]]
	731	then
	732	optin_pre[$iin]=yes
	733	else
	734	optin_pre[$iin]=no
	735	fi
[2605]	736
	737	# FILES WITH JOB-ATTRIBUTE ARE STORED IN THE SOURCES_FOR_RUN
	738	# FOLDER IF THE JOB IS RUNNING ON A REMOTE HOST
[2669]	739	if [[ $running_on_remote = true && "$s2b" = tr ]]
[2605]	740	then
[2610]	741	pathin_pre[$iin]=${fast_io_catalog}/${sources_for_run_catalog}
[2605]	742	fi
	743
[2610]	744	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	745	# THE WILDCARD FROM THE ENDING
	746	if [[ "${s5: -1}" = "*" ]]
	747	then
[2669]	748	if [[ "$s2b" = "di" ]]
[2610]	749	then
	750	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	751	printf "\n see file \"$fileconnection_file\", line"
	752	printf "\n$line"
	753	locat=iofiles_file; exit
	754	fi
	755	multin[$iin]=true
	756	string=${endin_pre[$iin]}
	757	endin_pre[$iin]="${string%?}"
	758	else
	759	multin[$iin]=false
	760	fi
[2380]	761	fi
[2669]	762	elif [[ "$s2a" = out && ! ( $create_remote_batch_job = true ) ]]
[2380]	763	then
	764	found=false
	765	for actual in $activation_string_list
	766	do
	767	for formal in $s3
	768	do
[2670]	769	[[ $actual = $formal \|\| $formal = wildcard ]] && found=true
[2380]	770	done
	771	done
	772	if [[ $found = true ]]
	773	then
	774	(( iout = iout + 1 ))
[2669]	775	localout_pre[$iout]=$s1; actionout_pre[$iout]=$s2b
[2610]	776	pathout_pre[$iout]=$s4; endout_pre[$iout]=$s5; extout_pre[$iout]=$s6
	777
[2669]	778	# CHECK IF WILDCARD IS USED AS ACTIVATION STRING
	779	# IN SUCH CASES, NO WARNING WILL LATER BE OUTPUT IF LOCAL FILES DO NOT EXIST
	780	if [[ $formal = wildcard ]]
	781	then
	782	warnout_pre[$iout]=false
	783	else
	784	warnout_pre[$iout]=true
	785	fi
	786
[2610]	787	# CHECK FOR MULTIPLE FILES, SET A RESPECTIVE FLAG AND REMOVE
	788	# THE WILDCARD FROM THE LOCAL FILENAME
	789	if [[ "${s1: -1}" = "*" ]]
	790	then
[2669]	791	if [[ "$s2b" = "di" ]]
[2610]	792	then
	793	printf "\n +++ wildcards (*) not allowed with \"di\" file attribute."
	794	printf "\n see file \"$fileconnection_file\", line"
	795	printf "\n$line"
	796	locat=iofiles_file; exit
	797	fi
	798	multout[$iout]=true
	799	string=${localout_pre[$iout]}
	800	localout_pre[$iout]="${string%?}"
	801	else
	802	multout[$iout]=false
	803	fi
[2380]	804	fi
[2669]	805	elif [[ "$s2a" != in && "$s2a" != inopt && "$s2a" != out ]]
[2380]	806	then
[2669]	807	printf "\n +++ I/O-attribute in file $fileconnection_file has invalid"
	808	printf "\n value \"$s2\". Only \"in\", \"inopt\", and \"out\" are allowed!"
[2380]	809	locat=connect; exit
	810	fi
	811	IFS="$IFSALT"
	812	fi
	813
	814	done < $fileconnection_file
	815
	816
	817
[2501]	818	# VALUES OF PALMRUN-OPTIONS OVERWRITE THOSE FROM THE CONFIGURATION-FILE
[3025]	819	[[ "$palmrun_memory" != "" ]] && memory=$palmrun_memory
	820	[[ "$palmrun_cpumax" != "" ]] && cpumax=$palmrun_cpumax
	821	[[ "$palmrun_cores" != "" ]] && cores=$palmrun_cores
[2501]	822	[[ "$max_par_io_str" != "" ]] && maximum_parallel_io_streams=$max_par_io_str
	823	[[ "$palmrun_tasks_per_node" != "" ]] && tasks_per_node=$palmrun_tasks_per_node
	824
	825
	826
[2380]	827	# EVALUATE MODEL COUPLING FEATURES (OPTION -Y)
	828	if [[ $run_coupled_model = true ]]
	829	then
	830
	831	cores_atmos=`echo $coupled_dist \| cut -d" " -s -f1`
	832	cores_ocean=`echo $coupled_dist \| cut -d" " -s -f2`
	833
	834	if (( $cores_ocean + $cores_atmos != $cores ))
	835	then
	836
	837	printf "\n +++ number of processors does not fit to specification by \"-Y\"."
	838	printf "\n PEs (total) : $cores"
	839	printf "\n PEs (atmosphere): $cores_atmos"
	840	printf "\n PEs (ocean) : $cores_ocean"
	841	locat=coupling; exit
	842
	843	fi
	844
	845	fi
	846
	847
	848	# IF I AM IN BATCH MODE, CHECK IF EXECUTABLE AND OTHER REQUIRED FILES
	849	# HAVE BEEN GENERATED BY PALMBUILD AND STORED IN THE SOURCES_FOR_RUN_...
	850	# FOLDER
	851	if [[ $running_in_batch_mode = true ]]
	852	then
	853
[2506]	854	if [[ ! -d ${fast_io_catalog}/${sources_for_run_catalog} ]]
[2380]	855	then
[2506]	856	printf "\n +++ directory ${fast_io_catalog}/${sources_for_run_catalog} is missing"
[2380]	857	printf "\n Please check the output of the palmrun-call"
	858	printf "\n that you did on your local host."
	859	locat=SOURCES_FOR_RUN; exit
	860	fi
	861
	862	else
	863
	864	# CREATE THE SOURCES_FOR_RUN_... FOLDER, BUT NOT IF I AM PART OF AN
	865	# AUTOMATIC RESTART RUN
	866	# AUTOMATIC RESTART RUNS JUST ACCESS THE DIRECTORY CREATED BY THE INITIAL RUN
	867	if [[ $restart_run = false ]]
	868	then
	869
	870	# COLLECT FILES TO BE COMPILED IN THE SOURCES_FOR_RUN_... FOLDER ON
	871	# THE LOCAL HOST
	872	if [[ ! -d $source_path ]]
	873	then
	874	printf "\n\n +++ source path \"$source_path\" on local host"
	875	printf "\n \"$(hostname)\" does not exist"
	876	locat=source_path; exit
	877	fi
	878
[2990]	879	rm -rf ${base_directory}/${sources_for_run_catalog}
	880	mkdir -p ${base_directory}/${sources_for_run_catalog}
[2380]	881
	882	if [[ "$source_list" = LM ]]
	883	then
	884
	885	# DETERMINE MODIFIED FILES OF THE SVN WORKING COPY
	886	source_list=""
	887	cd $source_path
	888
	889
[2512]	890	# CHECK, IF TRUNK-DIRECTORY IS UNDER SVN CONTROL
	891	if [[ ! -d ../.svn ]]
[2380]	892	then
	893	printf "\n\n +++ source directory"
	894	printf "\n \"$source_path\" "
	895	printf "\n is not under control of \"subversion\"."
[2512]	896	printf "\n Please do not use palmrun-option \"-s LM\"\n"
[2380]	897	fi
	898
	899
	900	# LIST ALL MODIFIED SOURCE CODE FILES
	901	Filenames=""
[2404]	902	svn status > tmp_svnstatus
[2380]	903	while read line
	904	do
	905	firstc=`echo $line \| cut -c1`
	906	if [[ $firstc = M \|\| $firstc = "?" ]]
	907	then
	908	Name=`echo "$line" \| cut -c8-`
	909	extension=`echo $Name \| cut -d. -f2`
	910	if [[ "$extension" = f90 \|\| "$extension" = F90 \|\| "$extension" = f \|\| "$extension" = F \|\| "$extension" = c ]]
	911	then
	912	Filenames="$Filenames "$Name
	913	fi
	914	fi
[2404]	915	done < tmp_svnstatus
	916	rm -rf tmp_svnstatus
[2380]	917
	918
	919	# COPY FILES TO SOURCES_FOR_RUN_...
	920	for filename in $Filenames
	921	do
[2990]	922	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	923	source_list=$source_list"$filename "
	924	done
	925
	926	cd - > /dev/null
	927
	928
	929	# COPY FILES GIVEN BY OPTION -s TO DIRECTORY SOURCES_FOR_RUN_...
	930	elif [[ "$source_list" != "" ]]
	931	then
	932
	933	cd $source_path
	934
	935	for filename in $source_list
	936	do
	937
	938	# SOURCE CODE FILE IS NOT ALLOWED TO INCLUDE PATH
	939	if [[ $(echo $filename \| grep -c "/") != 0 ]]
	940	then
	941	printf "\n +++ source code file: $filename"
	942	printf "\n must not contain (\"/\") "
	943	locat=source; exit
	944	fi
	945
	946	if [[ ! -f $filename ]]
	947	then
	948	printf "\n +++ source code file: $filename"
	949	printf "\n does not exist"
	950	locat=source; exit
	951	else
[2990]	952	cp $filename ${base_directory}/${sources_for_run_catalog}
[2380]	953	fi
	954
	955	done
	956
	957	cd - > /dev/null
	958
	959	fi
	960
	961	# CHECK, IF MAKEFILE EXISTS AND COPY IT TO THE SOURCES_FOR_RUN... DIRECTORY
	962	[[ "$makefile" = "" ]] && makefile=$source_path/Makefile
	963	if [[ ! -f $makefile ]]
	964	then
	965	printf "\n +++ file \"$makefile\" does not exist"
	966	locat=make; exit
	967	else
[2990]	968	cp $makefile ${base_directory}/${sources_for_run_catalog}/Makefile
[2380]	969	fi
	970
	971
	972	# COPY FILES FROM OPTIONAL SOURCE PATH GIVEN IN THE CONFIGURATION FILE
[2384]	973	if [[ "$user_source_path" != "" ]]
[2380]	974	then
	975
	976	# DOES THE DIRECTORY EXIST?
[2384]	977	if [[ ! -d $user_source_path ]]
[2380]	978	then
	979
	980	printf "\n\n *** INFORMATIVE: additional source code directory"
[2384]	981	printf "\n \"$user_source_path\" "
[2380]	982	printf "\n does not exist or is not a directory."
	983	printf "\n No source code will be used from this directory!\n"
[2384]	984	user_source_path=""
[2380]	985	if [[ $silent == false ]]
	986	then
	987	sleep 2
	988	fi
	989
	990	else
	991
[2384]	992	cd $user_source_path
[2380]	993
	994	Names=$(ls -1 *.f90 2>&1)
	995	[[ $(echo $Names \| grep -c '*.f90') = 0 ]] && AddFilenames="$Names"
	996	Names=$(ls -1 *.F90 2>&1)
	997	[[ $(echo $Names \| grep -c '*.F90') = 0 ]] && AddFilenames="$AddFilenames $Names"
	998	Names=$(ls -1 *.F 2>&1)
	999	[[ $(echo $Names \| grep -c '*.F') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1000	Names=$(ls -1 *.f 2>&1)
	1001	[[ $(echo $Names \| grep -c '*.f') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1002	Names=$(ls -1 *.c 2>&1)
	1003	[[ $(echo $Names \| grep -c '*.c') = 0 ]] && AddFilenames="$AddFilenames $Names"
	1004
	1005	cd - > /dev/null
[2990]	1006	cd ${base_directory}/${sources_for_run_catalog}
[2380]	1007
	1008	# COPY MAKEFILE IF EXISTING
[2384]	1009	if [[ -f $user_source_path/Makefile ]]
[2380]	1010	then
	1011	printf "\n\n *** user Makefile from directory"
[2384]	1012	printf "\n \"$user_source_path\" is used \n"
[2380]	1013	if [[ $silent == false ]]
	1014	then
	1015	sleep 1
	1016	fi
[2384]	1017	cp $user_source_path/Makefile .
[2380]	1018	fi
	1019
	1020	for filename in $AddFilenames
	1021	do
	1022	if [[ -f $filename ]]
	1023	then
	1024	printf "\n +++ source code file \"$filename\" found in additional"
[2384]	1025	printf "\n source code directory \"$user_source_path\" "
[2380]	1026	printf "\n but was also given with option \"-s\" which means that it should be taken"
	1027	printf "\n from directory \"$source_path\"."
	1028	locat=source; exit
	1029	fi
	1030
[2384]	1031	cp $user_source_path/$filename .
[2380]	1032	source_list="$source_list $filename"
	1033
	1034	# CHECK IF FILE IS CONTAINED IN MAKEFILE
	1035	if [[ $(grep -c $filename Makefile) = 0 ]]
	1036	then
	1037	printf "\n\n +++ user file \"$filename\" "
	1038	printf "\n is not listed in Makefile \n"
	1039	locat=source; exit
	1040	fi
	1041	done
	1042	cd - > /dev/null
	1043	fi
	1044	fi
	1045
	1046	# COPY CONFIGURATION FILES
[2990]	1047	cp $config_file ${base_directory}/${sources_for_run_catalog}
	1048	cp $fileconnection_file ${base_directory}/${sources_for_run_catalog}
[2380]	1049
	1050	# COPY SHELLSCRIPTS
[2990]	1051	cp ${source_path}/../SCRIPTS/palmrun ${base_directory}/${sources_for_run_catalog}
	1052	cp ${source_path}/../SCRIPTS/batch_scp ${base_directory}/${sources_for_run_catalog}
[2380]	1053
	1054	fi
	1055
	1056	fi
	1057
[2605]	1058
[2380]	1059	# GET THE GLOBAL REVISION-NUMBER OF THE SVN-REPOSITORY
	1060	# (HANDED OVER TO RESTART-RUNS USING OPTION -G)
	1061	if [[ "$global_revision" = "" ]]
	1062	then
	1063	global_revision=`svnversion $source_path 2>/dev/null`
	1064	global_revision="Rev: $global_revision"
	1065	fi
	1066
	1067
	1068	# IN CASE OF PARALLEL EXECUTION, CHECK SOME SPECIFICATIONS CONCERNING PROCESSOR NUMBERS
	1069	if [[ -n $cores ]]
	1070	then
	1071
	1072	# CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN
	1073	# INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X
[2501]	1074	if [[ $tasks_per_node = 0 ]]
[2380]	1075	then
[3025]	1076	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1077	then
	1078	printf "\n"
	1079	printf "\n +++ option \"-T\" (tasks per node) is missing"
	1080	printf "\n set -T option or define tasks_per_node in the config file"
	1081	locat=tasks_per_node; (( iec = 0 )); exit
	1082	else
	1083	# DEFAULT FOR INTERACTIVE RUN
	1084	tasks_per_node=$cores
	1085	fi
[2380]	1086	fi
	1087
	1088	if (( cores < tasks_per_node ))
	1089	then
	1090	printf "\n"
	1091	printf "\n +++ tasks per node (-T) cannot exceed total number of cores (-X)"
	1092	printf "\n given values: -T $tasks_per_node -X $cores"
	1093	locat=tasks_per_node; (( iec = 0 )); exit
	1094	fi
	1095
	1096	(( nodes = cores / ( tasks_per_node * threads_per_task ) ))
	1097	(( mpi_tasks = cores / threads_per_task ))
	1098	[[ $mpi_tasks = 0 ]] && (( mpi_tasks = 1 ))
	1099	(( ii = cores / tasks_per_node ))
	1100	(( remaining_cores = cores - ii * tasks_per_node ))
	1101	if (( remaining_cores > 0 ))
	1102	then
	1103	printf "\n"
	1104	printf "\n +++ WARNING: tasks per node (option \"-T\") is not an integral"
	1105	printf "\n divisor of the total number of cores (option \"-X\")"
	1106	printf "\n values of this palmrun-call: \"-T $tasks_per_node\" \"-X $cores\""
	1107	printf "\n One of the nodes is filled with $remaining_cores instead of $tasks_per_node tasks"
	1108	(( nodes = nodes + 1 ))
	1109	fi
	1110
	1111	fi
	1112
	1113
	1114	# SET DEFAULT VALUE FOR THE MAXIMUM NUMBER OF PARALLEL IO STREAMS
	1115	if [[ "$maximum_parallel_io_streams" = "" ]]
	1116	then
	1117	maximum_parallel_io_streams=$cores
	1118	fi
	1119
	1120
	1121	# SET PORT NUMBER OPTION FOR CALLS OF SSH/SCP AND batch_scp SCRIPT
	1122	if [[ "$scp_port" != "" ]]
	1123	then
	1124	PORTOPT="-P $scp_port"
	1125	SSH_PORTOPT="-p $scp_port"
	1126	fi
	1127
	1128
	1129	# DETERMINE THE SSH-OPTION IN CASE THAT AN SSH-KEY IS EXPLICITLY GIVEN IN THE
	1130	# CONFIG-FILE
	1131	if [[ "$ssh_key" != "" ]]
	1132	then
	1133	ssh_key="-i $HOME/.ssh/$ssh_key"
	1134	fi
	1135
	1136
	1137	# SET QUEUE, IF NOT GIVEN
	1138	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1139	then
	1140
	1141	if [[ $queue = none && "$defaultqueue" = "" ]]
	1142	then
	1143	printf "\n"
	1144	printf "\n +++ no default queue given in configuration file and no queue"
	1145	printf "\n given with option -q"
[2789]	1146	locat=queue; exit
[2380]	1147	fi
	1148	if [[ $queue = none ]]
	1149	then
	1150	queue=$defaultqueue
	1151	fi
	1152
	1153	fi
	1154
	1155
	1156	# GENERATE FULL FILENAMES OF INPUT-FILES, INCLUDING THEIR PATH
	1157	# CHECK, IF INPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST)
	1158	(( i = 0 ))
[2610]	1159	(( nr_of_input_files = 0 ))
[2380]	1160	while (( i < iin ))
	1161	do
	1162	(( i = i + 1 ))
	1163
	1164	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1165	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
[2610]	1166	if [[ "${actionin_pre[$i]}" = di ]]
[2380]	1167	then
[2610]	1168	eval filename=${pathin_pre[$i]}/${endin_pre[$i]}
[2380]	1169	else
[3236]	1170	eval filename=${pathin_pre[$i]}/${run_identifier}${endin_pre[$i]}
[2380]	1171	fi
	1172
[2610]	1173
[2380]	1174	# CHECK IF FILE EXISTS
	1175	if ! ls $filename* 1>/dev/null 2>&1
	1176	then
	1177
[2669]	1178	# FILES WITH ATTRIBUTE opt ARE OPTIONAL. NO ABORT, IF THEY DO NOT EXIST.
	1179	if [[ "${optin_pre[$i]}" != "yes" ]]
[2380]	1180	then
	1181	printf "\n\n +++ INPUT-file: "
[2610]	1182	if [[ "${extin_pre[$i]}" = "" \|\| "${extin_pre[$i]}" = " " ]]
[2380]	1183	then
	1184	printf "\n $filename"
	1185	else
[2610]	1186	printf "\n $filename.${extin_pre[$i]}"
[2380]	1187	fi
	1188	printf "\n does not exist\n"
	1189	locat=input; exit
	1190	else
[2610]	1191	(( nr_of_input_files = nr_of_input_files + 1 ))
	1192	localin[$nr_of_input_files]="${localin_pre[$i]}"
[2669]	1193	optin[$nr_of_input_files]="${optin_pre[$i]}"
	1194	actionin[$nr_of_input_files]="unavailable"
[2610]	1195	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1196	endin[$nr_of_input_files]="${endin_pre[$i]}"
	1197	extin[$nr_of_input_files]="${extin_pre[$i]}"
[2380]	1198	fi
[2605]	1199
[2380]	1200	else
	1201
[3236]	1202	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME BASENAME
	1203	# ($run_identifier) AND CREATE A LIST FOR THE DETECTED BASENAME
	1204	# ENDINGS
[2610]	1205	if [[ "${multin[$i]}" = true ]]
	1206	then
	1207	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	1208	ls -1 -d ${filename} > filelist 2>/dev/null
	1209	ls -1 -d ${filename}.* >> filelist 2>/dev/null
	1210	ls -1 -d ${filename}_* >> filelist 2>/dev/null
[2380]	1211
[2610]	1212	endings=""
	1213	while read line
	1214	do
	1215	# filename without path (i.e. after the last "/")
	1216	basefilename=$(basename ${line})
[2380]	1217
[2610]	1218	# check if there is an extension and remove it
	1219	ext=${basefilename##*.}
	1220	if [[ "$ext" = "${extin_pre[$i]}" ]]
	1221	then
	1222	basefilename=${basefilename%.*}
	1223	fi
[2380]	1224
[2610]	1225	# check for an existing cycle number and remove it
	1226	cycle=${basefilename##*.}
	1227	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1228	then
	1229	basefilename=${basefilename%.*}
	1230	fi
[2600]	1231
[3236]	1232	# remove the run_identifier from the beginning
	1233	length_run_identifier=${#run_identifier}
	1234	ending=${basefilename:${length_run_identifier}}
[2610]	1235
	1236	# remove the ending given in the .iofiles from the beginning
	1237	endingstring="${endin_pre[$i]}"
	1238	length_ending=${#endingstring}
	1239	ending=${ending:${length_ending}}
	1240
	1241	if [[ "$ending" = "" ]]
[2600]	1242	then
[2610]	1243	# standard ending as given in the .iofiles
	1244	if [[ $(echo $endings \| grep -c DEFAULT) = 0 ]]
	1245	then
	1246	endings="$endings DEFAULT"
	1247	fi
[2600]	1248	else
[2610]	1249	# ending must start with "_", otherwise its a different file
	1250	if [[ "${ending:0:1}" = "_" ]]
	1251	then
	1252	if [[ $(echo $endings \| grep -c "$ending") = 0 ]]
	1253	then
	1254	endings="$endings $ending"
	1255	fi
	1256	fi
[2600]	1257	fi
[2610]	1258
	1259	done <filelist
[2380]	1260
[2610]	1261	rm filelist
[2380]	1262
[2600]	1263	else
[2610]	1264
	1265	# SINGLE NAME
	1266	endings=DEFAULT
	1267
[2600]	1268	fi
	1269
[2610]	1270	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL INPUT FILE LIST
	1271	for ending in $endings
	1272	do
	1273
	1274	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	1275	if [[ $ending = DEFAULT ]]
[2380]	1276	then
[2610]	1277	ending=""
	1278	fi
	1279
	1280	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	1281	(( nr_of_input_files = nr_of_input_files + 1 ))
	1282	localin[$nr_of_input_files]="${localin_pre[$i]}"$ending
[2669]	1283	optin[$nr_of_input_files]="${optin_pre[$i]}"
[2610]	1284	actionin[$nr_of_input_files]="${actionin_pre[$i]}"
	1285	pathin[$nr_of_input_files]="${pathin_pre[$i]}"
	1286	endin[$nr_of_input_files]="${endin_pre[$i]}"$ending
	1287	extin[$nr_of_input_files]="${extin_pre[$i]}"
	1288
	1289
	1290	# GENERATE PATH AND FULL FILE NAME (then-BRANCH: FIXED FULL NAME IS GIVEN, I.E. THE
	1291	# FILE IDENTIFIER IS NOT PART OF THE FILENAME))
	1292	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1293	then
	1294	eval filename=${pathin[$nr_of_input_files]}/${endin[$nr_of_input_files]}
[2380]	1295	else
[3236]	1296	eval filename=${pathin[$nr_of_input_files]}/${run_identifier}${endin[$nr_of_input_files]}
[2380]	1297	fi
[2610]	1298
	1299	# DETERMINE THE FILE'S CYCLE NUMBER
	1300	(( maxcycle = 0 ))
	1301	ls -1 -d $filename > filelist 2>/dev/null
	1302	ls -1 -d $filename.* >> filelist 2>/dev/null
	1303	while read line
	1304	do
	1305	# filename without path (i.e. after the last "/")
	1306	basefilename=$(basename ${line})
	1307
	1308	# check if there is an extension
	1309	extension=${basefilename##*.}
	1310	if [[ "$extension" = "${extin[$nr_of_input_files]}" ]]
	1311	then
	1312	basefilename=${basefilename%.*}
	1313	fi
	1314
	1315	# check for an existing cycle number
	1316	cycle=${basefilename##*.}
	1317	if [[ $cycle =~ ^-?[0-9]+$ ]]
	1318	then
[2669]	1319	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	1320	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	1321	(( icycle = $((10#$cycle)) ))
[2610]	1322	else
	1323	(( icycle = 0 ))
	1324	fi
	1325
	1326	if (( icycle > maxcycle ))
	1327	then
	1328	(( maxcycle = icycle ))
	1329
	1330	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS
	1331	# CHECK IF CYCLE NUMBER CONTAINS LEADING ZEROS
	1332	if [[ $(echo $cycle \| cut -c1) = 0 ]]
	1333	then
	1334	leading_zero=true
	1335	else
	1336	leading_zero=false
	1337	fi
	1338	fi
	1339
	1340	done <filelist
	1341	rm filelist
	1342
	1343	# MAKE CYCLE NUMBER THREE DIGITS WIDE
	1344	if [[ $leading_zero = true ]]
[2380]	1345	then
[2610]	1346	cyclestring=`printf "%03d" $maxcycle`
	1347	else
	1348	cyclestring=$maxcycle
[2380]	1349	fi
[2610]	1350
	1351	# APPEND CYCLE NUMBER TO FILENAME
	1352	if (( maxcycle > 0 ))
[2380]	1353	then
[2610]	1354	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1355	then
	1356	filename=${filename}.$cyclestring.${extin[$nr_of_input_files]}
	1357	else
	1358	filename=${filename}.$cyclestring
	1359	fi
[2380]	1360	else
[2610]	1361	if [[ "${extin[$nr_of_input_files]}" != " " && "${extin[$nr_of_input_files]}" != "" ]]
	1362	then
	1363	filename=${filename}.${extin[$nr_of_input_files]}
	1364	fi
[2380]	1365	fi
[2610]	1366
	1367	# STORE FILENAME WITHOUT PATH BUT WITH CYCLE NUMBER,
	1368	# IS LATER USED FOR TRANSFERRING FILES WIHIN THE JOB (SEE END OF FILE)
	1369	absnamein[$nr_of_input_files]=$filename
	1370	if (( maxcycle > 0 ))
[2380]	1371	then
[2610]	1372	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1373	then
	1374	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}.$cyclestring
	1375	else
[3236]	1376	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}.$cyclestring
[2610]	1377	fi
[2380]	1378	else
[2610]	1379	if [[ "${actionin[$nr_of_input_files]}" = di ]]
	1380	then
	1381	frelin[$nr_of_input_files]=${endin[$nr_of_input_files]}
	1382	else
[3236]	1383	frelin[$nr_of_input_files]=${run_identifier}${endin[$nr_of_input_files]}
[2610]	1384	fi
[2380]	1385	fi
	1386
[2610]	1387	done
	1388
[2380]	1389	fi
[2610]	1390
[2380]	1391	done
	1392
[2610]	1393
[2380]	1394	# GENERATE FULL FILENAMES OF OUTPUT-FILES (WITHOUT $ OR ~),
	1395	# CHECK, IF OUTPUT-FILES EXIST, AND DETERMINE HIGHEST CYCLE NUMBER (IF CYCLES EXIST),
	1396	# OR, IN CASE THAT FILE DOES NOT EXIST, CHECK, IF IT CAN BE CREATED
[2610]	1397	# THESE ACTIONS ARE NOT CARRIED OUT, IF FILES SHALL BE TRANSFERRED FROM THE REMOTE TO
[2380]	1398	# THE LOCAL HOST (BECAUSE THEIR IS NO DIRECT ACCESS TO THE LOCAL DIRECTORIES FROM THE
	1399	# REMOTE HOST)
	1400	(( i = 0 ))
	1401	while (( i < iout ))
	1402	do
	1403	(( i = i + 1 ))
[2610]	1404	if [[ ! ( $running_on_remote = true && ( "${actionout_pre[$i]}" = tr \|\| "${actionout_pre[$i]}" = tra \|\| "${actionout_pre[$i]}" = trpe ) ) ]]
[2380]	1405	then
[2610]	1406	if [[ "${actionout_pre[$i]}" = tr ]]
[2380]	1407	then
[2610]	1408	actionout_pre[$i]=""
	1409	elif [[ "${actionout_pre[$i]}" = trpe ]]
[2380]	1410	then
[2610]	1411	actionout_pre[$i]=pe
	1412	elif [[ "${actionout_pre[$i]}" = tra ]]
[2380]	1413	then
[2610]	1414	actionout_pre[$i]=a
[2380]	1415	fi
	1416	(( maxcycle = 0 ))
[3236]	1417	eval filename=${pathout_pre[$i]}/${run_identifier}${endout_pre[$i]}
[2610]	1418	eval catalogname=${pathout_pre[$i]}
[2380]	1419	if ! ls $filename* 1>/dev/null 2>&1
	1420	then
	1421
	1422	# IF OUTPUT-FILE DOES NOT EXIST CHECK, IF IT CAN BE CREATED
	1423	if cat /dev/null > $filename
	1424	then
	1425	rm $filename
	1426	else
	1427
	1428	# CHECK, IF THE DIRECTORY WHERE FILE SHALL BE COPIED TO EXISTS
	1429	# IF IT DOES NOT EXIST, TRY TO CREATE IT
	1430	if [[ ! -d $catalogname ]]
	1431	then
	1432	if mkdir -p $catalogname
	1433	then
	1434	printf "\n\n *** directory:"
	1435	printf "\n $catalogname"
	1436	printf "\n was created\n"
	1437	else
	1438	printf "\n\n +++ OUTPUT-file:"
	1439	printf "\n $filename"
	1440	printf "\n cannot be created, because directory does not exist"
	1441	printf "\n and cannot be created either"
	1442	printf "\n"
	1443	locat=output ; exit
	1444	fi 2>/dev/null
	1445	else
	1446	printf "\n\n +++ OUTPUT-file:"
	1447	printf "\n $filename"
	1448	printf "\n cannot be created, although directory exists"
	1449	printf "\n"
	1450	locat=output ; exit
	1451	fi
	1452	fi 2>/dev/null
	1453
	1454	fi
	1455
	1456	fi
	1457	done
	1458
	1459
	1460	# DETERMINE THE NAME OF PALMRUN'S TEMPORARY WORKING DIRECTORY
	1461	if [[ $running_in_batch_mode = false ]]
	1462	then
[3236]	1463	run_id_number=$RANDOM
	1464	run_id=${run_identifier}.$run_id_number
[2380]	1465
[3236]	1466	tempdir=$fast_io_catalog/$run_id
[3346]	1467
	1468	# FOR COMPATIBILITY REASONS WITH OLDER VERSIONS SET JOB_ID
	1469	export job_id=$run_id
	1470
[2380]	1471	fi
	1472
	1473
	1474	# CHECK SETTINGS REQUIRED FOR BATCH JOBS
	1475	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1476	then
	1477
	1478	# CHECK, IF JOB DIRECTIVES HAVE BEEN GIVEN IN CONFIGURATION FILE
	1479	if [[ $ibd = 0 ]]
	1480	then
	1481	printf "\n"
	1482	printf "\n +++ no batch directives found in configuration file"
	1483	locat=config_file_batch_directives; (( iec = 0 )); exit
	1484	fi
	1485
	1486	# CHECK IF CPUTIME IS GIVEN FOR JOB
	1487	done=false
[2384]	1488	cputime=$cpumax
[2380]	1489	while [[ $done = false ]]
	1490	do
[2384]	1491	if (( cputime == 0 ))
[2380]	1492	then
	1493	printf "\n +++ cpu-time is undefined"
	1494	printf "\n >>> Please type CPU-time in seconds as INTEGER:"
	1495	printf "\n >>> "
[2384]	1496	read cputime 1>/dev/null 2>&1
[2380]	1497	else
	1498	done=true
	1499	fi
	1500	done
[2420]	1501	cpumax=$cputime
[2380]	1502
	1503	# CHECK THE MEMORY DEMAND
	1504	done=false
	1505	while [[ $done = false ]]
	1506	do
	1507	if (( memory == 0 ))
	1508	then
	1509	printf "\n +++ memory demand is undefined"
	1510	printf "\n >>> Please type memory in MByte per process as INTEGER:"
	1511	printf "\n >>> "
	1512	read memory 1>/dev/null 2>&1
	1513	else
	1514	done=true
	1515	fi
	1516	done
	1517
	1518	# IN CASE OF REMOTE-JOBS CHECK, IF A USERNAME FOR THE REMOTE HOST IS GIVEN
	1519	if [[ $create_remote_batch_job = true && -z $remote_username ]]
	1520	then
	1521	while [[ -z $remote_username ]]
	1522	do
[2420]	1523	printf "\n +++ username on remote host with IP \"$remote_ip\" is undefined"
[2380]	1524	printf "\n >>> Please type username:"
	1525	printf "\n >>> "
	1526	read remote_username
	1527	done
	1528	fi
	1529
	1530	else
	1531
[2420]	1532	if [[ $running_in_batch_mode = false ]]
	1533	then
	1534	cputime=10000000 # NO LIMT FOR INTERACTIVE RUNS
	1535	cpumax=$cputime
	1536	else
	1537	cputime=$cpumax
	1538	fi
[2380]	1539
	1540	fi
	1541
	1542
	1543	# CALCULATE HOURS/MINUTES/SECONDS, E.G. FOR BATCH-DIRECTIVES
	1544	(( cpu_hours = cputime / 3600 ))
	1545	(( resttime = cputime - cpu_hours * 3600 ))
	1546	(( cpu_minutes = resttime / 60 ))
	1547	(( cpu_seconds = resttime - cpu_minutes * 60 ))
	1548	timestring=${cpu_hours}:${cpu_minutes}:${cpu_seconds}
	1549
	1550
	1551	# OUTPUT OF THE PALMRUN-HEADER
	1552	calltime=$(date)
	1553	printf "\n"
	1554	printf "#------------------------------------------------------------------------# \n"
	1555	printf "\| %-35s%35s \| \n" "$version" "$calltime"
[3151]	1556	printf "\| %-35s%35s \| \n" "PALM code $global_revision" " "
[2380]	1557	printf "\| \| \n"
	1558	column1="called on:"; column2=$(hostname)
	1559	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1560	if [[ $create_remote_batch_job = true ]]
	1561	then
[3236]	1562	column1="execution on:"; column2="$configuration_identifier (username: $remote_username)"
[2380]	1563	else
	1564	if [[ $running_on_remote = true ]]
	1565	then
[3236]	1566	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $remote_ip)"
[2380]	1567	else
[3236]	1568	column1="config. identifier:"; column2="$configuration_identifier (execute on IP: $local_ip)"
[2380]	1569	fi
	1570	fi
	1571	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1572
	1573	column1="running in:"
	1574	if [[ $running_in_batch_mode = true ]]
	1575	then
	1576	column2="batch job mode"
	1577	else
	1578	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1579	then
	1580	column2="job creation mode"
	1581	else
	1582	column2="interactive run mode"
	1583	fi
	1584	fi
	1585	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1586
[2479]	1587	if [[ $running_in_batch_mode = true \|\| $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1588	then
[2480]	1589	if [[ "$project_account" != "" ]]
[2479]	1590	then
	1591	column1="project account number:"
	1592	column2="$project_account"
	1593	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1594	fi
	1595	fi
	1596
[2380]	1597	if [[ -n $cores ]]
	1598	then
	1599	if [[ $run_coupled_model = false ]]
	1600	then
	1601	column1="number of cores:"; column2=$cores
	1602	else
	1603	column1="number of cores:"; column2="$cores (atmosphere: $cores_atmos, ocean: $cores_ocean)"
	1604	fi
	1605	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1606	fi
	1607	if [[ -n $tasks_per_node ]]
	1608	then
	1609	column1="tasks per node:"; column2="$tasks_per_node (number of nodes: $nodes)"
	1610	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1611	if (( remaining_cores > 0 ))
	1612	then
	1613	column1=" "; column2="one of the nodes only filled with $remaining_cores tasks"
	1614	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1615	fi
	1616	fi
	1617	if [[ $maximum_parallel_io_streams != $cores ]]
	1618	then
	1619	column1="max par io streams:"; column2="$maximum_parallel_io_streams"
	1620	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1621	fi
	1622	if [[ $use_openmp = true ]]
	1623	then
	1624	column1="threads per task:"; column2="$threads_per_task"
	1625	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1626	fi
[2384]	1627	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true \|\| $running_in_batch_mode = true ]]
	1628	then
[2506]	1629	column1="memory demand / PE":; column2="$memory MB"
	1630	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2384]	1631	column1="job cpu time (h:m:s):"; column2="$timestring"
	1632	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1633	fi
[2380]	1634	printf "\| \| \n"
	1635	if [[ "$source_list" != "" ]]
	1636	then
	1637	if [[ "$make_options" != "" ]]
	1638	then
	1639	column1="make options:"; column2=$(echo "$make_options" \| cut -c-45)
	1640	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1641	line=$(echo "$make_options" \| cut -c46-)
	1642	while [[ "$line" != "" ]]
	1643	do
	1644	column1=""
	1645	column2=$(echo "$line" \| cut -c-45)
	1646	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1647	line=$(echo "$line" \| cut -c46-)
	1648	done
	1649	fi
	1650	fi
	1651
	1652	column1="cpp directives:"; column2=$(echo "$cpp_options" \| cut -c-45)
	1653	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1654	line=$(echo "$cpp_options" \| cut -c46-)
	1655	while [[ "$line" != "" ]]
	1656	do
	1657	column1=""
	1658	column2=$(echo "$line" \| cut -c-45)
	1659	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1660	line=$(echo "$line" \| cut -c46-)
	1661	done
	1662
	1663	column1="compiler options:"; column2=$(echo "$compiler_options" \| cut -c-45)
	1664	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1665	line=$(echo "$compiler_options" \| cut -c46-)
	1666	while [[ "$line" != "" ]]
	1667	do
	1668	column1=""
	1669	column2=$(echo "$line" \| cut -c-45)
	1670	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1671	line=$(echo "$line" \| cut -c46-)
	1672	done
	1673
[2388]	1674	column1="linker options:"; column2=$(echo "$linker_options" \| cut -c-45)
[2380]	1675	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
[2388]	1676	line=$(echo "$linker_options" \| cut -c46-)
[2380]	1677	while [[ "$line" != "" ]]
	1678	do
	1679	column1=""
	1680	column2=$(echo "$line" \| cut -c-45)
	1681	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1682	line=$(echo "$line" \| cut -c46-)
	1683	done
	1684
	1685	if [[ "$login_init_cmd" != "" ]]
	1686	then
	1687	column1="login init commands:"; column2=$(echo "$login_init_cmd" \| cut -c-45)
	1688	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1689	line=$(echo "$login_init_cmd" \| cut -c46-)
	1690	while [[ "$line" != "" ]]
	1691	do
	1692	column1=""
	1693	column2=$(echo "$line" \| cut -c-45)
	1694	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1695	line=$(echo "$line" \| cut -c46-)
	1696	done
	1697	fi
	1698
	1699	if [[ "$module_commands" != "" ]]
	1700	then
	1701	column1="module commands:"; column2=$(echo "$module_commands" \| cut -c-45)
	1702	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1703	line=$(echo "$module_commands" \| cut -c46-)
	1704	while [[ "$line" != "" ]]
	1705	do
	1706	column1=""
	1707	column2=$(echo "$line" \| cut -c-45)
	1708	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1709	line=$(echo "$line" \| cut -c46-)
	1710	done
	1711	fi
	1712	printf "\| \| \n"
[3236]	1713	column1="run identifier:"; column2=$run_identifier
[2380]	1714	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1715	column1="activation string list:"; column2=$(echo $activation_string_list)
	1716	printf "\| %-25s%-45s \| \n" "$column1" "$column2"
	1717
	1718	if [[ "$ocean_file_appendix" = true ]]
	1719	then
	1720	printf "\| %-35s%-35s \| \n" "suffix \"_O\" is added to local files" " "
	1721	fi
	1722
	1723	if [[ "$source_list" != "" ]]
	1724	then
	1725	printf "\| \| \n"
	1726	printf "\| Files to be compiled: \| \n"
	1727	line=$source_list
	1728	while [[ "$line" != "" ]]
	1729	do
	1730	linestart=$(echo $line \| cut -c-70)
	1731	printf "\| %-70s \| \n" "$linestart"
	1732	line=$(echo "$line" \| cut -c71-)
	1733	done
	1734	fi
	1735	printf "#------------------------------------------------------------------------#"
	1736
	1737
	1738
	1739	# OUTPUT OF FILE CONNECTIONS IN CASE OF TRACEBACK
	1740	if [[ $do_trace = true ]]
	1741	then
	1742	(( i = 0 ))
[2610]	1743	while (( i < nr_of_input_files ))
[2380]	1744	do
	1745	(( i = i + 1 ))
	1746	if (( i == 1 ))
	1747	then
	1748	printf "\n\n >>> INPUT-file assignments:\n"
	1749	fi
	1750	printf "\n ${localin[$i]} : ${absnamein[$i]}"
	1751	done
	1752	(( i = 0 ))
	1753	while (( i < iout ))
	1754	do
	1755	(( i = i + 1 ))
	1756	if (( i == 1 ))
	1757	then
	1758	printf "\n\n >>> OUTPUT-file assignments:\n"
	1759	fi
	1760	printf "\n ${localout[$i]} : ${pathout[$i]}"
	1761	done
	1762	(( i = 0 ))
	1763	while (( i < iic ))
	1764	do
	1765	(( i = i + 1 ))
	1766	if (( i == 1 ))
	1767	then
	1768	printf "\n\n >>> INPUT-commands:\n"
	1769	fi
	1770	printf "\n ${in_command[$i]}"
	1771	done
	1772	(( i = 0 ))
	1773	while (( i < ioc ))
	1774	do
	1775	(( i = i + 1 ))
	1776	if (( i == 1 ))
	1777	then
	1778	printf "\n\n >>> OUTPUT-commands:\n"
	1779	fi
	1780	printf "\n ${out_command[$i]}"
	1781	done
	1782	fi
	1783
	1784	# QUERY FOR CONTINUE
	1785	if [[ $silent = false && $running_in_batch_mode = false ]]
	1786	then
	1787	antwort=dummy
	1788	printf "\n\n"
	1789	printf " >>> everything o.k. (y/n) ? "
	1790	while read antwort
	1791	do
	1792	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1793	then
	1794	printf " >>> everything o.k. (y/n) ? "
	1795	else
	1796	break
	1797	fi
	1798	done
	1799	if [[ $antwort = n \|\| $antwort = N ]]
	1800	then
	1801	locat=user_abort; (( iec = 0 )); exit
	1802	fi
	1803	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1804	then
[2566]	1805	printf "\n *** batch-job will be created and submitted"
[2380]	1806	else
[2566]	1807	printf "\n *** PALMRUN will now continue to execute on this machine"
[2380]	1808	fi
	1809	fi
	1810
	1811
	1812
	1813	# PROVIDE FILES TO EXECUTE PALM AND CREATE THE EXECUTABLE
	1814	if [[ $restart_run = false && $running_in_batch_mode = false ]]
	1815	then
	1816
	1817	if [[ $create_batch_job = true \|\| $create_remote_batch_job = true ]]
	1818	then
[2566]	1819	printf "\n\n *** creating executable and other sources for the remote host\n"
[2380]	1820	else
[2566]	1821	printf "\n\n *** creating executable and other sources for the local host\n"
[2380]	1822	fi
	1823
[2422]	1824	# FIRST CHECK, IF A MAKE DEPOSITORY EXISTS, AND IF NOT, ASK THE USER IF
	1825	# IT SHALL BE CREATED
	1826	ask_for_make_depository=false
	1827	if [[ $create_remote_batch_job = true ]]
	1828	then
	1829
	1830	line=`grep %base_directory $config_file`
[3236]	1831	make_depository=`echo $line \| cut -d" " -s -f2`/MAKE_DEPOSITORY_${configuration_identifier}
[3534]	1832	### echo "[[ ! -d ${make_depository} ]] && echo depository not found" \| ssh -q $ssh_key ${remote_username}@${remote_ip} 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
	1833	ssh -q $ssh_key ${remote_username}@${remote_ip} "[[ ! -d ${make_depository} ]] && echo depository not found" 2>&1 \| tee ${configuration_identifier}_last_make_protokoll
[2422]	1834
[3236]	1835	if [[ $(grep -c "depository not found" ${configuration_identifier}_last_make_protokoll) != 0 ]]
[2422]	1836	then
	1837	printf "\n\n +++ make depository \"${make_depository}\""
	1838	printf "\n on remote host not found!"
	1839	ask_for_make_depository=true
	1840	fi
[3236]	1841	rm ${configuration_identifier}_last_make_protokoll
[2422]	1842
	1843	else
	1844
	1845	# CHECK FOR MAKE_DEPOSITORY ON THE LOCAL HOST
[3236]	1846	make_depository=${base_directory}/MAKE_DEPOSITORY_${configuration_identifier}
[2422]	1847	if [[ ! -d ${make_depository} ]]
	1848	then
	1849	printf "\n\n +++ make depository \"${make_depository}\""
	1850	printf "\n on local host not found!"
	1851	ask_for_make_depository=true
	1852	fi
	1853
	1854	fi
	1855
	1856	if [[ $ask_for_make_depository = true ]]
	1857	then
	1858
	1859	antwort=dummy
	1860	printf "\n\n"
	1861	printf " >>> Create a new one (y/n) ? "
	1862	while read antwort
	1863	do
	1864	if [[ "$antwort" != y && "$antwort" != Y && "$antwort" != n && "$antwort" != N ]]
	1865	then
	1866	printf " >>> Create a new one (y/n) ? "
	1867	else
	1868	break
	1869	fi
	1870	done
	1871	if [[ $antwort = n \|\| $antwort = N ]]
	1872	then
	1873	locat=user_abort; (( iec = 0 )); exit
	1874	fi
	1875
[2566]	1876	if [[ $do_trace = true ]]
	1877	then
[3455]	1878	palmbuild -c $configuration_identifier
[2566]	1879	else
[3455]	1880	palmbuild -v -c $configuration_identifier
[2566]	1881	fi
[2422]	1882
[3312]	1883	if [[ ${PIPESTATUS[0]} != 0 ]]
[2422]	1884	then
	1885
	1886	# ABORT IN CASE OF COMPILATION PROBLEMS
	1887	printf "\n +++ error while compiling for the MAKE_DEPOSITORY"
	1888	locat=make_depository
	1889	exit
	1890	else
	1891	echo " *** now continue with creating executable and other sources"
	1892	fi
	1893
	1894	fi
	1895
[2566]	1896	# NOW CREATE THE SOURCES_FOR_RUN FOLDER
[3455]	1897	palmbuild -v $use_existing_sources_folder -c $configuration_identifier -r $run_identifier
[2380]	1898
[3312]	1899	if [[ ${PIPESTATUS[0]} != 0 ]]
[2380]	1900	then
	1901
	1902	# ABORT IN CASE OF COMPILATION PROBLEMS
	1903	printf "\n +++ error while creating executable and/or other sources"
	1904	locat=execution
[2990]	1905	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1906	exit
	1907
	1908	else
	1909
[2566]	1910	printf " *** executable and other sources created\n"
[2990]	1911	rm -rf ${base_directory}/${sources_for_run_catalog}
[2380]	1912
	1913	fi
	1914
	1915	fi
	1916
	1917
[2669]	1918	# WHEN CREATING A REMOTE BATCH JOB, THOSE INPUT FILES WITH TRANSFER-ATTRIBUT
	1919	# WILL BE COPIED TO THE REMOTE HOST
[2605]	1920	if [[ $create_remote_batch_job = true ]]
	1921	then
	1922	(( i = 0 ))
[2610]	1923	while (( i < nr_of_input_files ))
[2605]	1924	do
	1925	(( i = i + 1 ))
[2669]	1926	if [[ "${actionin[$i]}" = tr ]]
[2605]	1927	then
	1928	eval inputfile=${pathin[$i]}/${frelin[$i]}
	1929	scp -q $ssh_key $PORTOPT $inputfile ${remote_username}@${remote_ip}:${fast_io_catalog}/${sources_for_run_catalog}/${frelin[$i]}
	1930	fi
	1931	done
	1932	if (( i > 0 ))
	1933	then
[3025]	1934	printf "\n\n *** input files have been copied to the remote host\n"
[2605]	1935	fi
	1936	fi
	1937
	1938
[2380]	1939	# NOW PERFORM THOSE ACTIONS REQUIRED TO EXECUTE THE PROGRAM (PALM) ON THIS MACHINE
	1940	# (COMPILING/LINKING, EXECUTING, COPYING I/O FILES)
	1941	if [[ $create_batch_job = false && $create_remote_batch_job = false ]]
	1942	then
	1943
	1944	# CHANGE TO THE TEMPORARY WORKING DIRECTORY
	1945	if [[ $running_in_batch_mode = false ]]
	1946	then
	1947	# CREATE THE DIRECTORY AND COPY FILES FROM SOURCES_FOR_RUN_... TO THAT
	1948	# FOLDER
[2566]	1949	mkdir -p $tempdir
	1950	chmod go+rx $tempdir
	1951	cd $tempdir
	1952	cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} $tempdir
	1953	printf "\n *** changed to temporary directory: $tempdir"
[2380]	1954
	1955	else
	1956
	1957	# IN BATCH MODE PALMRUN IS CALLED FROM TEMPDIR
[2566]	1958	printf "\n *** running in temporary directory: $tempdir"
[2380]	1959
	1960	fi
	1961
	1962
	1963	# PROVIDE THE INPUT FILES
	1964	# LOOP OVER ALL ACTIVATED FILES (LISTED IN THE CONFIGURATION FILE)
[2669]	1965	optional_files_missing=false
[2380]	1966	(( i = 0 ))
[2610]	1967	while (( i < nr_of_input_files ))
[2380]	1968	do
	1969	(( i = i + 1 ))
	1970	if (( i == 1 ))
	1971	then
	1972	printf "\n\n *** providing INPUT-files:\n$dashes"
	1973	fi
	1974
	1975
	1976	# SKIP OPTIONAL FILES, IF THEY DO NOT EXIST
[2669]	1977	if [[ "${actionin[$i]}" = unavailable ]]
[2380]	1978	then
[2669]	1979	optional_files_missing=true
[2380]	1980	continue
	1981	fi
	1982
	1983	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	1984	files_for_cores=false; filetype=file
	1985	if [[ "${actionin[$i]}" = pe && -n $cores ]]
	1986	then
	1987	files_for_cores=true; filetype=files
	1988	actionin[$i]=""
	1989	elif [[ "${actionin[$i]}" = pe && ! -n $cores ]]
	1990	then
	1991	actionin[$i]=""
	1992	elif [[ "${actionin[$i]}" = lnpe && -n $cores ]]
	1993	then
	1994	files_for_cores=true; filetype=files
	1995	actionin[$i]="ln"
	1996	elif [[ "${actionin[$i]}" = lnpe && ! -n $cores ]]
	1997	then
	1998	actionin[$i]="ln"
	1999	fi
	2000
	2001	if [[ $files_for_cores = true ]]
	2002	then
	2003	printf "\n >>> INPUT: ${absnamein[$i]}/.... to ${localin[$i]}"
	2004	else
	2005	printf "\n >>> INPUT: ${absnamein[$i]} to ${localin[$i]}"
	2006	fi
	2007
	2008	# INPUT-FILES TO BE LINKED
	2009	if [[ "${actionin[$i]}" = ln ]]
	2010	then
	2011
	2012	printf "\n $filetype will be linked"
	2013	if [[ $files_for_cores = false ]]
	2014	then
	2015	if [[ -f "${absnamein[$i]}" ]]
	2016	then
	2017	ln ${absnamein[$i]} ${localin[$i]}
	2018	got_tmp[$i]=true
	2019	fi
	2020	else
	2021	if [[ -d "${absnamein[$i]}" ]]
	2022	then
[2396]	2023	mkdir -p ${localin[$i]}
[2380]	2024	cd ${absnamein[$i]}
	2025	for file in $(ls *)
	2026	do
[2566]	2027	ln $file $tempdir/${localin[$i]}
[2380]	2028	done >\|/dev/null 2>&1
[2566]	2029	cd $tempdir
[2380]	2030	fi
	2031
	2032	# IF "ln -f" HAS FAILED DO A NORMAL COPY "cp -r"
	2033	if [[ ! -f "${localin[$i]}/_000000" ]]
	2034	then
	2035	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2036	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2037	fi
	2038
	2039	got_tmp[$i]=true
	2040	fi
	2041	fi
	2042
	2043	# FILE IS STORED IN THE RESPECTIVE DIRECTORY GIVEN IN THE CONFIGURATION FILE
[2669]	2044	if [[ "${actionin[$i]}" = "" \|\| "${actionin[$i]}" = "di" \|\| "${actionin[$i]}" = "tr" \|\| "${actionin[$i]}" = "npe" ]]
[2380]	2045	then
	2046
	2047	if [[ "${actionin[$i]}" = "npe" && -n $cores ]]
	2048	then
	2049
	2050	# FILE COPIES ARE PROVIDED FOR ALL CORES
	2051	# EACH FILE GETS A UNIQUE FILENAME WITH A FOUR DIGIT NUMBER
	2052	printf "\n file will be provided for $cores processors"
[2396]	2053	mkdir -p ${localin[$i]}
[2380]	2054	ival=$cores
	2055	(( ii = 0 ))
	2056	while (( ii <= ival-1 ))
	2057	do
	2058	if (( ii < 10 ))
	2059	then
	2060	cp ${absnamein[$i]} ${localin[$i]}/_000$ii
	2061	elif (( ii < 100 ))
	2062	then
	2063	cp ${absnamein[$i]} ${localin[$i]}/_00$ii
	2064	elif (( ii < 1000 ))
	2065	then
	2066	cp ${absnamein[$i]} ${localin[$i]}/_0$ii
	2067	else
	2068	cp ${absnamein[$i]} ${localin[$i]}/_$ii
	2069	fi
	2070	(( ii = ii + 1 ))
	2071	done
	2072
	2073	else
	2074
	2075	if [[ $files_for_cores = true ]]
	2076	then
	2077
	2078	# PROVIDE FILES FOR EACH CORE
	2079	# FIRST CREATE THE LOCAL DIRECTORY, THEN COPY FILES
	2080	# FROM THE PERMANENT DIRECTORY BY LINKING THEM TO THE LOCAL ONE
	2081	printf "\n providing $cores files for the respective cores"
[2396]	2082	mkdir -p ${localin[$i]}
[2380]	2083	if [[ $link_local_input = true ]]
	2084	then
	2085	printf " files will be linked\n"
	2086	cd ${absnamein[$i]}
	2087	for file in $(ls *)
	2088	do
	2089	ln -f $file ${localin[$i]}
	2090	done
[2566]	2091	cd $tempdir
[2380]	2092	fi
	2093
	2094	# IF "ln -f" FAILED OR IF "$link_local_input = false" DO A NORMAL "cp -r"
	2095	if [[ ! -f "${localin[$i]}/_000000" ]]
	2096	then
	2097	if [[ $link_local_input = true ]]
	2098	then
	2099	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2100	fi
	2101	cp -r ${absnamein[$i]}/* ${localin[$i]}
	2102	fi
	2103
	2104	else
	2105
	2106	# PROVIDE FILE FOR RUNS ON A SINGLE CORE
	2107	if [[ $link_local_input = true ]]
	2108	then
	2109	printf " file will be linked\n"
	2110	ln -f ${absnamein[$i]} ${localin[$i]}
	2111	fi
[2605]	2112	# If "ln -f" fails or if "$link_local_input = false" do a normal "cp"
[2380]	2113	if [[ ! -f "${localin[$i]}" ]]
	2114	then
	2115	if [[ $link_local_input = true ]]
	2116	then
	2117	printf "\n --- WARNING: ln failed, using cp instead (might be time consuming...)"
	2118	fi
[2669]	2119	if [[ $running_on_remote = true && "${actionin[$i]}" = tr ]]
[2605]	2120	then
	2121	mv ${absnamein[$i]} ${localin[$i]}
	2122	else
	2123	cp ${absnamein[$i]} ${localin[$i]}
	2124	fi
[2380]	2125	fi
	2126	fi
	2127	fi
	2128	fi
	2129
	2130	done
	2131	if (( i != 0 ))
	2132	then
[2669]	2133	if [[ $optional_files_missing = true ]]
	2134	then
	2135	printf "\n *** INFORMATIVE: some optional INPUT-files are not present"
	2136	fi
[2380]	2137	printf "\n$dashes\n *** all INPUT-files provided \n"
	2138	fi
	2139
	2140
	2141	# EXECUTE INPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2142	(( i = 0 ))
	2143	while (( i < iic ))
	2144	do
	2145	(( i = i + 1 ))
	2146	if (( i == 1 ))
	2147	then
	2148	printf "\n\n *** execution of INPUT-commands:\n$dashes"
	2149	fi
	2150	printf "\n >>> ${in_command[$i]}"
	2151	eval ${in_command[$i]}
	2152	if (( i == iic ))
	2153	then
	2154	printf "\n$dashes\n"
	2155	fi
	2156	done
	2157
	2158
[3313]	2159	# CHECK IF THE PROGRESS BAR NEEDS TO BE DISABLED
	2160	if [[ $running_in_batch_mode = true \|\| $running_in_test_mode = true ]]
	2161	then
	2162	progress_bar_disabled=true
	2163	else
	2164	progress_bar_disabled=false
	2165	fi
	2166
	2167
[2380]	2168	# CREATE THE NAMELIST-FILE WITH VALUES OF ENVIRONMENT-VARIABLES REQUIRED BY PALM
	2169	# (FILE ENVPAR WILL BE READ BY PALM)
	2170	cat > ENVPAR << EOF
[3236]	2171	&envpar run_identifier = '$run_identifier', host = '$configuration_identifier',
[2906]	2172	write_svf = .${write_svf}., write_binary = .${write_binary}.,
	2173	read_svf = .${read_svf}., tasks_per_node = $tasks_per_node,
[2380]	2174	maximum_parallel_io_streams = $maximum_parallel_io_streams,
	2175	maximum_cpu_time_allowed = ${cpumax}.,
	2176	revision = '$global_revision',
[3313]	2177	progress_bar_disabled = .${progress_bar_disabled}. /
[2380]	2178
	2179	EOF
	2180
	2181
	2182	# STARTING THE EXECUTABLE
	2183	printf "\n\n *** execution starts in directory\n \"`pwd`\"\n$dashes\n"
[2566]	2184	PATH=$PATH:$tempdir
[2380]	2185
	2186
	2187	# REPLACE PARAMETERS IN THE EXECUTION COMMAND WITH REAL VALUES
[2693]	2188	line=`echo "${execute_command}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2189	line2=`echo "${execute_command}" \| sed 's/{{mpi_tasks}}/1/g' \| sed 's/{{tasks_per_node}}/1/g' \| sed 's/palm/combine_plot_fields.x/g'`
[2380]	2190	eval line=\"$line\"
	2191	execute_command="$line"
	2192
	2193
	2194	# EXECUTION COMMAND FOR COMBINE_PLOT_FIELDS
[2566]	2195	if [[ "$execute_command_for_combine" = "" ]]
	2196	then
	2197	eval line2=\"$line2\"
	2198	execute_command_for_combine="$line2"
	2199	fi
	2200
[2380]	2201
	2202
	2203	# PROVIDE A HOSTFILE, IF REQUIRED
	2204	if [[ "$hostfile" != "" ]]
	2205	then
	2206
	2207	if [[ $hostfile = auto ]]
	2208	then
	2209	# CREATE A NEW HOSTFILE
	2210	(( ii = 1 ))
	2211	while (( ii <= cores / threads_per_task ))
	2212	do
	2213	echo $(hostname) >> hostfile
	2214	(( ii = ii + 1 ))
	2215	done
	2216	if (( cores / threads_per_task == 0 ))
	2217	then
	2218	echo $(hostname) >> hostfile
	2219	fi
	2220
	2221	else
	2222	cp $hostfile hostfile
	2223	fi
	2224	eval line=\"`head -n $ii hostfile`\"
	2225	printf "\n *** running on: $line"
	2226	fi
	2227
	2228
	2229
	2230	# SET THE NUMBER OF OPENMP-THREADS
	2231	if [[ $use_openmp = true ]]
	2232	then
	2233	export OMP_NUM_THREADS=$threads_per_task
	2234	printf "\n *** number of OpenMP threads per MPI-task: $OMP_NUM_THREADS"
	2235	else
	2236	export OMP_NUM_THREADS=1
	2237	fi
	2238
	2239
[2610]	2240	# PROVIDE DATA FOR ATMOSPHERE OCEAN COUPLING
[2380]	2241	if [[ $run_coupled_model = false ]]
	2242	then
	2243	if [[ "$ocean_file_appendix" = true ]]
	2244	then
	2245	echo "precursor_ocean" > coupling_steering
	2246	else
	2247	echo "precursor_atmos" > coupling_steering
	2248	fi
	2249	else
	2250	(( iia = $cores_atmos / $threads_per_task ))
	2251	(( iio = $cores_ocean / $threads_per_task ))
	2252	printf "\n coupled run ($iia atmosphere, $iio ocean)"
	2253	printf "\n\n"
	2254	echo "coupled_run $iia $iio" > coupling_steering
	2255	fi
	2256
	2257	printf "\n *** execute command:"
	2258	printf "\n \"$execute_command\" \n\n"
	2259
	2260
[3393]	2261	if [[ $progress_bar_disabled = true ]]
[2380]	2262	then
[3402]	2263	$execute_command < coupling_steering &> >(grep -v --line-buffered -e '^STOP 1$' -e '^1$' &> >(tee STDOUT) )
[3393]	2264	exit_code=${PIPESTATUS[0]}
	2265	else
	2266	$execute_command < coupling_steering &> >(tee STDOUT)
	2267	exit_code=${PIPESTATUS[0]}
	2268	fi
[2380]	2269
[3393]	2270	if [[ ${exit_code} != 0 ]]
	2271	then
	2272
[2380]	2273	# ABORT IN CASE OF RUNTIME ERRORS
	2274	printf "\n +++ runtime error occured"
	2275	locat=execution
	2276	exit
	2277
	2278	else
	2279
	2280	printf "\n$dashes\n *** execution finished \n"
	2281
	2282	fi
	2283
	2284
	2285	# CALL OF combine_plot_fields IN ORDER TO MERGE SINGLE FILES WRITTEN
	2286	# BY EACH CORE INTO ONE FILE
	2287	if [[ ! -f combine_plot_fields.x ]]
	2288	then
	2289
	2290	printf "\n\n\n +++ WARNING: no combine_plot_fields found"
	2291	printf "\n 2d- and/or 3d-data may be incomplete!"
	2292	printf "\n Your previous palmbuild may have failed. Please check.\n"
	2293
	2294	elif [[ "$combine_plot_fields" == true ]]
	2295	then
	2296
	2297	printf "\n\n\n *** post-processing: now executing \"$execute_command_for_combine\" ..."
	2298	$execute_command_for_combine
	2299
	2300	else
	2301
	2302	# TEMPORARY SOLUTION TO SKIP combine_plot_fields. THIS IS REQUIRED IN CASE OF HUGE AMOUNT OF
[2605]	2303	# DATA OUTPUT
[2380]	2304	printf "\n\n\n *** post-processing: skipping combine_plot_fields (-Z option set) ..."
	2305	fi
	2306
	2307
	2308
	2309	# EXECUTE OUTPUT-COMMANDS GIVEN IN THE CONFIGURATION FILE
	2310	(( i = 0 ))
	2311	while (( i < ioc ))
	2312	do
	2313	(( i = i + 1 ))
	2314	if (( i == 1 ))
	2315	then
	2316	printf "\n\n *** execution of OUTPUT-commands:\n$dashes"
	2317	fi
[2799]	2318
	2319	# REPLACE PARAMETERS IN THE OUTPUT COMMAND WITH REAL VALUES
	2320	out_command[$i]=`echo "${out_command[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
	2321
[2380]	2322	printf "\n >>> ${out_command[$i]}"
	2323	eval ${out_command[$i]}
	2324	if (( i == ioc ))
	2325	then
	2326	printf "\n$dashes\n"
	2327	fi
	2328	done
	2329
	2330
[2610]	2331	# IN A FIRST PASS, ADD ADDITIONAL OUTPUT FILE CONNECTIONS IN CASE OF
	2332	# WILDCARDS
[2380]	2333	(( i = 0 ))
[2610]	2334	(( nr_of_output_files = 0 ))
	2335
[2380]	2336	while (( i < iout ))
	2337	do
[2610]	2338
[2380]	2339	(( i = i + 1 ))
[2610]	2340
	2341	# FIRST CHECK FOR MULTIPLE NAMES WITH THE SAME LOCAL NAME AND
	2342	# CREATE A LIST FOR THE DETECTED ENDINGS
	2343	if [[ "${multout[$i]}" = true ]]
	2344	then
	2345	# DETERMINE THE EXISTING EXTENSIONS FROM THE LIST OF FILES
	2346	ls -1 -d ${localout_pre[$i]} > filelist 2>/dev/null
	2347	ls -1 -d ${localout_pre[$i]}_* >> filelist 2>/dev/null
	2348
	2349	endings="DEFAULT"
	2350	while read line
	2351	do
	2352	# remove the local name from the beginning
	2353	localnamestring="${localout_pre[$i]}"
	2354	length_localname=${#localnamestring}
	2355	ending=${line:${length_localname}}
	2356
	2357	if [[ "$ending" != "" ]]
	2358	then
	2359	endings="$endings $ending"
	2360	fi
	2361
	2362	done <filelist
	2363
	2364	rm filelist
	2365
	2366	else
	2367
	2368	# SINGLE NAME
	2369	endings=DEFAULT
	2370
	2371	fi
	2372
	2373	# FOR EACH BASENAME ENDING CREATE AN ENTRY IN THE FINAL OUTPUT FILE LIST
	2374	for ending in $endings
	2375	do
	2376
	2377	# DEFAULT MEANS THAT THE ENDING GIVEN IN .iofiles SHALL BE USED
	2378	if [[ $ending = DEFAULT ]]
	2379	then
	2380	ending=""
	2381	fi
	2382
	2383	# NEW ENTRY (ENDING IS ALSO ADDED TO LOCAL FILENAME READ BY PALM!)
	2384	(( nr_of_output_files = nr_of_output_files + 1 ))
	2385	localout[$nr_of_output_files]="${localout_pre[$i]}"$ending
	2386	transout[$nr_of_output_files]="${transout_pre[$i]}"
	2387	actionout[$nr_of_output_files]="${actionout_pre[$i]}"
	2388	pathout[$nr_of_output_files]="${pathout_pre[$i]}"
	2389	endout[$nr_of_output_files]="${endout_pre[$i]}"$ending
	2390	extout[$nr_of_output_files]="${extout_pre[$i]}"
[2669]	2391	warnout[$nr_of_output_files]="${warnout_pre[$i]}"
[2610]	2392
	2393	done
	2394
	2395	done
	2396
	2397
	2398
	2399
	2400	# COPY LOCAL OUTPUT-FILES TO THEIR PERMANENT DESTINATIONS
	2401	(( i = 0 ))
	2402	while (( i < nr_of_output_files ))
	2403	do
	2404	(( i = i + 1 ))
[2380]	2405	if (( i == 1 ))
	2406	then
	2407	printf "\n\n *** saving OUTPUT-files:"
	2408
	2409	# GET RUN NUMBER ASSIGNED BY PALM
	2410	if [[ -f RUN_NUMBER ]]
	2411	then
	2412	read run_number < RUN_NUMBER
	2413	printf "\n *** PALM generated run_number = "$run_number" will be used as unified cycle number for all output files"
	2414	usecycle_option="-U $run_number"
	2415	else
	2416	run_number=0
	2417	usecycle_option=""
	2418	fi
	2419	if [[ $running_on_remote = true && "$remote_loginnode" != "" ]]
	2420	then
[2404]	2421	printf "\n *** in case of SCP transfers to local host"
	2422	printf "\n they will be done via remote login-node \"$remote_loginnode\" "
[2380]	2423	fi
	2424	printf "\n$dashes"
	2425	fi
	2426
	2427	if [[ ! ( $running_on_remote = true && ( "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra \|\| "${actionout[$i]}" = trpe ) ) ]]
	2428	then
	2429
[3236]	2430	eval filename=${pathout[$i]}/${run_identifier}${endout[$i]}
[2610]	2431
	2432	# DETERMINE THE CYCLE NUMBER
	2433	ls -1 -d $filename > filelist 2>/dev/null
	2434	ls -1 -d $filename.* >> filelist 2>/dev/null
	2435	while read line
	2436	do
	2437
	2438	# filename without path (i.e. after the last "/")
	2439	basefilename=$(basename ${line})
	2440
	2441	# check if there is an extension
	2442	extension=${basefilename##*.}
	2443	if [[ "$extension" = "${extout[$i]}" ]]
	2444	then
	2445	basefilename=${basefilename%.*}
	2446	fi
	2447
	2448	# check for an existing cycle number
	2449	cycle=${basefilename##*.}
	2450	if [[ $cycle =~ ^-?[0-9]+$ ]]
	2451	then
[2669]	2452	# NUMBERS WITH LEADING ZEROS ARE INTERPRETED AS OCTAL NUMBERS
	2453	# 10# EXPLICITLY SPECIFIES THE NUMBER BASE AS 10
	2454	(( icycle = $((10#$cycle)) + 1 ))
[2610]	2455	else
	2456	(( icycle = 1 ))
	2457	fi
	2458
	2459	if (( icycle > maxcycle ))
	2460	then
	2461	(( maxcycle = icycle ))
	2462	fi
	2463
	2464	done <filelist
	2465	rm filelist
	2466
	2467
	2468	# SET THE CYCLE NUMBER
	2469	# IN CASE OF FILE-APPEND, IT MUST BE THE HIGHEST EXISTING CYCLE NUMBER
	2470	if [[ "${actionout[$i]}" = a ]]
	2471	then
	2472	(( maxcycle = maxcycle - 1 ))
	2473	fi
	2474
	2475	(( cycnum[$i] = maxcycle ))
	2476	pathout[$i]=$filename
	2477
	2478
	2479	# ADD CYCLE NUMBER TO FILENAME
	2480	# IN APPEND MODE, FILES KEEP THEIR CURRENT CYCLE NUMBER
[2380]	2481	if [[ "${actionout[$i]}" != "a" ]]
	2482	then
	2483	# SET RUN NUMBER AS CYCLE NUMBER, IF THERE IS NOT A CONFLICT
	2484	# WITH AN EXISTING CYCLE NUMBER
	2485	if (( run_number >= cycnum[$i] ))
	2486	then
	2487	(( cycnum[$i] = run_number ))
	2488	else
	2489	if (( run_number > 0 ))
	2490	then
	2491	printf "\n --- INFORMATIVE: The following file cannot get a unified cycle number"
	2492	fi
	2493	fi
	2494	fi
	2495	if (( cycnum[$i] > 0 ))
	2496	then
[2600]	2497	cyclestring=`printf "%03d" ${cycnum[$i]}`
	2498	pathout[$i]=${pathout[$i]}.$cyclestring
[2380]	2499	fi
	2500	fi
	2501
	2502	# CHECK FOR SINGLE FILE (SERIAL RUN) OR DIRECTORY (ONE FILE PER CORE FOR PARELLEL EXECUTION)
	2503	files_for_cores=false; filetype=file
	2504	link_local_output=false
	2505	if [[ "${actionout[$i]}" = pe && -n $cores ]]
	2506	then
	2507	files_for_cores=true; filetype=directory
	2508	actionout[$i]=""
	2509	elif [[ "${actionout[$i]}" = pe && ! -n $cores ]]
	2510	then
	2511	actionout[$i]=""
	2512	elif [[ "${actionout[$i]}" = lnpe && -n $cores ]]
	2513	then
	2514	files_for_cores=true; filetype=directory
	2515	link_local_output=true
	2516	actionout[$i]=""
	2517	elif [[ "${actionout[$i]}" = lnpe && ! -n $cores ]]
	2518	then
	2519	link_local_output
	2520	actionout[$i]=""
	2521	elif [[ "${actionout[$i]}" = trpe && -n $cores ]]
	2522	then
	2523	files_for_cores=true; filetype=directory
	2524	actionout[$i]="tr"
	2525	elif [[ "${actionout[$i]}" = trpe && ! -n $cores ]]
	2526	then
	2527	actionout[$i]="tr"
	2528	fi
	2529
	2530	if [[ ! -f ${localout[$i]} && $files_for_cores = false ]]
	2531	then
[2669]	2532	if [[ ${warnout[$i]} = true ]]
	2533	then
	2534	printf "\n +++ temporary OUTPUT-file ${localout[$i]} does not exist\n"
	2535	fi
[2380]	2536	elif [[ ! -d ${localout[$i]} && $files_for_cores = true ]]
	2537	then
[2669]	2538	if [[ ${warnout[$i]} = true ]]
	2539	then
	2540	printf "\n +++ temporary OUTPUT-file ${localout[$i]}/.... does not exist\n"
	2541	fi
[2380]	2542	else
	2543
	2544
	2545	# COPY VIA SCP TO LOCAL HOST (ALWAYS IN BINARY MODE USING batch_scp option -m)
	2546	# IF TARGET DIRECTORY DOES NOT EXISTS, TRY TO CREATE IT
	2547	if [[ "${actionout[$i]}" = tr \|\| "${actionout[$i]}" = tra ]]
	2548	then
	2549	if [[ $running_on_remote = true ]]
	2550	then
	2551
	2552	# SET OPTIONS FOR TRANSFER
	2553	if [[ "${actionout[$i]}" = tr ]]
	2554	then
	2555	if [[ $files_for_cores = false ]]
	2556	then
	2557	catalog_option=""
	2558	catalog_string=""
	2559	else
	2560	catalog_option="-c"
	2561	catalog_string="/"
	2562	fi
	2563	append_option=""
	2564	append_string=""
	2565	else
	2566	append_option="-A"
	2567	append_string="append"
	2568	fi
	2569
	2570	transfer_failed=false
	2571	printf "\n >>> OUTPUT: ${localout[$i]}$catalog_string $append_string by SCP to"
[3236]	2572	printf "\n ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}$catalog_string\n"
[2380]	2573
	2574	# TRANSFER VIA SCP
	2575	if [[ "$remote_loginnode" != "" ]]
	2576	then
[3534]	2577	### echo "cd $tempdir; ${fast_io_catalog}/${sources_for_run_catalog}/batch_scp $PORTOPT $catalog_option $append_option -b -m $usecycle_option -u $local_username $return_address ${localout[$i]} \"${pathout[$i]}\" ${configuration_identifier}_${run_identifier}${endout[$i]} ${extout[$i]}" \| ssh -q $remote_username@$remote_loginnode
	2578	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]	2579	else
[3236]	2580	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	fi
[3312]	2582	[[ ${PIPESTATUS[0]} != 0 ]] && transfer_failed=true
[2380]	2583
	2584
	2585	# IF TRANSFER FAILED, CREATE BACKUP COPY ON THIS MACHINE
	2586	if [[ $transfer_failed = true ]]
	2587	then
	2588	printf " +++ transfer failed. Trying to save a copy on this host under:\n"
[3236]	2589	printf " ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number\n"
[2380]	2590
	2591	# FIRST CHECK, IF DIRECTORY EXISTS, AND CREATE IT, IF NECESSARY
	2592	eval local_catalog=${pathout[$i]}
	2593	if [[ ! -d $local_catalog ]]
	2594	then
	2595	printf " *** local directory does not exist. Trying to create:\n"
	2596	printf " $local_catalog \n"
	2597	mkdir -p $local_catalog
	2598	fi
[3236]	2599	eval cp ${localout[$i]} ${pathout[$i]}/${configuration_identifier}_${run_identifier}${endout[$i]}_$run_id_number
[2380]	2600	transfer_problems=true
	2601	fi
	2602
	2603	else
	2604
	2605	# UNSET actionout. DUE TO THIS SETTING, FILE WILL LATER JUST
	2606	# BE COPIED OR APPENDED ON THIS MACHINE
	2607	if [[ "${actionout[$i]}" = tr ]]
	2608	then
	2609	actionout[$i]=""
	2610	else
	2611	actionout[$i]="a"
	2612	fi
	2613	fi
	2614	fi
	2615
	2616
	2617	# APPEND ON THIS MACHINE
	2618	if [[ "${actionout[$i]}" = "a" ]]
	2619	then
	2620	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2621	then
	2622	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2623	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2624	cat ${localout[$i]} >> ${pathout[$i]}.${extout[$i]}
	2625	else
	2626	printf "\n >>> OUTPUT: ${localout[$i]} append to"
	2627	printf "\n ${pathout[$i]}\n"
	2628	cat ${localout[$i]} >> ${pathout[$i]}
	2629	fi
	2630	fi
	2631
	2632	# COPY ON THIS MACHINE
	2633	# COPY HAS TO BE USED, BECAUSE MOVE DOES NOT WORK IF FILE-ORIGIN AND TARGET ARE
	2634	# ON DIFFERENT FILE-SYSTEMS
	2635	if [[ "${actionout[$i]}" = "" && $files_for_cores = false ]]
	2636	then
	2637
	2638	# COPY IN CASE OF RUNS ON SINGLE CORES
	2639	if [[ "${extout[$i]}" != " " && "${extout[$i]}" != "" ]]
	2640	then
	2641	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2642	printf "\n ${pathout[$i]}.${extout[$i]}\n"
	2643	if [[ $link_local_output = true ]]
	2644	then
	2645	printf " file will be linked\n"
	2646	ln -f ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2647	fi
	2648	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2649	if [[ ! -f "${pathout[$i]}.${extout[$i]}" ]]
	2650	then
	2651	if [[ $link_local_output = true ]]
	2652	then
	2653	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2654	fi
	2655	cp ${localout[$i]} ${pathout[$i]}.${extout[$i]}
	2656	else
	2657	printf "+++ no copy because file ${pathout[$i]}.${extout[$i]} exists\n"
	2658	fi
	2659	else
	2660	printf "\n >>> OUTPUT: ${localout[$i]} to"
	2661	printf "\n ${pathout[$i]}\n"
	2662	if [[ $link_local_output = true ]]
	2663	then
	2664	printf " file will be linked\n"
	2665	ln -f ${localout[$i]} ${pathout[$i]}
	2666	fi
	2667	# If "ln -f" fails of if "$link_local_output = false" do a normal "cp"
	2668	if [[ ! -f "${pathout[$i]}" ]]
	2669	then
	2670	if [[ $link_local_output = true ]]
	2671	then
	2672	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2673	fi
	2674	cp ${localout[$i]} ${pathout[$i]}
	2675	else
	2676	printf "+++ no copy because file ${pathout[$i]} exists\n"
	2677	fi
	2678	fi
	2679
	2680	elif [[ "${actionout[$i]}" = "" && $files_for_cores = true ]]
	2681	then
	2682
	2683	# FILES FROM THE DIFFERENT CORES ARE MOVED WITH ln-COMMAND TO THE PERMANENT DIRECTORY
	2684	# AS A FIRST STEP, THE PERMANENT DIRECTORY IS CREATED
	2685	printf "\n >>> OUTPUT: ${localout[$i]}/_.... to"
	2686	printf "\n ${pathout[$i]}\n"
	2687	if [[ $link_local_output = true ]]
	2688	then
	2689	printf " files will be linked\n"
[2396]	2690	mkdir -p ${pathout[$i]}
[2380]	2691	cd ${localout[$i]}
	2692	for file in $(ls *)
	2693	do
	2694	ln -f $file ${pathout[$i]}
	2695	done >\|/dev/null 2>&1
[2566]	2696	cd $tempdir
[2380]	2697	fi
	2698
	2699	# IF "ln -f" HAS FAILED OR IF "$link_local_output = false" DO A NORMAL COPY "cp -r"
	2700	if [[ ! -f "${pathout[$i]}/_000000" ]]
	2701	then
	2702	if [[ $link_local_output = true ]]
	2703	then
	2704	printf " --- WARNING: ln failed, using cp instead (might be time consuming...)\n"
	2705	fi
[3025]	2706	[[ ! -d "${pathout[$i]}" ]] && mkdir ${pathout[$i]}
[2380]	2707	cp -r ${localout[$i]}/* ${pathout[$i]}
	2708	fi
	2709
	2710	fi
	2711	fi
	2712	done
	2713
	2714	if (( i != 0 ))
	2715	then
	2716	if [[ $transfer_problems = true ]]
	2717	then
	2718	printf "\n$dashes\n *** OUTPUT-files saved"
	2719	printf "\n +++ WARNING: some data transfers failed! \n"
	2720	else
	2721	printf "\n$dashes\n *** all OUTPUT-files saved \n"
	2722	fi
	2723	fi
	2724
	2725
	2726	# IF REQUIRED, START A RESTART-JOB
	2727	# FILE CONTINUE_RUN MUST HAVE BEEN CREATED BY THE EXECUTABLE (PALM)
	2728	if [[ -f CONTINUE_RUN ]]
	2729	then
	2730
	2731	# ADD RESTART-OPTIONS TO THE PALMRUN-CALL (IF THEY ARE NOT USED ALREADY):
	2732	# -C TELLS PALMRUN THAT IT IS A RESTART-RUN
	2733	# -v SILENT MODE WITHOUT INTERACTIVE QUERIES
	2734	# -b START A BATCH JOB
	2735	[[ $(echo $prc \| grep -c "\-C") = 0 ]] && prc="$prc -C"
	2736	[[ $(echo $prc \| grep -c "\-v") = 0 ]] && prc="$prc -v"
	2737	[[ $(echo $prc \| grep -c "\-b") = 0 ]] && prc="$prc -b"
	2738
[2957]	2739	# REPLACE SVFOUT IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2740	# SO THAT RESTARTS USE SVF DATA CREATED BY THE INITIAL RUN
	2741	if [[ $(echo $prc \| grep -c "svfout") != 0 ]]
	2742	then
	2743	prc=`echo $prc \| sed 's/svfout/svfin/g'`
	2744	fi
[2380]	2745
	2746	# REPLACE THE HASH IN THE ACTIVATION STRINGS (GIVEN WITH OPTION -a)
	2747	# SO THAT RESTARTS ACCESS DIFFERENT FILES THAN THE INITIAL RUN
	2748	if [[ $(echo $prc \| grep -c "#") != 0 ]]
	2749	then
[2381]	2750	prc=`echo $prc \| sed 's/#/r/g'`
[2380]	2751	fi
	2752
	2753
	2754	# START THE RESTART-JOB
	2755	printf "\n\n *** initiating restart-run on \"$local_ip\" using command:\n"
	2756	echo " $prc"
	2757	printf "\n$dashes\n"
	2758	if [[ $running_on_remote = true ]]
	2759	then
	2760
	2761	echo "*** ssh will be used to initiate restart-runs!"
	2762	echo " return_address=\"$return_address\" "
	2763	echo " return_username=\"$local_username\" "
	2764
	2765	if [[ "$remote_loginnode" != "" ]]
	2766	then
[3534]	2767	ssh -q $remote_username@$remote_loginnode "ssh -q $SSH_PORTOPT $local_username@$return_address \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" " \| tee palmrun_restart.log
[2380]	2768	else
[3534]	2769	### echo \" PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc\" \| ssh -q $SSH_PORTOPT $local_username@$return_address \| tee palmrun_restart.log
	2770	ssh -q $SSH_PORTOPT $local_username@$return_address " PATH=\\\$PATH:$LOCAL_PALMRUN_PATH; cd $LOCAL_PWD; $prc" \| tee palmrun_restart.log
[2380]	2771	fi
	2772
	2773	# WAIT TO ALLOW THE RESTART-JOB TO BE QUEUED, BEFORE THE CURRENT JOB IS FINISHED
	2774	sleep 30
	2775
	2776	else
	2777
	2778	# START THE RESTART JOB ON THE LOCAL HOST
[3132]	2779	eval $prc \| tee palmrun_restart.log # THE ' MUST BE EVALUATED
[2380]	2780	cd - > /dev/null
	2781
	2782	fi
	2783
[3132]	2784	# CHECK, IF RESTART JOB HAS BEEN STARTED
	2785	if [[ $( grep -c "+++ palmrun killed" palmrun_restart.log ) != 0 ]]
	2786	then
	2787	printf "\n$dashes\n +++ creating restart run failed \n"
	2788	locat=create_restart
[3455]	2789	rm palmrun_restart.log
[3132]	2790	exit
	2791	else
	2792	printf "\n$dashes\n *** restart run initiated \n"
	2793	rm palmrun_restart.log
	2794	fi
[2380]	2795
[3132]	2796
[2380]	2797	# DELETE INPUT-(RESTART)FILES, WHICH HAVE BEEN FETCHED FROM THE TEMPORARY DATA
	2798	# DIRECTORY, BACAUSE THEY ARE NOT REQUIRED BY THE RESTART-JOB.
	2799	# THIS IS DONE IN ORDER TO AVOID EXCEEDING DISC QUOTAS OR DISC SPACE (RESTART-FILES
	2800	# MAY BE VERY HUGE)
	2801	(( i = 0 ))
[2610]	2802	while (( i < nr_of_input_files ))
[2380]	2803	do
	2804	(( i = i + 1 ))
	2805	if [[ "${got_tmp[$i]}" = true && $keep_data_from_previous_run = false ]]
	2806	then
	2807	rm -r ${absnamein[$i]}
	2808	fi
	2809	done
	2810
	2811	fi
	2812
	2813
	2814	# ALL ACTIONS FINISHED, TEMPORARY WORKING-DIRECTORY CAN BE DELETED
	2815	cd $HOME
[2566]	2816	[[ $delete_temporary_catalog = true ]] && rm -rf $tempdir
[2380]	2817
	2818
	2819	else
	2820
	2821
	2822	# PREPARING ACTIONS,
	2823	# IF A BATCH-JOB IS TO BE GENERATED AND TO BE STARTED ON A LOCAL OR REMOTE-MACHINE
	2824
	2825	# BUILD THE PALMRUN-COMMAND TO BE CALLED IN THE BATCH-JOB
[3455]	2826	palmrun_com="$palmrun_script_name -r $run_identifier -c $configuration_identifier -m $memory -t $cpumax -q $queue -i $run_id_number -U $local_username"
[2380]	2827	[[ "$activation_string_list" != "" ]] && palmrun_com=${palmrun_com}" -a \"$activation_string_list\""
	2828	[[ "$global_revision" != "" ]] && palmrun_com=${palmrun_com}" -G \"$global_revision\""
	2829	[[ $keep_data_from_previous_run = true ]] && palmrun_com=${palmrun_com}" -k"
	2830	[[ $do_trace = true ]] && palmrun_com=${palmrun_com}" -x"
	2831	[[ "$cores" != "" ]] && palmrun_com=${palmrun_com}" -X $cores"
	2832	[[ $use_openmp = true ]] && palmrun_com=${palmrun_com}" -O $threads_per_task"
[2501]	2833	[[ $tasks_per_node != 0 ]] && palmrun_com=${palmrun_com}" -T $tasks_per_node"
[2380]	2834	[[ $delete_temporary_catalog = false ]] && palmrun_com=${palmrun_com}" -B"
	2835	[[ "$ocean_file_appendix" = true ]] && palmrun_com=${palmrun_com}" -y"
	2836	[[ $run_coupled_model = true ]] && palmrun_com=${palmrun_com}" -Y \"$coupled_dist\""
	2837	[[ "$combine_plot_fields" = false ]] && palmrun_com=${palmrun_com}" -Z"
	2838	[[ "$max_par_io_str" != "" ]] && palmrun_com=${palmrun_com}" -w $max_par_io_str"
[2479]	2839	[[ "$project_account" != "" ]] && palmrun_com=${palmrun_com}" -A $project_account"
[2380]	2840	if [[ $create_remote_batch_job = true ]]
	2841	then
	2842	palmrun_com=${palmrun_com}" -j -u $remote_username -R $local_ip"
[2420]	2843	if [[ $do_trace = true ]]
	2844	then
	2845	printf "\n *** PALMRUN-command on remote host:\n $palmrun_com \n"
	2846	fi
[2380]	2847	elif [[ $create_batch_job = true ]]
	2848	then
	2849	palmrun_com=${palmrun_com}" -j"
[2420]	2850	if [[ $do_trace = true ]]
	2851	then
	2852	printf "\n *** PALMRUN-command on local host:\n $palmrun_com \n"
	2853	fi
[2380]	2854	fi
	2855
	2856
	2857	# DETERMINE THE FULL PATHS FOR THE JOB PROTOCOL FILES ON THE LOCAL AND
	2858	# REMOTE HOST
[3236]	2859	job_protocol_file_local=${local_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2860	job_protocol_file=$job_protocol_file_local
	2861	if [[ $create_remote_batch_job = true ]]
	2862	then
[3236]	2863	job_protocol_file_remote=${remote_jobcatalog}/${configuration_identifier}_${run_id}
[2380]	2864	job_protocol_file=$job_protocol_file_remote
	2865	job_transfer_protocol_file=${remote_jobcatalog}/last_job_transfer_protocol
[3236]	2866	scpjob_file=${remote_jobcatalog}/scpjob.$run_id_number
[2380]	2867	fi
	2868
	2869
	2870	# BUILD THE JOB-SCRIPTS ON FILE jobfile
[3236]	2871	jobfile=jobfile.$run_id_number
[2380]	2872
	2873
	2874	# FIRST CREATE THE BATCH DIRECTIVES
	2875	(( i = 0 ))
	2876	while (( i < ibd ))
	2877	do
	2878	(( i = i + 1 ))
[2693]	2879	line=`echo "${batch_directive[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2880	eval line=\"$line\"
	2881	echo "$line" >> $jobfile
	2882	done
	2883	echo " " >> $jobfile
	2884
	2885
	2886	# FOR BATCH JOBS ON REMOTE HOSTS, ADD THE JOBFILE TO SEND BACK THE JOB
	2887	# PROTOCOL
	2888	if [[ $create_remote_batch_job = true ]]
	2889	then
[3236]	2890	echo "set +vx" >> $jobfile
	2891	echo "trap '" >> $jobfile
	2892	echo "set +vx" >> $jobfile
	2893	echo "cd ${remote_jobcatalog}" >> $jobfile
	2894	echo "cat > scpjob.$run_id_number << %%END%%" >> $jobfile
[2380]	2895
	2896	# ADD THE BATCH DIRECTIVES
	2897	(( i = 0 ))
	2898	while (( i < ibdt ))
	2899	do
	2900	(( i = i + 1 ))
[2693]	2901	line=`echo "${batch_directive_transfer[$i]}" \| sed 's/{{/$/g' \| sed 's/}}//g'`
[2380]	2902	eval line=\"$line\"
	2903	echo "$line" >> $jobfile
	2904	done
	2905	echo " " >> $jobfile
	2906
	2907	echo "set -x" >> $jobfile
[3534]	2908	if [[ "$remote_loginnode" != "" ]]
	2909	then
	2910	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}\" " >> $jobfile
	2911	else
	2912	echo "${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
	2913	fi
[2380]	2914	echo "%%END%%" >> $jobfile
	2915	echo "echo \" *** submitting job for transfering the job protocol file to $local_ip\" " >> $jobfile
[3534]	2916	echo "$submit_command $scpjob_file" >> $jobfile
[2380]	2917	echo "rm $scpjob_file" >> $jobfile
[2404]	2918	echo "rm -rf $job_transfer_protocol_file" >> $jobfile
[2380]	2919	echo "set -x" >> $jobfile
	2920	echo " ' exit" >> $jobfile
	2921	fi
	2922
	2923
	2924	# ACTIVATE ERROR-TRACEBACK
	2925	if [[ $do_trace = true ]]
	2926	then
	2927	echo "set -x" >> $jobfile
	2928	else
	2929	echo "set +vx" >> $jobfile
	2930	fi
	2931
	2932
	2933	# INITIALIZE THE ENVIRONMENT AND LOAD MODULES
	2934	if [[ "$login_init_cmd" != "" ]]
	2935	then
	2936	echo "$login_init_cmd" >> $jobfile
	2937	fi
	2938	if [[ "$module_commands" != "" ]]
	2939	then
	2940	echo "$module_commands" >> $jobfile
	2941	fi
	2942
	2943
	2944	# CREATE TEMPORARY DIRECTORY AND SWITCH TO IT
[2566]	2945	if [[ $create_remote_batch_job = true ]]
	2946	then
	2947	echo "mkdir $tempdir" >> $jobfile
	2948	echo "chmod go+rx $tempdir" >> $jobfile
	2949	else
	2950	# DIRECTORY FOR LOCAL BATCH JOBS IS CREATED NOW, DUE TO A
	2951	# REQUIREMENT OF THE GRID ENGINE BATCH SYSTEM (WORKING DIR IS GIVEN IN
	2952	# BATCH DIRECTIVE -wd AND MUST ALREADY EXIST WHEN THE JOB IS SUBMITTED)
	2953	mkdir $tempdir
	2954	chmod go+rx $tempdir
	2955	fi
	2956	echo "cd $tempdir" >> $jobfile
	2957	echo "export tempdir=$tempdir" >> $jobfile
[2506]	2958	echo "cp ${fast_io_catalog}/${sources_for_run_catalog}/{,.[!.]} ." >> $jobfile
[2380]	2959	echo "export PATH=.:\$PATH" >> $jobfile
	2960	echo "export execute_palmrun=true" >> $jobfile
	2961
	2962
	2963	# PROVIDE NAME OF THE CURRENT WORKING-DIRECTORY ON THE LOCAL MACHINE (FROM WHERE THE JOB IS
	2964	# STARTED) BY SETTING AN ENVIRONMENT-VARIABLE. THIS INFORMATION IS USED IN THE JOB BY PALMRUN
	2965	# IN CASE THAT RESTART-RUNS HAVE TO BE GENERATED
	2966	echo "LOCAL_PWD=$working_directory" >> $jobfile
	2967	echo "export LOCAL_PWD" >> $jobfile
	2968
	2969
	2970	# PROVIDE THE PATH OF THE LOCAL PALMRUN-SCRIPT FOR THE SAME REASON
[2420]	2971	echo "LOCAL_PALMRUN_PATH=${source_path}/../SCRIPTS" >> $jobfile
[2380]	2972	echo "export LOCAL_PALMRUN_PATH" >> $jobfile
	2973
	2974
	2975	# CALL PALMRUN WITHIN THE JOB
	2976	# AS FINAL ACTION, REMOVE THE TEMPORARY DIRECTORY CREATED AT THE BEGINNING OF THE JOB
	2977	echo "set -x" >> $jobfile
	2978	echo "[[ \$execute_palmrun = true ]] && $palmrun_com" >> $jobfile
	2979
	2980
	2981	# TRANSFER JOBFILE TO THE TARGET HOST
	2982	if [[ $create_jobfile_only = false ]]
	2983	then
	2984
[3505]	2985	# CREATE LOCAL JOB FOLDER
	2986	eval local_jobcatalog=$local_jobcatalog
	2987	if [[ ! -d $local_jobcatalog ]]
	2988	then
	2989	echo " "
	2990	echo " *** local jobcatalog \"$local_jobcatalog\" does not exist and will be created now"
	2991	mkdir $local_jobcatalog
	2992	fi
	2993
[2380]	2994	if [[ $create_remote_batch_job = true ]]
	2995	then
	2996
[2420]	2997	echo " "
[2566]	2998	echo " *** transfer of job to remote host via scp"
[3505]	2999
	3000	# CREATE REMOTE JOB FOLDER, IF IT DOES NOT EXIST
[3534]	3001	### echo "[[ ! -d $remote_jobcatalog ]] && mkdir $remote_jobcatalog" \| ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} 2>&1
	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
[2566]	3012	printf " *** submit the job (output of submit command, e.g. the job-id, may follow)"
[2420]	3013	if [[ $do_trace = true ]]
	3014	then
[3534]	3015	### 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>&1"
	3016	echo " ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} \"cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}\" 2>&1"
[2420]	3017	fi
[3236]	3018	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>&1
[3534]	3019	### ssh -q $ssh_key $SSH_PORTOPT ${remote_username}@${remote_ip} "cd $remote_jobcatalog; $submit_command ${configuration_identifier}_${run_id}; rm ${configuration_identifier}_${run_id}" 2>&1
[2380]	3020
	3021	elif [[ $create_batch_job = true ]]
	3022	then
	3023
[2385]	3024	eval local_jobcatalog=$local_jobcatalog
[3236]	3025	cp $jobfile ${local_jobcatalog}/${configuration_identifier}_${run_id}
[2385]	3026	cd $local_jobcatalog
[2380]	3027	echo " "
[2420]	3028	echo " *** submit the job"
	3029	if [[ $do_trace = true ]]
	3030	then
[3236]	3031	echo "$submit_command ${configuration_identifier}_${run_id}"
[2420]	3032	fi
[3236]	3033	$submit_command ${configuration_identifier}_${run_id}
	3034	rm ${configuration_identifier}_${run_id}
[2380]	3035	cd - > /dev/null
	3036
	3037	fi
	3038
	3039	rm -rf $jobfile
	3040
	3041	else
	3042
	3043	printf "\n *** jobfile created under name \"$jobfile\" "
	3044	printf "\n no batch-job has been sent!"
	3045
	3046	fi
	3047
	3048	fi # END OF REMOTE-PART

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